Genetic Diversity and Population Structure of F3:6 Nebraska Winter Wheat Genotypes Using Genotyping-By-Sequencing

Genetic diversity and population structure in banana (Musa spp.) breeding germplasm

Bananas (Musa spp.) are one of the most highly consumed fruits globally, grown in the tropical and sub-tropical regions. We evaluated 856 Musa accessions from the breeding programs of the International Institute of Tropical Agriculture of Nigeria, Tanzania, and Uganda; the National Agricultural Research Organization of Uganda; the Brazilian Agricultural Research Corporation (Embrapa); and the National Research Centre for Banana of India. Accessions from the in vitro gene bank at the International Transit Centre in Belgium were included to provide a baseline of available global diversity. A total of 16,903 informative single nucleotide polymorphism markers were used to estimate and characterize the genetic diversity and population structure and identify overlaps and unique material among the breeding programs. Analysis of molecular variance displayed low genetic variation among accessions and diploids and a higher variation among tetraploids (p < 0.001). Structure analysis revealed two major clusters corresponding to genomic composition. The results indicate that there is potential for the banana breeding programs to increase the diversity in their breeding materials and should exploit this potential for parental improvement and to enhance genetic gains in future breeding efforts.

Molecular genetic diversity and linkage disequilibrium structure of the Egyptian faba bean using Single Primer Enrichment Technology (SPET)

Faba bean is an important legume crop. The genetic diversity among faba bean genotypes is very important for the genetic improvement of target traits. A set of 128 fab bean genotypes that are originally from Egypt were used in this study to investigate the genetic diversity and population structure. The 128 genotypes were genotyped using the Single Primer Enrichment Technology (SPET) by which a set of 6759 SNP markers were generated after filtration. The SNP markers were distributed on all chromosomes with a range extending from 822 (Chr. 6) to 1872 (Chr.1). The SNP markers had wide ranges of polymorphic information content (PIC), gene diversity (GD), and minor allele frequency. The analysis of population structure divided the Egyptian faba bean population into five subpopulations. Considerable genetic distance was found among all genotypes, ranging from 0.1 to 0.4. The highly divergent genotype was highlighted in this study and the genetic distance among genotypes ranged from 0.1 and 0.6. Moreover, the structure of linkage disequilibrium was studied, and the analysis revealed a low level of LD in the Egyptian faba bean population. A slow LD decay at the genomic and chromosomal levels was observed. Interestingly, the distribution of haplotype blocks was presented in each chromosome and the number of haplotype block ranged from 65 (Chr. 4) to 156 (Chr. 1). Migration and genetic drift are the main reasons for the low LD in the Egyptian faba bean population. The results of this study shed light on the possibility of the genetic improvement of faba bean crop in Egypt and conducting genetic association analyses to identify candidate genes associated with target traits (e.g. protein content, grain yield, etc.) in this panel.

Genetic diversity and population structure of Piper nigrum (black pepper) accessions based on next-generation SNP markers

Despite the economic importance of Piper nigrum (black pepper), a highly valued crop worldwide, development and utilization of genomic resources have remained limited, with diversity assessments often relying on only a few samples or DNA markers. Here we employed restriction-site associated DNA sequencing to analyze 175 P. nigrum accessions from eight main black pepper growing regions in Sri Lanka. The sequencing effort resulted in 1,976 million raw reads, averaging 11.3 million reads per accession, revealing 150,356 high-quality single nucleotide polymorphisms (SNPs) distributed across 26 chromosomes. Population structure analysis revealed two subpopulations (K = 2): a dominant group consisting of 152 accessions sourced from both home gardens and large-scale cultivations, and a smaller group comprising 23 accessions exclusively from native collections in home gardens. This clustering was further supported by principal component analysis, with the first two principal components explaining 35.2 and 12.1% of the total variation. Genetic diversity analysis indicated substantial gene flow (Nm = 342.21) and a low fixation index (FST = 0.00073) between the two subpopulations, with no clear genetic differentiation among accessions from different agro-climatic regions. These findings demonstrate that most current black pepper genotypes grown in Sri Lanka share a common genetic background, emphasizing the necessity to broaden the genetic base to enhance resilience to biotic and abiotic stresses. This study represents the first attempt at analyzing black pepper genetic diversity using high-resolution SNP markers, laying the foundation for future genome-wide association studies for SNP-based gene discovery and breeding.

Genetic Diversity and Population Structure of a Large USDA Sesame Collection

Sesame, Sesamum indicum L., is one of the oldest domesticated crops used for its oil and protein in many parts of the world. To build genomic resources for sesame that could be used to improve sesame productivity and responses to stresses, a USDA sesame germplasm collection of 501 accessions originating from 36 countries was used in this study. The panel was genotyped using genotyping-by-sequencing (GBS) technology to explore its genetic diversity and population structure and the relatedness among its accessions. A total of 24,735 high-quality single-nucleotide polymorphism (SNP) markers were identified over the 13 chromosomes. The marker density was 1900 SNP per chromosome, with an average polymorphism information content (PIC) value of 0.267. The marker polymorphisms and heterozygosity estimators indicated the usefulness of the identified SNPs to be used in future genetic studies and breeding activities. The population structure, principal components analysis (PCA), and unrooted neighbor-joining phylogenetic tree analyses classified two distinct subpopulations, indicating a wide genetic diversity within the USDA sesame collection. Analysis of molecular variance (AMOVA) revealed that 29.5% of the variation in this population was due to subpopulations, while 57.5% of the variation was due to variation among the accessions within the subpopulations. These results showed the degree of differentiation between the two subpopulations as well as within each subpopulation. The high fixation index (FST) between the distinguished subpopulations indicates a wide genetic diversity and high genetic differentiation among and within the identified subpopulations. The linkage disequilibrium (LD) pattern averaged 161 Kbp for the whole sesame genome, while the LD decay ranged from 168 Kbp at chromosome LG09 to 123 Kbp in chromosome LG05. These findings could explain the complications of linkage drag among the traits during selections. The selected accessions and genotyped SNPs provide tools to enhance genetic gain in sesame breeding programs through molecular approaches.

Genome-Wide Association Analysis of Yield-Related Traits and Candidate Genes in Vegetable Soybean

Owing to the rising demand for vegetable soybean products, there is an increasing need for high-yield soybean varieties. However, the complex correlation patterns among quantitative traits with genetic architecture pose a challenge for improving vegetable soybean through breeding. Herein, a genome-wide association study (GWAS) was applied to 6 yield-related traits in 188 vegetable soybean accessions. Using a BLINK model, a total of 116 single nucleotide polymorphisms (SNPs) were identified for plant height, pod length, pod number, pod thickness, pod width, and fresh pod weight. Furthermore, a total of 220 genes were found in the 200 kb upstream and downstream regions of significant SNPs, including 11 genes encoding functional proteins. Among them, four candidate genes, Glyma.13G109100, Glyma.03G183200, Glyma.09G102200, and Glyma.09G102300 were analyzed for significant haplotype variations and to be in LD block, which encode MYB-related transcription factor, auxin-responsive protein, F-box protein, and CYP450, respectively. The relative expression of candidate genes in V030 and V071 vegetable soybean (for the plant height, pod number, and fresh pod weight of V030 were lower than those of the V071 strains) was significantly different, and these genes could be involved in plant growth and development via various pathways. Altogether, we identified four candidate genes for pod yield and plant height from vegetable soybean germplasm. This study provides insights into the genomic basis for improving soybean and crucial genomic resources that can facilitate genome-assisted high-yielding vegetable soybean breeding.

Genome-Wide Association Study of Rice Diversity Panel Reveals New QTLs for Tolerance to Water Deficit Under the Egyptian Conditions

Drought has a significant impact on rice yield by restricting the crop's ability to grow and develop. Producing rice cultivars adapted to water deficit conditions is still the main interest of rice breeders and geneticists. To address this challenge, a set of 413 highly diverse rice populations were evaluated under normal and water deficit conditions for two growing seasons of 2021 and 2022. High genetic variation was found among genotypes for all studied traits. The heritability estimates ranged from 0.82 (panicle length) to 0.95 (plant height). Sterility percentage (SET%) was the most trait affected by water deficit in two growing seasons. 22 Rice genotypes were classified as drought tolerant in both years. Genome-wide association mapping was performed for all traits in the two growing seasons under both conditions using a total of 700,000 SNPs. The GWAS results revealed important and major SNPs associated with all traits. 26 Significant SNPs with stable allele effects were found to be associated with yield traits under water deficit conditions in both years. The results of this study provided rice genotypes that can be adapted under water deficit conditions and important stable SNP markers that can be used for marker-assisted selection after validation in different genetic backgrounds.

Genomic wide association study and selective sweep analysis identify genes associated with improved yield under drought in Turkish winter wheat germplasm

A panel comprising of 84 Turkish winter wheat landraces (LR) and 73 modern varieties (MV) was analyzed with genome wide association study (GWAS) to identify genes/genomic regions associated with increased yield under favorable and drought conditions. In addition, selective sweep analysis was conducted to detect signatures of selection in the winter wheat genome driving the differentiation between LR and MV, to gather an understanding of genomic regions linked to adaptation and yield improvement. The panel was genotyped with 25 K wheat SNP array and phenotyped for agronomic traits for two growing seasons (2018 and 2019) in Konya, Turkey. Year 2018 was treated as drought environment due to very low precipitation prior to heading whereas year 2019 was considered as a favorable season. GWAS conducted with SNPs and haplotype blocks using mixed linear model identified 18 genomic regions in the vicinities of known genes i.e., TaERF3-3A, TaERF3-3B, DEP1-5A, FRIZZY PANICLE-2D, TaSnRK23-1A, TaAGL6-A, TaARF12-2A, TaARF12-2B, WAPO1, TaSPL16-7D, TaTGW6-A1, KAT-2B, TaOGT1, TaSPL21-6B, TaSBEIb, trs1/WFZP-A, TaCwi-A1-2A and TaPIN1-7A associated with grain yield (GY) and yield related traits. Haplotype-based GWAS identified five haplotype blocks (H1A-42, H2A-71, H4A-48, H7B-123 and H7B-124), with the favorable haplotypes showing a yield increase of > 700 kg/ha in the drought season. SNP-based GWAS, detected only one larger effect genomic region on chromosome 7B, in common with haplotype-based GWAS. On an average, the percentage variation (PV) explained by haplotypes was 8.0% higher than PV explained by SNPs for all the investigated traits. Selective sweep analysis detected 39 signatures of selection between LR and MV of which 15 were within proximity of known functional genes controlling flowering (PRR-A1, PPR-D1, TaHd1-6B), GY and GY components (TaSus2-2B, TaGS2-B1, AG1-1A/WAG1-1A, DUO-A1, DUO-B1, AG2-3A/WAG2-3A, TaLAX1, TaSnRK210-4A, FBP, TaLAX1, TaPIL1 and AP3-1-7A/WPA3-7A) and 10 regions underlying various transcription factors and regulatory genes. The study outcomes contribute to utilization of LR in breeding winter wheat.

Understanding genetic diversity in drought-adaptive hybrid parental lines in pearl millet

Information on genetic diversity and population structure is helpful to strategize enhancing the genetic base of hybrid parental lines in breeding programs. The present study determined the population structure and genetic diversity of 109 pearl millet hybrid parental lines, known for their better adaptation and performance in drought-prone environments, using 16,472 single nucleotide polymorphic (SNP) markers generated from GBS (genotyping-by-sequencing) platforms. The SNPs were distributed uniformly across the pearl millet genome and showed considerable genetic diversity (0.337), expected heterozygosity (0.334), and observed heterozygosity (0.031). Most of the pairs of lines (78.36%) had Identity-by-State (IBS) based genetic distances of more than 0.3, indicating a significant amount of genetic diversity among the parental lines. Bayesian model-based population stratification, neighbor-joining phylogenetic analysis, and principal coordinate analysis (PCoA) differentiated all hybrid parental lines into two clear-cut major groups, one each for seed parents (B-lines) and pollinators (R-lines). Majority of parental lines sharing common parentages were found grouped in the same cluster. Analysis of molecular variance (AMOVA) revealed 7% of the variation among subpopulations, and 93% of the variation was attributable to within sub-populations. Chromosome 3 had the highest number of LD regions. Genomic LD decay distance was 0.69 Mb and varied across the different chromosomes. Genetic diversity based on 11 agro-morphological and grain quality traits also suggested that the majority of the B- and R-lines were grouped into two major clusters with few overlaps. In addition, the combined analysis of phenotypic and genotypic data showed similarities in the population grouping patterns. The present study revealed the uniqueness of most of the inbred lines, which can be a valuable source of new alleles and help breeders to utilize these inbred lines for the development of hybrids in drought-prone environments.

Population structure and genetic diversity in Eucalyptus pellita based on SNP markers

Eucalyptus pellita has the characteristics of rapid growth and high resistance. However, there is little research on molecular breeding of E. pellita, which is essential to shortening breeding life and selecting quality varieties. Therefore, a crucial step before selective breeding can be carried out to increase the wood quality of E. pellita is identifying genetic diversity and population structure using single nucleotide polymorphism (SNP) markers. In this study, the genetic diversity of 1st generation 196 E. pellita families from 23 geographically defined was assessed using 1,677,732 SNP markers identified by whole genome resequencing. SNP annotation showed that the ratio of non-synonymous to synonymous coding mutations was 0.83. Principal component analysis (PCA), phylogenetic tree, and population structure analysis permitted the families to be categorized into three groups, one of which (G2) contains most of the Indonesian (IDN) and Papua New Guinea (PNG) families. Genetic relationship analysis showed that IDN was closely related to PNG. Genetic diversity analysis showed that He, PIC, I, and H mean values were 0.2502, 0.2027, 0.3815, and 0.2680, respectively. PCA analysis classified various provenances in QLD into two categories (G1 and G3). The genetic diversity of G3 was higher than that of G2. The results of genetic differentiation (Fst) showed that PNG region was divided into two groups (PNG1 and PNG2), the Fst (0.172) between QLD and PNG2 region was higher than QLD and PNG1, and the Fst (0.024) between IDN and PNG1 is smaller than IDN and PNG2. A Mantel test revealed a positive correlation between the genetic and geographic distance of E. pellita. This study has a certain reference value for genetic identification, germplasm preservation, and breeding of E. pellita. Also, it provides a basis for subsequent association analysis to explore excellent alleles and introduction.

Genetic diversity and population structure of modern wheat (Triticum aestivum L.) cultivars in Henan Province of China based on SNP markers

BACKGROUND

Henan is the province with the greatest wheat production in China. Although more than 100 cultivars are used for production, many cultivars are still insufficient in quality, disease resistance, adaptability and yield potential. To overcome these limitations, it is necessary to constantly breed new cultivars to maintain the continuous and stable growth of wheat yield and quality. To improve breeding efficiency, it is important to evaluate the genetic diversity and population genetic structure of its cultivars. However, there are no such reports from Henan Province. Therefore, in this study, single nucleotide polymorphism (SNP) markers were used to study the population genetic structure and genetic diversity of 243 wheat cultivars included in a comparative test of wheat varieties in Henan Province, aiming to provide a reference for the utilization of backbone parents and the selection of hybrid combinations in the genetic improvement of wheat cultivars.

RESULTS

In this study, 243 wheat cultivars from Henan Province of China were genotyped by the Affymetrix Axiom Wheat660K SNP chip, and 21 characteristics were investigated. The cultivars were divided into ten subgroups; each subgroup had distinct characteristics and unique utilization value. Furthermore, based on principal component analysis, Zhoumai cultivars were the main hybrid parents, followed by Aikang 58, high-quality cultivars, and Shandong cultivars. Genetic diversity analysis showed that 61.3% of SNPs had a high degree of genetic differentiation, whereas 33.4% showed a moderate degree. The nucleotide diversity of subgenome B was relatively high, with an average π value of 3.91E-5; the nucleotide diversity of subgenome D was the lowest, with an average π value of 2.44E-5.

CONCLUSION

The parents used in wheat cross-breeding in Henan Province are similar, with a relatively homogeneous genetic background and low genetic diversity. These results will not only contribute to the objective evaluation and utilization of the tested cultivars but also provide insights into the current conditions and existing challenges of wheat cultivar breeding in Henan Province, thereby facilitating the scientific formulation of breeding objectives and strategies to improve breeding efficiency.

Genome-wide association mapping highlights candidate genes and immune genotypes for net blotch and powdery mildew resistance in barley

Net blotch (NB) and powdery mildew (PM) are major barley diseases with the potential to cause a dramatic loss in grain yield. Breeding for resistant barley genotypes in combination with identifying candidate resistant genes will accelerate the genetic improvement for resistance to NB and PM. To address this challenge, a set of 122 highly diverse barley genotypes from 34 countries were evaluated for NB and PM resistance under natural infection for in two growing seasons. Moreover, four yield traits; plant height (Ph), spike length (SL), spike weight (SW), and the number of spikelets per spike (NOS) were recorded. High genetic variation was found among genotypes in all traits scored in this study. No significant phenotypic correlation was found in the resistance between PM and NB. Immune genotypes for NB and PM were identified. A total of 21 genotypes were immune to both diseases. Of the 21 genotypes, the German genotype HOR_9570 was selected as the most promising genotype that can be used for future breeding programs. Furthermore, a genome-wide association study (GWAS) was used to identify resistant alleles to PM and NB. The results of GWAS revealed a set of 14 and 25 significant SNPs that were associated with increased resistance to PM and NB, respectively. This study provided very important genetic resources that are highly resistant to the Egyptian PM and NB pathotypes and revealed SNP markers that can be utilized to genetically improve resistance to PM and NB.

Genome-wide association mapping for yield-related traits in soybean (Glycine max) under well-watered and drought-stressed conditions

Soybean (Glycine max) productivity is significantly reduced by drought stress. Breeders are aiming to improve soybean grain yields both under well-watered (WW) and drought-stressed (DS) conditions, however, little is known about the genetic architecture of yield-related traits. Here, a panel of 188 soybean germplasm was used in a genome wide association study (GWAS) to identify single nucleotide polymorphism (SNP) markers linked to yield-related traits including pod number per plant (PN), biomass per plant (BM) and seed weight per plant (SW). The SLAF-seq genotyping was conducted on the population and three phenotype traits were examined in WW and DS conditions in four environments. Based on best linear unbiased prediction (BLUP) data and individual environmental analyses, 39 SNPs were significantly associated with three soybean traits under two conditions, which were tagged to 26 genomic regions by linkage disequilibrium (LD) analysis. Of these, six QTLs qPN-WW19.1, qPN-DS8.8, qBM-WW1, qBM-DS17.4, qSW-WW4 and qSW-DS8 were identified controlling PN, BM and SW of soybean. There were larger proportions of favorable haplotypes for locus qPN-WW19.1 and qSW-WW4 rather than qBM-WW1, qBM-DS17.4, qPN-DS8.8 and qSW-DS8 in both landraces and improved cultivars. In addition, several putative candidate genes such as Glyma.19G211300, Glyma.17G057100 and Glyma.04G124800, encoding E3 ubiquitin-protein ligase BAH1, WRKY transcription factor 11 and protein zinc induced facilitator-like 1, respectively, were predicted. We propose that the further exploration of these locus will facilitate accelerating breeding for high-yield soybean cultivars.

Morpho-physiological traits and SSR markers-based analysis of relationships and genetic diversity among fodder maize landraces in India

BACKGROUND

Maize is an excellent fodder crop due to its high biomass, better palatability, succulency, and nutrition. Studies on morpho-physiological and biochemical characterization of fodder maize are limited. The present study aimed to explore the genetic variation in fodder maize landraces for various morpho-physiological traits and estimation of genetic relationship and population structure.

METHODS AND RESULTS

The study on 47 fodder maize landraces revealed significant variation for all morpho-physiological traits except leaf-stem ratio. Plant height, stem girth, leaf-width and number of leaves showed positive correlation with green fodder yield. Morpho-physiological traits-based clustering grouped the landraces into three major clusters, whereas neighbour joining cluster and population structure analysis using 40 SSR markers revealed four and five major groups, respectively. Most landraces of Northern Himalaya-Kashmir and Ludhiana fall into a single group, whereas rest groups mainly had landraces from North-Eastern Himalaya. A total of 101 alleles were generated with mean polymorphic information content value of 0.36 and major allele frequency of 0.68. The pair wise genetic dissimilarity between genotypes ranged from 0.21 to 0.67. Mantel test revealed weak but significant correlation between morphological and molecular distance. Biochemical characterisation of superior landraces revealed significant variation for neutral detergent fibre, acid detergent fibre, cellulose and lignin content.

CONCLUSION

Interestingly, significant, and positive correlation of SPAD with lignin content can be explored to bypass the costly affair of invitro quality assessment for digestibility parameters. The study identified superior landraces and demonstrated the use of molecular markers in genetic diversity assessment and grouping of genotypes for fodder maize improvement.

Genetic Diversity and Population Structure of African Sorghum (Sorghum bicolor L. Moench) Accessions Assessed through Single Nucleotide Polymorphisms Markers

Assessing the genetic diversity and population structure of cultivated sorghum is important for heterotic grouping, breeding population development, marker-assisted cultivar development, and release. The objectives of the present study were to assess the genetic diversity and deduce the population structure of 200 sorghum accessions using diversity arrays technology (DArT)-derived single nucleotide polymorphism (SNP) markers. The expected heterozygosity values ranged from 0.10 to 0.50 with an average of 0.32, while the average observed heterozygosity (0.15) was relatively low, which is a typical value for autogamous crops species like sorghum. Moderate polymorphic information content (PIC) values were identified with a mean of 0.26, which indicates the informativeness of the chosen SNP markers. The population structure and cluster analyses revealed four main clusters with a high level of genetic diversity among the accessions studied. The variation within populations (41.5%) was significantly higher than that among populations (30.8%) and between samples within the structure (27.7%). The study identified distantly related sorghum accessions such as SAMSORG 48, KAURA RED GLUME; Gadam, AS 152; CSRO1, ICNSL2014-062; and YALAI, KAFI MORI. The accessions exhibited wide genetic diversity that will be useful in developing new gene pools and novel genotypes for West Africa sorghum breeding programs.

Harnessing genome-wide genetic diversity, population structure and linkage disequilibrium in Ethiopian durum wheat gene pool

Yanyang Liu, Henan Academy of Agricultural Sciences (HNAAS), China; Landraces are an important genetic source for transferring valuable novel genes and alleles required to enhance genetic variation. Therefore, information on the gene pool's genetic diversity and population structure is essential for the conservation and sustainable use of durum wheat genetic resources. Hence, the aim of this study was to assess genetic diversity, population structure, and linkage disequilibrium, as well as to identify regions with selection signature. Five hundred (500) individuals representing 46 landraces, along with 28 cultivars were evaluated using the Illumina Infinium 25K wheat SNP array, resulting in 8,178 SNPs for further analysis. Gene diversity (GD) and the polymorphic information content (PIC) ranged from 0.13-0.50 and 0.12-0.38, with mean GD and PIC values of 0.34 and 0.27, respectively. Linkage disequilibrium (LD) revealed 353,600 pairs of significant SNPs at a cut-off (r2 > 0.20, P < 0.01), with an average r2 of 0.21 for marker pairs. The nucleotide diversity (π) and Tajima's D (TD) per chromosome for the populations ranged from 0.29-0.36 and 3.46-5.06, respectively, with genome level, mean π values of 0.33 and TD values of 4.43. Genomic scan using the Fst outlier test revealed 85 loci under selection signatures, with 65 loci under balancing selection and 17 under directional selection. Putative candidate genes co-localized with regions exhibiting strong selection signatures were associated with grain yield, plant height, host plant resistance to pathogens, heading date, grain quality, and phenolic content. The Bayesian Model (STRUCTURE) and distance-based (principal coordinate analysis, PCoA, and unweighted pair group method with arithmetic mean, UPGMA) methods grouped the genotypes into five subpopulations, where landraces from geographically non-adjoining environments were clustered in the same cluster. This research provides further insights into population structure and genetic relationships in a diverse set of durum wheat germplasm, which could be further used in wheat breeding programs to address production challenges sustainably.

Genetic Diversity and Population Structure in Türkiye Bread Wheat Genotypes Revealed by Simple Sequence Repeats (SSR) Markers

Wheat genotypes should be improved through available germplasm genetic diversity to ensure food security. This study investigated the molecular diversity and population structure of a set of Türkiye bread wheat genotypes using 120 microsatellite markers. Based on the results, 651 polymorphic alleles were evaluated to determine genetic diversity and population structure. The number of alleles ranged from 2 to 19, with an average of 5.44 alleles per locus. Polymorphic information content (PIC) ranged from 0.031 to 0.915 with a mean of 0.43. In addition, the gene diversity index ranged from 0.03 to 0.92 with an average of 0.46. The expected heterozygosity ranged from 0.00 to 0.359 with a mean of 0.124. The unbiased expected heterozygosity ranged from 0.00 to 0.319 with an average of 0.112. The mean values of the number of effective alleles (Ne), genetic diversity of Nei (H) and Shannon's information index (I) were estimated at 1.190, 1.049 and 0.168, respectively. The highest genetic diversity (GD) was estimated between genotypes G1 and G27. In the UPGMA dendrogram, the 63 genotypes were grouped into three clusters. The three main coordinates were able to explain 12.64, 6.38 and 4.90% of genetic diversity, respectively. AMOVA revealed diversity within populations at 78% and between populations at 22%. The current populations were found to be highly structured. Model-based cluster analyses classified the 63 genotypes studied into three subpopulations. The values of F-statistic (Fst) for the identified subpopulations were 0.253, 0.330 and 0.244, respectively. In addition, the expected values of heterozygosity (He) for these sub-populations were recorded as 0.45, 0.46 and 0.44, respectively. Therefore, SSR markers can be useful not only in genetic diversity and association analysis of wheat but also in its germplasm for various agronomic traits or mechanisms of tolerance to environmental stresses.

Effectiveness of TaDreb-B1 and 1-FEH w3 KASP Markers in Spring and Winter Wheat Populations for Marker-Assisted Selection to Improve Drought Tolerance

Due to the advances in DNA markers, kompetitive allele-specific PCR (KASP) markers could accelerate breeding programs and genetically improve drought tolerance. Two previously reported KASP markers, TaDreb-B1 and 1-FEH w3, were investigated in this study for the marker-assisted selection (MAS) of drought tolerance. Two highly diverse spring and winter wheat populations were genotyped using these two KASP markers. The same populations were evaluated for drought tolerance at seedling (drought stress) and reproductive (normal and drought stress) growth stages. The single-marker analysis revealed a high significant association between the target allele of 1-FEH w3 and drought susceptibility in the spring population, while the marker-trait association was not significant in the winter population. The TaDreb-B1 marker did not have any highly significant association with seedling traits, except the sum of leaf wilting in the spring population. For field experiments, SMA revealed very few negative and significant associations between the target allele of the two markers and yield traits under both conditions. The results of this study revealed that the use of TaDreb-B1 provided better consistency in improving drought tolerance than 1-FEH w3.

Novel genomic regions on chromosome 5B controlling wheat powdery mildew seedling resistance under Egyptian conditions

Wheat powdery mildew (PM) causes significant yield losses worldwide. None of the Egyptian wheat cultivars was detected to be highly resistant to such a severe disease. Therefore, a diverse spring wheat panel was evaluated for PM seedling resistance using different Bgt conidiospores collected from Egyptian fields in two growing seasons. The evaluation was done in two separate experiments. Highly significant differences were found between the two experiments suggesting the presence of different isolates populations. Highly significant differences were found among the tested genotypes confirming the ability to improve PM resistance using the recent panel. Genome-wide association study (GWAS) was done for each experiment separately and a total of 71 significant markers located within 36 gene models were identified. The majority of these markers are located on chromosome 5B. Haplotype block analysis identified seven blocks containing the significant markers on chromosome 5B. Five gene models were identified on the short arm of the chromosome. Gene enrichment analysis identified five and seven pathways based on the biological process and molecular functions respectively for the detected gene models. All these pathways are associated with disease resistance in wheat. The genomic regions on 5B seem to be novel regions that are associated with PM resistance under Egyptian conditions. Selection of superior genotypes was done and Grecian genotypes seem to be a good source for improving PM resistance under Egyptian conditions.

Genetic Diversity and Population Structure of Sorghum (Sorghum bicolor (L.) Moench) Landraces Using DArTseq-Derived Single-Nucleotide Polymorphism (SNP) Markers

Genetic integrity of an accession should be preserved in the conservation of germplasm. Characterization of diverse germplasm based on a molecular basis enhances its conservation and use in breeding programs. The aim of this study was to assess the genetic diversity of 169 sorghum accessions using a total of 6977 SNP markers. The polymorphic information content of the markers was 0.31 which is considered to be moderately high. Structure analysis using ADMIXTURE program revealed a total of 10 subpopulations. Neighbor-joining tree revealed the presence of six main clusters among these subpopulations whereas in principal component analysis, seven clusters were identified. Cluster analysis grouped most populations depending on source of collection although other accessions originating from the same source were grouped under different clusters. Analysis of molecular variance (AMOVA) revealed 30% and 70% of the variation occurred within and among accessions, respectively. Gene flow within the populations was, however, limited indicating high differentiation within the subpopulation. Observed heterozygosity among accessions varied from 0.03 to 0.06 with a mean of 0.05 since sorghum is a self-pollinating crop. High genetic diversity among the subpopulations can be further explored for superior genes to develop new sorghum varieties.

A novel SNP panel developed for targeted genotyping-by-sequencing (GBS) reveals genetic diversity and population structure of Musa spp. germplasm collection

The Philippines is situated in the geographic region regarded as the center of diversity of banana and its wild relatives (Musa spp.). It holds the most extensive collection of B-genome germplasm in the world along with A-genome groups and several natural hybrids with A- and B-genome combinations. Management of this germplasm resource has relied immensely on identification using local names and morphological characters, and the extent of genetic diversity of the collection has not been achieved with molecular markers. A high-throughput and reliable genotyping method for banana and its relatives will facilitate germplasm management and support breeding initiatives toward a marker-based approach. Here, we developed a 1 K SNP genotyping panel based on filtering of high-quality genome-wide SNPs from the Musa Germplasm Information System and used it to assess the genetic diversity and population structure of 183 accessions from a Musa spp. germplasm collection containing Philippine and foreign accessions. Targeted GBS using SeqSNP™ technology generated 70,376,284 next-generation sequencing (NGS) reads with an average effective target SNP coverage of 340 × . Bioinformatics pipeline revealed 971 polymorphic SNPs containing 76.9% homozygous calls, 23.1% heterozygous calls and 4% with missing data. A final set of 952 SNPs detected 2,092 alleles. Pairwise genetic distance varied from 0.0021 to 0.3325 with most pairs of accessions distinguished with 250 to 300 loci. The SNP panel was able to detect seven (k = 7) genetically differentiated groups and its composition through Principal Component Analysis (PCA) with k-means clustering algorithm and Discriminant Analysis of Principal Components (DAPC). Accession-specific SNPs were also identified. The 1 K SNP panel effectively distinguishes between genomic groups and provides relatively good resolution of genome-wide nucleotide diversity of Musa spp. This panel is recommended for low-density genotyping for application in marker-assisted breeding and germplasm management, and could be further enhanced to increase marker density for other applications like genetic association and genomic selection in bananas.

Genome-wide association study of leaf-related traits in tea plant in Guizhou based on genotyping-by-sequencing

BACKGROUND

Studying the genetic characteristics of tea plant (Camellia spp.) leaf traits is essential for improving yield and quality through breeding and selection. Guizhou Plateau, an important part of the original center of tea plants, has rich genetic resources. However, few studies have explored the associations between tea plant leaf traits and single nucleotide polymorphism (SNP) markers in Guizhou.

RESULTS

In this study, we used the genotyping-by-sequencing (GBS) method to identify 100,829 SNP markers from 338 accessions of tea germplasm in Guizhou Plateau, a region with rich genetic resources. We assessed population structure based on high-quality SNPs, constructed phylogenetic relationships, and performed genome-wide association studies (GWASs). Four inferred pure groups (G-I, G-II, G-III, and G-IV) and one inferred admixture group (G-V), were identified by a population structure analysis, and verified by principal component analyses and phylogenetic analyses. Through GWAS, we identified six candidate genes associated with four leaf traits, including mature leaf size, texture, color and shape. Specifically, two candidate genes, located on chromosomes 1 and 9, were significantly associated with mature leaf size, while two genes, located on chromosomes 8 and 11, were significantly associated with mature leaf texture. Additionally, two candidate genes, located on chromosomes 1 and 2 were identified as being associated with mature leaf color and mature leaf shape, respectively. We verified the expression level of two candidate genes was verified using reverse transcription quantitative polymerase chain reaction (RT-qPCR) and designed a derived cleaved amplified polymorphism (dCAPS) marker that co-segregated with mature leaf size, which could be used for marker-assisted selection (MAS) breeding in Camellia sinensis.

CONCLUSIONS

In the present study, by using GWAS approaches with the 338 tea accessions population in Guizhou, we revealed a list of SNPs markers and candidate genes that were significantly associated with four leaf traits. This work provides theoretical and practical basis for the genetic breeding of related traits in tea plant leaves.

Analysis of genetic diversity and agronomic variation in banana sub-populations for genomic selection under drought stress in southern Benin

In the perspective of investigating genomic selection (GS) among Musa genotypes in West and Central Africa, banana accessions were phenotyped under natural drought stress in Benin and genotyped using genotyping by sequencing. Sixty-one (61) accessions grouped into three major genomic groups AAA, AAB and ABB and those without genomic affiliation information were used. Variation within the population was determined by phenotypic variables while population structure and clustering analysis were carried out to understand the genetic diversity at the molecular level. Among the genomic groups evaluated, the group AAB showed the best performance for fruit weight at maturity, (3.41 ± 1.99 kg) and for plant height (198.46 ± 12.66 cm). At the accession level, HD 117 S1 and NIA 27 showed the best plant height (263.16 ± 20.98 cm) and the best fruit weight at maturity (9.43 ± 0.0 kg) respectively. Phenotypic data did not reveal clear genetic diversity among accessions; however, the genetic diversity was conspicuous at the molecular level using 5000 markers. The affiliations of local accessions in genomic groups were determined for the first time based on the phenotypic and molecular data obtained in this study. The knowledge generated allows the possibility to apply GS in banana.

Utilizing Genomics to Characterize the Common Oat Gene Pool—The Story of More than a Century of Polish Breeding

This study was undertaken to investigate the diversity and population structure of 487 oat accessions, including breeding lines from the ongoing programs of the three largest Polish breeding companies, along with modern and historical Polish and foreign cultivars. The analysis was based on 7411 DArTseq-derived SNPs distributed among three sub-genomes (A, C, and D). The heterogeneity of the studied material was very low, as only cultivars and advanced breeding lines were examined. Principal component analysis (PCA), principal coordinate analysis (PCoA), and cluster and STRUCTURE analyses found congruent results, which show that most of the examined cultivars and materials from Polish breeding programs formed major gene pools, that only some accessions derived from Strzelce Plant Breeding, and that foreign cultivars were outside of the main group. During the 120 year oat breeding process, only 67 alleles from the old gene pool were lost and replaced by 67 new alleles. The obtained results indicate that no erosion of genetic diversity was observed within the Polish native oat gene pool. Moreover, current oat breeding programs have introduced 673 new alleles into the gene pool relative to historical cultivars. The analysis also showed that most of the changes in relation to historical cultivars occurred within the A sub-genome with emphasis on chromosome 6A. The targeted changes were the rarest in the C sub-genome. This study showed that Polish oat breeding based mainly on traditional breeding methods—although focused on improving traits typical to this crop, i.e., enhancing the grain yield and quality and improving adaptability—did not significantly narrow the oat gene pool and in fact produced cultivars that are not only competitive in the European market but are also reservoirs of new alleles that were not found in the analyzed foreign materials.

Assessment of the Genetic Diversity and Population Structure of the Peruvian Andean Legume, Tarwi (Lupinus mutabilis), with High Quality SNPs

Lupinus mutabilis Sweet (Fabaceae), “tarwi” or “chocho”, is an important grain legume in the Andean region. In Peru, studies on tarwi have mainly focused on morphological features; however, they have not been molecularly characterized. Currently, it is possible to explore the genetic parameters of plants with reliable and modern methods such as genotyping by sequencing (GBS). Here, for the first time, we used single nucleotide polymorphism (SNP) markers to infer the genetic diversity and population structure of 89 accessions of tarwi from nine Andean regions of Peru. A total of 5922 SNPs distributed along all chromosomes of tarwi were identified. STRUCTURE analysis revealed that this crop is grouped into two clusters. A dendrogram was generated using the UPGMA clustering algorithm and, like the principal coordinate analysis (PCoA), it showed two groups that correspond to the geographic origin of the tarwi samples. AMOVA showed a reduced variation between clusters (7.59%) and indicated that variability within populations is 92.41%. Population divergence (Fst) between clusters 1 and 2 revealed low genetic difference (0.019). We also detected a negative Fis for both populations, demonstrating that, like other Lupinus species, tarwi also depends on cross-pollination. SNP markers were powerful and effective for the genotyping process in this germplasm. We hope that this information is the beginning of the path towards a modern genetic improvement and conservation strategies of this important Andean legume.

Full-sib progenies show greater genetic diversity than half-sib progenies in sour passion fruit: an approach by ssr markers

BACKGROUND

Genetic variability is the most important parameter in plant breeding based on selection. There is a need for morpho-agronomic and molecular characterization of Passiflora species, to exploit their genetic resources more efficiently. No study has yet been carried out to compare half-sib and full-sib families in relation to the magnitude of the genetic variability obtained in them, and then to elucidate the advantages or disadvantages of each one.

METHODS AND RESULTS

In the present study, SSR markers were used to evaluate the genetic structure and diversity of half-sib and full-sib progenies of sour passion fruit. Two full-sib progenies (PSA and PSB), and a half-sib progeny (PHS), together with their parents, were genotyped with a set of eight pairs of SSR markers. Discriminant Analysis of Principal Components (DAPC) and Structure software were used to study the genetic structure of the progenies. The results indicate that the half-sib progeny has lower genetic variability, although it has higher allele richness. By the AMOVA most of the genetic variability was found within the progenies. Three groups were clearly observed in the DAPC analysis, while two hypothetical groups (k = 2) were observed in the Bayesian approach. The PSB progeny showed a high genetic mixture between the PSA and PHS progenies.

CONCLUSION

Lower genetic variability is found in half-sib progenies. The results obtained here allow us to suppose that the selection within full-sib progenies will possibly provide better estimates of genetic variance in sour passion fruit breeding programs, since they provide greater genetic diversity.

Genetic diversity and population structure of Uganda's yam (Dioscorea spp.) genetic resource based on DArTseq

Assessing the genetic diversity of yam germplasm from different geographical origins for cultivation and breeding purposes is an essential step for crop genetic resource conservation and genetic improvement, especially where the crop faces minimal attention. This study aimed to classify the population structure, and assess the extent of genetic diversity in 207 Dioscorea rotundata genotypes sourced from three different geographical origins. A total of 4,957 (16.2%) single nucleotide polymorphism markers were used to assess genetic diversity. The SNP markers were informative, with polymorphic information content ranging from 0.238 to 0.288 and a mean of 0.260 across all the genotypes. The observed and expected heterozygosity was 0.12 and 0.23, respectively while the minor allele frequency ranged from 0.093 to 0.124 with a mean of 0.109. The principal coordinate analysis, model-based structure and discriminant analysis of principal components, and the Euclidean distance matrix method grouped 207 yam genotypes into three main clusters. Genotypes from West Africa (Ghana and Nigeria) had significant similarities with those from Uganda. Analysis of molecular variance revealed that within-population variation across three different geographical origins accounted for 93% of the observed variation. This study, therefore, showed that yam improvement in Uganda is possible, and the outcome will constitute a foundation for the genetic improvement of yams in Uganda.

Genome-wide association analysis revealed genetic variation and candidate genes associated with the yield traits of upland cotton under drought conditions

Drought is one of the major abiotic stresses seriously affecting cotton yield. At present, the main cotton-producing areas in China are primarily arid and semiarid regions. Therefore, the identification of molecular markers and genes associated with cotton yield traits under drought conditions is of great importance for stabilize cotton yield under such conditions. In this study, resequencing data were used to conduct a genome-wide association study (GWAS) on 8 traits of 150 cotton germplasms. Under drought stress, 18 SNPs were significantly correlated with yield traits (single-boll weight (SBW) and seed (SC)), and 8 SNPs were identified as significantly correlated with effective fruit shoot number (EFBN) traits (a trait that is positively correlated with yield). Finally, a total of 15 candidate genes were screened. The combined results of the GWAS and transcriptome data analysis showed that four genes were highly expressed after drought stress, and these genes had significantly increased expression at 10, 15 and 25 DPA of fiber development. qRT-PCR was performed on two samples with drought tolerance extremes (drought-resistant Xinluzao 45 and drought-sensitive Xinluzao 26), revealing that three of the genes had the same differential expression pattern. This study provides a theoretical basis for the genetic analysis of cotton yield traits under drought stress, and provides gene resources for improved breeding of cotton yield traits under drought stress.

Population Genomics Study and Implications for the Conservation of Zabelia tyaihyonii Based on Genotyping-By-Sequencing

Zabelia tyaihyonii (Nakai) Hisauti and H. Hara is a perennial shrub endemic to Republic of Korea that grows naturally in only a very limited region of the dolomite areas of Gangwon-do and Chungcheongbuk-do Provinces in the Republic of Korea. Given its geographical characteristics, it is more vulnerable than more widely distributed species. Despite the need for comprehensive information to support conservation, population genetic information for this species is very scarce. In this study, we analyzed the genetic diversity and population structure of 94 individuals from six populations of Z. tyaihyonii using a genotyping-by-sequencing (GBS) approach to provide important information for proper conservation and management. Our results, based on 3088 single nucleotide polymorphisms (SNPs), showed a mean expected heterozygosity (He) of 0.233, no sign of within-population inbreeding (G_IS that was close to or even below zero in all populations), and a high level of genetic differentiation (F_ST = 0.170). Analysis of molecular variance (AMOVA) indicated that the principal molecular variance existed within populations (84.5%) rather than among populations (17.0%). We suggested that six management units were proposed for conservation considering Bayesian structure analysis and phylogenetic analysis, and given the various current situations faced by Z. tyaihyonii, it is believed that not only the in situ conservation but also the ex situ conservation should be considered.

Analysis of Genetic Diversity and Population Structure of Cowpea (Vigna unguiculata (L.) Walp) Genotypes Using Single Nucleotide Polymorphism Markers

Cowpea (Vigna unguiculata (L.) Walp) is an important legume crop with immense potential for nutritional and food security, income generation, and livestock feed in Sub-Saharan Africa. The crop is highly tolerant to heat and drought stresses which makes it an extremely important crop for improving resilience in crop production in the face of climate change. This study was carried out to assess the genetic diversity and population structure of 90 cowpea accessions using single nucleotide polymorphism (SNP) markers. Out of 11,940 SNPs used, 5864 SNPs were polymorphic and maintained for genome diversity analysis. Polymorphic information content (PIC) values ranged from 0.22 to 0.32 with a mean value of 0.27. The model-based Bayesian STRUCTURE analysis classified 90 cowpea accessions into four subpopulations at K = 4, while the distance-based cluster analysis grouped the accessions into three distinct clusters. The analysis of molecular variance (AMOVA) revealed that 59% and 69% of the total molecular variation was attributed to among individual variation for model-based and distance-based populations, respectively, and 18% was attributed to within individual variations. Furthermore, the low heterozygosity among cowpea accessions and the high inbreeding coefficient observed in this study suggests that the accessions reached an acceptable level of homozygosity. This study would serve as a reference for future selection and breeding programs of cowpea with desirable traits and systematic conservation of these plant genetic resources.

Development of the maize 5.5K loci panel for genomic prediction through genotyping by target sequencing

Genotyping platforms are important for genetic research and molecular breeding. In this study, a low-density genotyping platform containing 5.5K SNP markers was successfully developed in maize using genotyping by target sequencing (GBTS) technology with capture-in-solution. Two maize populations (Pop1 and Pop2) were used to validate the GBTS panel for genetic and molecular breeding studies. Pop1 comprised 942 hybrids derived from 250 inbred lines and four testers, and Pop2 contained 540 hybrids which were generated from 123 new-developed inbred lines and eight testers. The genetic analyses showed that the average polymorphic information content and genetic diversity values ranged from 0.27 to 0.38 in both populations using all filtered genotyping data. The mean missing rate was 1.23% across populations. The Structure and UPGMA tree analyses revealed similar genetic divergences (76-89%) in both populations. Genomic prediction analyses showed that the prediction accuracy of reproducing kernel Hilbert space (RKHS) was slightly lower than that of genomic best linear unbiased prediction (GBLUP) and three Bayesian methods for general combining ability of grain yield per plant and three yield-related traits in both populations, whereas RKHS with additive effects showed superior advantages over the other four methods in Pop1. In Pop1, the GBLUP and three Bayesian methods with additive-dominance model improved the prediction accuracies by 4.89-134.52% for the four traits in comparison to the additive model. In Pop2, the inclusion of dominance did not improve the accuracy in most cases. In general, low accuracies (0.33-0.43) were achieved for general combing ability of the four traits in Pop1, whereas moderate-to-high accuracies (0.52-0.65) were observed in Pop2. For hybrid performance prediction, the accuracies were moderate to high (0.51-0.75) for the four traits in both populations using the additive-dominance model. This study suggests a reliable genotyping platform that can be implemented in genomic selection-assisted breeding to accelerate maize new cultivar development and improvement.

Construction of an SNP fingerprinting database and population genetic analysis of 329 cauliflower cultivars

Cauliflower is one of the most important vegetable crops grown worldwide. However, the lack of genetic diversity information and efficient molecular markers hinders efforts to improve cauliflower. This study aims to construct DNA fingerprints for 329 cauliflower cultivars based on SNP markers and the KASP system. After rigorous filtering, a total of 1662 candidate SNPs were obtained from nearly 17.9 million SNP loci. The mean values of PIC, MAF, heterozygosity and gene diversity of these SNPs were 0.389, 0.419, 0.075, and 0.506, respectively. We developed a program for in silico simulations on 153 core germplasm samples to generate ideal SNP marker sets from the candidates. Finally, 41 highly polymorphic KASP markers were selected and applied to identify 329 cauliflower cultivars, mainly collected from the public market. Furthermore, based on the KASP genotyping data, we performed phylogenetic analysis and population structure analysis of the 329 cultivars. As a result, these cultivars could be classified into three major clusters, and the classification patterns were significantly related to their curd solidity and geographical origin. Finally, fingerprints of the 329 cultivars and 2D barcodes with the genetic information of each sample were generated. The fingerprinting database developed in this study provides a practical tool for identifying the authenticity and purity of cauliflower seeds and valuable genetic information about the current cauliflower cultivars.

Growth responses and genetic variation among highly ecologically diverse spring wheat genotypes grown under seawater stress

Most of the freshwaters worldwide are used for agriculture. Freshwater sources are expected to decline and will not suffice to support the food production needed for the growing population. Therefore, growing crops with seawater might constitute a solution. However, very little work has been done on the effect of seawater stress on wheat, an important cereal crop. The present study aimed to determine whether particular wheat genotypes provided better resistance to seawater stress. A set of 80 highly diverse spring wheat genotypes collected from different countries in Europe, Asia, Africa, North and South America was exposed to 50% seawater stress at the early growth stage. Four seeding shoot and root traits were scored for all genotypes. High genetic variations were found among all genotypes for the epicotyl length (EL), hypocotyl length (HL), number of radicles (NOR), and fresh weight (FW). Eight genotypes with high-performance scores of seedling traits were selected. The correlation analyses revealed highly significant correlations among all traits scored in this study. The strongest correlation was found between the NOR and the other seeding traits. Thus, the NOR might be an important adaptive trait for seawater tolerance. The genetic diversity among all genotypes was investigated based on genetic distance. A wide range of genetic distances among all genotypes was found. There was also a great genetic distance among the eight selected genotypes. In particular, the genetic distance between ATRI 5310 (France) and the other seven genotypes was the greatest. Such high genetic diversity might be utilized to select highly divergent genotypes for crossing in a future breeding program. The present study provides very useful information on the presence of different genetic resources in wheat for seawater tolerance.

Genetic and morpho-physiological analyses of the tolerance and recovery mechanisms in seedling stage spring wheat under drought stress

Drought is one of the complex abiotic stresses that affect the growth and production of wheat in arid and semiarid countries. In this study, a set of 172 diverse spring wheat genotypes from 20 different countries were assessed under drought stress at the seedling stage. Besides seedling length, two types of traits were recorded, namely: tolerance traits (days to wilting, leaf wilting, and the sum of leaf wilting), and recovery traits (days to regrowth, regrowth biomass, and drought survival rate). In addition, tolerance index, recovery index, and drought tolerance index (DTI) were estimated to select the most drought tolerant genotypes. Moreover, leaf protein content (P), amino acid (AM), proline content (PRO), glucose (G), fructose (F), and total soluble carbohydrates (TSC) were measured under control and drought conditions to study the changes in each physiological trait due to drought stress. All genotypes showed a high significant genetic variation in all the physio-morphological traits scored under drought stress. High phenotypic and genotypic correlations were found among all seedling morphological traits. Among the studied indices, the drought tolerance index (DTI) had the highest phenotypic and genotypic correlations with all tolerance and recovery traits. The broad-sense heritability (H²) estimates were high for morphological traits (83.85–92.27), while the physiological traits ranged from 96.41 to 98.68 under the control conditions and from 97.13 to 99.99 under drought stress. The averages of the physiological traits (proteins, amino acids, proline, glucose, fructose, and total soluble carbohydrates) denoted under drought stress were higher than those recorded under well-watered conditions except for proteins. In this regard, amino acids, glucose, and total soluble carbohydrates had a significant correlation with all morphological traits. The selection for drought tolerance revealed 10 tolerant genotypes from different countries (8 genotypes from Egypt, one from Morocco, and one from the United States). These selected genotypes were screened for the presence of nine specific TaDREB1 alleles. Six primers were polymorphic among the selected genotypes. Genetic diversity among the selected genotypes was investigated using 21,450 SNP markers. The results of the study shed light on the different mechanisms for drought tolerance that wheat plants use to tolerate and survive under drought stress. The genetic analysis performed in this study suggested the most suitable genotypes for selective breeding at the seedling stage under water deficit.

Genetic diversity and population structure of wild and cultivated Crotalaria species based on genotyping-by-sequencing

Crotalaria is a plant genus that is found all over the world, with over 700 species of herbs and shrubs. The species are potential alternative food and industrial crops due to their adaptability to different environments. Currently, information on the genetic diversity and population structure of these species is scanty. Genotyping-by-sequencing (GBS) is a cost-effective high-throughput technique in diversity evaluation of plant species that have not been fully sequenced. In the current study, de novo GBS was used to characterize 80 Crotalaria accessions from five geographical regions in Kenya. A total of 9820 single nucleotide polymorphism (SNP) markers were obtained after thinning and filtering, which were then used for the analysis of genetic diversity and population structure in Crotalaria. The proportion of SNPs with a minor allele frequency (maf) > = 0.05 was 45.08%, while the Guanine-Cytosine (GC) content was 0.45, from an average sequence depth of 455,909 reads per base. The transition vs transversion ratio was 1.81 and Heterozygosity (He) ranged between 0.01–0.07 in all the sites and 0.04 to 0.52 in the segregating sites. The mean Tajima’s D value for the population was -0.094, suggesting an excess of rare alleles. The fixation index (Fst) between the different populations based on the Wright Fst (1943) ranged from 0.0119 to 0.066 for the Eastern-Western and Nairobi-Western populations. Model based techniques of population structure analysis including structure, k-means and cross-entropy depicted eight clusters in the study accessions. Non-model based techniques especially DAPC depicted poor population stratification. Correspondence Analysis (CA), Principal coordinate analyses (PCoA) and phylogenetic analysis identified a moderate level of population stratification. Results from this study will help conservationists and breeders understand the genetic diversity of Crotalaria. The study also provides valuable information for genetic improvement of domesticated species.

Genetic diversity and population structure of pigeonpea (Cajanus cajan [L.] Millspaugh) landraces grown in Benin revealed by Genotyping-By-Sequencing

Genetic diversity studies provide important details on target trait availability and its variability, for the success of breeding programs. In this study, GBS approach was used to reveal a new structuration of genetic diversity and population structure of pigeonpea in Benin. We used a total of 688 high-quality Single Nucleotide Polymorphism markers for a total of 44 pigeonpea genotypes. The distribution of SNP markers on the 11 chromosomes ranged from 14 on chromosome 5 to 133 on chromosome 2. The Polymorphism Information Content and gene diversity values were 0.30 and 0.34 respectively. The analysis of population structure revealed four clear subpopulations. The Weighted Neighbor Joining tree agreed with structure analyses by grouping the 44 genotypes into four clusters. The PCoA revealed that genotypes from subpopulations 1, 2 and 3 intermixed among themselves. The Analysis of Molecular Variance showed 7% of the total variation among genotypes while the rest of variation (93%) was within genotypes from subpopulations indicating a high gene exchange (Nm = 7.13) and low genetic differentiation (PhiPT = 0.07) between subpopulations. Subpopulation 2 presented the highest mean values of number of different alleles (Na = 1.57), number of loci with private alleles (Pa = 0.11) and the percentage of polymorphic loci (P = 57.12%). We discuss our findings and demonstrate how the genetic diversity and the population structure of this specie can be used through the Genome Wide Association Studies and Marker-Assisted Selection to enhance genetic gain in pigeonpea breeding programs in Benin.

Genetic Diversity and Selection Signatures in Synthetic-Derived Wheats and Modern Spring Wheat

Synthetic hexaploid wheats and their derived advanced lines were subject to empirical selection in developing genetically superior cultivars. To investigate genetic diversity, patterns of nucleotide diversity, population structure, and selection signatures during wheat breeding, we tested 422 wheat accessions, including 145 synthetic-derived wheats, 128 spring wheat cultivars, and 149 advanced breeding lines from Pakistan. A total of 18,589 high-quality GBS-SNPs were identified that were distributed across the A (40%), B (49%), and D (11%) genomes. Values of population diversity parameters were estimated across chromosomes and genomes. Genome-wide average values of genetic diversity and polymorphic information content were estimated to be 0.30 and 0.25, respectively. Neighbor-joining (NJ) tree, principal component analysis (PCA), and kinship analyses revealed that synthetic-derived wheats and advanced breeding lines were genetically diverse. The 422 accessions were not separated into distinct groups by NJ analysis and confirmed using the PCA. This conclusion was validated with both relative kinship and Rogers' genetic distance analyses. EigenGWAS analysis revealed that 32 unique genome regions had undergone selection. We found that 50% of the selected regions were located in the B-genome, 29% in the D-genome, and 21% in the A-genome. Previously known functional genes or QTL were found within the selection regions associated with phenology-related traits such as vernalization, adaptability, disease resistance, and yield-related traits. The selection signatures identified in the present investigation will be useful for understanding the targets of modern wheat breeding in Pakistan.

Genetic Diversity and Population Structure of Schima superba From Southern China

The tree Schima superba is important for afforestation and fire prevention in southern China. The wood of this tree can also be used for furniture and buildings. However, the lack of genetic background and genomic information for this species has lowered wood yield speed and quality improvement. Here, we aimed to discover genome-wide single nucleotide polymorphisms (SNPs) in 302 S. superba germplasms collected from southern China and to use these SNPs to investigate the population structure. Using genotyping by sequencing, a total of 785 high-quality SNP markers (minor allele frequency [MAF] ≥ 0.05) were identified from 302 accessions collected from seven geographical locations. Population structure analyses and principal coordinate analyses (PCoAs) indicated that these germplasm resources can be clearly separated into different populations. The S. superba accessions originating from Yunnan (YN) and Guangxi (GX) fell into the same population, separate from the accessions originating from Guangdong (GD), which indicated that these two regions should be regarded as major provenances of this species. In addition, two independent core germplasm sets with abundant genetic polymorphisms were constructed to support the breeding work. The identification of SNP markers, analyses of population genetics, and construction of core germplasm sets will greatly promote the molecular breeding work of S. superba.

Exploring the Genetic Diversity and Population Structure of Wheat Landrace Population Conserved at ICARDA Genebank

Landraces are considered a valuable source of potential genetic diversity that could be used in the selection process in any plant breeding program. Here, we assembled a population of 600 bread wheat landraces collected from eight different countries, conserved at the ICARDA's genebank, and evaluated the genetic diversity and the population structure of the landraces using single nucleotide polymorphism (SNP) markers. A total of 11,830 high-quality SNPs distributed across the genomes A (40.5%), B (45.9%), and D (13.6%) were used for the final analysis. The population structure analysis was evaluated using the model-based method (STRUCTURE) and distance-based methods [discriminant analysis of principal components (DAPC) and principal component analysis (PCA)]. The STRUCTURE method grouped the landraces into two major clusters, with the landraces from Syria and Turkey forming two clusters with high proportions of admixture, whereas the DAPC and PCA analysis grouped the population into three subpopulations mostly according to the geographical information of the landraces, i.e., Syria, Iran, and Turkey with admixture. The analysis of molecular variance revealed that the majority of the variation was due to genetic differences within the populations as compared with between subpopulations, and it was the same for both the cluster-based and distance-based methods. Genetic distance analysis was also studied to estimate the differences between the landraces from different countries, and it was observed that the maximum genetic distance (0.389) was between the landraces from Spain and Palestine, whereas the minimum genetic distance (0.013) was observed between the landraces from Syria and Turkey. It was concluded from the study that the model-based methods (DAPC and PCA) could dissect the population structure more precisely when compared with the STRUCTURE method. The population structure and genetic diversity analysis of the bread wheat landraces presented here highlight the complex genetic architecture of the landraces native to the Fertile Crescent region. The results of this study provide useful information for the genetic improvement of hexaploid wheat and facilitate the use of landraces in wheat breeding programs.

Genetic Diversity Assessment of the International Maize and Wheat Improvement Center and Chinese Wheat Core Germplasms by Non-Denaturing Fluorescence In Situ Hybridization

Germplasm is the material basis for crop genetic improvement and related basic research. Knowledge of genetic diversity present in wheat is the prerequisite for wheat breeding and improvement. Non-denaturing fluorescence in situ hybridization (ND-FISH) is a powerful tool to distinguish chromosomal polymorphisms and evaluate genetic diversity in wheat. In this study, ND-FISH using Oligo-pSc119.2-1, Oligo-pTa535-1, and Oligo-(GAA)7 as probes were used to analyze the genetic diversity among 60 International Maize and Wheat Improvement Center (CIMMYT) derived wheat lines, and 93 cultivated wheat and landraces from the Chinese wheat core germplasm. A total of 137 polymorphic FISH patterns were obtained, in which 41, 65, and 31 were from A-, B-, and D-genome chromosomes, respectively, indicating polymorphism of B-genome > A-genome > D-genome. In addition, 22 and 51 specific FISH types were observed in the two germplasm resource lines. Twelve types of rearrangements, including seven new translocations, were detected in all 153 wheat lines. Genetic relationships among 153 wheat lines were clustered into six groups. Our research provides cytological information for rational utilization of wheat germplasm resources.

Genome-Wide Association Analysis Reveals Genetic Architecture and Candidate Genes Associated with Grain Yield and Other Traits under Low Soil Nitrogen in Early-Maturing White Quality Protein Maize Inbred Lines

Maize production in the savannas of sub-Saharan Africa (SSA) is constrained by the low nitrogen in the soils. The identification of quantitative trait loci (QTL) conferring tolerance to low soil nitrogen (low-N) is crucial for the successful breeding of high-yielding QPM maize genotypes under low-N conditions. The objective of this study was to identify QTLs significantly associated with grain yield and other low-N tolerance-related traits under low-N. The phenotypic data of 140 early-maturing white quality protein maize (QPM) inbred lines were evaluated under low-N. The inbred lines were genotyped using 49,185 DArTseq markers, from which 7599 markers were filtered for population structure analysis and genome-wide association study (GWAS). The inbred lines were grouped into two major clusters based on the population structure analysis. The GWAS identified 24, 3, 10, and 3 significant SNPs respectively associated with grain yield, stay-green characteristic, and plant and ear aspects, under low-N. Sixteen SNP markers were physically located in proximity to 32 putative genes associated with grain yield, stay-green characteristic, and plant and ear aspects. The putative genes GRMZM2G127139, GRMZM5G848945, GRMZM2G031331, GRMZM2G003493, GRMZM2G067964, GRMZM2G180254, on chromosomes 1, 2, 8, and 10 were involved in cellular nitrogen assimilation and biosynthesis, normal plant growth and development, nitrogen assimilation, and disease resistance. Following the validation of the markers, the putative candidate genes and SNPs could be used as genomic markers for marker-assisted selection, to facilitate genetic gains for low-N tolerance in maize production.

Combined GWAS and QTL mapping revealed candidate genes and SNP network controlling recovery and tolerance traits associated with drought tolerance in seedling winter wheat

To date, very little research on drought tolerance has been conducted at the seedling stage in winter wheat. In this study, two types of traits, namely tolerance and recovery traits, associated with drought tolerance were scored in biparental mapping population (BPP) and association mapping population (A-set). The results of this study revealed no or weak significant correlation between the two types of traits. Based on GWAS and QTL mapping analyses, all QTLs associated with recovery traits were completely different from those associated with tolerance traits except one QTL in each population that was found to be associated with one tolerance trait and one recovery trait. The analysis of SNP and gene networks confirmed the results of combined GWAS and QTL mapping. One SNP marker located on the 2B chromosome (S2B_26494801) was found to be associated with recovery traits in both populations. The results of this study provided new information on understanding and improving drought tolerance in winter wheat.

Genotyping-by-Sequencing Based Molecular Genetic Diversity of Pakistani Bread Wheat (Triticum aestivum L.) Accessions

Spring wheat (Triticum aestivum L.) is one of the most imperative staple food crops, with an annual production of 765 million tons globally to feed ∼40% world population. Genetic diversity in available germplasm is crucial for sustainable wheat improvement to ensure global food security. A diversity panel of 184 Pakistani wheat accessions was genotyped using 123,596 high-quality single nucleotide polymorphism (SNP) markers generated by genotyping-by-sequencing with 42% of the SNPs mapped on B, 36% on A, and 22% on D sub-genomes of wheat. Chromosome 2B contains the most SNPs (9,126), whereas 4D has the least (2,660) markers. The mean polymorphic information content, genetic diversity, and major allele frequency of the population were 0.157, 0.1844, and 0.87, respectively. Analysis of molecular variance revealed a higher genetic diversity (80%) within the sub-population than among the sub-populations (20%). The genome-wide linkage disequilibrium was 0.34 Mbp for the whole wheat genome. Among the three subgenomes, A has the highest LD decay value (0.29 Mbp), followed by B (0.2 Mbp) and D (0.07 Mbp) genomes, respectively. The results of population structure, principal coordinate analysis, phylogenetic tree, and kinship analysis also divided the whole population into three clusters comprising 31, 33, and 120 accessions in group 1, group 2, and group 3, respectively. All groups were dominated by the local wheat accessions. Estimation of genetic diversity will be a baseline for the selection of breeding parents for mutations and the genome-wide association and marker-assisted selection studies.

Genetic Diversity and Association Analysis for Carotenoid Content among Sprouts of Cowpea (Vigna unguiculata L. Walp)

The development and promotion of biofortified foods plants are a sustainable strategy for supplying essential micronutrients for human health and nutrition. We set out to identify quantitative trait loci (QTL) associated with carotenoid content in cowpea sprouts. The contents of carotenoids, including lutein, zeaxanthin, and β-carotene in sprouts of 125 accessions were quantified via high-performance liquid chromatography. Significant variation existed in the profiles of the different carotenoids. Lutein was the most abundant (58 ± 12.8 mg/100 g), followed by zeaxanthin (14.7 ± 3.1 mg/100 g) and β-carotene (13.2 ± 2.9 mg/100 g). A strong positive correlation was observed among the carotenoid compounds (r ≥ 0.87), indicating they can be improved concurrently. The accessions were distributed into three groups, following their carotenoid profiles, with accession C044 having the highest sprout carotenoid content in a single cluster. A total of 3120 genome-wide SNPs were tested for association analysis, which revealed that carotenoid biosynthesis in cowpea sprouts is a polygenic trait controlled by genes with additive and dominance effects. Seven loci were significantly associated with the variation in carotenoid content. The evidence of variation in carotenoid content and genomic regions controlling the trait creates an avenue for breeding cowpea varieties with enhanced sprouts carotenoid content.

Genetic mapping of powdery mildew resistance genes in wheat landrace Guizi 1 via genotyping by sequencing

BACKGROUND

Wheat (Triticum aestivum L.) powdery mildew (Pm), which caused by Blumeria graminis f. sp. tritici (Bgt), is a destructive disease worldwide that causes severe yield losses in wheat. Resistant wheat cultivars easily lose their ability to effectively resist newly emerged Bgt strains; therefore, identifying new resistance genes is necessary for breeding resistant cultivars.

METHODS AND RESULTS

Guizi 1 (GZ1) is a Chinese wheat cultivar with moderate and stable resistance to Pm. Genetic analysis indicated that the Pm resistance of GZ1 was controlled by a single dominant gene, designated PmGZ1. In total, 110 F₂ individual plants and their 2 parents were subjected to genotyping by sequencing (GBS), which yielded 23,134 high-quality single-nucleotide polymorphisms (SNPs). The SNP distributions across the 21 chromosomes ranged from 134 on chromosome 6D to 6288 on chromosome 3B. Chromosome 6A has 1866 SNPs, among which 16 are physically located between positions 307,802,221 and 309,885,836 in an approximate 2.3-cM region; this region also had the greatest SNP density. The average map distance between SNP markers was 0.1 cM. A quantitative trait locus (QTL) with a significant epistatic effect on Pm resistance was mapped to chromosome 6A. The logarithm of odds (LOD) value of PmGZ1 was 34.8, and PmGZ1 was located within the confidence interval marked by chr6a-307802221 and chr6a-309885836. Moreover, 74.7% of the phenotypic variance was explained by PmGZ1. Four candidate genes (which encoded two TaAP2-A and two actin proteins) were annotated maybe as resistance genes.

CONCLUSIONS

The present results provide valuable information for wheat genetic improvement, QTL fine mapping, and candidate gene validation.

Population Genetics and Development of a Core Collection from Elite Germplasms of Xanthoceras sorbifolium Based on Genome-Wide SNPs

Xanthoceras sorbifolium is one of the most important species of woody oil. In this study, whole genome re-sequencing of 119 X. sorbifolium germplasms was conducted and, after filtering, 105,685,557 high-quality SNPs were identified, which were used to perform population genetics and core collection development analyses. The results from the phylogenetic, population structure, and principal component analyses showed a high level of agreement, with 119 germplasms being classified into three main groups. The germplasms were not completely classified based on their geographical origins and flower colors; furthermore, the genetic backgrounds of these germplasms were complex and diverse. The average polymorphsim information content (PIC) values for the three inferred groups clustered by structure analysis and the six classified color groups were 0.2445 and 0.2628, respectively, indicating a low to medium informative degree of genetic diversity. Moreover, a core collection containing 29.4% (35) out of the 119 X. sorbifolium germplasms was established. Our results revealed the genetic diversity and structure of X. sorbifolium germplasms, and the development of a core collection will be useful for the efficient improvement of breeding programs and genome-wide association studies.

Genetic diversity and population structure of rice (Oryza sativa L.) landraces from Kerala, India analyzed through genotyping-by-sequencing

Researchers stand at the vanguard of advancement and application of next-generation sequencing technology for developing dominant strategies for the sustainable management of genetically diverse crops. We attempt to fill the existing research lacuna in the molecular characterization of potent rice landraces in Kerala. Genotyping-by-sequencing (GBS) was performed on 96 Kerala rice accessions to identify single-nucleotide polymorphisms (SNPs), to examine the genetic diversity, population structure, and to delineate linkage disequilibrium (LD) pattern. GBS identified 5856 high-quality SNPs. The structure analysis indicated three subpopulations with the highest probability for population clustering with significant genetic differentiation, confirmed by principal component analysis. The genome-wide LD decay distance was 772 kb, at which the r² dropped to half its maximum value. The analysis of genetic properties of the identified SNP panel with an average polymorphism information content (PIC) value of 0.22 and a minor allele frequency (MAF) > 0.1 unveiled their efficacy in genome-wide association studies (GWAS). High F_ST (0.266) and low Nm (0.692) portray a strong genetic differentiation among the rice landraces, complementing the genetic structuring observed in the studied population. Slow LD decay in the rice landraces reflects their self-pollinating behavior and the indirect selection of desired traits by domestication. Moreover, the high LD entails only a minimum number of SNP markers for detecting marker-trait association. The diverse germplasm utilized in this study can be further utilized to disclose genetic variants associated with phenotypic traits and define signatures of selection via GWAS and selective sweep, respectively.

Assessment of the Genetic Structure and Diversity of Soybean (Glycine&nbsp;max L.) Germplasm Using Diversity Array Technology and Single Nucleotide Polymorphism Markers

Knowledge of the genetic structure and diversity of germplasm collections is crucial for sustainable genetic improvement through hybridization programs and rapid adaptation to changing breeding objectives. The objective of this study was to determine the genetic diversity and population structure of 281 International Institute of Tropical Agriculture (IITA) soybean accessions using diversity array technology (DArT) and single nucleotide polymorphism (SNP) markers for the efficient utilization of these accessions. From the results, the SNP and DArT markers were well distributed across the 20 soybean chromosomes. The cluster and principal component analyses revealed the genetic diversity among the 281 accessions by grouping them into two stratifications, a grouping that was also evident from the population structure analysis, which divided the 281 accessions into two distinct groups. The analysis of molecular variance revealed that 97% and 98% of the genetic variances using SNP and DArT markers, respectively, were within the population. Genetic diversity indices such as Shannon's diversity index, diversity and unbiased diversity revealed the diversity among the different populations of the soybean accessions. The SNP and DArT markers used provided similar information on the structure, diversity and polymorphism of the accessions, which indicates the applicability of the DArT marker in genetic diversity studies. Our study provides information about the genetic structure and diversity of the IITA soybean accessions that will allow for the efficient utilization of these accessions in soybean improvement programs, especially in Africa.

Genetic Diversity and Population Structure Analysis of the USDA Olive Germplasm Using Genotyping-By-Sequencing (GBS)

Olives are one of the most important fruit and woody oil trees cultivated in many parts of the world. Olive oil is a critical component of the Mediterranean diet due to its importance in heart health. Olives are believed to have been brought to the United States from the Mediterranean countries in the 18th century. Despite the increase in demand and production areas, only a few selected olive varieties are grown in most traditional or new growing regions in the US. By understanding the genetic background, new sources of genetic diversity can be incorporated into the olive breeding programs to develop regionally adapted varieties for the US market. This study aimed to explore the genetic diversity and population structure of 90 olive accessions from the USDA repository along with six popular varieties using genotyping-by-sequencing (GBS)-generated SNP markers. After quality filtering, 54,075 SNP markers were retained for the genetic diversity analysis. The average gene diversity (GD) and polymorphic information content (PIC) values of the SNPs were 0.244 and 0.206, respectively, indicating a moderate genetic diversity for the US olive germplasm evaluated in this study. The structure analysis showed that the USDA collection was distributed across seven subpopulations; 63% of the accessions were grouped into an identifiable subpopulation. The phylogenetic and principal coordinate analysis (PCoA) showed that the subpopulations did not align with the geographical origins or climatic zones. An analysis of the molecular variance revealed that the major genetic variation sources were within populations. These findings provide critical information for future olive breeding programs to select genetically distant parents and facilitate future gene identification using genome-wide association studies (GWAS) or a marker-assisted selection (MAS) to develop varieties suited to production in the US.

Identification of a Diverse Core Set Panel of Rice From the East Coast Region of India Using SNP Markers

In India, rice (Oryza sativa L.) is cultivated under a variety of climatic conditions. Due to the fragility of the coastal ecosystem, rice farming in these areas has lagged behind. Salinity coupled with floods has added to this trend. Hence, to prevent genetic erosion, conserving and characterizing the coastal rice, is the need of the hour. This work accessed the genetic variation and population structure among 2,242 rice accessions originating from India’s east coast comprising Andhra Pradesh, Orissa, and Tamil Nadu, using 36 SNP markers, and have generated a core set (247 accessions) as well as a mini-core set (30 accessions) of rice germplasm. All the 36 SNP loci were biallelic and 72 alleles found with average two alleles per locus. The genetic relatedness of the total collection was inferred using the un-rooted neighbor-joining tree, which grouped all the genotypes (2,242) into three major clusters. Two groups were obtained with a core set and three groups obtained with a mini core set. The mean PIC value of total collection was 0.24, and those of the core collection and mini core collection were 0.27 and 0.32, respectively. The mean heterozygosity and gene diversity of the overall collection were 0.07 and 0.29, respectively, and the core set and mini core set revealed 0.12 and 0.34, 0.20 and 0.40 values, respectively, representing 99% of distinctiveness in the core and mini core sets. Population structure analysis showed maximum population at K = 4 for total collection and core collection. Accessions were distributed according to their population structure confirmed by PCoA and AMOVA analysis. The identified small and diverse core set panel will be useful in allele mining for biotic and abiotic traits and managing the genetic diversity of the coastal rice collection. Validation of the 36-plex SNP assay was done by comparing the genetic diversity parameters across two different rice core collections, i.e., east coast and northeast rice collection. The same set of SNP markers was found very effective in deciphering diversity at different genetic parameters in both the collections; hence, these marker sets can be utilized for core development and diversity analysis studies.