Next Article in Journal
Effects of Plant Density and Fertilization on Agronomic Traits and Yield of Flax (Linum usitatissimum L.)
Previous Article in Journal
Integrative Machine Learning Approaches for Identifying Loci Associated with Anthracnose Resistance in Strawberry
Previous Article in Special Issue
Taxonomy, Lectotypification, and Conservation of the Genus Phyllodium (Fabaceae: Desmodieae) in Cambodia, Laos, and Vietnam
 
 
Search for Articles:
Title / Keyword
Author / Affiliation / Email
Journal
Article Type
 
 
Advanced Search
 
Section
Special Issue
Volume
Issue
Number
Page
 
Journals
Plants
Volume 14
Issue 18
10.3390/plants14182890
plants-logo
Submit to this Journal Review for this Journal Propose a Special Issue
► Article Menu

Article Menu

share Share announcement Help format_quote Cite question_answer Discuss in SciProfiles
first_page
settings
Order Article Reprints
Font Type:
Arial Georgia Verdana
Font Size:
Aa Aa Aa
Line Spacing:
Column Width:
Background:
Article

Integral Assessment of Species of the Genus Allium L. (Amaryllidaceae) in the Western Part of the Kyrgyz Alatau

by
Polina V. Vesselova
1,
Gulmira M. Kudabayeva
1,
Daulet Sh. Abdildanov
1,2,*,
Bektemir B. Osmonali
1,
Serikbay Ussen
1,2,
Mikhail V. Skaptsov
3 and
Nikolai Friesen
4
1
Institute of Botany and Phytointroduction, 36D Timiryazev Str., Almaty 050040, Kazakhstan
2
Faculty of Biology and Biotechnology, Al-Farabi Kazakh National University, al-Farabi Ave 71., Almaty 050040, Kazakhstan
3
South Siberian Botanical Garden, Altai State University, Lesosechnaya Str. 25, 656906 Barnaul, Russia
4
Botanical Garden, Osnabruck University, Albrechtstrasse 29, 49076 Osnabruck, Germany
*
Author to whom correspondence should be addressed.
Plants 2025, 14(18), 2890; https://doi.org/10.3390/plants14182890
Submission received: 22 July 2025 / Revised: 21 August 2025 / Accepted: 8 September 2025 / Published: 18 September 2025
(This article belongs to the Collection Feature Papers in Plant Systematics, Taxonomy, Nomenclature and Classification)
Browse Figures
Versions Notes

Abstract

This paper presents the results of the current present species composition of the genus Allium L. (Amaryllidaceae) of the western part of the Kyrgyz Alatau. The phylogeny, ploidy, and chorological data are presented, and a checklist of species of the genus Allium in the study area is compiled. The large subgenera of Allium, including Melanocrommyum, have been identified, reflecting their prevalence in the mountainous regions of Central Asia. Ploidy of some species (A. artrosanguineum and A. turkestanicum) of the genus Allium growing in the western part of the Kyrgyz Alatau were studied for the first time using flow cytometry methods. The nrITS sequencing was used to construct a phylogenetic tree including sequences from the NCBI database. The phylogenetic tree of species of the genus Allium of the Kyrgyz Alatau was compiled taking into account previously published data. The list of studied Allium species in the Kyrgyz Alatau is represented by 25 species, which include seven subgenera and 17 sections. Also, the nomenclature of onion species is brought to the modern understanding of some species names. Based on specimens of the genus Allium collected in the western part of the Kyrgyz Alatau, an integral assessment of the current species composition using molecular–genetic, cytometric, and traditional botanical methods was carried out.

1. Introduction

The genus Allium L. (Amaryllidaceae J. St.-Hil.), which is a complex systematic group, includes more than 1000 species [1,2]. The ecological range of Allium representatives extends from the alpine and subalpine belts to deserts. Almost one third of them grow in the mountains of Central Asia—the world’s largest centre of diversity of Allium species. Only in the Tien Shan mountains, which are characterised by a high degree of endemism, there are 13 major subgenera of the genus Allium, including 56 species endemic to this mountain system [3,4]. According to the literature data, there are from 9 to 21 endemic species of this genus and 14 subendemic taxa in the flora of Kazakhstan [5,6,7]. The Kyrgyz Alatau is located at the junction of the Northern and Western Tien Shan and characterised by a correspondingly transitional composition of the flora.
According to the botanical and geographical zoning of Kazakhstan, the Kyrgyz Alatau belongs to the Saharan–Gobi desert region, Iran-Turan subregion, Dzungar-North Tien Shan province, and Kyrgyz mountain subprovince [8] (Figure 1).
In one of the fundamental works on the genus Allium, the Flora of the USSR [5], the genus was divided into nine sections. In the Flora of Kazakhstan [6], for the territory of the republic as a whole, 108 species of Alliums are indicated, 29 of which are stated as endemic. According to the data of Flora of Kazakhstan Vol. 2. Generic composition of the flora [9], the genus Allium in the flora of Kazakhstan is represented by 140 species.
The list of representatives of the Allium genus in the flora of Kazakhstan, published in Plantarium [10], includes 128 species. At that, 25 species from seven subgenera and 17 sections are represented in the Kazakh part of the Kyrgyz Alatau range. The Kyrgyz Alatau is a transboundary range; it is possible to expand the list by onion species growing in the territories bordering Kyrgyzstan.
The aim of this study was to conduct a phylogenetic and taxonomic assessment of species of the genus Allium L. found in the Kyrgyz Alatau, using data on the internal transcribed spacer (ITS) sequence in order to clarify the systematic position of individual taxa within modern classification systems.

2. Results

2.1. Distribution Analyses

As a result of the analysis of the literature data, herbarium materials, and our own field research, an annotated checklist of 25 species of the genus Allium growing in the Kyrgyz Alatau was compiled. Among the identified species, one is endemic (A. oreoprasoides); two subendemic (A. margaritae, A. trachyscordum), which are also distributed in Kyrgyzstan; and one is a rare species listed in the Red Book of the Republic (A. suworowii) [11,12].
Three species of Alliums, which, according to the literature data [13], were cited for the Kazakhstan part of the Kyrgyz Alatau (Allium altissimum, Allium schoenoprasum, A. kokanicum), were excluded from the list, because no herbarium specimens for these three species from the Kyrgyz Alatau exist, as well as no references in the literature and no image evidence in Internet sources [14,15]. One of the largest subgenera of the studied genus includes two main groups: subgenus Allium, consisting of six sections, and subgenera Melanocrommyum and Reticulatobulbosa, including three sections. All species of the genus Allium growing in the western part of the Kyrgyz Alatau are presented in the illustrations provided in Figure 2a,b. For two species, new names have been given: Allium pallasii s. l. is divided into two species—Allium caricifolium is distributed west of Lake Saisan and in the southeast and south Kazakhstan and Kyrgyzstan, and A. pallasii is distributed in northern Kazakhstan to the Siberian Altai [16]. Allium carolinianum is also divided into two species—Allium polyphylum is now valid for Tianshan and Dzhungar Alatau; A. carolinianum is only distributed in the Himalayas [17].
Meanwhile, in other subgenera, several large sections are also distinguished, each with an equal number of species: Acmopetala (Subgenus Melanocrommyum) and Falcatifolia (Subgenus Polyprason).
An annotated checklist of the species of the genus Allium currently found in the Kyrgyz Alatau is presented below.
  • Subgenus Allium.
    Section Allium.
    Allium sativum L. (1753 in Sp. Pl. 1: 296)—syn. A. longicuspis Regel (1875 in Trudy Imp. S.-Peterburgsk. Bot. Sada 3.2: 45).
    The wild plants described as A. longicuspis Regel are feral cultivated garlic [31].
    Perennial. Grows in shrubs and along the banks of streams at the bottom of gorges in the lower belt of mountains. Flowering VI–VIII.
    Examined herbarium specimens from the Kyrgyz Alatau: AA (Geographic area: the southwestern extremity of the Kyrgyz range, the foothills to the northwest, from Almaly-sai, along the meadow slopes, date 03.VI.1963, author Goloskokov V. P.).
    Distribution in Kazakhstan: 25. Zailiyskiy-Kungei Alatau, 25a. Ketmen-Terskey Alatau, 26. Chu-Ili mountains, 27. Kyrgyz Alatau, 28. Karatau, 29. Western Tien-Shan.
    General distribution: Iranian–mountain–Middle Asian cultivated species (cultivated worldwide).
  • Section Brevispatha Valsecchi (1974 in Giorn. Bot. Ital. 108(1–2): 92).
    Type species Allium parciflorum Viv.
    Allium margaritae B. Fedtsch. (1918 in Izv. Glavn. Bot. Sada R.S.F.S.R. 18: 14.).
    Perennial. Grows on rubbly outcrops of variegated rocks. Flowering V–VI.
    Examined herbarium specimens from the Kyrgyz Alatau: AA (Geographic area: Kyrgyz Alatau, Zhambyl region, Ulken Almalysay gorge, southern slope. Coordinates: N 42°53′56″ E 71°42′43″ altitude—h-1200 m, date: 26.VIII.2024, authors: Vesselova P.V., Bilibayeva B.K., Abdildanov D.Sh., Ussen S., Akhmetzhanova R.K.).
    Distribution in Kazakhstan: 16. Betpakdala, 26. Chu-Ili mountains, 27. Kyrgyz Alatau.
    General distribution: Betpakdala-North Tyanshan (endemic).
  • Section Caerulea (Omelcz.) F. O. Khass. (1996 in Öztürk, Seqmen & Gork (eds.) Plant Life in South-West and Central Asia: 150).
    Type species Allium caeruleum Pall.
    Allium caesium Schrenk (1844 in Bull. Cl. Phys.-Math. Acad. Imp. Sci. Saint-Pétersbourg 2: 113).
    Perennial. Grows in steppes and deserts, on plumes and mountain slopes up to the middle belt. Flowering IV–VII.
    Examined herbarium specimens from the Kyrgyz Alatau: MW (foothills of the Kyrgyz range, feather grass steppe, 08. VI. 1958, collector Gubanov I.; northwestern extremity of the Kirghiz range, Syugaty gorge in the lower tichi of the river, along the southern rocky slopes, 05. VI. 1963, collector: Goloskokov V.P.); AA (Western tip of the Kyrgyz Alatau, valley of the Merke River, left-bank slope among bushes. 29.V.1985, Chubarova T.U. Northwestern Tip of the Kirghiz Range. Syugata Gorge in the lower reaches of the river. Along the southern rocky slopes.05.VI.1963. Goloskokov V.P. Kyrgyz Alatau, Kyzylsu river gorge, foothills, northeastern slopes, altitude –1500 m 16.VII.1948. Rubtsov N. I. Kyrgyz range. Almalyk-sai gorge, a gap west of the beginning of the gorge, feather grass steppe with spirea bushes and groups of St. John’s wort. 25.V.1961. Fisyun V.V. Chibindy Gorge, range crest, near the rocks. 04.VI.1960. Gamayunova A.P. Zhambyl region, Turar, Ryskulovsky district, Makpal gorge N 42.8651568 E 71.9170940 03.V.2025. Vesselova P.V., Kudabayeva G.M., Friesen N.V., Abdildanov D.Sh., Kenesbay A.Kh., Akhmetzhanova R.K.).
    Distribution in Kazakhstan: 3. Irtysh, 9. Turgai, 10. Western Shallow Soil, 11. Eastern Cretaceous-Popochon, 16. Betpakdala, 17. Moyinkum, 18. Balkhash-Alakol, 21. Turkestan, 24. Dzungarian Alatau, 25. Zailiyskiy-Kungei Alatau, 25a. Ketmen-Terskey Alatau, 26. Chu-Ili Mountains, 27. Kyrgyz Alatau, 28. Karatau, 29. Western Tien Shan.
    General distribution: North-Turanian–Mountain–Middle Asian (Kazakhstan, Kyrgyzstan, Tajikistan, Uzbekistan, Xinjiang).
  • Allium caeruleum Pall. (1773 Reise Russ. Reich 2: 737).
    Perennial. Grows on high dry steppes, in foothills and mountains, in wet meadows and shrubs. Flowering V–VI.
    Examined herbarium specimens from the Kyrgyz Alatau: MW (Akyrtobe, Taldybulak gorge, date 11.VII. 1924, authors: Popov M.G., Makieva E.M.); AA (Kara-Bulak gorge, the bottom of the gorge, among the high mint. date 07.VI.1961 author: Gamayunova A. P. Geographic area: Syugates. A damp meadow along the bottom of the gorge in the upper reaches. date 03.VI.1961, author: Gamayunova A.P. Geographic area: Southwestern Extremity of the Kyrgyz ange. Almaly-Sai gorge. Along the southern rocky slopes. date 03.VI.1963. Goloskokov V. P. Geographic area: Right side of the sh.r. Merke. Southwestern rocky slope. date 03.VII.1947, authors: Rubtsov N.I., Stepanova E.F.).
    Distribution in Kazakhstan: 2. Tobyl-Ishim, 4. Semipalatinsk hog, 9. Turgai, 10. Western Shallow Soil, 11. Eastern Shallow Soil, 12. Zaisan, 16. Betpakdala, 18. Balkhash-Alakol, 24. Dzungarian Alatau, 25. Zailiyskiy-Kungei Alatau, 25a. Ketmen-Terskey Alatau, 26. Chu-Ili Mountains, 27. Kyrgyz Alatau.
    General distribution: Central Palaearctic (Russia: Altai, Kazakhstan, Kyrgyzstan, Tajikistan, Uzbekistan, China: Xinjiang).
  • Section Pallasia (Tzag.) F.O.Khass., R.M. Fritsch & N. Friesen (2017 in Flora Uzbekistana 1: 87). Type species A. pallasii Murrai.
    Allium caricifolium Kar et Kir. (1841 in Bull. Soc. Imp. Naturalistes Moscou 14: 854)—Allium pallasii Murrai pro parte [16].
    Perennial. Grows on rubbly and stony slopes, outcrops of variegated rocks, less often in the upper belts of mountains. Flowering V–VI.
    Examined herbarium specimens from the Kyrgyz Alatau: AA (Zhambyl region, Merken district, Molaly gorge. Coordinates: N 42°45′35″ E 73°1′29″ altitude h-1230 m. date 24.V.2023. authors: Vesselova P.V., Kudabayeva G.M., Shormanova A.A., Osmonali B.B., Abdildanov D.Sh., Ussen S.; Geographic area: Zhambyl region, Turar Ryskulov district, Makpal gorge. Coordinates: N 42.8651568 E 71.9170940, date 03.V.2025. authors: Vesselova P.V., Kudabayeva G.M., Friesen N.V., Abdildanov D.Sh., Kenesbay A.Kh., Akhmetzhanova R.K.).
    Distribution in Kazakhstan: 24. Dzungarian Alatau, 25. Zailiyskiy-Kungei Alatau, 25a. Ketmen-Terskey Alatau, 26. Chu-Ili Mountains, 27. Kyrgyz Alatau.
    General distribution: mountain–central Asian (Kazakhstan, Kyrgyzstan, Tajikistan, Uzbekistan, China: Xinjiang).
  • Section Mediasia F. O. Khass., Yengal. & N. Friesen (2006 in Aliso 22: 386).
    Type species A. turkestanicum Regel.
    Allium turkestanicum Regel (1875 in Trudy Imp. S.-Peterburgsk. Bot. Sada 3.2: 197).
    Perennial. Grows in clay, sandy and rubbly desert steppes. Flowering VI–VII.
    Examined herbarium specimens from the Kyrgyz Alatau: AA (Geographic area: Kyrgyz range, northern gorges, Katudzhan gorge, dry slopes of the left bank; on shallow earth in groups. date 16.VI.1961 author: Gamayunova A.P.).
    Distribution in Kazakhstan: 15. Kyzylorda, 16. Betpakdala, 18. Balkhash-Alakol, 21. Turkestan, 25. Zailiyskiy-Kungei Alatau, 26. Chu-Ili Mountains, 27. Kyrgyz Alatau, 28. Karatau.
    General distribution: North Turanian–mountain–Middle Asian (Kazakhstan, Kyrgyzstan, Tajikistan, Turkmenistan, Uzbekistan).
  • Section Minuta F. O. Khass. (1996 In Öztürk, Seqmen & Gork (eds.) Plant Life in South-West and Central Asia: 150).
    Type species A. minutum Vved.
    Allium parvulum Vved. (1934 in Byull. Sredne-Aziatsk. Gosud. Univ. xix. 124).
    Perennial. Grows on rubbly variegated plumes of mountains. Flowering V–VI.
    Examined herbarium specimens from the Kyrgyz Alatau: AA (Geographic area: Dzhambi region, steppe hillock between Chu and Lugovaya stations. date 25.V.1948. Pavlov N.V. Geographic area: South-Kazakh region. Department of Land Management, Aulie-Ata district. Plain from Ak-Chulak. Bluegrass-sedge steppe with coarse forbs. date 14.V.1933, author: Kornilova V.S.).
    Distribution in Kazakhstan: 25. Zailiyskiy-Kungai Alatau, 27. Kyrgyz Alatau, 28. Karatau.
    General distribution: Prityanshansky (Kazakhstan, Kyrgyzstan).
  • Subgenus Butomissa (Salish.) N. Friesen (2006 in Aliso 22: 387)—Genus Butomissa Salisb. 1866 in Gen. Pl. fragm. Cont. part. Liriogamae: 90.
    Section Austromontana N. Friesen (2006 in Aliso 22: 387).
    Type species Allium oreoprasum Schrenk.
    Allium oreoprasum Schrenk (1842 in Bull. Acad. Imp. Sci. Saint-Pétersbourg 10.23: 354).
    Perennial. Inhabits rocks and rocky slopes of mountains. Flowering V–VII.
    Examined herbarium specimens from the Kyrgyz Alatau: AA (Geographic area: Kyrgyz Alatau, valley of the Merke River, right side of the Taldysu tract, southern slope. date 26.VI.1985. author: Chubarova T.U. Geographic area: Western Extremity of the Kyrgyz Alatau, Kaindy River Valley, Dry Eastern Rocky Slope in the Lower Cordon Area. date 20.V.1984. author: Nelina N.V. Geographic area: West part of the Kyrgyz Alatau, southern. macroslope. the valley of the Nelda River. Rocky slope of the southeastern exposure, thickets. date 21.VI.1984. author: Nelina N.V.).
    Distribution in Kazakhstan: 24. Dzungarian Alatau, 25. Zailiyskiy-Kungei Alatau, 25a. Ketmen-Terskey Alatau, 27. Kyrgyz Alatau, 29. Western Tien Shan.
    General distribution: Mountain–central Asian (Afghanistan, Kazakhstan, Kyrgyzstan, Pakistan, Tajikistan, Tibet, Uzbekistan, Western Himalayas, Xinjiang).
  • Subgenus Cepa (Mill.) Prokh. (1990 in Razp. Slov. Akad. Znanosti Umetn., Razr. Nar. Vede (SAZU) 31: 250, 251)—Cepa Mill. 1754 in Gard. Dict. Abr., ed. 4.
    Type species Allium cepa L.
    Section Annuloprason T.V. Egorova (1977 in Rast. Tsent. Azii, Mater. Bot. Inst. Komarova 7: 57).
    Type species Allium atrosanguineum Schrenk.
    Allium atrosanguineum Schrenk (1842 in Bull. Acad. Imp. Sci. Saint-Pétersbourg 10.23: 355).
    Perennial. Grows on stony and fine-grained places in alpine and subalpine belts of mountains, often in huge thickets. Flowering VI–VIII.
    Examined herbarium specimens from the Kyrgyz Alatau: AA (Geographic area: Western part of the Kyrgyz Alatau, Southern macroslope, Kenkol valley, date 04.VI.1984. author: Karmysheva N.Kh. Geographic area: Western extremity of the Kyrgyz Alatau, the valley of the Aspara river, the Kumbel Pass, a wet meadow and a southeastern stony–rubble slope. date 12.VII.1984. author: Zaripov R.G. Geographic area: Kyrgyz range, upper reaches of the gorge. Solver. Alpine lawn on compacted soil. date 17.VI.1961. Fisyun V.V. Geographic area: Kyrgyz Alatau range, Zhambyl region, Turar Ryskulov district, Karakystak. Coordinates: N 42°40′7″ E 72°50′26″ altitude—h-2530m. date 19.07.2023. authors: Vesselova P.V., Kudabayeva G.M., Friesen N.V., Osmonali B.B., Abdildanov D.Sh., Ussen S.).
    Distribution in Kazakhstan: 23. Tarbagatai, 24. Dzungarian Alatau, 25. Zailiyskiy-Kungei Alatau, 25a. Ketmen-Terskey Alatau, 27. Kyrgyz Alatau, 29. Western Tien Shan.
    General distribution: mountain–central Asian (Afghanistan, China, Kazakhstan, Kyrgyzstan, Pakistan, Tajikistan, Uzbekistan).
    Allium semenovii Regel (1986 in Bull. Soc. Imp. Naturalistes Moscou 41.1: 449).
    Perennial. Grows in alpine meadows. Flowering VI–VII.
    Examined herbarium specimens from the Kyrgyz Alatau: AA (Geographic area: Kyrgyz range, Chungur Gorge, upper reaches of the Solyusher river, date 17.VI.1961. author: Fisyun V.V.).
    Distribution in Kazakhstan: 24. Dzungarian Alatau, 25. Zailiyskiy-Kungei Alatau, 25a. Ketmen-Terskey Alatau, 27. Kyrgyz Alatau.
    General distribution: Mountain–Middle Asian–Himalayan (Kazakhstan, Kyrgyzstan, Tajikistan, Western China, India: Himalayas).
  • Subgenus Melanocrommyum (Webb & Berth.) Rouy (1910 in Fl. France 12: 378)—Allium sect. Melanocrommyum Webb et Berth (1846 in Phytogr. Canar. 3: 347).
    Type species Allium nigrum L.
    Section Acmopetala R.M. Fritsch (1992 in Hanelt et al. (eds.), The genus Allium: taxonomical problems and genetic resources: 74).
    Type species Allium backhousianum Regel.
    Allium dasyphyllum Vved. (1925 in Byull. Sredne-Aziatsk. Gosud. Univ. ix. Suppl. 6).
    Perennial. Grows on stony slopes in the upper belt of mountains. Flowering VII.
    Distribution in Kazakhstan: 27. Kyrgyz Alatau [32].
    General distribution: Kyrgyz-Alatau (endemic to the Kyrgyz Alatau (Kyrgyzstan, Kazakhstan—subendemic).
    Allium taschkenticum F.O. Khass. et R.M. Fritsch (1994 in Linz. Biol. Beitr. 26: 971).
    Perennial. Grows on shrubby and herbaceous slopes in the lower belt of mountains. Flowering V–VI.
    Distribution in Kazakhstan: 26. Chu-Ili Mountains, 27. Kyrgyz Alatau, 29. Western Tien Shan.
    A. taschkenticum occurs in the Kyrgyz Alatau [33], but so far, we have not seen any herbarium specimens.
    General distribution: Western Tien Shan (Kazakhstan—subendem, Kyrgyzstan, Uzbekistan).
    Allium suworowii Regel (1881 in Gartenflora 30: 356).
    Perennial. Grows on shrubby and herbaceous slopes and plumes of mountains. Flowering V–VI.
    Examined herbarium specimens from the Kyrgyz Alatau: AA (Geographic area: A saline damp meadow in the steppe between Chu and Lugovaya stations. date 24.V.1948. author: Pavlov N.V. Geographic area: Kyrgyz Alatau, the valley of the Kaindy river, near the road in the vicinity of the lower cordon. date 20.V.1984. author: Nelina N.V. Geographic area: Kyrgyz Alatau, uroch. Chungur (Slutorsky) gorge Kara-Archa. date 28.V.1984. author: Nelina N. V. Geographic area: Zhambyl Region, Turar Ryskulov district, Makpal gorge. Coordinates N 42.8651568 E 71. 9170940 altitude h-1182 m. date 03.V.2025. authors: Vesselova P.V., Kudabayeva G.M., Friesen N.V., Abdildanov D.Sh., Kenesbay A.Kh., Akhmetzhanova R.K.).
    Distribution in Kazakhstan: 18. Balkhash-Alakol, 21. Turkestan, 27. Kyrgyz Alatau, 28. Karatau, 29. Western Tien Shan.
    General distribution: Near-North Tien Shan (Afghanistan, Kazakhstan, Kyrgyzstan, Tadzhikistan, Turkmenistan, Uzbekistan).
  • Section Longibidentata (R.M. Fritsch) R.M. Fritsch (2009 in Bot. Jahrb. Syst. 127.4: 465)—1994 in in Khassanov & Fritsch, Linzer Biol. Beiträge 26: 974.
    Type species Allium fetisowi Regel.
    Allium fetisowi Regel (1877 in Trudy Imp. S.-Peterburgsk. Bot. Sada 5: 631).
    Perennial. Grows on shrubby and herbaceous slopes in the lower belt of mountains. Flowering V–VI.
    Examined herbarium specimens from the Kyrgyz Alatau: MW (Geographic area: Akyrtobe, Taldybulak gorge, subalpine and alpine cereals, date 12. VII. 1924, author: Popov M.G.); AA (Geographic area: Western part of the Kyrgyz Alatau, Chungur gorge, right bank of the river, southeastern slope and top of the mountain. 28.VI.1985. Chubarova T.U. Geographic area: Northwestern part of the Kyrgyz range. Syugata gorge in the upper reaches of the river. Along the steep northern slope. date 07.VI.1963. author: Goloskokov V.P. Geographic area: Kyrgyz range, northern gorges. Almalyk-sai gorge, steppe slopes with shrubs, at the top of the spurs, altitude—1500 m, date 23.V.1963. author: Gamayunova A.P. Geographic area: Kyrgyz range, Almalyk-sai gorge. Steppe meadows in the middle part of the range along the wide saddle of the Kaindy. date 01.VI.1961 author: Gamayunova A.P. Geographic area: Kyrgyz range, Almalyk-sai gorge 3rd gap to the west of the main gorge. Steppe slopes of the southern exposure, stony places. date 26.V.1961. author: Fisyun V. V.).
    Distribution in Kazakhstan: 25. Zailiyskiy-Kungei Alatau, 26. Chu-Ili Mountains, 27. Kyrgyz Alatau, 29. Western Tien Shan.
    General distribution: Tien Shan (Kazakhstan, Kyrgyzstan, China).
  • Section Miniprason R.M. Fritsch (1992 in Hanelt et al. (eds.), The genus Allium: taxonomical problems and genetic resources: 74).
    Type species Allium karataviense Regel.
    Allium karataviense Regel (1875 in Acta Horti Petropolit. 3.2: 243).
    Perennial. Grows on rubbly mobile placers in the lower and middle belts of mountains.
    Flowering IV–VI.
    Examined herbarium specimens from the Kyrgyz Alatau: AA (Geographic area: Kyrgyz Range. 03.VII.1947. Rubtsov N. I., Stepanova E. F. Geographic area: Kyrgyz range. The vicinity of the city of Dzhambul, foothills, the beginning of the Butumainak gorge, scree, date 18.V.1961, author: Fisyun V.V. Geographic area: Western part of the Kyrgyz Alatau, valley of the Syugatti River, rocky canyon, thalweg. date 24.V.1984. author: Nelina N. V.).
    Distribution in Kazakhstan: 26. Chu-Ili Mountains, 27. Kyrgyz Alatau, 28. Karatau, 29. Western Tien-Shan.
    General distribution: Iranian–mountain–Middle Asian (Afghanistan, Kazakhstan, Kyrgyzstan, Tajikistan, Uzbekistan).
  • Subgenus Polyprason Radic (1990 in Razp. Slov. Akad. Znan. Umet. 31: 253).
    Type species Allium moschatum L.
    Section Falcatifolia N. Friesen (2006 in Aliso 22: 390).
    Type species Allium carolinianum DC.
    Allium platyspathum Schrenk (1841 in Enum. Pl. Nov.:7).
    Perennial. Grows in subalpine and alpine meadows. Flowering VI–VII.
    Examined herbarium specimens from the Kyrgyz Alatau: AA (Geographic area: Kyrgyz Alatau. Kaindy tract, grass–sedge bog with birch and spruce, h–2200 m above sea level. date 18.VII.1948. author: Rubtsov N. I. Geographic area: Aspara Forest, Kumbel pass, southeastern slope, altitude—h–3000–3500, date 12.VIII.1980. author: Zaripov R.G. Geographic area: Kyrgyz Alatau, Karabalty gorge, near the Tyuzashu pass. Along the wet sais, 2750 m. date 16.VII.1970. author: Roldugin I. I.).
    Distribution in Kazakhstan: 22. Altai, 23. Tarbagatai, 24. Dzungarian Alatau, 25. Zailiyskiy-Kungei Alatau, 25a. Ketmen-Terskey Alatau, 27. Kyrgyz Alatau, 29. Western Tien Shan.
    General distribution: mountain–central Asian (Afghanistan, Altai, Kazakhstan, Kyrgyzstan, Mongolia, Mongolia, Pakistan, Tajikistan, Uzbekistan, Western China).
    Allium polyhyllum Kar. et Kir. (1842 in Bull. Soc. Imp. Naturalistes Moscou 15: 509)—syn. A. carolinianum Redoute pro parte [17].
    Perennial. Occurs on rubbly slopes, in alpine and subalpine belts of mountains. Flowering VII–VIII.
    Examined herbarium specimens from the Kyrgyz Alatau: MW (Geographic area: upper reaches of the Kishi Kaindy, rocky slope, date 19.VII. 1951, author: Golubev V.); AA (Geographic area: Kyrgyz range, 4–5 km west of the Merke river gorge. date 18.VII.1947. author: Rubtsov N.I., Stepanova E.F. Geographic area: Northern macroslope, shch. Nelds. Rocky slopes. date 15.VI.1984. author: Nelina N.V. Geographic area: Kyrgyz range, gorge sulyusher. Alpine lawns near snowfields. date 17.VI.1961. author: Fisyun V.V. Geographic area: Kyrgyz Alatau range, Shaldy in the rocks. 27.VIII.1951. author: Baitenov M.S.).
    Distribution in Kazakhstan: 24. Dzungarian Alatau, 25. Zailiyskiy-Kungei Alatau, 25a. Ketmen-Terskey Alatau, 27. Kyrgyz Alatau, 29. Western Tien Shan.
    General distribution: mountain–central Asian (Afghanistan, Kazakhstan, Kyrgyzstan, Mongolia, Nepal, Pakistan, Tajikistan, Tibet, Uzbekistan, China).
    Allium hymenorhizum Ledeb. (1830 in Fl. Altaica 2:12).
    Perennial. Inhabits damp saline meadows, in mountains on grassy marshes and meadows.
    Flowering VI–VII.
    Examined herbarium specimens from the Kyrgyz Alatau: AA (Geographic area: Western part of the Kyrgyz Alatau, valley of the Aspara river, Archaly tract. date 15.07.1984. author: Zaripov R.G. Geographic area: Western part of the Kyrgyz Alatau, the valley of the Aspara river, the Kumbel Pass, a wet meadow. date 16.08.1984. author: Zaripov R.G. Geographic area: Kyrgyz range. The Aral-Tyube river gorge, a gravelly slope among fescue vegetation. date 05.08.1947. authors: Rubtsov N.I., Stepanova E.F. Geographic area: Kyrgyz Alatau range, Zhambyl region, Turar Ryskulov district, serpentine. Coordinates: N 42°40′26″ E72°50′31″ altitude—h-2290m. date 19.07.2023. authors: Vesselova P.V., Kudabayeva G.M., Friesen N.V., Osmonali B.B., Abdildanov D.Sh., Ussen S.).
    Distribution in Kazakhstan: 18. Balkhash-Alakol, 22. Altai, 23. Tarbagatai, 24. Dzungarian Alatau, 25. Zailiyskiy-Kungei Alatau, 25a. Ketmen-Terskey Alatau, 26. Chu-Ili Mountains, 27. Kyrgyz Alatau, 28. Karatau, 29. Western Tien-Shan.
    General distribution: Iranian–mountain–central Asian (Afghanistan, Russia, Iran, Kazakhstan, Kyrgyzstan, Mongolia, Tajikistan, Turkey, Uzbekistan, China).
  • Section Oreiprason F. Herm. (1939 in Feddes Repert. 46: 57).
    Type species Allium saxatile M.Bieb.
    Allium leptomorphum Vved. (1952 in Bot. Mater. Gerb. Inst. Bot. Akad. Nauk Uzbeksk. S.S.R. xiii. 29).
    Perennial. Grows on rocks and placers of mountains. Flowering VII–VIII.
    Distribution in Kazakhstan: 25. Zailiyskiy-Kungei Alatau, 26. Chu-Ili Mountains, 27. Kyrgyz Alatau.
    General distribution: North Tianshanian (Kazakhstan, Kyrgyzstan).
    Allium obliquum L. (1753 in Sp. Pl. 1: 296).
    Perennial. Grows on rocks and stony slopes in foothills and lower belt of mountains. Flowering VI–VII.
    Examined herbarium specimens from the Kyrgyz Alatau: AA (Geographic area: Kyrgyz Alatau, Kultakhr gorge, scree, date 19.08.1948. author: Rubtsov N. I.).
    Distribution in Kazakhstan: 23. Tarbagatai, 24. Dzungarian Alatau, 25. Zailiyskiy Kungei, Alatau, 25a. Ketmen-Terskey Alatau, 26. Chu-Ili Mountains, 27. Kyrgyz Alatau, 28. Karatau.
    General distribution: Central Palaearctic (Romania, Ukraine, Russia (Southern Urals, Siberia), Kazakhstan, Kyrgyzstan, Mongolia, China (western).
  • Subgenus Porphyroprason (Ekberg) R.M. Fritsch (2006 in Aliso 22: 386—Allium sect. Porphyroprason Ekberg 1969 in Bot. Not. 122: 65).
    Type species Allium oreophilum C.A:Mey.
    Section Porphyroprason Ekberg (1969 in Bot. Not. 122: 65).
    Type species A. oreophilum C. A. Mey.
    Allium platystemon Kar. & Kir. (1842 in Bull. Soc. Imp. Naturalistes Moscou 15(2): 514).—Syn. A. oreophillum C.A.Mey. pro parte [34].
    Perennial. Grows on rubbly slopes in the upper belt of mountains. Flowering VI–VIII.
    Examined herbarium specimens from the Kyrgyz Alatau: MW (Geographic area: Kishi Kaindy, the top of the mountain range, 19.VII. 1951, collector Golubev V.); AA (Geographic area: Kyrgyz Alatau range, 4–5 km west of the Merke river gorge, northern gravelly slope, altitude—2700 m. date 14.VII.1947. authors: Rubtsov N.I., Stepanova E.F. Geographic area: Kyrgyz Alatau. Upper reaches of the Shamsi River, alpine meadow, on crushed stone, date 31.VII.1948. Rubtsov N.I.).
    Distribution in Kazakhstan: 23. Tarbagatai, 24. Dzungarian Alatau, 25. Zailiyskiy-Kungei Alatau, 25a. Ketmen-Terskey Alatau, 27. Kyrgyz Alatau, 29. Western Tien Shan.
    General distribution: mountain–central Asian (Afghanistan, Kazakhstan, Kyrgyzstan, Pakistan, Tajikistan, Uzbekistan, China).
  • Subgenus Reticulatobulbosa (Kamelin) N. Friesen (2005 in Aliso 22: 389).
    Type species Allium lineare L.
    Section Campanulata Kamelin (1980 in Bot. Journ. 65.10: 1461).
    Type species Allium xiphopetalum Aitch. & Baker.
    Allium barsczewskii Lipsky (1900 in Acta Horti Petropolit. 18: 114).
    Perennial. Occurs on fine-grained or rubbly steppes, slopes of foothills and mountains.
    Flowering V–VII.
    Examined herbarium specimens from the Kyrgyz Alatau: AA (Geographic area: Aulie-Ata district. Trails of the Kyrgyz range. To the northeast of the Ak-Chulak base of the Konesovkhoz, date 13.V.1933. author: Kornilova V.S. Geographic area: Kyrgyz Alatau Suyundyk-sai river. The northern slope is about 2500 m above sea level. date 22.VII.1947. authors: Rubtsov N. I., Stepanova E. F. Geographic area: Kyrgyz range. Sundyk-sai river gorge, northern slope, altitude 2500 m. date 28.VII.1947. authors: Rubtsov N.I., Stepanova E.F. Geographic area: Dzhamb. region, steppe trail of the mountain between the village of Chulak-Tau and Kok-Tal. date 30.V.1948. Pavlov N.V. Geographic area: Kyrgyz range, western extremity. Butumainak gorge. Limestone cliffs, southern slope. date 19.V.1961. author: Fisyun V.V. Geographic area: Kyrgyz range, northern gorges. Almalyk-sai gorge, southern steppe slopes. date 22.V.1961. author: Fisyun V.V. Geographic area: Kyrgyz Alatau range the central part of Almalyk-say. Southern steppe slope among Carex pachystilis. 22.V.1961. author: Gamayunova A.P. Geographic area: Kyrgyz range, Northern Gorges. Almaly-Sai Gorge. Meadow-Steppe Slopes. date 24.V.1961. author: Fisyun V.V. Geographic area: Kyrgyz range, Almalyk-sai gorge, eastern slit. date 24.V.1961 author: Gamayunova A.P. Geographic area: Kyrgyz range, northern gorges. Uzunbulak gorge, ranges of spurs. date 28.V.1961. author: Fisyun V.V. Geographic area: Kyrgyz range, the upper reaches of the Kaindy river, near the top of Mount Tegres, at an altitude of altitude h–1500 m. date 01.VI.1961. author: Gamayunova A. P. Geographic area: Kyrgyz range, northern gorges. Slopes of the Dzhaksalyk-Sai range. date 01.VI.1961. author: Gamayunova A. P. Geographic area: Foothill loess plain of the Kyrgyz range between Lugovoy and Dzhambul. Among the ephemerae. date 15.V.1963. author: Goloskokov V.P. Geographic area: Foothill loess plain of the Kyrgyz range between Merke and Meadow. Among the ephemeral meadow. date 15.V.1963. author: Goloskokov V.P. Geographic area: Southwestern part of the Kyrgyz range. Almaly-sai gorge. Along the southern rocky slopes. date 02.VI.1963. author: Goloskokov V.P. Geographic area: Western part of the Kyrgyz Alatau, valley of the Syugatti river, stony red range of low mountains. date 24.V.1984 author: Nelina N.V. Geographic area: Kyrg. Alat. river Aspara, tract. Char, watershed. date 22.VI.1985. author: Chubarova T.U. Geographic area: Zhambyl region, Kyrgyz Alatau. Merke Gorge, near the outpost date 12.V.2018 authors: Vesselova P.V., Mukhtubayeva S.K., Danilov M.P. Geographic area: Zhambyl region, Kyrgyz Alatau. Merke gorge, near the outpost, date 12.V.2018, authors: Vesselova P.V., Mukhtubayeva S.K., Danilov M.P.).
    Distribution in Kazakhstan: 21. Turkestan, 25. Zailiyskiy-Kungei Alatau, 26. Chu-Ili Mountains, 27. Kyrgyz Alatau, 28. Karatau, 29. Western Tien-Shan.
    General distribution: Iranian–Mountain–Middle Asian–Western Himalayan (Afghanistan, Iran, Kazakhstan, Kirgizstan, Pakistan, Tadzhikistan, Uzbekistan, West Himalaya).
    Allium longiradiatum (Regel) Vved. (1923 in Vved. & al., Key Fl. Tashkent Pt. 1—Allium tataricum var. longiradiatum Regel 1875 in Acta Horti Petropolit. 3.2: 180).
    Examined herbarium specimens from the Kyrgyz Alatau: AA (Kyrgyz Alatau range, foothills. date 25.V.1986. author: Kamenetskaya I.I.).
    Perennial. Inhabits loess plains and foothills. Flowering IV–V.
    Distribution in Kazakhstan: 27. Kyrgyz Alatau, 29. Western Tien Shan.
    General distribution: Western Tien Shan (Kazakhstan, Uzbekistan).
  • Section Scabriscapa (Tscholok.) N. Friesen (2006 in Aliso 22: 389).
    Type species Allium scabriscapum Boiss.
    Allium trachyscordum Vved. (1925 in Byull. Sredne-Aziatsk. Gosud. Univ. ix. Suppl. 11).
    Perennial. Occurs on rubbly mountain slopes. Flowering VI–VII.
    Examined herbarium specimens from the Kyrgyz Alatau: AA (Geographic area: Southwestern part of the Kyrgyz range, foothills to the northwest of Almaly-Say. date 03.VI.1963. author: Goloskokov V.P. Geographic area: Western part of the Kyrgyz Alatau, dale Sugats, left-bank lowlands from the cordon 2–3 km up, date 15.VI.1985 author: Karmysheva N.Kh. Geographic area: Western part of the Kyrgyz Alatau, northern macroslope, valley of the Syugata river, red hills adjacent to the mouth of the river, date 05.VIII.1988. author: Karmysheva N.Kh.).
    Distribution in Kazakhstan: 16. Betpakdala, 26. Chu-Ili Mountains, 27. Kyrgyz Alatau, 28. Karatau.
    General distribution: Betpakdala-Severoturan-Tianshanian (Kazakhstan, Kyrgyzstan).
  • Section Nigrimontana N. Friesen (2006 in Aliso 22:390).
    Type species Allium drobovii Vved.
    Allium oreoprasoides Vved. (1925 in Trudy Turkestansk. Nauchn. Obshch. 2: 29).
    Perennial. Inhabits rubbly mountain slopes. Flowering V–VI.
    Examined herbarium specimens from the Kyrgyz Alatau: AA (Geographic area: The western part of the Kyrgyz Alatau, the valley of the Aspara River, the Archaly tract, date 19.VIII.1984. author: Zaripov R.G. Geographic area: Western part Kyrgyz Alatau, northern macroslope, mouth of the Syugatta river, red-crushed stone ranges, date 24.V.1984. author: Nelina N.V.).
    Distribution in Kazakhstan: 27. Kyrgyz Alatau, 28. Karatau.
    General distribution: Western Tianshan (Kazakhstan (Endem).
The areal analysis of the studied group of species showed that 16 types of ranges were distributed among seven arealological groups: Central Palearctic (two species), Mountain–Central Asian (seven species), Mountain–Middle Asian (five species), North-Turano–Mountain–Middle Asian (two species), Betpakdalin-Tianshan (two species), Tianshan (six species), Prityanshan (two species). Such a distribution of species suggests that most of the species studied originated in the mountains.

2.2. Flow Cytometry

For six species collected during expedition trips (Allium turkestanicum, A. suworowii, A. barzsczewskii, A. artrosanguineum, A. margaritae, A. caeruleum), flow cytometry analysis was performed. In addition, literary information on the karyology of species of the genus Allium growing in the Kyrgyz Alatau is presented (Table 1).
According to the data (Table 1), most species demonstrate diploidy (2n = 16), which indicates the predominance of x = 8. For A. leptomorphum, A. parvulum, and A. semenowii, there is no information available on the number of chromosomes. Data on the genome size of these samples were obtained (Table 2 and Figure 3).

2.3. Phylogenetic Analysis

Due to the fact that out of 25 species noted for the Kazakhstan part of the flora of the Kyrgyz Alatau range, we had actual genetic material at our disposal for only 6 species (Figure 4), we were able to obtain ITS sequences only for these 6 species (eight specimens) (Table 1); the remaining ITS sequences were taken from the NCBI database [53]. It should be noted that most of the sequences used in this paper (for the missing species from the NCBI database) were sequenced earlier also by the authors of this paper.
The ITS tree of sequences is made using the studied specimens and supplemented with specimens from the NCBI database [53]. Samples of our own materials are highlighted in bold in the tree. For ease of visual perception, colour highlighting is provided.
The tree shows not only the species affiliation, but also the subgenus and sectional divisions (Figure 5). For Allium caeruleum, two different sequence types are present. Our accession A121 from the Kyrgyz Alatau, along with accession MG772547, is a sister group to Allium caesium. However, there are also three accessions in the NCBI GenBank [53], AJ412729, AJ411903, and MT923833, that act as sister groups to A. caesium and A. caeruleum, respectively (Figure 5). All other accessions of Allium taxa from the Kyrgyz Alatau are in the expected position, and each species forms a clear monophyletic clade.

3. Discussion

The analysis of species composition shows that within the Kyrgyz Alatau, representatives of subgenera Allium and Melanocrommyum are the most widely distributed among seven subgenera of the studied genus.
The subgenus Allium includes the largest number of species—nine (five sections), belonging mainly to the Allium section and characterised by adaptation to growing in the upper belt of mountains (subalpine and alpine belts). Representatives of the subgenus Allium are characterised by a wide ecological amplitude and play a key role in the vegetation cover of mountain ecosystems of the Kyrgyz Alatau. The subgenus Melanocrommyum is represented by five species (three sections), characterised by characteristic large inflorescences, which underlines their potential ornamental value. Representatives of the subgenus are adapted to arid conditions and are confined to stony places. Phenological plasticity and distinct ecological specialisation indicate a high degree of adaptability of the genus to various altitudinal zones of the region.
The richness of species and their specialisation underline the floristic uniqueness of the Kyrgyz Alatau as an important centre of biodiversity of the genus Allium in Central Asia. The majority of species are regionally confined to the Tien Shan floristic province. Some species are also found in the neighbouring ranges: Terskey Alatau, Zailiyskiy Alatau, Karatau [54]. Allium species in the Kyrgyz Alatau are clearly differentiated by altitudinal and microclimatic conditions, which indicates their high ecological plasticity and adaptation to extreme mountain conditions. Distribution by belts reflects the gradient from xerophytic steppes to mesophytic high-mountain meadows. Species of the genus Allium within the Kyrgyz Alatau in the territory of Kazakhstan demonstrate clear confinement to certain altitudinal belts and habitat types. The majority of species are found in mountain, subalpine, and alpine regions, where they are adapted to particular environmental conditions [13].
According to the results of the analysis by flow cytometry, data were obtained for six species of the genus Allium, represented in four subgenera and belonging to different sections. The following species were identified in the subgenus Allium: A. turkestanicum from section Mediasia with DNA content of 22.310 ± 0.566 pg, A. margaritae from section Brevispatha with 13.907 ± 0.047 pg, and A. caeruleum from section Caerulea with 20.043 ± 0.796 pg. In subgenus Melanocrommyum, A. suworiwii, a representative of section Acmopetala, is characterised by a value of 44.159 ± 0.446 pg. The subgenus Reticulatobulbosa is represented by the species A. barzschzewskii from section Campanulata (21.948 ± 0.624 pg), and subgenus Cepa by the species A. artrosanguineum from section Annuloprason with DNA content of 22.740 ± 0.018 pg (Table 2).
In the Plant DNA database [55], for most species characteristic of the Kyrgyz Alatau, the DNA content varies within 20–30 pg, with some exceptions showing much higher values. For example, Allium karataviense recorded 39.68 pg, A. platystemon 38.80 pg, and A. suworowii 37.62 pg. According to Jones and Rees [56], the minimum amount of DNA within the genus Allium was previously recorded in A. schoenoprasum (16.90 pg). It should be noted that for a significant number of species of the genus Allium, the size of the nuclear genome has not been determined so far, which opens prospects for further studies.
Within the framework of the present work, for A. margaritae, we recorded the minimum value of DNA content in the genus Allium equal to 13.907 ± 0.047 pg (Table 2; Figure 3). This is significantly lower than the value reported in Vakhtina et al. [43], where 31.50 pg is stated for the same species. This discrepancy probably indicates the possible presence of polyploid forms within A. margaritae. Considering the low coefficient of variation of our measurements (0.34%), the data obtained seem reliable.
Similar discrepancies between published data and our results were found for Allium barzschzewskii and A. suworowii. For A. barzschzewskii, we determined the DNA content at 21.948 pg, while a number of earlier publications for this species state a value of 31.60 pg [43]. Taking into account outdated methods of analysis and possible methodological differences, a discrepancy of about 10 pg can be considered acceptable.
For A. suworowii, we obtained a value of 44.159 pg, whereas the database states 37.62 pg [57,58]. Despite some difference, both values are in a close range and probably reflect both intraspecific variability and differences in the methods used. It should be emphasised that modern flow cytometry technologies provide higher accuracy and reproducibility of results, which increases the reliability of our measurements.
The species A. caeruleum showed a genome size of 20.043 pg, which is comparable to the previously published value of 23.50 pg [42]. Notably, the presence of polyploid forms (2n = 24, 32) (Table 1) in A. caeruleum indicates the species capacity for polyploidisation, which may be associated with adaptive responses or geographical variability.
For the two species studied, A. artrosanguineum and A. turkestanicum, the results of flow cytometry are presented for the first time. The values obtained are 22.740 ± 0.018 pg and 22.310 ± 0.566 pg, respectively.
Although the species are most likely diploid, differences in chromosome numbers within the section [59] suggest possible cytogenetic variation.
The discrepancy between our data and that of the published literature may be attributable to instrumental error, variations in the applied standards, and the utilisation of microdensitometry in certain studies.
Molecular phylogenetic data are of particular interest: based on the analysis of ITS-sequences, it was found that the studied onion species from the Kyrgyz Alatau occupy the expected phylogenetic positions and correspond to previously published phylogenetic reconstructions [60,61,62,63,64,65], with barely significant deviations detected. It is interesting that in Allium caeruleum, two different sequence types are present. Our accession A121, along with accessions MG772547 and AJ411903, is a sister group to Allium caesium. However, there are also two accessions, AJ412729 and MT923833, that act as sister groups to A. caesium and A. caeruleum, respectively. A broader study of A. caeruleum is warranted. Allium caeruleum is known to exhibit a ploidy range (see Table 1).
However, given that only 5 of the 25 Allium species distributed in the Kyrgyz Alatau were sampled directly from the Kyrgyz range (see Table 2), further sequencing may reveal new or refined phylogenetic relationships.

4. Material and Methods

4.1. Distribution Analyses

The objects of the present study were species of the genus Allium L. of the western part of the Kyrgyz Alatau.
Field studies were conducted during 2024–2025 in the territory of the western part of the Kyrgyz Alatau. The research included route surveys covering various types of habitats. In the course of field work, a targeted collection of herbarium material and samples of representatives of the genus Allium L. growing in this territory was carried out [5,6]. Along with this, they were photographed (Figure 2) and geographically referenced using a GPS device (Figure 4).
The identification of the collected materials was based on fundamental works on the genus Allium [3,5,6,66], and all recent publications concerning Allium species found in the Kyrgyz Alatau were also taken into account [60,61,62,63,64,65].
An areological analysis of Allium species was conducted to determine their geographical distribution and areal status within the study area. The geographical affiliation and nature of the range of each species were assessed based on a combination of floristic and areological sources, including fundamental reference books on the flora of Central Asia and neighbouring regions [67,68,69].
Each species was assigned an areological status according to its distribution outside the study area. Endemism was assessed based on information from modern POWO databases.
The herbarium collections of the Institute of Botany and Phytointroduction (AA, Almaty, Kazakhstan) and the Moscow State University named after M.V. Lomonosov (MW, Moscow, Russia) were studied. The names of taxa are provided according to the databases International Plant Names Index (IPNI) [70] and Plants of the World Online (POWO) [2]. Materials from the Plantarium website [14] were also used.
The QGIS 3.34.13 program was used for data mapping (https://qgis.org, accessed on 5 June 2025).

4.2. Flow Cytometry

The DNA content was determined by flow cytometry techniques with propidium iodide (PI) staining. Leaves dried with silica gel were used as samples. Samples were chopped as is standard, using a sharp razor blade in LB01 buffer containing PI (50 µg/mL), RNase (50 µg/mL) [71] supplemented with 12 mM sodium thiosulfate, and 1% polyvinylpyrrolidone [72]. The nuclear suspension was filtered through a nylon filter with a pore size of 30 μm. Analyses were performed on a Cytoflex (Beckman Coulter, Inc.) cytometer. Peaks with at least 1000 nuclei and a CV of less than 5% were used for analysis. Histograms were visualised and processed using CytExpert version 2.4 (Beckman Coulter, Inc., Brea, CA, USA). Descriptive statistics were calculated using XLStat (Addinsoft). As an internal standard, we used the Pisum sativum ‘Ctirad’, 2C = 9.09 pg and Vicia faba ‘Inovec’, 2C = 26.9 pg [71,73].

4.3. Phylogenetic Analyses

ITS DNA fragments were sequenced for the species studied of the genus Allium. The primers ITS1 (5′-TCCGTAGGTGAACCTGCGG-3′) and ITS4 (5′-TCCTCCTCCGCTTATTGATATATGC-3′) were used for ITS fragments. Polymerase chain reaction was performed in 50 µL of reaction mixture, using the Biomaster HS-Taq PCR-Color 2x PCR kit (Biolabmix LLC, Novosibirsk, Russia) in the following composition—per sample: 25 µL of ready PCR mixture, 21 µL of H2O, 1 µL of 10 mM respective primers, 2 µL of total DNA. The amplification protocol was as follows: 95 °C (3 min); 35 cycles: 95 °C (20 s), 57 °C (30 s), 72 °C (30 s); 72 °C (5 min). Amplification products were purified using microcolumns. Sequencing was performed by the Sanger method, using an ABI PRISM 3500 XL sequencer. Sequence chromatograms were manually edited using Chromas Lite 2.1, aligned with ClustalX [74], and manually refined in MEGA 11 software 11.0. 13 [75].
NrITS datasets were analysed separately through Fitch parsimony with the heuristic search option in PAUP version 4.0 b10 [76], with MULTREES, TBR branch swapping, and 100 replicates of random addition sequence. Gaps were treated as missing data. The consistency index (CI) was calculated to estimate the amount of homoplasy in the character set [77]. The most parsimonious trees returned by the analysis were summarised in one consensus tree using the strict consensus method. Bootstrap support (BS) was performed using 1000 pseudoreplicates to assess the support of the clades [78]. Bayesian phylogenetic analyses were also performed using MrBayes 3.1.23 [79]. The sequence evolution model was chosen by following the Akaike information criterion (AIC) obtained from jModelTest2 [80]. Two independent analyses with four Markov chains were run for 10 million generations, sampling trees every 100 generations. The first 25% of the trees were discarded as burn-in. The remaining 150,000 trees were combined into a single dataset, and a majority-rule consensus tree was obtained, along with posterior probabilities (PPs).
Two species were selected as an outgroup: Tulbaghia violacea Harv. and Nothoscordum bivalve (L.) Britton [65].

5. Conclusions

Thus, as a result of field studies, molecular–genetic analysis, flow cytometry, and a critical review of the literature, it has been established that the flora of the genus Allium within the Kyrgyz Alatau includes 25 species belonging to seven subgenera and 17 sections. These data represent the most complete taxonomic assessment of Allium species diversity in this region to date. As part of the work, the nomenclature of a number of taxa was updated in accordance with modern systematic approaches (for example, Allium polyphyllum is treated as a synonym of A. carolinianum, and A. caricifolium as a synonym of A. pallasii), which is important for the harmonisation of regional and global botanical databases.
Analysis of areal data indicates a predominance of mountain species, highlighting the importance of the Kyrgyz Alatau as one of the key centres for the formation and preservation of high-altitude flora in Central Asia. The results of flow cytometry and karyological (the literature data) analysis showed that, with the same, presumably diploid, level of ploidy, representatives of the genus demonstrate wide variability in nuclear genome size.
Phylogenetic analysis confirmed that most of the studied species corresponded to the expected taxonomic relationships, but also revealed potential taxonomic inconsistencies. This highlights the need for further research on representatives of the genus Allium in the western part of the Kyrgyz Alatau, which could lead to a refinement of the species composition, the discovery of new species or species not previously recorded in this region, and the exclusion of erroneously identified taxa.

Author Contributions

Conceptualisation, D.S.A.; methodology, D.S.A., N.F., B.B.O., S.U. and M.V.S.; formal analysis, N.F., P.V.V. and G.M.K.; writing—preparation of initial draft, D.S.A., P.V.V., G.M.K. and N.F.; writing—editing, N.F., D.S.A., P.V.V. and G.M.K.; author’s supervision, N.F.; project administration, D.S.A. and N.F.; acquisition of funding, P.V.V. All authors have read and agreed to the published version of the manuscript.

Funding

This research is funded by the Science Committee of the Ministry of Science and Higher Education of the Republic of Kazakhstan (Grant AP23484591 “Comprehensive research (floristic, molecular genetic and resource) on the Allium L. genus of the Kyrgyz Alatau cross-border range—a scientific foundation for the management of the region’s natural resources” (2024–2026)).

Data Availability Statement

All data supporting this study’s findings are available in the main text or Appendix A.

Conflicts of Interest

All authors declare that they have no competing interests and personal relationships and agree on the contents of the paper.

Appendix A

Plants 14 02890 i001a
Plants 14 02890 i001b

References

  1. Friesen, N. Chapter 1. Introduction to Edible Alliums: Evolution, Classification and Domestication. In Edible Allium: Botany, Production and Uses; Rabinowich, H.D., Thomas, B., Eds.; CAB International: Wallingford, UK, 2023; pp. 1–19. [Google Scholar] [CrossRef]
  2. POWO Royal Botanic Gardens. Plants of the World Online. Facilitated by the Royal Botanic Gardens, Kew. Available online: http://www.plantsoftheworldonline.org (accessed on 10 June 2025).
  3. Vvedensky, A.I. Identifier of Plants of Central Asia Genus Allium L.; FAN Uzbek SSR: Tashkent, Uzbekistan, 1971; pp. 39–89. (In Russian) [Google Scholar]
  4. Khassanov, F.O. Taxonomical and Etnobotanical aspect of Allium species from Midle Asia with particular reference to subgenus Allium. In The Allium Genomes. Compedium of Plant Genomes; Shigyo, M., Khar, A., Abdelrahman, M., Eds.; Springer Nature: Cham, Switzerland, 2018. [Google Scholar] [CrossRef]
  5. Vvedensky, A.I. Flora of the USSR Genus Allium L.; Publishing House of the USSR Academy of Sciences: Leningrad, Russia, 1935; Volume 4, pp. 112–280. (In Russian) [Google Scholar]
  6. Pavlov, N.V. Flora of Kazakhstan; Academy of Sciences of the Kazakh SSR: Alma-Ata, Kazakhstan, 1958; Volume 2. (In Russian) [Google Scholar]
  7. Kubentayev, S.A.; Alibekov, D.T.; Perezhogin, Y.V.; Lazkov, G.A.; Kupriyanov, A.N.; Ebel, A.L.; Izbastina, K.; Borodulina, O.; Kubentayeva, B.B. Revised checklist of endemic vascular plants of Kazakhstan. PhytoKeys 2024, 238, 241–279. [Google Scholar] [CrossRef]
  8. Rachkovskaya, E.I.; Volkova, E.A.; Khramtsov, V.N. Botanical Geography of Kazakhstan and Central Asia (Within the Desert Region); Komarov Botanical Institute: Sankt Petersburg, Russia, 2003; p. 424. (In Russian) [Google Scholar]
  9. Bajtenov, M.S. Flora Kazahstana. Rodovoj Kompleks Flory [Flora of Kazakhstan. Generic Complex of Flora]; Gylym: Almaty, Kazakhstan, 2001. (In Russian) [Google Scholar]
  10. Epiktetov, V. The Genus Allium in the Flora of Kazakhstan. Floristic List. Available online: https://www.plantarium.ru/page/flora/id/1087.html (accessed on 10 June 2025). (In Russian).
  11. Red Book of Kazakhstan, 2nd ed.; ArtPrintXXI: Astana, Kazakhstan, 2014; Volume 2. (In Russian)
  12. Abdildanov, D.S.; Vesselova, P.V.; Kudabayeva, G.M.; Osmonali, B.B.; Shormanova, A.A.; Ussen, S. To the Distribution of Allium suworowii Regel Within Kazakhstan. Redaksyalyk Alka. 29 June 2023, 13. Available online: https://astanabotsad.kz/storage/app/media/uploaded-files/Conference%20.pdf (accessed on 7 September 2025). (In Russian).
  13. Gemejiyeva, N.; Abdildanov, D.; Kudabayeva, G.; Vesselova, P.; Nelina, N.; Friesen, N. Species of the genus Allium L. of the western part of the Kyrgyz Alatau range: The current status and prospects of studying. Fundam. Exp. Biol. 2025, 11830, 13–25. [Google Scholar] [CrossRef]
  14. Plantarium (2007–2025): An Open Online Atlas—Definition of Plants and Lichens of Russia and Neighbouring Countries. Available online: http://www.plantarium.ru/ (accessed on 10 June 2025). (In Russian).
  15. INaturalist. Available online: https://www.inaturalist.org/search?q=Allium (accessed on 10 August 2025).
  16. Friesen, N.; Grützmacher, L.; Skaptsov, M.; Vesselova, P.; Dorofeyev, V.; Luferov, A.N.; Hurka, H. Allium pallasii and A. caricifolium—Surprisingly diverse old steppe species, showing a clear geographical barrier in Lake Zaysan. Plants 2022, 11, 1465. [Google Scholar] [CrossRef]
  17. Sennikov, A.N.; Lazkov, G.A.; Ganabyeva, M.R.; Friesen, N.; German, D.A. Taxonomic corrections and new records for vascular plants of Kyrgyzstan, 6. Nord. J. Bot. 2025, 2025, e04731. [Google Scholar] [CrossRef]
  18. Kolbintsev, V. Image of Allium caeruleum Pall.//Plantarium. Plants and Lichens of Russia and Neighboring Countries: Open Online Galleries and Plant Identification Guide. 2014. Available online: https://www.plantarium.ru/lang/en/page/image/id/261564.html (accessed on 6 August 2025).
  19. Kolbintsev, V. Image of Allium dasyphyllum Vved.//Plantarium. Plants and Lichens of Russia and Neighboring Countries: Open Online Galleries and Plant Identification Guide. 2014. Available online: https://www.plantarium.ru/lang/en/page/image/id/567120.html (accessed on 6 August 2025).
  20. Epiktetov, V. Image of Allium leptomorphum Vved.//Plantarium. Plants and Lichens of Russia and Neighboring Countries: Open Online Galleries and Plant Identification Guide. 2015. Available online: https://www.plantarium.ru/lang/en/page/image/id/406739.html (accessed on 9 August 2025).
  21. Belousov, E. Image of Allium longiradiatum (Regel) Vved.//Plantarium. Plants and Lichens of Russia and Neighboring Countries: Open Online Galleries and Plant Identification Guide. 2022. Available online: https://www.plantarium.ru/lang/en/page/image/id/754544.html (accessed on 6 August 2025).
  22. Kolbintsev, V. Image of Allium margaritae B. Fedtsch.//Plantarium. Plants and Lichens of Russia and Neighboring Countries: Open Online Galleries and Plant Identification Guide. 2018. Available online: https://www.plantarium.ru/lang/en/page/image/id/570673.html (accessed on 6 August 2025).
  23. Ebel, A.L. Image of Allium oreoprasoides Vved.//Plantarium. Plants and Lichens of Russia and Neighboring Countries: Open Online Galleries and Plant Identification Guide. 2018. Available online: https://www.plantarium.ru/lang/en/page/image/id/596196.html (accessed on 9 August 2025).
  24. Kolbintsev, V. Image of Allium parvulum Vved.//Plantarium. Plants and Lichens of Russia and Neighboring Countries: Open Online Galleries and Plant Identification Guide. 2017. Available online: https://www.plantarium.ru/lang/en/page/image/id/510761.html (accessed on 6 August 2025).
  25. Kolbintsev, V. Image of Allium platystemon Kar. & Kir.//Plantarium. Plants and Lichens of Russia and Neighboring Countries: Open Online Galleries and Plant Identification Guide. 2018. Available online: https://www.plantarium.ru/lang/en/page/image/id/580173.html (accessed on 6 August 2025).
  26. Epiktetov, V. Image of Allium carolinianum DC.//Plantarium. Plants and Lichens of Russia and Neighboring Countries: Open Online Galleries and Plant Identification Guide. 2013. Available online: https://www.plantarium.ru/lang/en/page/image/id/194632.html (accessed on 6 August 2025).
  27. Kolbintsev, V. Image of Allium semenowii Regel//Plantarium. Plants and Lichens of Russia and Neighboring Countries: Open Online Galleries and Plant Identification Guide. 2014. Available online: https://www.plantarium.ru/lang/en/page/image/id/253469.html (accessed on 6 August 2025).
  28. Epiktetov, V. Image of Allium taschkenticum F.O. Khass. & R.M. Fritsch//Plantarium. Plants and Lichens of Russia and Neighboring Countries: Open Online Galleries and Plant Identification Guide. 2015. Available online: https://www.plantarium.ru/lang/en/page/image/id/403084.html (accessed on 6 August 2025).
  29. Kolbintsev, V. Image of Allium trachyscordum Vved.//Plantarium. Plants and Lichens of Russia and Neighboring Countries: Open Online Galleries and Plant Identification Guide. 2014. Available online: https://www.plantarium.ru/lang/en/page/image/id/253715.html (accessed on 7 August 2025).
  30. Kolbintsev, V. Image of Allium turkestanicum Regel//Plantarium. Plants and Lichens of Russia and Neighboring Countries: Open Online Galleries and Plant Identification Guide. 2016. Available online: https://www.plantarium.ru/lang/en/page/image/id/459840.html (accessed on 6 August 2025).
  31. Tokenova, A.; Sitpayeva, G.; Gemejiyeva, N.; Suleimenova, S.; Friesen, N.; Batayeva, D. Wild Allium longicuspis Regel is a Feral Form of Allium sativum L. in Kazakhstan: A Comparative Molecular Genetic Analysis. Online J. Biol. Sci. 2023, 23, 33–43. [Google Scholar] [CrossRef]
  32. Kolbintsev, V. Image of Allium dasyphyllum Vved.//Plantarium. Plants and Lichens of Russia and Neighboring Countries: Open Online Galleries and Plant Identification Guide. 2018. Available online: https://www.plantarium.ru/lang/en/page/image/id/566975.html (accessed on 10 June 2025).
  33. Fritsch, R.M. A Preliminary Review of Allium subg. Melanocrommyum in Central Asia; Leibniz-Institut für Pflanzengenetik und Kulturpflanzenforschung Gatersleben (IPK): Gatersleben, Germany, 2016. [Google Scholar]
  34. Friesen, N.; Lazkov, G.; Levichev, I.G.; Leweke, M.; Abdildanov, D.; Turdumatova, N.; Murtazaliev, R.; Dzumanov, S.; Sitpayeva, G.T.; Vesselova, P.; et al. Taxonomy and dated molecular phylogeny of Allium oreophilum sensu lato (A. subg. Porphyroprason) uncover a surprising number of cryptic taxa. Taxon, 2025; early view. [Google Scholar] [CrossRef]
  35. Zakirova, R.O.; Nafanailova, I.I. Chromosome numbers in members of some families of the Kazakhstan flora. Bot. Zhurn. 1992, 77, 71–72. [Google Scholar]
  36. Vakhtina, L.I. Chromosome numbers in some species of the genus Allium (Alliaceae) in the flora of the USSR. Bot. Zhurn. 1985, 70, 700–701. [Google Scholar]
  37. He, X.-J.; Xu, J.-M. Karyotypes of 4 species in Allium sect. Haplostemon Boiss. from China. J. Syst. Evol. 2001, 39, 423–432. [Google Scholar]
  38. Tang, H.; Lihua, M.; Shiqimg, A.; Jianquaan, L. Origin of the Qinghai-Tibetan Plateau endemic Milula (Liliaceae): Further insights from karyological comparisons with Allium. Caryologia 2005, 58, 320–331. [Google Scholar] [CrossRef]
  39. Löve, Á. IOPB chromosome number reports LVI. Taxon 1977, 26, 257–274. [Google Scholar] [CrossRef]
  40. Pogosian, A.I.; Seisums, A.G. Chromosome numbers in some species of Allium (Alliaceae) from the Afganistan, Turkey and states of Middle Asia. Bot. Zhurn. 1992, 77, 103–104. [Google Scholar]
  41. Al-Sheikh Hussain, L.A.; Elkington, T.T. Giemsa C-band karyotypes of diploid and triploid Allium caeruleum and their genomic relationship. Cytologia 1978, 43, 405–410. [Google Scholar]
  42. Ohri, D.; Pistrick, K. Phenology and genome size variation in Allium L.—A tight correl correlation? Plant Biol. 2001, 3, 654–660. [Google Scholar] [CrossRef]
  43. Vakhtina, L.I.; Zakirova, R.O.; Vakhtin, Y.B. Interspecific differences in DNA content and taxonomically significant characters in the genus Allium L. (Liliaceae). Bot. Zhurnal 1977, 62, 677–684. [Google Scholar]
  44. Zakirova, R.O. Chromosome numbers of some Alliaceae, Salicaceae, Polygonaceae, and Chenopodiaceae of the South Balkhash territory. Citologija 1999, 41, 1064. [Google Scholar]
  45. Friesen, N.V. Chromosome numbers of the representatives of the family Alliaceae from Siberia. Bot. Zhurnal 1986, 71, 113–115. [Google Scholar]
  46. Zakirova, R.O. Chromosome Numbers of Flowering Plants of the Flora of Kazakhstan; Nauka: Almaty, Kazakhstan, 2003; 278p. (In Russian) [Google Scholar]
  47. Friesen, N. Allium ubsicolum Regel—A new species for the Flora of USSR. Nov. Syst. Vyssh. Rast. 1988, 25, 47–48. [Google Scholar]
  48. Friesen, N.; Vesselova, P.; Osmonaly, B.; Sitpaeva, G.; Luferov, A.; Shmakov, A. Allium toksanbaicum (Amaryllidaceae), a new species from Southeast Kazachstan. Phytotaxa 2021, 494, 251–267. [Google Scholar] [CrossRef]
  49. Kaul, R. In Chromosome number reports LXXII. Taxon 1981, 30, 707. [Google Scholar] [CrossRef]
  50. Zakirova, R.O.; Nafanailova, I.I. Chromosome numbers in some species of the Kazakhstan flora. Bot. Zhurn. 1988, 73, 1493–1494. [Google Scholar]
  51. Fritsch, R.M.; Astanova, S.B. Uniform karyotypes in different sections of Allium L. subgenus Melanocrommyum (Webb & Berth.) Rouy from central Asia. Feddes Repert. 1998, 109, 539–549. [Google Scholar]
  52. Vakhtina, L.I.; Kudrjaschova, G.L. Cytotaxonomical study in some Allium species of the subgenus Rhizirideum (Koch) Wendelbo (section Reticulato-bulbosa R. Kam). Sist. I Evol. Vyss. Rastenii 1980, 75–82. Available online: https://ccdb.tau.ac.il/Angiosperms/Amaryllidaceae/Allium/Allium%20dolichomischum%20Vved./ (accessed on 7 September 2025).
  53. National Center for Biotechnology Information (NCBI). Available online: https://www.ncbi.nlm.nih.gov/ (accessed on 10 June 2025).
  54. Tojibaev, K.S.; Jang, C.G.; Lazkov, G.A.; Chang, K.S.; Sitpayeva, G.T.; Safarov, N.; Oh, S.H. An annotated checklist of endemic vascular plants of the Tian-Shan Mountains in Central Asian countries. Phytotaxa 2020, 464, 117–158. [Google Scholar] [CrossRef]
  55. Leitch, I.J.; Johnston, E.; Pellicer, J.; Hidalgo, O.; Bennett, M.D. Plant DNA C-values Database (release 9.0, April 2019). Available online: https://cvalues.science.kew.org/ (accessed on 10 June 2025).
  56. Jones, R.N.; Rees, H. The influence of B-chromosomes upon the nuclear phenotype in rye. Chromosoma 1968, 24, 158–176. [Google Scholar] [CrossRef]
  57. Gurushidze, M.; Fritsch, R.M.; Blattner, F.R. Phylogenetic analysis of Allium subgenus Melanocrommyum infers cryptic species and demands a new sectional classification. Mol. Phylogenet. Evol. 2008, 49, 997–1007. [Google Scholar] [CrossRef]
  58. Gurushidze, M.; Fuchs, J.; Blattner, F.R. The evolution of genome size variation in drumstick onions (Allium subgenus Melanocrommyum). Syst. Bot. 2012, 37, 96–104. [Google Scholar] [CrossRef]
  59. Kobrlová, L.; Jandová, M.; Vojtěchová, K.; Šafářová, L.; Duchoslav, M. New estimates and synthesis of chromosome numbers, ploidy levels and genome size variation in Allium sect. Codonoprasum: Advancing our understanding of the unresolved diversification and evolution of this section. Bot. Stud. 2024, 65, 40. [Google Scholar] [CrossRef]
  60. Friesen, N.; Fritsch, R.M.; Blattner, F. Phylogeny and new intrageneric classification of Allium L. (Alliaceae) based on nuclear ribosomal DNA ITS sequences. Aliso 2006, 22, 372–395. [Google Scholar] [CrossRef]
  61. Li, Q.Q.; Zhou, S.D.; He, X.J.; Yu, Y.; Zhang, Y.C.; Wei, X.Q. Phylogeny and biogeography of Allium (Amaryllidaceae: Allieae) based on nuclear ribosomal internal transcribed spacer and chloroplast rps16 sequences, focusing on the inclusion of species endemic to China. Ann. Bot. 2010, 106, 709–733. [Google Scholar] [CrossRef]
  62. Abdildanov, D.S.; Vesselova, P.V.; Kudabayeva, G.M.; Osmonali, B.B.; Skaptsov, M.V.; Friesen, N. Endemic of Kazakhstan Allium lehmannianum Merckl. Ex Bunge and Its Position Within the Genus Allium. Plants 2025, 14, 1113. [Google Scholar] [CrossRef]
  63. Yusupov, Z.; Ergashov, I.; Volis, S.; Makhmudjanov, D.; Dekhkonov, D.; Khassanov, F.; Sun, H. Seed macro-and micromorphology in Allium (Amaryllidaceae) and its phylogenetic significance. Ann. Bot. 2022, 129, 869–911. [Google Scholar] [CrossRef] [PubMed]
  64. Seregin, A.P.; Friesen, N. Molecular and morphological revision reveals different evolution patterns in Allium sect. Oreiprason and sect. Falcatifolia (Amaryllidaceae). In Semicentenary After Konstantin Meyer: XIII Moscow Symposium on Plant Phylogeny; Timonin, A.C., Ed.; Moscow MAKS Press: Moscow, Russia, 2015; pp. 353–356. [Google Scholar] [CrossRef]
  65. Friesen, N.; Herden, T.; Leweke, M.; Grützmacher, L.; Fragman-Sapir, O.; Hurka, H.; Frank, R.; Blattner, F.R.; Fritsch, R.M. Dated phylogeny, phylogeography, and classification of Allium subgenus Amerallium (Amaryllidaceae) from the Old World, based on six DNA fragments. Taxon 2024, 73, 971–991. [Google Scholar] [CrossRef]
  66. Goloskokov, V.P. Illustrated Identifier of Plants of Kazakhstan; Nauka Kazahskoj SSR: Alma-Ata, Kazakhstan, 1969; Volume 1. (In Russian) [Google Scholar]
  67. Kamelin, R.V. Florogenetic Analysis of the Natural Flora of Mountainous Central Asia; Nauka: Leningrad, Russia, 1973; 355p. [Google Scholar]
  68. Tolmachev, A.I. Floristic Zoning of the World; Nauka: Leningrad, Russia, 1974. [Google Scholar]
  69. Hultén, E.; Fries, M. Atlas of North European Vascular Plants North of the Tropic of Cancer; Koeltz Scientific Books: Königstein, Germany, 1986. [Google Scholar]
  70. The Royal Botanic Gardens Kew; Harvard University Herbaria; Libraries and Australian National Botanic Gardens. IPNI International Plant Names Index. Available online: http://www.ipni.org (accessed on 10 June 2025).
  71. Doležel, J.; Sgorbati, S.; Lucretti, S. Comparison of three DNA fluorochromes for flow cytometric estimation of nuclear DNA content in plants. Physiol. Plant. 1992, 85, 625–631. [Google Scholar] [CrossRef]
  72. Skaptsov, M.V.; Kutsev, M.G.; Smirnov, S.V.; Vaganov, A.V.; Uvarova, O.V.; Shmakov, A.I. Standards in plant flow cytometry: An overview, polymorphism and linearity issues. Turczaninowia 2024, 27, 86–104. [Google Scholar] [CrossRef]
  73. Doležel, J.; Greilhuber, J.; Lucretti, S.; Meister, A.; Lysák, M.; Nardi, L.; Obermayer, R. Plant genome size estimation by flow cytometry: Inter-laboratory comparison. Ann. Bot. 1998, 82, 17–26. [Google Scholar] [CrossRef]
  74. Thompson, J.D.; Gibson, T.J.; Plewniak, F.; Jeanmougin, F.; Higgins, D.G. The Clustal X windows interface: Flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res. 1997, 25, 4876–4882. [Google Scholar] [CrossRef]
  75. Tamura, K.; Stecher, G.; Kumar, S. MEGA11: Molecular evolutionary genetics analysis version 11. Mol. Biol. Evol. 2021, 38, 3022–3027. [Google Scholar] [CrossRef]
  76. Swofford, D.L. PAUP*: Phylogenetic Analysis Using Parsimony (*and Other Methods); Version 4.0b10; Sinauer Associates: Sunderland, MA, USA, 2002. [Google Scholar]
  77. Kluge, A.G.; Farris, J.S. Quantitative phyletic and the evolution of anurans. Syst. Biol. 1969, 18, 1–32. [Google Scholar] [CrossRef]
  78. Felsenstein, J. Confidence limits on phylogenies: An approach using the bootstrap. Evolution 1985, 39, 783–791. [Google Scholar] [CrossRef]
  79. Ronquist, F.; Huelsenbeck, J.P. MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 2003, 19, 1572–1574. [Google Scholar] [CrossRef]
  80. Darriba, D.; Taboada, G.L.; Doallo, R.; Posada, D. jModelTest 2: More models, new heuristics and parallel computing. Nat. Methods 2012, 9, 772. [Google Scholar] [CrossRef]
Plants 14 02890 g001
Figure 1. The study area is the Kazakh part of the Kyrgyz Alatau range.
Figure 1. The study area is the Kazakh part of the Kyrgyz Alatau range.
Plants 14 02890 g001
Plants 14 02890 g002aPlants 14 02890 g002b
Figure 2. (a) Photographs of Allium species from the Kyrgyz Alatau. A—A. atrosanguineum (photo N. Friesen), B—A. barsczewskii (photo Abdildanov), C—A. caeruleum [18], D—A. caesium (photo Abdildanov), E—A. caricifolium (photo Abdildanov), F—A. dasyphyllum [19], G—A. fetisowii (photo N. Friesen), H—A. hymenorhizum (photo Abdildanov), I—A. karataviense (photo Abdildanov), J—A. leptomorphum [20], K—A. longiradiatum [21], L—A. margaritae [22]. (b) M—A. obliquum (photo Abdildanov), N—A. oreoprasoides [23], O—A. oreoprasum (photo N. Friesen), P—A. parvulum [24], Q—A. platyspathum (photo Vesselova), R—A. platystemon [25], S—A. polyphyllum [26], T—A. sativum (photo N. Friesen), U—A. semenowii [27], V—A. suworowii (photo Abdildanov), W—A. taschkenticum [28], X—A. trachyscordum [29], Y—A. turkestanicum [30].
Figure 2. (a) Photographs of Allium species from the Kyrgyz Alatau. A—A. atrosanguineum (photo N. Friesen), B—A. barsczewskii (photo Abdildanov), C—A. caeruleum [18], D—A. caesium (photo Abdildanov), E—A. caricifolium (photo Abdildanov), F—A. dasyphyllum [19], G—A. fetisowii (photo N. Friesen), H—A. hymenorhizum (photo Abdildanov), I—A. karataviense (photo Abdildanov), J—A. leptomorphum [20], K—A. longiradiatum [21], L—A. margaritae [22]. (b) M—A. obliquum (photo Abdildanov), N—A. oreoprasoides [23], O—A. oreoprasum (photo N. Friesen), P—A. parvulum [24], Q—A. platyspathum (photo Vesselova), R—A. platystemon [25], S—A. polyphyllum [26], T—A. sativum (photo N. Friesen), U—A. semenowii [27], V—A. suworowii (photo Abdildanov), W—A. taschkenticum [28], X—A. trachyscordum [29], Y—A. turkestanicum [30].
Plants 14 02890 g002aPlants 14 02890 g002b
Plants 14 02890 g003
Figure 3. Examples of ungated flow cytometric histograms of the Allium samples (log scale). (A) A. barzsczewskii; (B) A. turkestanicum; (C) A. atrosanguineum; (D) A. margaritae; (E,F) A. suworowii. P.s.—Pisum sativum internal standard, V.f.—Vicia faba internal standard.
Figure 3. Examples of ungated flow cytometric histograms of the Allium samples (log scale). (A) A. barzsczewskii; (B) A. turkestanicum; (C) A. atrosanguineum; (D) A. margaritae; (E,F) A. suworowii. P.s.—Pisum sativum internal standard, V.f.—Vicia faba internal standard.
Plants 14 02890 g003
Plants 14 02890 g004
Figure 4. Map of specimen collection points of Allium species.
Figure 4. Map of specimen collection points of Allium species.
Plants 14 02890 g004
Plants 14 02890 g005
Figure 5. ITS tree of species of the genus Allium. The joint presence of Bayesian with a probability greater than 0.98 and bootstrap support greater than 95% is indicated by a black dot. The samples we investigated are highlighted in bold. The following data were obtained by running the data through the JModeltest software: 2.1.10. 010234+G+F, -lnL 7923.16582, AIC 16137.894239, weight 0.493067.
Figure 5. ITS tree of species of the genus Allium. The joint presence of Bayesian with a probability greater than 0.98 and bootstrap support greater than 95% is indicated by a black dot. The samples we investigated are highlighted in bold. The following data were obtained by running the data through the JModeltest software: 2.1.10. 010234+G+F, -lnL 7923.16582, AIC 16137.894239, weight 0.493067.
Plants 14 02890 g005
Table 1. Karyological data of species of the genus Allium growing in the Kyrgyz Alatau.
Table 1. Karyological data of species of the genus Allium growing in the Kyrgyz Alatau.
No.Species of the Genus AlliumNumber of ChromosomesLiterature
1A. atrosanguineum2n = 16[35]
2A. barsczewskii2n = 16[36]
3A. caeruleum2n = 16, 24, 32
2n = 16; 24
2n = 16		[37,38]
[39,40]
[41,42]
4A. caesium2n = 16[43,44]
5A. caricifolium2n = 16[16,43]
6A. dasyphyllum2n = 16[40]
7A. fetisowii2n = 16[35,40]
8A. hymenorhizum2n = 16[35,39,42,43,45]
9A. karataviense2n = 18[35,39,40]
10A. leptomorphum--
11A. longiradiatum2n = 16[35]
12A. margaritae2n = 16[46]
13A. obliquum2n = 16[45,47,48]
14A. oreoprasoides2n = 16[46]
15A. oreoprasum2n = 16[43,49]
16A. parvulum--
17A. platyspathum2n = 16[43,50]
18A. platystemon2n = 16[17]
19A. polyphyllum2n = 16[35]
20A. sativum2n = 16[31,43]
21A. semenowii--
22A. suworowii2n = 16[43,49]
23A. taschkenticum2n = 16[35,51]
24A. trachyscordum2n = 16[52]
25A. turkestanicum2n = 16[46]
Table 2. Collection points of genetic material of species of the genus Allium, accessions number of ITS sequences, and DNA content of the studied species.
Table 2. Collection points of genetic material of species of the genus Allium, accessions number of ITS sequences, and DNA content of the studied species.
No.Sample NumberSpeciesLocation of Material CollectionVoucher NumberITSMean 2C ± SD, pgCVNStd.
1Al16Allium turkestanicumBetpakdala floristic region, Zhambyl region, southern part of Betpakdala
N 45.839444 E 73.413889		AA0003680PV91572222.310 ± 0.5662.54%5P.s.
Al22A. turkestanicumKyrgyz Alatau, Zhambyl region
N 42.889830 E 71.801594		AA0003685PV915719
2Al17A. suworowiiMoyinkum floristic area, Zhambyl region, Chui district, close to the road, Moyinkum-Chu highway, sands. Saxaulnik.
N 44.257222 E 73.190556		AA0003681PV91572444.159 ± 0.4461.01%4P.s., V.f.
3Al18A. barsczewskiiMoyinkum floristic area, Zhambyl region, Chui district, close to the road on the left side of the road in the town of Chu.
N 43.3925 E 74.026111		AA0003682
(Appendix A)		PV91572121.948 ± 0.6242.84%4P.s.
4Al19A. barsczewskiiKyrgyz Alatau, Zhambyl region, T. Ryskulov district, Karakystak village.
N 42.792222 E 72.9		AA0003683PV915720
5Al21A. caeruleumKyrgyz Alatau, Zhambyl region, T. Ryskulov district, Karakystak.
N 42.792222 E 72.9		AA0003684PV91572320.043 ± 0.7963.97%3P.s., V.f.
7Al23A. atrosanguineumKyrgyz Alatau, Zhambyl Oblast, Kaskasu gorge.
N 42.543611 E 73.203333		AA0003686PV91571822.740 ± 0.0180.08%3P.s.
8Al24A. margaritaeKyrgyz Alatau, Zhambyl region, Zhambyl district, Ulken Almalysay, southern slope.
N 42.898889 E 71.711944		AA0003687
(Appendix A)		PV91571713.907 ± 0.0470.34%3P.s.
Note: pg—picogram, CV—coefficient of variation sample, N—number of analysed individuals, Std.—standard deviation.
Disclaimer/Publisher’s Note: The statements, opinions and data contained in all publications are solely those of the individual author(s) and contributor(s) and not of MDPI and/or the editor(s). MDPI and/or the editor(s) disclaim responsibility for any injury to people or property resulting from any ideas, methods, instructions or products referred to in the content.

Share and Cite

MDPI and ACS Style

Vesselova, P.V.; Kudabayeva, G.M.; Abdildanov, D.S.; Osmonali, B.B.; Ussen, S.; Skaptsov, M.V.; Friesen, N. Integral Assessment of Species of the Genus Allium L. (Amaryllidaceae) in the Western Part of the Kyrgyz Alatau. Plants 2025, 14, 2890. https://doi.org/10.3390/plants14182890

AMA Style

Vesselova PV, Kudabayeva GM, Abdildanov DS, Osmonali BB, Ussen S, Skaptsov MV, Friesen N. Integral Assessment of Species of the Genus Allium L. (Amaryllidaceae) in the Western Part of the Kyrgyz Alatau. Plants. 2025; 14(18):2890. https://doi.org/10.3390/plants14182890

Chicago/Turabian Style

Vesselova, Polina V., Gulmira M. Kudabayeva, Daulet Sh. Abdildanov, Bektemir B. Osmonali, Serikbay Ussen, Mikhail V. Skaptsov, and Nikolai Friesen. 2025. "Integral Assessment of Species of the Genus Allium L. (Amaryllidaceae) in the Western Part of the Kyrgyz Alatau" Plants 14, no. 18: 2890. https://doi.org/10.3390/plants14182890

APA Style

Vesselova, P. V., Kudabayeva, G. M., Abdildanov, D. S., Osmonali, B. B., Ussen, S., Skaptsov, M. V., & Friesen, N. (2025). Integral Assessment of Species of the Genus Allium L. (Amaryllidaceae) in the Western Part of the Kyrgyz Alatau. Plants, 14(18), 2890. https://doi.org/10.3390/plants14182890

Note that from the first issue of 2016, this journal uses article numbers instead of page numbers. See further details here.

Article Metrics

Back to TopTop