Search Results (88)

The undertaking of distant hybridization holds paramount significance for the innovation of tea germplasm resources and the cultivation of superior, specialized tea varieties. However, challenges manifest during the process of tea plant distant hybridization breeding, with reproductive barriers impeding the successful acquisition of hybrid progeny; the precise stages at which these barriers occur remain unclear. In this study, utilizing Camellia sinensis cv. Jinxuan as the maternal parent, as well as C. gymnogyna Chang and C. sinensis cv. Yinghong No.9 as the paternal parents, interspecific distant hybridization (DH) and intraspecific hybridization (IH) were conducted. The investigation involved the observation of pollen germination and pollen tube behavior on the stigma, the scrutiny of the developmental dynamics of the ovary post-hybridization, and the examination of the stages and reasons for reproductive disorders during tea tree distant hybridization. The findings indicate that both IH and DH exhibit pre-fertilization barriers. The pre-embryonic development of hybrids obtained from DH is normal, but there is a significant fruit drop during the stage of fruit development. The germination rate of mature seeds obtained from DH is low, and there are pronounced post-fertilization disorders, which are the primary reasons for the difficulty in achieving successful tea plant distant hybridization. An analysis of the genetic variation in phenotypes and chemical components in the progeny after distant hybridization revealed widespread variation and rich genetic diversity. The identification of progeny with a high amino acid and caffeine content holds promise for future production and breeding, providing valuable theoretical references for the selection of parents in the creation of low-caffeine-content tea germplasm resources. Full article

Nightlily (Hemerocallis citrina Baroni) is mainly cultivated for bud consumption with medicinal, nutritional, and economic value. Enhancing nightlily yield is one of the most significant breeding goals of modern agriculture of H. citrina breeding objective, but it also faces great challenges. In this study, an intraspecific hybridization population crossed between two varieties, ‘Liuyuehua’ and ‘Datong Huanghua’ of Hemerocallis, was used to establish 715 F₁ individuals. Phenotypic data for eight floral traits, including scape number, bud number, scape length, scape diameter, bud length, bud diameter, fresh flower bud weight, and dry flower bud weight, were collected from 715 F₁ individuals over a three-year period (2022, 2023, and 2024). The Simple Repeat Sequence (SSR) markers were validated to genotype the 116 random F₁ individuals and to construct a linkage map. The intraspecific hybridization map contained 11 linkage groups. A total of 169 SSR markers were used to construct a linkage map, spanning a total map length of 1605.3 cM, with an average marker interval of 9.50 cM. The linkage map revealed 11 floral QTLs from 7.21% to 24.29% of phenotypic variation. Through collinearity analysis, it was found that 122 markers could be aligned to the published genome sequence of H. citrina. A total of five candidate genes for floral traits were predicted. The linkage map is essential for mapping and marker-assisted progeny selection that will accelerate the pace of nightlily breeding. Full article

Leaves are the most ubiquitous plant organs, whose macrostructures exhibit close correlations with environmental factors while simultaneously reflecting inherent genetic and evolutionary patterns. These characteristics render them highly significant for plant taxonomy, ecology, and related disciplines. Therefore, this study presents the first comprehensive evaluation of Malus leaf macrostructures for infraspecific classification. By establishing a trait-screening system, we conducted a numerical taxonomic analysis of leaf phenotypic variation across 73 Malus germplasm (34 species and 39 cultivars). Through ancestor-inclined distribution characteristic analysis, we investigated phylogenetic relationships at both the genus level and infraspecific ranks within Malus. A total of 21 leaf phenotypic traits were selected from 50 candidate traits based on the following criteria: high diversity, abundance, and evenness (D ≥ 0.50, H ≥ 0.80, and E ≥ 0.60); significant intraspecific uniformity and interspecific distinctness ($\overline{CV}$ ≤ 10% and $CV$ ≥ 15%). Notably, the selected traits with low intraspecific variability ($\overline{CV}$ ≤ 10%) exhibit environmental robustness, likely reflecting low phenotypic plasticity of these specific traits under varying conditions. This stability enhances their taxonomic utility. It was found that the highest ancestor-inclined distribution probability reached 90% for 10 traceable cultivars, demonstrating reliable breeding lines. Based on morphological evidence, there was a highly significant correlation between the evolutionary orders of (Sect. Docyniopsis → Sect. Sorbomalus → Sect. Malus) and group/sub-groups (B₁ → B₂ → A). This study demonstrates that phenotypic variation in leaf macrostructures can effectively explore the affinities among Malus germplasm, exhibiting taxonomic significance at the infraspecific level, thereby providing references for variety selection. However, hybrid offspring may exhibit mixed parental characteristics, leading to blurred species boundaries. And convergent evolution may create false homologies, potentially misleading morphology-based taxonomic inferences. The inferred taxonomic relationships present certain limitations that warrant further investigation. Full article

Blueberry breeding requires a significant commitment of time, skilled labour, and financial resources, but it is essential to develop new cultivars that can meet challenges such as climate change, disease resistance, and changing market preferences. Intraspecific hybridisationis a widely used breeding strategy to increase genetic diversity, broaden the selection base, and develop new cultivars. By crossing different varieties and making advanced selections, breeders can introduce desirable traits such as improved fruit quality, increased yield, improved disease resistance and greater adaptability to environmental conditions. The present study aimed to evaluate the heritability of some key biometric and biochemical parameters inblueberry hybrids derived from intraspecific crosses to assess their inheritance patterns. The results can guide breeders in selecting parent combinations that maximise genetic gain, ultimately supporting the advancement of commercial blueberry production. The ‘Delicia × 4/6’ hybrid combination showed excellent performance for total polyphenol content, flavonoids, tannins, and ascorbic acid, with high genetic gain and near complete heritability, making it a promising candidate for improving antioxidant activity. The ‘Azur × Northblue’ hybrid had favourable total anthocyanin and tannin content, but an unfavourable sugar and ascorbic acid profile.The ‘Simultan × Duke’ hybrid combination showed the highest genetic gain for total soluble solids and firmness, together with high positive heterosis and heterotic progress, highlighting its potential for high-quality cultivars suitable for mechanical harvesting and storage. This research provides valuable insights into the efficiency of intraspecific hybridisationin the development of new blueberry cultivars with improved agronomic and nutritional qualities. Full article

Background/Objectives: The genus Vitis comprises approximately 70 species with high genetic diversity, among which Vitis vinifera is the most economically significant. Despite numerous studies on the genetic characterizations of V. vinifera, selecting optimal chloroplast DNA barcoding regions for intraspecific differentiation remains unresolved. Most studies have focused on nuclear markers (SSRs, SNPs) or widely used chloroplast loci (e.g., matk, rbcl), which have shown limited resolution at the subspecies level. In this study, the complete chloroplast genomes of 34 V. vinifera accessions from different varieties and hybrids (vinifera, sylvestris, caucasica, and labrusca) were analyzed to identify the key genomic regions for DNA barcoding. Methods: Using bioinformatics tools, we assessed the genome structure, nucleotide variability, microsatellites, codon usage bias, and phylogenetic relationships among the investigated varieties. Results: The chloroplast genomes displayed a quadripartite structure, with lengths ranging from 160,906 to 160,929 bp and a guanine–cytosine (GC) content of ~37.4%. Phylogenetic analysis revealed an unusual position for VV-5 vini and VVVL-3 lab, suggesting potential taxonomic misclassification or hybridization effects. A single locus showed low discrimination power, but the concatenation of five loci (ccsA-trnN-GUU, rpl16, rpl2-rps19, rpoC2, and trnM-CAU) exhibited significantly improved resolution (44.11% K2P), surpassing traditional markers. Conclusions: This study addresses the gap in the literature regarding the use of concatenated chloroplast loci for subspecies research; the results validate these markers across a broader range of Vitis accessions and integrate nuclear and mitochondrial data to achieve a more comprehensive understanding of the evolutionary history and genetic diversity of V. vinifera. Full article

This study investigated seed storage behavior and seedling development patterns in the genus Phoenix L. (Arecaceae), addressing the knowledge gap regarding orthodox versus recalcitrant characteristics in these ecologically and economically significant palms. We examined the germination capacity and subsequent growth in 31 seed samples from various Phoenix species stored for up to 10 years at approximately 5 °C, at the Germplasm Bank at the Escuela Politécnica Superior de Orihuela, comprising 465 seeds monitored over a one-year period. The seed germination trials involved planting seeds in pots placed in an open-air greenhouse after ambient temperatures consistently exceeded 20 °C, typically after mid-June. Phoenix dactylifera, P. canariensis, P. theophrasti, the hybrid P. dactylifera × P. canariensis, and P. × “Palmeri” demonstrated orthodox seed storage behavior, maintaining viability for up to nine years. Conversely, P. sylvestris, P. pusilla, P. rupicola, and P. loureiroi consistently failed to germinate despite previous germination success, suggesting potential recalcitrant characteristics. Statistical analyses revealed that species identity and geographic origin exerted greater influence on germination success than seed age. Seedling development exhibited a conserved seasonal pattern across all species, with synchronized leaf emergence in September and March–July, followed by winter dormancy. Significant intraspecific variation was observed, particularly within P. dactylifera varieties, in both leaf production and final leaf length. These findings provide valuable insights into germplasm preservation and cultivation strategies, demonstrating that while some Phoenix species are suitable for long-term seed banking, others may require alternative conservation approaches. The observed species-specific and variety-specific differences offer important selection criteria for horticultural applications and conservation efforts. Full article

Sicily, Southern Italy, has important genetic resources for azarole (Crataegus azarolus). The region hosts both spontaneous wild populations and various forms of the genus, some of which belong to well-defined specific or intraspecific taxa, while others are hybrids of unclear origin. Not all wild forms can be considered related to C. azarolus, but those included in the sect. Azaroli and thus C. aronia (= C. azarolus var. aronia), which is widespread in western Sicily, certainly can. All these populations are morphologically distinct but coexist in the same area. This preliminary genetic study aims to establish the genetic relationships between wild populations of Crataegus taxa and azarole (C. azarolus). Furthermore, the research addresses the lack of clear taxonomic information regarding the different phenotypes found in Sicily, including both recognized taxa and those still critically underreported. The study is based on SSR (Simple Sequence Repeat) molecular markers, isolated from other Rosaceae species. The findings indicate that at least two groups affiliated with C. azarolus, yet distinct, are present in Sicilian populations. These results could have significant implications for systematics and taxonomy, as well as for conservation and the valorization of plant biodiversity. Full article

Interspecific hybridization serves as a crucial strategy for innovating sugarcane germplasms. Currently, nearly all modern sugarcane varieties that incorporate genetic material are derived from Saccharum spontaneum. The number of chromosomes in S. spontaneum ranges from 40 to 128, contributing significantly to the diversity of its genetic resources. However, the genetic mechanisms driving chromosome number variation in S. spontaneum remain to be fully elucidated. Here, oligonucleotide fluorescence in situ hybridization (Oligo-FISH) was conducted to identify individual chromosomes and explore chromosome transmission during the intraspecific hybridization of S. spontaneum. The results indicate that from the progenies generated from S. spontaneum Yunnan2017-22 (2n = 8x = 64) and Yunnan82-1 (2n = 8x = 64) emerged two distinct karyotypes, 2n = 12x = 96 (A1) and 2n = 8x = 64 (A2, A33-1, A18). This implies that the chromosome inheritances were 2n + n and n + n in the progenies. However, self-pollinated samples of A1 (2n = 12x = 96) produced normal offspring C1 (2n = 94) and C2 (2n = 96). The 2n + n inheritance pattern did not continue. In another cross, the progenies derived from S. spontaneum Yunnan2017-41 (2n = 8x = 64) and Yunnan8 (2n = 10x = 80) carried a karyotype of 2n = 9x = 72, with n + n inheritance mode. These findings highlight the existence of two chromosome inheritance modes, 2n + n and n + n, in the context of the intraspecific hybridization of S. spontaneum. Additionally, hybridization between different ploidy S. spontaneum was also accompanied by chromosomal translocations (A1, A2, A18, A18) and loss (A2, A33-1, AA-4, and C2) that further resulted in the complexity of the S. spontaneum genome. Together, these findings highlight diverse chromosome inheritance in S. spontaneum hybridization, and provide a theoretical foundation for the further utilization of S. spontaneum germplasm in sugarcane breeding. Full article

Nightlily (Hemerocallis citrina Baroni) is an important vegetable with edible floral organs. It possesses considerable economic value due to its edibility, ornamental, and medicinal properties. However, the genetic linkage map construction and quantitative trait locus (QTL) mapping of nightlily have not been performed. This study used two varieties ‘Dongzhuanghuanghua’ and ‘Chonglihua’ of nightlily as cross parents to establish an intraspecific hybridization population of 120 F₁ progenies. The ‘Datonghuanghua’ (female) variety of nightlily and ‘Lullaby Baby’ (male) variety of daylily were selected to construct an interspecific hybridization population of 55 F₁ progenies. A total of 965 expressed sequence tag–simple sequence repeats (EST-SSRs), along with 20 SSR markers from various sources, were used for genetic mapping. Among these markers, CT/TC (9.24%) of the dinucleotide and GGA/GAG/AGG (4.67%) of the trinucleotide repeat motifs were most abundant. In the intraspecific hybridization genetic map, a total of 124 markers were resolved into 11 linkage groups, with a total map length of 1535.07 cM and an average interval of 12.38 cM. Similarly, the interspecific hybridization map contained 11 linkage groups but with 164 markers, a total map length of 2517.06 cM, and an average interval of 15.35 cM. The two constructed maps had 48 identical markers and demonstrated good collinearity. The collinearity analysis showed that 161 markers hit the genomic sequence of the published H. citrina genome, indicating that the two constructed genetic maps had high accuracy. Phenotypic data were investigated over two consecutive years (2018 and 2019) for flower bud fresh weight, dry weight, and bud length in two hybridization populations. A total of nine QTLs associated with flower bud-related traits were identified, among which those located on linkage group 8 of the intraspecific genetic map and linkage group 4 of the interspecific genetic map showed good stability. All nine QTLs had LOD values of not less than 4 and PVE values of not less than 15% over two years. This is the first report about the intra- and interspecific genetic map construction and QTL mapping of the flower bud-related traits in nightlily based on a genetic map. The results promote marker-assisted breeding and offer insights into the mechanisms underlying important traits of the genus Hemerocallis. Full article

The trans-Palearctic moth Phyllonorycter populifoliella (Lepidoptera: Gracillariidae) is a major pest of the North American Populus balsamifera and its hybrids widely planted as ornamentals in North Asia (i.e., the Asian part of Russia). We DNA barcoded Ph. populifoliella from distant geographical populations in Russia and analyzed them together with the data from eight European countries and India to estimate intraspecific variability and the haplotype richness in the Palearctic, and specifically in North Asia. Furthermore, using next-generation sequencing (NGS, Sequel platform, PacBio), we investigated larval and pupal remnants found in an old herbarium from the Nearctic, where P. balsamifera occurs naturally, to verify if any events of the moth introduction to this biogeographic zone happened in the past. Relatively high intraspecific variability in the COI gene of mtDNA, reaching 3.73%, was recorded in Ph. populifoliella. Overall, 30 COI haplotypes were defined in 83 specimens from the Palearctic, with a noticeable richness in North Asia (21 haplotypes). Using NGS, the remnants of 14 Phyllonorycter specimens dissected from up to 174-year-old herbaria from the Palearctic and Nearctic were sequenced, and four moth species were identified. Among them, there were three Palearctic species, Ph. populifoliella, Ph. pastorella (Zeller), and Ph. apparella (Herrich-Schäffer), and one Nearctic, Ph. nipigon (Freeman). No evidence of Ph. populifoliella introduction to North America was documented based on the examination of the herbarium dated 1850–1974. Three specimens of Ph. populifoliella identified from herbaria from Austria and Poland (dated 1879–1931) represented one haplotype (H7) known from the recent time. Overall, our study clarifies the modern range, provides insights into phylogeography, and defines the haplotype richness of the native leafminer outbreaking on the alien host. Furthermore, it underlines the use of old herbaria to explore the historical distribution of endophagous insect species. Full article

The high leaf morphological variability of European white oaks is largely documented in the botanical literature, and several papers have been published in the last two decades focusing on inter- and intraspecific leaf phenotypic plasticity. Studies involving landmark-based geometric morphometrics proved to be useful in highlighting relationships between leaf size and shape variation and environmental factors, phylogenetic patterns, or hybridization events. In this paper, the leaf size and shape variations of 18 populations of Quercus petraea distributed throughout a wide geographical area were analyzed by means of geometric morphometric methods (GMMs). This study involved 10 European countries and investigated the intraspecific leaf variability of Q. petraea within a wide latitudinal and longitudinal gradient. Analyses of variance for shape and centroid size were performed through Procrustes ANOVA. Multivariate analysis procedures, partial least squares method, and regression analyses were used to highlight possible patterns of covariation between leaf shape and size and geographical/environmental variables. The results revealed that the Q. petraea populations analyzed mainly differed in their leaf size, where a decrease was observed according to a north to south geographical gradient. Both leaf size and shape were found to be significantly related to latitude, and, to a lesser extent, to mean annual temperature and the leaf isotopic signature of ¹⁵N. All the other variables considered did not provide significant results. Unexpected differences observed comparing the leaf traits of geographically strictly adjacent populations suggest the involvement of local hybridization/introgression events. However, with a few exceptions, Q. petraea turned out to be quite conservative in its leaf shape and size at both the local and continental scale. Full article

Background/Objectives: The classification and phylogenetic relationships of Gossypium hirsutum L. landraces, despite their proximity to southern Mexico, remain unresolved. This study aimed to clarify these relationships using SSR markers and hybridization methods, focusing on subspecies and race differentiation within G. hirsutum L. Methods: Seventy polymorphic SSR markers (out of 177 tested) were used to analyze 141 alleles and calculate genetic distances among accessions. Phylogenetic relationships were determined using MEGA software (version 11.0.13) and visualized in a phylogenetic tree. ANOVA in NCSS 12 was used for statistical analysis. Over 1000 inter-race crosses were conducted to assess boll-setting rates. Results: Distinct phylogenetic patterns were identified between G. hirsutum subspecies and races, correlating with boll-setting rates. Latifolium, richmondii, and morilli showed no significant increase in boll-setting rates in reciprocal crosses. Cultivars Omad and Bakht, as paternal parents, yielded higher boll-setting rates. Religiosum and yucatanense displayed high boll- and seed-setting rates as maternal parents but low rates as paternal parents. Additionally, phylogenetic analysis revealed a close relationship between cultivars ‘Omad’ and ‘Bakht’ with G. hirsutum race richmondii, indicating their close evolutionary relationship. Conclusions: Reciprocal differentiation characteristics of G. hirsutum subspecies and races, particularly religiosum and yucatanense, should be considered during hybridization for genetic and breeding studies. Understanding the phylogenetic relationships among G. hirsutum taxa is crucial for exploring the genetic diversity of this economically important species. Full article

The radiation of cichlid species in the East African Great Lakes is remarkable and rapid. The population genetics of two deep-water Cyphotilapia species along the east coast of Lake Tanganyika from Burundi to southern Tanzania was determined using ddRAD-seq. A combination of ADMIXTURE, PCA, genome polarization, and 2D site frequency spectrum analyses confirmed the presence of two species, C. frontosa in the north and C. gibberosa in the south, as documented in other studies. We also found evidence of a potential hybrid zone connecting the two species at a sharp genetic cline centered in the middle of the lake and apparent introgression in both directions, but predominantly from ‘gibberosa’ into ‘frontosa’. The highest proportion of introgressed ‘gibberosa’ ancestry was present in the southernmost populations of C. frontosa collected near Karilani Island and Cape Kabogo. At the intra-specific level, there was support for between 1 and 3 populations of C. frontosa, whereas the results indicated only a single homogeneous population of C. gibberosa. The presence of different morphs in the lake despite the low levels of heterozygosity suggests that a small number of loci may be involved in the morphological variation and/or that there is a more complex interplay between genetics and the environment in different locations. Full article

Hairy vetch (Vicia villosa Roth) and smooth vetch (V. villosa Roth var. glabrescens) are important cover crops and legume forage with great economic and ecological values. Due to the large and highly heterozygous genome, full-length transcriptome reconstruction is a cost-effective route to mining their genetic resources. In this study, a hybrid sequencing approach combining SMRT and NGS technologies was applied. The results showed that 28,747 and 40,600 high-quality non-redundant transcripts with an average length of 1808 bp and 1768 bp were generated from hairy vetch and smooth vetch, including 24,864 and 35,035 open reading frames (ORFs), respectively. More than 96% of transcripts were annotated to the public databases, and around 25% of isoforms underwent alternative splicing (AS) events. In addition, 987 and 1587 high-confidence lncRNAs were identified in two vetches. Interestingly, smooth vetch contains more specific transcripts and orthologous clusters than hairy vetch, revealing intraspecific transcript diversity. The phylogeny revealed that they were clustered together and closely related to the genus Pisum. Furthermore, the estimation of Ka/Ks ratios showed that purifying selection was the predominant force. A putative 3-dehydroquinate dehydratase/shikimate dehydrogenase (DHD/SDH) gene underwent strong positive selection and might regulate phenotypic differences between hairy vetch and smooth vetch. Overall, our study provides a vital characterization of two full-length transcriptomes in Vicia villosa, which will be valuable for their molecular research and breeding. Full article

Naturally transgenic plants are plants that have undergone Agrobacterium-mediated transformation under natural conditions without human involvement. Among Arachis hypogaea L., A. duranensis Krapov. & W.C. Greg, A. ipaensis Krapov. & W.C. Greg, A. monticola Krapov. & Rigoni, and A. stenosperma Krapov. & W.C. Greg are known to contain sequences derived from the T-DNA of “Agrobacterium”. In the present study, using molecular genetics and bioinformatic methods, we characterized natural transgenes in 18 new species from six sections of the genus Arachis. We found that small fragments of genes for enzymes of the agropine synthesis pathway were preserved only in some of the studied samples and were lost in the majority of the species during evolution. At the same time, genes, similar to cucumopine synthases (cus-like), remained intact in almost all of the investigated species. In cultivated peanuts, they are expressed in a tissue-specific manner. We demonstrated the intraspecific variability of the structure and expression of the cus-like gene in cultivated peanuts. The described diversity of gene sequences horizontally transferred from Agrobacterium to plants helps to shed light on the phylogeny of species of the genus Arachis and track possible hybridization events. Data on the ability of certain species to hybridize are useful for planning breeding schemes aimed at transferring valuable traits from wild species into cultivated peanuts. Full article