Editorial

7 pages, 229 KiB

Open AccessEditorial

Analysis of Crop Genetic and Germplasm Diversity

by Antonio M. De Ron and Ana Paula Rodiño

Agronomy 2022, 12(1), 91; https://doi.org/10.3390/agronomy12010091 - 30 Dec 2021

Cited by 1 | Viewed by 1371

Plant genetic resources are the basis for the genetic improvement of cultivated plants and future food and feed security [...] Full article

(This article belongs to the Special Issue Analysis of Crop Genetic and Germplasm Diversity)

Research

Jump to: Editorial, Review

15 pages, 1812 KiB

Open AccessArticle

Implications of the Symbiotic Nitrogen Fixation in Common Bean under Seasonal Water Stress

by Ana P. Rodiño, Manuel Riveiro and Antonio M. De Ron

Agronomy 2021, 11(1), 70; https://doi.org/10.3390/agronomy11010070 - 31 Dec 2020

Cited by 4 | Viewed by 2802

Abstract

The objective of this research was to study the performance of 10 common bean genotypes under water deficit stress and how it affects to their symbiotic relationship with 10 Rhizobium strains in both greenhouse and field conditions. PHA-0471, a small seeded genotype had [...] Read more.

The objective of this research was to study the performance of 10 common bean genotypes under water deficit stress and how it affects to their symbiotic relationship with 10 Rhizobium strains in both greenhouse and field conditions. PHA-0471, a small seeded genotype had the best yield under irrigation and under water stress. Other genotypes with tolerance to drought were the large-seeded PHA-0432 and PHA-0683. In the Rhizobium inoculation tests it was observed that the increase of dry nodular weight produced less seed yield in beans. PHA-0683 genotype presented a great uniformity on nodule size and an association with yield when it displays the big nodule phenotype. Further research about this would be interesting because this fact could be due to the existence of a plant blocking mechanism for inefficient strain nodules. The inoculated plants were productive in irrigated fields and in drought ones and their productivity was the same or even better than the N supplemented plant control. The genotype-strain relationship was very specific and the local strains achieved the greatest productivity with some genotypes in irrigated and drought conditions that make possible their use as inoculating strains, with relevance for the environmental impact of agriculture. Full article

(This article belongs to the Special Issue Analysis of Crop Genetic and Germplasm Diversity)

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15 pages, 2644 KiB

Open AccessArticle

Genetic Diversity among Cowpea (Vigna unguiculata (L.) Walp.) Landraces Suggests Central Mozambique as an Important Hotspot of Variation

by Ana Maria Figueira Gomes, David Draper, Pedro Talhinhas, Paula Batista Santos, Fernanda Simões, Nascimento Nhantumbo, Rafael Massinga, José C. Ramalho, Isabel Marques and Ana I. Ribeiro-Barros

Agronomy 2020, 10(12), 1893; https://doi.org/10.3390/agronomy10121893 - 30 Nov 2020

Cited by 11 | Viewed by 3482

Abstract

Cowpea is a multiple-purpose drought-tolerant leguminous pulse crop grown in several dry tropical areas. Its domestication center is thought to be East or West Africa, where a high level of genetic diversity is apparently still found. However, detailed genetic information is lacking in [...] Read more.

Cowpea is a multiple-purpose drought-tolerant leguminous pulse crop grown in several dry tropical areas. Its domestication center is thought to be East or West Africa, where a high level of genetic diversity is apparently still found. However, detailed genetic information is lacking in many African countries, limiting the success of breeding programs. In this work, we assessed the genetic variation and gene flow in 59 Vigna unguiculata (cowpea) accessions from 10 landraces spanning across six agro-ecological zones of Mozambique, based on nuclear microsatellite markers. The results revealed the existence of high genetic diversity between the landraces, even in comparison to other world regions. Four genetic groups were found, with no specific geographic pattern, suggesting the presence of gene flow between landraces. In comparison, the two commercial varieties had lower values of genetic diversity, although still close to the ones found in local landraces. The high genetic diversity found in Mozambique sustains the importance of local genetic resources and farm protection to enhance genetic diversity in modern varieties of cowpea worldwide. Full article

(This article belongs to the Special Issue Analysis of Crop Genetic and Germplasm Diversity)

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13 pages, 1508 KiB

Open AccessArticle

Inheritance and Expressivity of Neoplasm Trait in Crosses between the Domestic Pea (Pisum sativum subsp. sativum) and Tall Wild Pea (Pisum sativum subsp. elatius)

by Hatice Sari, Duygu Sari, Tuba Eker, Bilal Aydinoglu, Huseyin Canci, Cengiz Ikten, Ramazan S. Gokturk, Ahmet Zeybek, Melike Bakir, Petr Smykal and Cengiz Toker

Agronomy 2020, 10(12), 1869; https://doi.org/10.3390/agronomy10121869 - 27 Nov 2020

Cited by 5 | Viewed by 2280

Abstract

The Neoplasm trait in pea pods is reported to be due to the lack of ultraviolet (UV) light in glasshouse conditions or in response to pea weevil (Bruchus pisorum L.) damage. This pod deformation arises from the growth of non-meristematic tissue on [...] Read more.

The Neoplasm trait in pea pods is reported to be due to the lack of ultraviolet (UV) light in glasshouse conditions or in response to pea weevil (Bruchus pisorum L.) damage. This pod deformation arises from the growth of non-meristematic tissue on pods of domesticated peas (Pisum sativum L. subsp. sativum). Neither expressivity, nor the effect of pea weevil on neoplasm in the tall wild pea (P. sativum L. subsp. elatius (M. Bieb.) Asch. & Graebn.), have been adequately studied. We aimed to study the expression and inheritance of neoplasm in the tall wild pea and crosses between domesticated and tall wild peas grown in the glasshouse (without pea weevils) and in the field (with pea weevils) under natural infestation conditions. Neoplasm was found in all pods in tall wild peas when grown in the glasshouse, while it was not detected on pods of field-grown plants despite heavy pea weevil damage. In inter-subspecific crosses between P. sativum subsp. sativum and P. sativum subsp. elatius, all F₁ plants had neoplastic pods, and the F₂ populations segregated in a good fit ratio of 3 (neoplasm): 1 (free from neoplasm) under glasshouse conditions, which suggests that neoplasm on pods of the tall wild pea was controlled by a single dominant gene. Expressivity of neoplasm in the progeny differed from parent to parent used in inter-subspecific crosses. There was no relationship between neoplasm and damage by pea weevil under heavy insect epidemics under field conditions. The neoplasm occurring under glasshouse conditions may be due to one or to a combination of environmental factors. Since wild peas are useful genetic resources for breeding programs aiming at fresh pea production that could be utilized under glasshouse conditions, negative selection could be considered in segregating populations. Full article

(This article belongs to the Special Issue Analysis of Crop Genetic and Germplasm Diversity)

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8 pages, 12308 KiB

Open AccessArticle

Resistance to Anthracnose (Colletotrichum lentis, Race 0) in Lens spp. Germplasm

by Eleonora Barilli, Juan Moral, Thaïs Aznar-Fernández and Diego Rubiales

Agronomy 2020, 10(11), 1799; https://doi.org/10.3390/agronomy10111799 - 16 Nov 2020

Cited by 6 | Viewed by 2543

Abstract

Anthracnose, caused by the fungal pathogen Colletotrichum lentis, is a severe disease of lentil (Lens culinaris) causing premature defoliation, necrotic stem lesions that lead to plant wilting and death in susceptible varieties. Two races of C. lentis (0 and 1) [...] Read more.

Anthracnose, caused by the fungal pathogen Colletotrichum lentis, is a severe disease of lentil (Lens culinaris) causing premature defoliation, necrotic stem lesions that lead to plant wilting and death in susceptible varieties. Two races of C. lentis (0 and 1) have been described so far. Race 0 is the most virulent one and limited genetic resistance is available to date. To address this scarcity of resistance, we screened a germplasm collection covering different Lens spp. originating from different countries for C. lentis race 0 resistance. Leaf and stem damage and plant mortality were assessed on seedlings inoculated under controlled conditions. A significant variability was observed among accession. Most of the collection studied was highly susceptible, but some levels of resistance were identified in about 15% of the accessions. The highest levels of resistance were identified in L. ervoides accessions PI572330, PI572334 and PI572338. Moderate resistance was also identified in 10 L. culinaris ssp. culinaris accessions but not in the remaining species studied. Selected accessions showed potential to integrate several breeding programs. Full article

(This article belongs to the Special Issue Analysis of Crop Genetic and Germplasm Diversity)

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18 pages, 924 KiB

Open AccessArticle

Morphological, Sensorial and Chemical Characterization of Chilli Peppers (Capsicum spp.) from the CATIE Genebank

by Nelly Judith Paredes Andrade, Alvaro Monteros-Altamirano, Cesar Guillermo Tapia Bastidas and Marten Sørensen

Agronomy 2020, 10(11), 1732; https://doi.org/10.3390/agronomy10111732 - 06 Nov 2020

Cited by 12 | Viewed by 4372

Abstract

In order to assess the potential of 192 accessions of Capsicum L., from 21 countries, a morphological and agronomic characterization was carried out by applying 57 qualitative and quantitative descriptors. Multivariate analyses identified two large groups: the first including C. annuum (G3, G5, [...] Read more.

In order to assess the potential of 192 accessions of Capsicum L., from 21 countries, a morphological and agronomic characterization was carried out by applying 57 qualitative and quantitative descriptors. Multivariate analyses identified two large groups: the first including C. annuum (G3, G5, G7 and G8) and the second C. frutescens, C. baccatum, C. chinense and C. pubescens (G1, G2, G4, G6 and G9). The discriminant qualitative descriptors were the colour of the corolla, the colour of the anthers and position of the flower. The quantitative discriminant characteristics were length, weight and width of the fruit. The participatory selection identified 15 materials by colour, aroma, texture, flavour, size and thickness of fruits. Chemical analyses determined the highest concentration of flavonoids in the accessions 10,757 (16.64 mg/g) and 15,661 (15.77 mg/g). Accessions 17,750 (11.68 mg/g) and 10,757 (11.41 mg/g) presented the highest polyphenol contents. The highest capsaicin concentration was recorded in accessions 16,209 (55.90 mg/g) and 10,757 (48.80 mg/g). The highest antioxidant value was recorded in accessions 17,750 (90.85 mg/g) and 15,661 (87.03 mg/g). All these characteristics are important with a view to increasing industrial use and genetic improvement processes. These results show the existence of significant genetic variability within the genus Capsicum. Full article

(This article belongs to the Special Issue Analysis of Crop Genetic and Germplasm Diversity)

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15 pages, 1033 KiB

Open AccessArticle

Natural Genetic Diversity of Nutritive Value Traits in the Genus Cynodon

by Cleber de Souza, Yolanda Lopez, Patricio Munoz, William Anderson, Miguel Dall’Agnol, Marcelo Wallau and Esteban Rios

Agronomy 2020, 10(11), 1729; https://doi.org/10.3390/agronomy10111729 - 06 Nov 2020

Cited by 7 | Viewed by 1954

Abstract

The Cynodon spp. collection maintained by United States Department of Agriculture National Plant Germplasm System (USDA-NPGS) has limited information on nutritive value (NV) traits. In this study, crude protein (CP), phosphorous concentration (P), in vitro digestible organic matter (IVDOM), and neutral detergent fiber [...] Read more.

The Cynodon spp. collection maintained by United States Department of Agriculture National Plant Germplasm System (USDA-NPGS) has limited information on nutritive value (NV) traits. In this study, crude protein (CP), phosphorous concentration (P), in vitro digestible organic matter (IVDOM), and neutral detergent fiber (NDF) were determined to (i) estimate genetic parameters for NV, (ii) obtain genetic values for the whole population across two harvests, (iii) estimate genotype by harvest interaction (GHI) for NV traits, and (iv) select accessions exhibiting improved NV traits compared to ‘Tifton 85′. The experiment was setup as a row-column design with two replicates and augmented representation of controls: Tifton 85, ‘Jiggs’, and ‘Coastal’. The whole-population was harvested twice, and data were analyzed using linear mixed models with repeated measures. In addition, a selected population of 15 genotypes were evaluated across 11 harvests to determine the extent of GHI. Genetic parameters revealed the presence of significant genetic variability, indicating potential improvements for NV through breeding. Specifically, P and IVDOM presented large variation, while NDF had lower diversity but some accessions exhibited lower NDF than Tifton 85. Low GHI, except for IVDOM, indicated genotypic stability and potential for selecting improved accessions under fewer harvests. Breeding line 240, PI-316510, and PI-3166536 presented superior NV than Tifton 85. Full article

(This article belongs to the Special Issue Analysis of Crop Genetic and Germplasm Diversity)

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18 pages, 1599 KiB

Open AccessArticle

Phenotypic Divergence Analysis in Pigeonpea [Cajanus cajan (L.) Millspaugh] Germplasm Accessions

by Esnart Nyirenda Yohane, Hussein Shimelis, Mark Laing, Isack Mathew and Admire Shayanowako

Agronomy 2020, 10(11), 1682; https://doi.org/10.3390/agronomy10111682 - 30 Oct 2020

Cited by 11 | Viewed by 2907

Abstract

Pigeonpea (Cajanus cajan (L.) Millspaugh) is an important source of grain protein for low-income countries such as Malawi. Knowledge of the genetic diversity in pigeonpea is essential for an effective breeding program. The study objective was to assess the genetic diversity among [...] Read more.

Pigeonpea (Cajanus cajan (L.) Millspaugh) is an important source of grain protein for low-income countries such as Malawi. Knowledge of the genetic diversity in pigeonpea is essential for an effective breeding program. The study objective was to assess the genetic diversity among diverse pigeonpea accessions to select complementary and unique genotypes for breeding. Eighty-one pigeonpea accessions were evaluated in six environments in Malawi using a 9 × 9 alpha-lattice design with two replications. The cross-tabulation analysis revealed a significant genotype variation on plant growth, flower, and seed traits. The combined analysis of variance identified genotypes MWPLR 14, ICEAP 01170, ICEAP 871091, and ICEAP 01285 as early maturing varieties, while Kachangu, MWPLR 16, TZA 5582, No. 40, and MWPLR 14 were identified as high-yielding genotypes. The correlation analysis revealed a significant positive correlation between grain yield and a hundred seed weight (HSWT) (r = 0.50, p < 0.01), suggesting the usefulness of this trait for selection. The nonlinear principal component analysis identified grain yield (GDY), days to 50% flowering (DTF), days to 75% maturity (DTM), number of pods per plant (NPP), number of racemes per plant (NRP), 100 seed weight (HSWT), leaf hairiness (LH), and number of seeds per pod (NSP) as the most discriminated traits among the test genotypes. The cluster analysis using morphological traits delineated the accessions into three clusters. The selected high-yielding and early-maturing genotypes may be recommended as parental lines for breeding and grain yield improvement in Malawi or similar agro-ecologies. Full article

(This article belongs to the Special Issue Analysis of Crop Genetic and Germplasm Diversity)

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18 pages, 2190 KiB

Open AccessArticle

Utilization of Phytochemical and Molecular Diversity to Develop a Target-Oriented Core Collection in Tea Germplasm

by Do Yoon Hyun, Gwang-Yeon Gi, Raveendar Sebastin, Gyu-Taek Cho, Seong-Hoon Kim, Eunae Yoo, Sookyeong Lee, Dong-Mo Son and Kyung Jun Lee

Agronomy 2020, 10(11), 1667; https://doi.org/10.3390/agronomy10111667 - 29 Oct 2020

Cited by 6 | Viewed by 2197

Abstract

Tea has received attention due to its phytochemicals. For the direct use of tea germplasm in breeding programs, a core collection that retains the genetic diversity and various phytochemicals in tea is needed. In this study, we evaluated the content of eight phytochemicals [...] Read more.

Tea has received attention due to its phytochemicals. For the direct use of tea germplasm in breeding programs, a core collection that retains the genetic diversity and various phytochemicals in tea is needed. In this study, we evaluated the content of eight phytochemicals over two years and the genetic diversity through 33 SSR (simple sequence repeats) markers for 462 tea accessions (entire collection, ENC) and developed a target-oriented core collection (TOCC). Significant phytochemical variation was observed in the ENC between genotypes and years. The genetic diversity of ENC showed high levels of molecular variability. These results were incorporated into developing TOCCs. The TOCC showed a representation of the ENC, where the mean difference percentage, the variance difference percentage, the variable rate of coefficient of variance percentage, and the coincidence rate of range percentage were 7.88, 39.33, 120.79, and 97.43, respectively. The Shannon’s diversity index (I) and Nei’s gene diversity (H) of TOCC were higher than those of ENC. Furthermore, the accessions in TOCC were shown to be selected proportionally, thus accurately reflecting the distribution of the overall accessions for each phytochemical. This is the first report describing the development of a TOCC retaining the diversity of phytochemicals in tea germplasm. This TOCC will facilitate the identification of the genetic determinants of trait variability and the effective utilization of phytochemical diversity in crop improvement programs. Full article

(This article belongs to the Special Issue Analysis of Crop Genetic and Germplasm Diversity)

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19 pages, 3311 KiB

Open AccessArticle

Agromorphological Characterization Revealed Three Phenotypic Groups in a Region-Wide Germplasm of Fonio (Digitaria exilis (Kippist) Stapf) from West Africa

by Abdou R. Ibrahim Bio Yerima, Enoch G. Achigan-Dako, Mamadou Aissata, Emmanuel Sekloka, Claire Billot, Charlotte O. A. Adje, Adeline Barnaud and Yacoubou Bakasso

Agronomy 2020, 10(11), 1653; https://doi.org/10.3390/agronomy10111653 - 27 Oct 2020

Cited by 9 | Viewed by 2999

Abstract

Fonio is an ancient orphan cereal, cultivated by resource-poor farmers in arid and semi-arid regions of West Africa, who conserved and used the cereal for nutrition and income generation. However, the extent and patterns of phenotypic variation within the fonio germplasm remain scarcely [...] Read more.

Fonio is an ancient orphan cereal, cultivated by resource-poor farmers in arid and semi-arid regions of West Africa, who conserved and used the cereal for nutrition and income generation. However, the extent and patterns of phenotypic variation within the fonio germplasm remain scarcely evaluated to inform breeding decisions. In this study, we used alpha lattice design to assess the phenotypic variability of 180 fonio accessions using 20 agro morphological descriptors, including both qualitative and quantitative traits at Bengou research station in 2018 and 2019. Descriptive statistics, combined analysis and multivariate analyses, including principal components analysis (PCA), hierarchical clustering, and multiple factor analysis (MFA) were performed. As results, we found significant differences among fonio accessions and among agro ecological zones of provenance for most of the quantitative traits. Furthermore, highly significant positive correlations were found between grain yield and other yield-related attributes such as harvest index and thousand seeds weight, whereas significant negative correlations were found between grain yield and flowering and maturity times. Clusters analysis revealed three phenotypic groups. Group 1 was characterized by early maturing fonio accessions with higher grain yield. Groups 2 and 3 were characterized by late maturing accessions with intermediate to moderate grain yield. The accessions from Group 1 are candidate for yield improvement and development of fonio lines with enhanced lodging resistance. Accessions from Group 2 and 3 can be improved for yield through marker-assisted selection of best thousand seed weight. This study highlights how traits are correlated within the major phenotypic groups of fonio in West Africa, and we discussed how these groups could be further exploited for improving traits of economic importance. Furthermore, this study exhibited agro morphological descriptors that discriminate fonio accessions and provide useful information for parental selection with economically important agronomic traits. Full article

(This article belongs to the Special Issue Analysis of Crop Genetic and Germplasm Diversity)

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13 pages, 13579 KiB

Open AccessArticle

Genetic Composition of Korean Ginseng Germplasm by Collection Area and Resource Type

by Kyung Jun Lee, Raveendar Sebastin, Seong-Hoon Kim, Eunae Yoo, Sookyeong Lee, Gyu-Taek Cho, Manjung Kang and Do Yoon Hyun

Agronomy 2020, 10(11), 1643; https://doi.org/10.3390/agronomy10111643 - 26 Oct 2020

Cited by 5 | Viewed by 2146

Abstract

To improve crops, it is important to secure plant genetic source material and evaluate the genetic diversity. Ginseng (Panax ginseng C.A. Meyer) has long been used as a medicinal herb in Korea and China. Since ginseng originated from wild ginseng with low [...] Read more.

To improve crops, it is important to secure plant genetic source material and evaluate the genetic diversity. Ginseng (Panax ginseng C.A. Meyer) has long been used as a medicinal herb in Korea and China. Since ginseng originated from wild ginseng with low genetic diversity, it is also expected to have low genetic diversity. In this study, the genetic diversity of 451 ginseng accessions conserved in the National Agrobiodiversity Center (NAC) at Korea was analyzed using 33 SSR markers. Another objective was to establish a strategy for NAC to manage ginseng germplasm based on these results. The 451 accessions were collected from 22 cities in six provinces in South Korea. Among the 451 ginseng accessions, 390 (86.5%) and 61 (13.5%) were landraces and breeding lines, respectively. In the STRUCTURE results for the accessions, there was no relationship between assigned genotypes and collection areas, but there was a population genetic structure. In addition, genetic differentiation within populations of each analysis was low, indicating that the ginseng accessions conserved at NAC are extensively dispersed throughout the collection areas. The results of this study suggest that NAC should increase the genetic diversity of ginseng accessions for breeding programs, and alternatives are needed for securing ginseng genetic resources. Full article

(This article belongs to the Special Issue Analysis of Crop Genetic and Germplasm Diversity)

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14 pages, 2322 KiB

Open AccessArticle

Congruity of the Polymorphisms in the Expressed and Noncoding Parts of the Gli-B1 Locus in Common Wheat

by Yulia Popovych, Sabina Chebotar, Viktor Melnik, Marta Rodriguez-Quijano, Laura Pascual, William John Rogers and Eugene Metakovsky

Agronomy 2020, 10(10), 1510; https://doi.org/10.3390/agronomy10101510 - 04 Oct 2020

Cited by 2 | Viewed by 1744

Abstract

The previously defined pairs of primers GliB1.1 and GliB1.2 were found to produce three and four principal variants, respectively, of PCR sequence length for the γ-gliadin pseudogene in 46 Triticum aestivum L. cultivars from 15 countries carrying 19 known alleles at the Gli-B1 [...] Read more.

The previously defined pairs of primers GliB1.1 and GliB1.2 were found to produce three and four principal variants, respectively, of PCR sequence length for the γ-gliadin pseudogene in 46 Triticum aestivum L. cultivars from 15 countries carrying 19 known alleles at the Gli-B1 locus. A congruity was established between this polymorphism, allelic sets of the Gli-B1-produced gliadins (especially of the electrophoretic mobility in acid gels of the encoded γ-gliadin) and the presence in the wheat genotype of the Gli-B5b + Rg-1 allelic combination. Six different alleles at the Gli-B1 locus encoding an identical γ-gliadin produced a PCR sequence of about 400 bp (GliB1.1). Nine Gli-B1d-carrying genotypes from four countries produced an identical sequence of about 409 bp (GliB1.2), while three cultivars with Gli-B1h and four with Gli-B1b produced three and two specific sequences, respectively, of slightly different length. Allele Gli-B1j might be the result of recombination between coding and noncoding DNA sequences within the Gli-B1 locus. These observations imply that genetic diversity of the agriculturally important region of chromosome 1B marked by variants of the Gli-B1 locus is rather limited among common wheat cultivars of the 20th century, specifically to eight principal versions. These might have been incorporated into common wheat from diverged genotypes of diploid donor(s), and, due to the scarcity of recombination, subsequently maintained relatively intact. As well as its evolutionary significance, this information is of potential use in wheat breeding and we consider it likely that novel variants of the Gli-B1 locus will be found in hitherto unstudied germplasm. Full article

(This article belongs to the Special Issue Analysis of Crop Genetic and Germplasm Diversity)

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14 pages, 6846 KiB

Open AccessArticle

Salt Stress Induces Differentiated Nitrogen Uptake and Antioxidant Responses in Two Contrasting Barley Landraces from MENA Region

by Fatma Ezzahra Ben Azaiez, Sawsen Ayadi, Giorgia Capasso, Simone Landi, Valeria Paradisone, Salma Jallouli, Zied Hammami, Zoubeir Chamekh, Inès Zouari, Youssef Trifa and Sergio Esposito

Agronomy 2020, 10(9), 1426; https://doi.org/10.3390/agronomy10091426 - 19 Sep 2020

Cited by 16 | Viewed by 2556

Abstract

The interaction between salinity and nitrogen metabolism has been investigated in two barley landraces, one tolerant (“100/1B”) and one susceptible to salinity (“Barley medenine”) from the Middle East and North Africa (MENA) region. Barley plants were exposed to 50 mM NaCl for 7 [...] Read more.

The interaction between salinity and nitrogen metabolism has been investigated in two barley landraces, one tolerant (“100/1B”) and one susceptible to salinity (“Barley medenine”) from the Middle East and North Africa (MENA) region. Barley plants were exposed to 50 mM NaCl for 7 days; then, salinity was increased to 150 mM NaCl in the presence (10 mM) or limitation (1 mM) of ammonium as a nitrogen source. Upon salinity, “100/1B” was shown to support N assimilation by enhancing the glutamine synthetase (GS) and glutamine oxoglutarate aminotransferase (GOGAT) cycle under high N, and the stimulation of the glutamate dehydrogenase (GDH) pathway under low N treatment. In “Barley medenine”, salinity reduced the GS/GOGAT cycle, and increased GDH activity. Upon salinity, Heat Shock Proteins 70 and PEPC remained unchanged in “100/1B”, while they decreased in “Barley medenine”. The tolerance degree is a determining factor in enzymes’ occurrence and regulation: exposed to salinity, “100/1B” rapidly increased APX and PEPC activities, while this was delayed in “Barley medenine”. Salinity increased cyt-G6PDH levels in “100/1B”, while “Barley medenine” showed a decrease in G6PDH isoforms. Correlation analyses confirm GOGAT was related to G6PDH; GDH and APX with PEPC in “100/1B” under moderate salinity; severe salinity correlated GDH with G6PDH and PEPC. In “Barley medenine” under salinity, GOGAT was correlated with G6PDH, while APX showed a relation with PEPC. Therefore, specific enzymatic activities and occurrence can be used to determine stress responsiveness of different landraces. We suggest that the rapid increase in G6PDH, APX, and nitrogen assimilation enzymes activities represents an index of tolerance in “100/1B” and a stress symptom in “Barley medenine”. Full article

(This article belongs to the Special Issue Analysis of Crop Genetic and Germplasm Diversity)

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19 pages, 3253 KiB

Open AccessArticle

Genetic Diversity, Population Structure and Inter-Trait Relationships of Combined Heat and Drought Tolerant Early-Maturing Maize Inbred Lines from West and Central Africa

by Alimatu Sadia Osuman, Baffour Badu-Apraku, Beatrice E. Ifie, Pangirayi Tongoona, Ebenezer Obeng-Bio and Ana Luísa Garcia-Oliveira

Agronomy 2020, 10(9), 1324; https://doi.org/10.3390/agronomy10091324 - 04 Sep 2020

Cited by 10 | Viewed by 3792

Abstract

Adequate knowledge and understanding of the genetic diversity and inter-trait relationships among elite maize inbred lines are crucial for determining breeding strategies and predicting hybrid performance. The objectives of this study were to investigate the genetic diversity of 162 early maturing white and [...] Read more.

Adequate knowledge and understanding of the genetic diversity and inter-trait relationships among elite maize inbred lines are crucial for determining breeding strategies and predicting hybrid performance. The objectives of this study were to investigate the genetic diversity of 162 early maturing white and yellow tropical maize inbred lines, and to determine the population structure, heterotic groups and inter-trait relationships among the lines. Using 9684 DArT single nucleotide polymorphism (SNP) markers, a gene diversity (GD) of 0.30 was recorded for the inbred lines with polymorphic information content (PIC) ranging from 0.08 to 0.38. The genetic relatedness among the inbred lines evaluated revealed six different groups based on the history of selection, colour of endosperm and pedigree. The genotype-by-trait (GT) biplot analysis identified inbred 1 (TZEI 935) as outstanding in terms of combined heat and drought (HD) tolerance with the base index analysis identifying 15 superior inbreds in the HD environment. A wide range of genetic variability was observed among the inbred lines, indicating that they are an invaluable resource for breeding for HD tolerance in maize breeding programmes, especially in West and Central Africa. Full article

(This article belongs to the Special Issue Analysis of Crop Genetic and Germplasm Diversity)

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17 pages, 1045 KiB

Open AccessArticle

Assessment of Agro-Morphologic Performance, Genetic Parameters and Clustering Pattern of Newly Developed Blast Resistant Rice Lines Tested in Four Environments

by Raieah Saiyedah Sabri, Mohd Y. Rafii, Mohd Razi Ismail, Oladosu Yusuff, Samuel C. Chukwu and Nor’Aishah Hasan

Agronomy 2020, 10(8), 1098; https://doi.org/10.3390/agronomy10081098 - 29 Jul 2020

Cited by 34 | Viewed by 3578

Abstract

Multi-environmental yield trial is very vital in assessing newly developed rice lines for its adaptability and stability across environments especially prior to release of the newly developed variety for commercial cultivation. The growth performance and phenotypic variability of these genotypes are the combination [...] Read more.

Multi-environmental yield trial is very vital in assessing newly developed rice lines for its adaptability and stability across environments especially prior to release of the newly developed variety for commercial cultivation. The growth performance and phenotypic variability of these genotypes are the combination of environment, genotype and genotype by environment (G×E) interaction factors. Thus, evaluation creates an opportunity for effective selection of superior genotypes. The objectives of this study were to evaluate the newly developed blast resistant rice lines in varied environmental conditions, precisely measure the response of the advanced lines in multiple environments and classify the genotypes into groups that could serve as varieties for commercial cultivation. Genetic materials included 18 improved blast resistant rice lines and the recipient parent MR219. The total of 19 newly developed genotypes was evaluated under four varied environments in Peninsular Malaysia. The experiments were carried out using randomized complete block design (RCBD) with three replications at each environment. Data were collected on the vegetative, yield and yield component traits. Descriptive statistics (mean performance) and analysis of variance were conducted using SAS Software version 9.4. Genotypic and phenotypic coefficients, phenotypic variance component, heritability and genetic advance were also determined. Analysis of variance revealed that all traits were significantly different for genotypes except days to maturity, number of filled grains and total number of grains. Meanwhile, all the traits differed significantly for genotype × environment (G×E) except number of tillers per hill and number of panicles per hill. Low heritability (<30%) was found for all the traits. Similarly, low genetic advance was also observed for all the traits except for number of tillers per hill and number of panicles per hill. yield per hectare had significant and positive correlation with most evaluated traits except for days to flowering, days to maturity, plant height and number of unfilled grains. Cluster analysis classified the 19 evaluated genotypes into six groups. Therefore, the six clusters/groups of genotypes were recommended as varieties for commercial cultivation in Malaysia and other rice growing regions. Full article

(This article belongs to the Special Issue Analysis of Crop Genetic and Germplasm Diversity)

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28 pages, 12377 KiB

Open AccessArticle

Isolate-Dependent Inheritance of Resistance Against Pseudoperonospora cubensis in Cucumber

by Tomer Chen, Daniel Katz, Yariv Ben Naim, Rivka Hammer, Bat Hen Ben Daniel, Avia E. Rubin and Yigal Cohen

Agronomy 2020, 10(8), 1086; https://doi.org/10.3390/agronomy10081086 - 27 Jul 2020

Cited by 4 | Viewed by 4292

Abstract

Six wild accessions of Cucumis sativum were evaluated for resistance against each of the 23 isolates of the downy mildew oomycete Pseudoperonospora cubensis. The isolates originated from Israel, Europe, USA, and Asia. C. sativum PI 197088 (India) and PI 330628 (Pakistan) exhibited [...] Read more.

Six wild accessions of Cucumis sativum were evaluated for resistance against each of the 23 isolates of the downy mildew oomycete Pseudoperonospora cubensis. The isolates originated from Israel, Europe, USA, and Asia. C. sativum PI 197088 (India) and PI 330628 (Pakistan) exhibited the highest level of resistance against multiple isolates of P. cubensis. Resistance was manifested as reduced lesion number, lesion size, sporangiophores and sporangia per lesion and enhanced encasement of haustoria with callose and intensive accumulation of lignin in lesions of both Plant Introductions (PIs) compared to the susceptible C. sativum SMR-18. In the field, much smaller AUDPC (Area Under Disease Progress Curve) values were recorded in PI 197088 or PI 330628 as compared to SMR-18. Each PI was crossed with SMR-18 and offspring progeny plants were exposed to inoculation with each of several isolates of P. cubensis in growth chambers and the field during six growing seasons. F1 plants showed partial resistance. F2 plants showed multiple phenotypes ranging from highly susceptible (S) to highly resistant (R, no symptoms) including moderately resistant (MR) phenotypes. The segregation ratio between phenotypes in growth chambers ranged from 3:1 to 1:15, depending on the isolate used for inoculation, suggesting that the number of genes, dominant, partially dominant, or recessive are responsible for resistance. In the field, the segregation ratio of 1:15, 1:14:1, or 1:9:6 was observed. F2 progeny plants of the cross between the two resistant PI’s were resistant, except for a few plants that were partially susceptible, suggesting that some of the resistance genes in PI 197088 and PI 330328 are not allelic. Full article

(This article belongs to the Special Issue Analysis of Crop Genetic and Germplasm Diversity)

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12 pages, 1416 KiB

Open AccessArticle

The Variability of Puroindoline-Encoding Alleles and Their Influence on Grain Hardness in Modern Wheat Cultivars Cultivated in Poland, Breeding Lines and Polish Old Landraces (Triticum aestivum L.)

by Mateusz Przyborowski, Sebastian Gasparis, Maciej Kała, Wacław Orczyk and Anna Nadolska-Orczyk

Agronomy 2020, 10(8), 1075; https://doi.org/10.3390/agronomy10081075 - 25 Jul 2020

Cited by 8 | Viewed by 2476

Abstract

Wheat (Triticum aestivum L.) grain hardness is determined mainly by variations in puroindoline genes (Pina-D1 and Pinb-D1), which are located on the short arm of chromosome 5D. This trait has a direct effect on the technological properties of the flour [...] Read more.

Wheat (Triticum aestivum L.) grain hardness is determined mainly by variations in puroindoline genes (Pina-D1 and Pinb-D1), which are located on the short arm of chromosome 5D. This trait has a direct effect on the technological properties of the flour and the final product quality. The objective of the study was to analyze the mutation frequency in both Pin genes and their influence on grain hardness in 118 modern bread wheat cultivars and breeding lines cultivated in Poland, and 80 landraces from Poland. The PCR products containing the Pin gene coding sequences were sequenced by the Sanger method. Based on detected the SNPs (single-nucleotide polymorphisms) we designed CAPS (cleaved amplified polymorphic sequence) markers for the fast screening of Pinb alleles in a large number of genotypes. All analyzed cultivars, breeding lines, and landraces possess the wild-type Pina-D1a allele. Allelic variation was observed within the Pinb gene. The most frequently occurring allele in modern wheat cultivars and breeding lines (over 50%) was Pinb-D1b. The contribution of the remaining alleles (Pinb-D1a, Pinb-D1c, and Pinb-D1d) was much less (approx. 15% each). In landraces, the most frequent allele was Pinb-D1a (over 70%), followed by Pinb-D1b (21% frequency). Pinb-D1c and Pinb-D1g were found in individual varieties. SKCS (single-kernel characterization system) analysis revealed that grain hardness was strictly connected with Pinb gene allelic variation in most tested cultivars. The mean grain hardness values were significantly greater in cultivars with mutant Pinb variants as compared to those with the wild-type Pinb-D1a allele. Based on grain hardness measured by SKCS, we classified the analyzed cultivars and lines into different classes according to a previously proposed classification system. Full article

(This article belongs to the Special Issue Analysis of Crop Genetic and Germplasm Diversity)

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23 pages, 2339 KiB

Open AccessArticle

Analysis of Proteomic Profile of Contrasting Phosphorus Responsive Rice Cultivars Grown under Phosphorus Deficiency

by Aadil Yousuf Tantray, Hayssam M. Ali and Altaf Ahmad

Agronomy 2020, 10(7), 1028; https://doi.org/10.3390/agronomy10071028 - 16 Jul 2020

Cited by 9 | Viewed by 2749

Abstract

Phosphorus (P) deficiency is one of the major limiting factors for crop productivity. The yield of rice (Oryza sativa L.) is severely limited by phosphorus deficiency. An attempt has been made in this study to identify P deficiency responsive differentially expressed proteins [...] Read more.

Phosphorus (P) deficiency is one of the major limiting factors for crop productivity. The yield of rice (Oryza sativa L.) is severely limited by phosphorus deficiency. An attempt has been made in this study to identify P deficiency responsive differentially expressed proteins of rice through analysis of leaf proteome of contrasting P-responsive rice cultivars under P deficiency conditions because genetic variability has been found in the rice cultivars for adaptive response to P deficiency and a controlled regulatory system is involved in the P deficiency adaptation response. Phosphorus-efficient (cv. Panvel) and P-inefficient (cv. Nagina 22) rice cultivars were hydroponically grown in the nutrient medium under control environmental conditions at low-P level (2.0 µM) and optimum-P level (320 µM) treatments. Expression patterns of the proteins of the leaves of both the cultivars were analyzed in 30-day-old plants. The identification of these proteins through mass spectrometry and MASCOT software (Matrix Science Inc., Boston, USA) revealed that these differentially expressed proteins were homologous to known functional proteins involved in energy metabolism, biosynthesis, photosynthesis, signaling, protein synthesis, protein folding, phospholipid metabolism, oxidative stress, transcription factors, and phosphorus metabolism. It has been observed that rice cultivars responded differently to low-P treatment through modification in protein expressions pattern to maintain the growth of the plants. Therefore, the expression patterns of proteins were different in both of the cultivars under low-P treatment. Higher potential of protein stability, stress tolerance, osmo-protection, and regulation of phosphorus uptake was observed in cv. Panvel than cv. Nagina 22. This study could help to unravel the complex regulatory process that is involved in adaptation to P deficiency in rice. Full article

(This article belongs to the Special Issue Analysis of Crop Genetic and Germplasm Diversity)

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23 pages, 4009 KiB

Open AccessArticle

Genetic Variation and Sequence Diversity of Starch Biosynthesis and Sucrose Metabolism Genes in Sweet Potato

by Kai Zhang, Kai Luo, Shixi Li, Deliang Peng, Daobin Tang, Huixiang Lu, Yong Zhao, Changwen Lv and Jichun Wang

Agronomy 2020, 10(5), 627; https://doi.org/10.3390/agronomy10050627 - 29 Apr 2020

Cited by 6 | Viewed by 2784

Abstract

Knowledge of genetic variations can provide clues into the molecular mechanisms regulating key crop traits. Sweet potato (Ipomoea batatas (L.) Lam.) is an important starch-producing crop, but little is known about the genetic variations in starch biosynthesis and sucrose metabolism genes. Here, [...] Read more.

Knowledge of genetic variations can provide clues into the molecular mechanisms regulating key crop traits. Sweet potato (Ipomoea batatas (L.) Lam.) is an important starch-producing crop, but little is known about the genetic variations in starch biosynthesis and sucrose metabolism genes. Here, we used high-throughput sequencing of pooled amplicons of target genes to identify sequence variations in 20 genes encoding key enzymes involved in starch biosynthesis and sucrose metabolism in 507 sweet potato germplasms. After filtering potential variations between gene copies within the genome, we identified 622 potential allelic single nucleotide polymorphisms (SNPs) and 85 insertions/deletions (InDels), including 50 non-synonymous SNPs (nsSNPs) and 12 frameshift InDels. Three nsSNPs were confirmed to be present in eight sweet potato varieties with various starch properties using cleaved amplified polymorphic sequence (CAPS) markers. Gene copy with loss of the fifth intron was detected in IbAGPb3 genes, and loss of multiple introns were observed in IbGBSS1-1 genes and various among germplasms based on intron length polymorphism (ILP) markers. Thus, we identified sequence variations between germplasms in 20 genes involved in starch biosynthesis and sucrose metabolism, and demonstrated the diversity in intron-loss alleles among sweet potato germplasms. These findings provide critical genetic information and useful molecular markers for revealing regulatory mechanism of starch properties. Full article

(This article belongs to the Special Issue Analysis of Crop Genetic and Germplasm Diversity)

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16 pages, 2074 KiB

Open AccessArticle

Development of a Multipurpose Core Collection of Bread Wheat Based on High-Throughput Genotyping Data

by Laura Pascual, Mario Fernández, Nieves Aparicio, Matilde López-Fernández, Rosario Fité, Patricia Giraldo and Magdalena Ruiz

Agronomy 2020, 10(4), 534; https://doi.org/10.3390/agronomy10040534 - 08 Apr 2020

Cited by 17 | Viewed by 2938

Abstract

Modern plant breeding practices have narrowed the genetic base of wheat throughout the world, increasing crop vulnerability. Therefore, there is clearly a need for introducing new germplasm in breeding programs to search for variability related to traits of agronomic interest for wheat improvement. [...] Read more.

Modern plant breeding practices have narrowed the genetic base of wheat throughout the world, increasing crop vulnerability. Therefore, there is clearly a need for introducing new germplasm in breeding programs to search for variability related to traits of agronomic interest for wheat improvement. The existence of subsets of accessions (core collections) that represent the diversity conserved in germplasm collections is a favored approach for breeders to explore novel variation and enhance the use of germplasm. In this study, a core collection of Spanish landraces of bread wheat has been created using high-throughput genotyping technologies (DArTseq), which yielded more than 50 K molecular markers. This marker system not only provides a robust estimate of the diversity, but also information about its distribution in the genome. Two core collections of 94 entries were created by using two common sampling strategies: the maximization strategy and the population structure-based method. Both core collections showed high geographic, phenotypic and genetic representativeness, but the collection obtained with the maximization strategy captured better the diversity displayed by the initial collection. This core collection, which includes a broad range of adapted genotypes, can be efficiently utilized for mining new alleles for useful traits in wheat breeding. Full article

(This article belongs to the Special Issue Analysis of Crop Genetic and Germplasm Diversity)

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17 pages, 2524 KiB

Open AccessArticle

Biomorphological Characterization of Brazilian Capsicum Chinense Jacq. Germplasm

by Paola Alvares Bianchi, Lígia Renata Almeida da Silva, Antônio André da Silva Alencar, Pedro Henrique Araújo Diniz Santos, Samy Pimenta, Cláudia Pombo Sudré, Lígia Erpen-Dalla Corte, Leandro Simões Azeredo Gonçalves and Rosana Rodrigues

Agronomy 2020, 10(3), 447; https://doi.org/10.3390/agronomy10030447 - 24 Mar 2020

Cited by 24 | Viewed by 5275

Abstract

Loss of biodiversity and ecosystem degradation become major concerns worldwide, making the conservation process an important strategy for maintaining biodiversity. Capsicum chinense Jacq. is the most Brazilian species of the genus, with representatives in different biomes. Anthropic pressure, such as burns, real estate [...] Read more.

Loss of biodiversity and ecosystem degradation become major concerns worldwide, making the conservation process an important strategy for maintaining biodiversity. Capsicum chinense Jacq. is the most Brazilian species of the genus, with representatives in different biomes. Anthropic pressure, such as burns, real estate speculation, and changing cultivation habit has led to risks of genetic erosion. Conservation and characterization of conserved accessions are paramount to ensure genetic diversity, useful for the bioeconomy and for genetic improvement. We report the characterization of 55 C. chinense accessions from four different regions of Brazil and one accession from Peru. The accessions were characterized based on 37 morpho-agronomic variables, Inter Simple Sequence Repeats—ISSR and Simple Sequence Repeat—SSR. Qualitative descriptors were analyzed using a descriptive statistical, while the quantitative descriptors were analyzed via F test and significant differences in mean values were separated using Scott-Knott test. The relative contribution of each quantitative trait was determined. A correlation between morphological and molecular distances was calculated. Color of ripe fruit and fruit shape had the largest number of observed classes. Six distinct groups and the joint analysis presented an entanglement rate of 0.58, evidencing the divergence of accessions between the groups of both dendrograms. Bayesian analysis allowed the distinction of two clusters for SSR. A significant variability was observed among accession with potential to integrate several breeding programs. Full article

(This article belongs to the Special Issue Analysis of Crop Genetic and Germplasm Diversity)

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17 pages, 489 KiB

Open AccessArticle

Genetic Variability of Eggplant Germplasm Evaluated under Open Field and Glasshouse Cropping Conditions

by Nur Nadzirah Mat Sulaiman, Mohd Y. Rafii, Janejira Duangjit, Shairul Izan Ramlee, Chalermpol Phumichai, Yusuff Oladosu, Debi Rani Datta and Ibrahim Musa

Agronomy 2020, 10(3), 436; https://doi.org/10.3390/agronomy10030436 - 23 Mar 2020

Cited by 23 | Viewed by 3901

Abstract

Knowledge of agro-morphological genetic variation and cropping conditions on vegetative and yield-related traits plays a significant role in varietal improvement and production of eggplant (Solanum melongena L.). Following this premise, the current study was conducted to critically asses the genetic variation of [...] Read more.

Knowledge of agro-morphological genetic variation and cropping conditions on vegetative and yield-related traits plays a significant role in varietal improvement and production of eggplant (Solanum melongena L.). Following this premise, the current study was conducted to critically asses the genetic variation of 29 eggplant accessions by using agro-morphological characterization evaluated under two cropping conditions, namely, glasshouse and open field. The experiments were laid out in randomized complete block design (RCBD) with three replications. Data on vegetative and yield characteristics were collected and subjected to analysis of variance (ANOVA) using SAS 9.4, while variance components were estimated manually. The results obtained from the analysis of variance indicated a highly significant difference (p ≤ 0.01) for all characteristics studied in both cropping conditions. The evaluated accessions were grouped into six major clusters based on agro-morphological traits using Unweighted Pair Group Method with Arithmetic mean (UPGMA) dendrogram. Hence, crosses between group I with VI or V could be used to attain higher heterosis and vigor among the accessions. Also, this evaluation could be used as a selection criterion for important yield agronomic traits in eggplant. The methodology and the approaches used may provide a model for the enhancement of other vegetable crop diversity towards adaptability to the cropping condition decision. This result displayed importance for preserving eggplant germplasm for future varietal development and revealed that open field cropping condition is more suitable under Malaysia’s agroecology. Full article

(This article belongs to the Special Issue Analysis of Crop Genetic and Germplasm Diversity)

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14 pages, 3242 KiB

Open AccessArticle

Genetic Basis Dissection for Eating and Cooking Qualities of Japonica Rice in Northeast China

by Yaolong Yang, Xin Xu, Mengchen Zhang, Qun Xu, Yue Feng, Xiaoping Yuan, Hanyong Yu, Yiping Wang and Xinghua Wei

Agronomy 2020, 10(3), 423; https://doi.org/10.3390/agronomy10030423 - 20 Mar 2020

Cited by 10 | Viewed by 2315

Abstract

The japonica rice in Northeast China is famous because of its high quality. Eating and cooking qualities (ECQs) are the most important factors that determine cooked rice quality. However, the genetic basis of ECQ of japonica varieties in Northeast China needs further study. [...] Read more.

The japonica rice in Northeast China is famous because of its high quality. Eating and cooking qualities (ECQs) are the most important factors that determine cooked rice quality. However, the genetic basis of ECQ of japonica varieties in Northeast China needs further study. In this study, 200 japonica varieties that are widely distributed in Northeast China were collected to evaluate the physicochemical indices of grain ECQs. The distribution of each trait was concentrated without large variations. Correlation analysis indicated that gel consistency (GC) had a significantly negative correlation with gelatinization temperature (GT). By integrating various analyses including kinship calculation, principal component analysis (PCA), linkage disequilibrium (LD) analysis, and original parent investigation, we found that the japonica varieties in Northeast China exhibited a narrow genetic basis. An association study for grain ECQs was performed and eight quantitative trait loci (QTLs) were detected. ALK was the major locus that regulated GT and also significantly affecting GC. Through the linkage disequilibrium (LD) and expression pattern analysis, one possible candidate gene (LOC_Os02g29980) was predicted and required further research for validation. Additionally, a different allele of Wx was identified in the variety CH4126, and ALK was not fixed in these japonica varieties. These results further elucidate the genetic basis of ECQs of japonica varieties in Northeast China and provide local breeders some assistance for improving ECQs of rice grain in rice breeding. Full article

(This article belongs to the Special Issue Analysis of Crop Genetic and Germplasm Diversity)

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13 pages, 2143 KiB

Open AccessArticle

Nucleotide Diversity and Association Analysis of ZmMADS60 with Root Length in the Maize Seedling Stage

by Pengcheng Li, Zhenzhen Ge, Houmiao Wang, Jie Wei, Yunyun Wang, Yang Xu, Zefeng Yang and Chenwu Xu

Agronomy 2020, 10(3), 342; https://doi.org/10.3390/agronomy10030342 - 02 Mar 2020

Cited by 5 | Viewed by 2471

Abstract

Root length is a determining factor of the root system architecture, which is essential for the uptake of water, nutrients and plant anchorage. In this study, ZmMADS60 was resequenced in 285 inbred lines, 68 landraces and 32 teosintes to detect the nucleotide diversity [...] Read more.

Root length is a determining factor of the root system architecture, which is essential for the uptake of water, nutrients and plant anchorage. In this study, ZmMADS60 was resequenced in 285 inbred lines, 68 landraces and 32 teosintes to detect the nucleotide diversity and natural variations associated with root length. Nucleotide diversity and neutral tests revealed that ZmMADS60 might be selected in domestication and improvement processes. ZmMADS60 in maize retained only 40.1% and 66.9% of the nucleotide diversity found in teosinte and landrace, respectively. Gene-based association analysis of inbred lines identified nine variants that were significantly associated with primary root length (PRL), lateral root length (LRL), root length between 0 mm and 0.5 mm in diameter (RL005) and total root length (TRL). One single-nucleotide polymorphism SNP1357 with pleiotropic effects was significantly associated with LRL, RL005 and TRL. The frequency of the increased allele T decreased from 68.8% in teosintes to 52.9% and 38.9% in the landrace and inbred lines, respectively. The frequency of the increased allele of another significant SNP723 associated with PRL also decreased during the maize domestication and improvement processes. The results of this study reveal that ZmMADS60 may be involved in the elongation of primary and lateral roots in the seedling stage and that significant variants can be used to develop functional markers to improve root length in maize. Full article

(This article belongs to the Special Issue Analysis of Crop Genetic and Germplasm Diversity)

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11 pages, 1994 KiB

Open AccessArticle

A 1Ns Disomic Addition from Psathyrostachys Huashanica Keng Confers Resistance to Powdery Mildew in Wheat

by Jing Han, Yuxiu Liu, Chenchen Hou, Jiachuang Li, Jinglin Wang, Qiaoying Zhang, Qunhui Yang, Xinhong Chen and Jun Wu

Agronomy 2020, 10(2), 312; https://doi.org/10.3390/agronomy10020312 - 24 Feb 2020

Cited by 9 | Viewed by 2880

Abstract

Powdery mildew is a fungal disease that threatens wheat production throughout the world. Breeding resistant cultivars is an effective way to reduce harm caused by powdery mildew. In this study, 35 wheat-Psathyrostachys huashanica-derived lines were developed by crossing common wheat and [...] Read more.

Powdery mildew is a fungal disease that threatens wheat production throughout the world. Breeding resistant cultivars is an effective way to reduce harm caused by powdery mildew. In this study, 35 wheat-Psathyrostachys huashanica-derived lines were developed by crossing common wheat and P. huashanica Keng (2n = 2x = 14, NsNs) using embryo culture. Resistance to powdery mildew in the derived lines was identified at the seedling and adult stages. Line H5-5-4-2 was selected with immunity to powdery mildew at both growth stages. The chromosome structure of this line was characterized by cytology, genomic in situ hybridization (GISH), and expressed sequence tag-sequence-tagged site (EST-STS) analysis. The chromosome configuration was 2n = 44 = 22II. Two P. huashanica chromosomes with strong hybridization signals were detected by GISH analysis. Among 83 EST-STS markers that covered all seven homologous groups in wheat, three pairs of STS markers, BE497584, BF202643, and BG262410, located in wheat homologous group 1 amplified clear specific bands related to P. huashanica. The results indicated that resistant line H5-5-4-2 was a wheat-P. huashanica 1Ns disomic addition line. Full article

(This article belongs to the Special Issue Analysis of Crop Genetic and Germplasm Diversity)

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12 pages, 978 KiB

Open AccessArticle

Estimation of Genetic Diversity in Seven Races of Native Maize from the Highlands of Mexico

by Mario Rocandio-Rodríguez, Amalio Santacruz-Varela, Leobigildo Córdova-Téllez, Higinio López-Sánchez, Aurelio Hernández-Bautista, Fernando Castillo-González, Ricardo Lobato-Ortiz, J. Jesús García-Zavala and Pedro Antonio López

Agronomy 2020, 10(2), 309; https://doi.org/10.3390/agronomy10020309 - 22 Feb 2020

Cited by 1 | Viewed by 3233

Abstract

Characterizing the genetic diversity of maize (Zea mays L.) populations by their morphological and molecular attributes makes it possible to place populations into specific groups; thus, facilitating the design of procedures for their optimum and sustainable use. In this study, data from [...] Read more.

Characterizing the genetic diversity of maize (Zea mays L.) populations by their morphological and molecular attributes makes it possible to place populations into specific groups; thus, facilitating the design of procedures for their optimum and sustainable use. In this study, data from two lines of evidence were analyzed simultaneously to robustly classify maize populations and to determine their genetic relationships. Seven maize races of the central high plateau of Mexico were characterized using a combined analysis of 13 morphological traits and 31 microsatellite loci. The germplasm assessed included samples of 119 accessions held at Mexican germplasm banks. Cluster and principal component analyses were performed. Also, genetic and geographic relationships among the accessions were determined. Principal component analysis separated the different accessions into well-defined groups using first three principal components. The accessions of Arrocillo Amarillo and Elotes Cónicos races did not exhibit a grouping pattern, indicating greater genetic complexity. Better grounded grouping and phylogenetic relationships were obtained when traits of both lines of evidence were used simultaneously. Full article

(This article belongs to the Special Issue Analysis of Crop Genetic and Germplasm Diversity)

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18 pages, 1786 KiB

Open AccessArticle

Allelic Variation for Prolamins in Spanish Durum Wheat Landraces and Its Relationship with Quality Traits

by Efraín A. Chacón, Francisco J. Vázquez, Patricia Giraldo, José M. Carrillo, Elena Benavente and Marta Rodríguez-Quijano

Agronomy 2020, 10(1), 136; https://doi.org/10.3390/agronomy10010136 - 16 Jan 2020

Cited by 20 | Viewed by 3554

Abstract

Wheat landraces are currently being explored mainly as a source of allelic variation related to crop resilience and low-input adaptation. Characterization of their high- and low-molecular weight glutenin subunits can aid breeders to select as donor local materials those ensuring good end-use properties [...] Read more.

Wheat landraces are currently being explored mainly as a source of allelic variation related to crop resilience and low-input adaptation. Characterization of their high- and low-molecular weight glutenin subunits can aid breeders to select as donor local materials those ensuring good end-use properties in the derived elite cultivars. By using protein electrophoretic methods, we have determined the prolamin allelic profile of 116 Spanish durum wheat landraces. Their quality properties (as defined by grain protein content, sodium dodecyl sulfate (SDS) sedimentation volume and mixograph behavior) have also been assessed. The study has identified six novel glutenin alleles plus some other rare alleles some of which have been associated with improved durum wheat quality. Most of the novel variation detected needs to be characterized in a wider sample of varieties to establish any eventual beneficial effect on functional quality. Further analysis of the quality properties associated to specific allele combinations of Glu-A3, Glu-B3, and Glu-A1 has disclosed some clues on the influence on quality of certain non-allelic interactions between these main prolamin-encoding loci. Some of the landraces, showing outstanding values for the gluten quality parameters analyzed, might be directly used by farmers interested in the cultivation of traditional varieties for specialized food markets. Full article

(This article belongs to the Special Issue Analysis of Crop Genetic and Germplasm Diversity)

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12 pages, 1045 KiB

Open AccessArticle

Molecular Genetic Diversity and Population Structure of Ginseng Germplasm in RDA-Genebank: Implications for Breeding and Conservation

by Kyung Jun Lee, Jung-Ro Lee, Raveendar Sebastin, Gyu-Taek Cho and Do Yoon Hyun

Agronomy 2020, 10(1), 68; https://doi.org/10.3390/agronomy10010068 - 03 Jan 2020

Cited by 19 | Viewed by 3856

Abstract

Ginseng (Panax ginseng C.A. Meyer), commonly known as Korean or Asian ginseng, is a perennial herb native to Korea and China. There has been limited research effort to analyze the genetic diversity and population structure of ginseng germplasm because of its growth [...] Read more.

Ginseng (Panax ginseng C.A. Meyer), commonly known as Korean or Asian ginseng, is a perennial herb native to Korea and China. There has been limited research effort to analyze the genetic diversity and population structure of ginseng germplasm because of its growth habits. In the present study, genetic diversity and population structure of ginseng germplasm conserved in the National Agrobiodiversity Center (NAC) of South Korea were analyzed to provide basic data for future preservation and breeding of ginseng genetic resources. Seventeen simple sequence repeat (SSR) markers were used to assess the genetic diversity and population structure of 1109 ginseng accessions. Among 1109 ginseng accessions, 1042 (94.0%) accessions were landraces and 66 (6.0%) accessions were breeding lines (61 accessions, 5.5%) or cultivars (5 accessions, 0.5%). SSR markers revealed 56 different alleles with an average of 3.29 alleles per locus. The average gene diversity was 0.49. Analysis of molecular variance showed that 91% of allelic diversity was attributed to individual accessions within clusters while only 9% was distributed among clusters. Using discriminant analysis of principal components, 12 clusters were detected in 1109 ginseng accessions. The results of this study provide molecular evidence for the narrow genetic base of ginseng germplasm in NAC. For the broad understanding and efficient use of ginseng germplasm, it is necessary to analyze functional factors and to evaluate morphological traits. Full article

(This article belongs to the Special Issue Analysis of Crop Genetic and Germplasm Diversity)

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20 pages, 1361 KiB

Open AccessArticle

Multi-Level Characterization of Eggplant Accessions from Greek Islands and the Mainland Contributes to the Enhancement and Conservation of this Germplasm and Reveals a Large Diversity and Signatures of Differentiation between both Origins

by Pietro Gramazio, Eleni Chatziefstratiou, Constantinos Petropoulos, Vasileia Chioti, Photini Mylona, George Kapotis, Santiago Vilanova, Jaime Prohens and Vasileios Papasotiropoulos

Agronomy 2019, 9(12), 887; https://doi.org/10.3390/agronomy9120887 - 13 Dec 2019

Cited by 12 | Viewed by 3328

Abstract

Crop landraces are found in many inhabited islands of Greece. Due to the particularity of environment and isolation from the mainland, Greek islands represent a natural laboratory for comparing the diversity of landraces from the islands with those of the Greek mainland. A [...] Read more.

Crop landraces are found in many inhabited islands of Greece. Due to the particularity of environment and isolation from the mainland, Greek islands represent a natural laboratory for comparing the diversity of landraces from the islands with those of the Greek mainland. A collection of 36 Greek eggplant landraces and traditional cultivars from the mainland and the islands has been phenotypically and genetically characterized using 22 morphological descriptors and 5 SSR markers. The mineral composition (K, Mg, Cu, Fe, Mn, Zn) of fruits was also determined. The objectives of this study include the multi-level characterization of eggplant local landraces and the comparison of diversity among accessions from the Greek mainland and the islands. Characterization of eggplant landraces will contribute to the enhancement and prevention of genetic erosion in this local group and will provide a resource for future investigation and breeding. PCA analysis of morphological traits explained 45.4% of the total variance revealing the formation of two clusters, one with most of the island accessions, and another with most of the mainland ones. The SSR markers used exhibited high average values for the number of alleles/locus (4.6), expected heterozygosity (0.60) and PIC (0.55), while the observed heterozygosity was low (0.13). Both STRUCTURE and PCoA analyses based on SSR data revealed two genetic clusters, one made up mainly by the mainland accessions, while the other one was mainly made up by the island accessions. Although there was considerable variation among the landraces for the concentration of minerals studied, only average Mg concentration was significantly different between mainland and island accessions. Based on our data, the Greek eggplant landraces present considerable morphological and genetic diversity with some differentiation signatures between the island and the mainland accessions. Our results have implications for conservation of Greek landraces and suggest that Greece might be considered as part of a secondary center of diversity for eggplant in the Mediterranean basin. Full article

(This article belongs to the Special Issue Analysis of Crop Genetic and Germplasm Diversity)

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13 pages, 2051 KiB

Open AccessArticle

Variability in Nutraceutical Lipid Content of Selected Rice (Oryza sativa L. spp. indica) Germplasms

by Bhornchai Harakotr, Kasidid Prompoh, Supakorn Boonyuen, Bhalang Suriharn and Kamol Lertrat

Agronomy 2019, 9(12), 823; https://doi.org/10.3390/agronomy9120823 - 30 Nov 2019

Cited by 6 | Viewed by 2966

Abstract

Rice (Oryza sativa L.) contains many high-value nutritional compounds, including nutraceutical lipid compounds that offer health benefits. An understanding of the genetic variability in the lipid contents of different rice germplasms is necessary to support breeding programs. The goals of this study [...] Read more.

Rice (Oryza sativa L.) contains many high-value nutritional compounds, including nutraceutical lipid compounds that offer health benefits. An understanding of the genetic variability in the lipid contents of different rice germplasms is necessary to support breeding programs. The goals of this study were: i) to investigate varietal differences in levels of the nutraceutical lipid α-tocopherol, γ-oryzanol, campesterol, β-sitosterol, octacosanol, and squalene and ii) to identify clusters of rice germplasms based on their lipid contents. Eighty-three indica rice subspecies were evaluated using a randomized complete block design with three replications. Research was conducted in Thailand during the 2016 rice-growing season. Significant differences were found among genotypes across all traits. The largest variation was found for β-sitosterol, followed by campesterol, octacosanol, and α-tocopherol. Variation in squalene content was small. Four principal components were found that accounted for 93.47% of overall variability. β-sitosterol, campesterol, and squalene were the principal discriminatory constituents. No significant correlation was found between color parameters and levels of these compounds, suggesting that former are of little use as an indirect marker for selection of fat-soluble nutraceuticals. Cluster analysis sorted the germplasm into nine clusters, based on their nutraceutical lipid content. TU-010, TU-027, TU-093, and TU-244 genotypes had the highest levels, making them a potentially useful genetic resource in breeding programs for nutraceutically-improved rice. The findings of this study can support the introduction of novel rice varieties with high added-value bioactive properties. Full article

(This article belongs to the Special Issue Analysis of Crop Genetic and Germplasm Diversity)

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11 pages, 1015 KiB

Open AccessArticle

Genetic Diversity of Sweet Potato (Ipomoea batatas L. Lam) Germplasms Collected Worldwide Using Chloroplast SSR Markers

by Kyung Jun Lee, Gi-An Lee, Jung-Ro Lee, Raveendar Sebastin, Myoung-Jae Shin, Gyu-Taek Cho and Do Yoon Hyun

Agronomy 2019, 9(11), 752; https://doi.org/10.3390/agronomy9110752 - 13 Nov 2019

Cited by 8 | Viewed by 4316

Abstract

Sweet potato (Ipomoea batatas L. Lam) is an important food crop widely cultivated in the world. In this study, nine chloroplast simple sequence repeat (cpSSR) markers were used to analyze the genetic diversity and relationships of 558 sweet potato accessions in the [...] Read more.

Sweet potato (Ipomoea batatas L. Lam) is an important food crop widely cultivated in the world. In this study, nine chloroplast simple sequence repeat (cpSSR) markers were used to analyze the genetic diversity and relationships of 558 sweet potato accessions in the germplasm collection of the National Agrobiodiversity Center (NAC). Eight of the nine cpSSR showed polymorphisms, while Ibcp31 did not. The number of alleles per locus ranged from two to four. In general, the Shannon index for each cpSSR ranged from 0.280 to 1.123 and the diversity indices and unbiased diversity ranged from 0.148 to 0.626, and 0.210 to 0.627, respectively. Results of the median-joining network showed 33 chlorotypes in 558 sweet potato accessions. In factor analysis, 558 sweet potato accessions were divided into four clusters, with clusters I and II composed only of the sweet potato accessions from Korea, Japan, Taiwan, and the USA. The results of this study confirmed that the genetic diversity of the female parents of sweet potato accessions conserved at the NAC is low and therefore more sweet potato accessions need to be collected. These results will help to establish an efficient management plan for sweet potato genetic germplasms at the NAC. Full article

(This article belongs to the Special Issue Analysis of Crop Genetic and Germplasm Diversity)

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14 pages, 2138 KiB

Open AccessArticle

Exploring the Genetic Diversity and Population Structure of Turkish Laurel Germplasm by the iPBS-Retrotransposon Marker System

by Ünal Karık, Muhammad Azhar Nadeem, Ephrem Habyarimana, Sezai Ercişli, Mehtap Yildiz, Abdurrahim Yılmaz, Seung Hwan Yang, Gyuhwa Chung and Faheem Shehzad Baloch

Agronomy 2019, 9(10), 647; https://doi.org/10.3390/agronomy9100647 - 17 Oct 2019

Cited by 24 | Viewed by 3971

Abstract

Laurel is a medicinally important plant and is known to the world for its essential oil. Turkey is the main market in the laurel leaf trade by sharing about 90% of the world trade. Here we made an effort to elucidate genetic diversity [...] Read more.

Laurel is a medicinally important plant and is known to the world for its essential oil. Turkey is the main market in the laurel leaf trade by sharing about 90% of the world trade. Here we made an effort to elucidate genetic diversity and population structure of 94 Turkish laurel genotypes collected from 26 provinces and four geographical regions using inter-primer binding site (iPBS) retrotransposon markers. A total of 13 most polymorphic primers were selected which yielded 195 total bands, of which 84.10% were found polymorphic. Mean polymorphism information content (PIC) was (0.361) and diversity indices including mean effective number of alleles (1.36), mean Shannon’s information index (0.35) and overall gene diversity (0.22) revealed the existence of sufficient amount of genetic diversity in the studied plant material. Most diversity was found in genotypes collected from the Mediterranean region. Analysis of molecular variance (AMOVA) revealed that most of the variation (85%) in Turkish laurel germplasm is due to differences within populations. Model-based structure, principal coordinate analysis (PCoA) and neighbor-joining algorithms were found in agreement and clustered the studied germplasm according to their collection provinces and regions. This is a very first study exploring the genetic diversity and population structure of laurel germplasm using iPBS-retrotransposon marker system. We believe that information provided in this work will be helpful for the scientific community to take more interest in this forgotten but the medicinally important plant. Full article

(This article belongs to the Special Issue Analysis of Crop Genetic and Germplasm Diversity)

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Review

Jump to: Editorial, Research

8 pages, 2736 KiB

Open AccessReview

Aegilops Species for the Improvement of the Leaf and Stripe Rust Resistance in Cultivated Triticale (×Triticosecale Wittmack)

by Waldemar Ulaszewski and Michał Tomasz Kwiatek

Agronomy 2020, 10(12), 1991; https://doi.org/10.3390/agronomy10121991 - 18 Dec 2020

Cited by 2 | Viewed by 2107

Abstract

Hexaploid triticale (×Triticosecale Wittmack, 2n = 6x = 42 chromosomes, AABBRR) is a cultivated hybrid, which combines wheat (Triticum aestivum L.) and rye (Secale cereale L.) properties. It has a better ability to be grown on poor soils, [...] Read more.

Hexaploid triticale (×Triticosecale Wittmack, 2n = 6x = 42 chromosomes, AABBRR) is a cultivated hybrid, which combines wheat (Triticum aestivum L.) and rye (Secale cereale L.) properties. It has a better ability to be grown on poor soils, compared to wheat. Mainly, triticale is produced for forage feed and bioethanol. Considering the limited diversity of this human-made crop, there is a need to widen its genetic variability, especially to introduce new genes, responsible for agronomic traits, such as resistance to biotic stresses. Leaf rust caused by Puccinia triticina Eriks. and stripe rust caused by Puccinia striiformis Westend are the most destructive foliar diseases of triticale and related cereals. Developing resistant triticale varieties is an important strategy for the control of these diseases. A number of leaf and stripe rust resistance genes have been already introduced into bread wheat from related species using chromosome manipulations. Exploitation of related species conferring desirable loci is the most effective non-GMO way of improving the rust resistance of triticale. The procedure encompasses chromosome doubling of obtained hybrids followed by a number of backcrosses to eliminate unnecessary alien chromatin and to reduce the linkage drag. In this review, we show the recent status of pre-breeding studies, which are focused on transfer of leaf and stripe rust resistance genes from Aegilops species into cultivated triticale using distant crossing and chromosome engineering. Full article

(This article belongs to the Special Issue Analysis of Crop Genetic and Germplasm Diversity)

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