Characterization of genetic diversity and population structure in wheat using array based SNP markers

Industry perspective, genetics and genomics of peanut blanchability

Blanching is the process of removing the testa or seed coat (skin) from peanuts, and a genotype's capacity to release its testa is referred to as its blanchability. The genotype, seed quality, harvest date, level of maturity, as well as the length of time and temperature of the post-harvest storage period, all influence peanut's blanchability. This characteristic holds significant value in the production of food items made from peanuts. However, major research on this economically significant trait in breeding programmes has been limited. Blanchability is reported to be a highly heritable and genetically regulated trait, thus breeding and selection should be effective. Blanchability reports to be fixed in the early generations due to its relatively simple genetic control, hence choice of parents which have good blanchability is of utmost importance in a breeding programme. Since blanching percentage possess high genetic control with very low genotype × environment (G×E) interactions, effective selection for improved blanchability can be conducted in early generations. In peanut, blanchability is a great target trait for marker-assisted selection (MAS), but possess few factors that makes it difficult breeding target. These factors, include the high cost operations to measure blanchability and the relatively large seed size in particular, prevent testing in early generations. In this review, we emphasize genetic research on this trait, its relationship to other traits, factors influencing it, methods of measurement, its industrial significance, as well as initiatives and difficulties related to its improvement.

Population structure, genetic diversity, and GWAS analyses with GBS-derived SNPs and silicodart markers unveil genetic potential for breeding and candidate genes for agronomic and root quality traits in an international sugar beet germplasm collection

BACKGROUND

Knowledge about the degree of genetic diversity and population structure is crucial as it facilitates novel variations that can be used in breeding programs. Similarly, genome-wide association studies (GWAS) can reveal candidate genes controlling traits of interest. Sugar beet is a major industrial crops worldwide, generating 20% of the world's total sugar production. In this work, using genotyping by sequencing (GBS)-derived SNP and silicoDArT markers, we present new insights into the genetic structure and level of genetic diversity in an international sugar beet germplasm (94 accessions from 16 countries). We also performed GWAS to identify candidate genes for agriculturally-relevant traits.

RESULTS

After applying various filtering criteria, a total of 4,609 high-quality non-redundant SNPs and 6,950 silicoDArT markers were used for genetic analyses. Calculation of various diversity indices using the SNP (e.g., mean gene diversity: 0.31, MAF: 0.22) and silicoDArT (mean gene diversity: 0.21, MAF: 0.12) data sets revealed the existence of a good level of conserved genetic diversity. Cluster analysis by UPGMA revealed three and two distinct clusters for SNP and DArT data, respectively, with accessions being grouped in general agreement with their geographical origins and their tap root color. Coincidently, structure analysis indicated three (K = 3) and two (K = 2) subpopulations for SNP and DArT data, respectively, with accessions in each subpopulation sharing similar geographic origins and root color; and comparable clustering patterns were also found by principal component analysis. GWAS on 13 root and leaf phenotypic traits allowed the identification of 35 significant marker-trait associations for nine traits and, based on predicted functions of the genes in the genomic regions surrounding the significant markers, 25 candidate genes were identified for four root (fresh weight, width, length, and color) and three leaf traits (shape, blade color, and veins color).

CONCLUSIONS

The present work unveiled conserved genetic diversity-evidenced both genetically (by SNP and silicoDArT markers) and phenotypically- exploitable in breeding programs and germplasm curation of sugar beet. Results from GWAS and candidate gene analyses provide a frame work for future studies aiming at deciphering the genetic basis underlying relevant traits for sugar beet and related crop types within Beta vulgaris subsp. vulgaris.

Exploring the genetic diversity and population structure of an ancient hexaploid wheat species Triticum sphaerococcum using SNP markers

BACKGROUND

Understanding genetic diversity and population structure is crucial for strategizing and enhancing breeding efficiency. Wheat, a globally cultivated crop, is a significant source of daily calories for humans. To overcome challenges such as extreme climatic fluctuations, stagnant yields, and diminishing genetic variation, it is essential to develop diverse germplasms with new alleles. Triticum sphaerococcum, an underutilized ancient hexaploid wheat species, shows promise for contributing beneficial alleles. However, the genetic diversity of its germplasms remains unstudied. This is the first report where we have examined the genetic diversity and population structure of 116 T. sphaerococcum accessions using a 35 K SNP Array. The objective of this study is to apply these findings to improve wheat breeding programs.

RESULTS

Analysis of the population's genetic structure identified four potential subpopulations, which was supported by principal coordinate analysis. Allele neutrality tests showed an abundance of intermediate genotypes, suggesting that many beneficial alleles are maintained through balancing selection. Among the three subgenomes, subgenome B exhibited the highest genetic diversity. AMOVA (Analysis of Molecular Variance) revealed significant variation both among (35%) and within (65%) the four subpopulations. The high genetic differentiation between subpopulations was corroborated by a moderate level of haploid migrant numbers (Nm = 1.286), indicating sufficient gene flow. SP4 emerged as the most diverse subpopulation, showing the highest values for allelic pattern indices due to its larger size and higher percentage of polymorphic loci. The D subgenome displayed a faster linkage disequilibrium (LD) decay rate compared to the A and B subgenomes. Haplotype block analysis identified 260 haplotype blocks of varying sizes distributed across the genome.

CONCLUSIONS

This research demonstrates that Indian dwarf wheat accessions, sourced from three distinct gene banks and local collections, possess considerable genetic diversity. These germplasm collections offer valuable opportunities to investigate their unexplored genetic potential. They can be utilized in wheat improvement initiatives to tackle both present and future breeding challenges. Furthermore, these accessions can introduce new alleles to broaden the genetic base of modern wheat varieties, enhancing their overall diversity.

The genetic diversity and population structure of wild and cultivated Avena species in Ethiopia using a SSR markers

Oats are grains that can be consumed by both animals and humans. They have thrived in Ethiopia, where certain oat species are considered native to the region. This work represents the first investigation of the population structure and genetic diversity of Ethiopian and other country oats. This led the scientists to explore the genetic diversity and population structure of wild and cultivated Ethiopian oats (Avena) species as well as oat cultivated in USA, the Netherlands and Austria. This study's main objective looks to be to investigate the variation in genetic makeup of cultivated and wild oat species. Studying the population structure of the oat species in the germplasm of Ethiopia, USA, the Netherlands and Austria. We used nineteen fluorescent SSR (simple sequence repeat) markers since previous research had indicated that these markers had high PIC (polymorphism information content) values. Five species of Avena were studied among the 176 oat accessions: A. sativa (cultivated oats) and four wild oats, such as A. abyssinica, A. vaviloviana, A. fatua, and A. sterilis. The AMOVA investigation revealed significant genetic distinctions among populations, individuals, and within individuals, explaining 18 % of the variance within populations, 4 % among populations, and 78 % within individuals. The AMOVA analysis of Avena species demonstrated extensive variance, with 33 % variation among species and 67 % within each species, underscoring robust species differentiation. The study also discovered gene interchange between wild oat and cultivated populations, defining two Avena species: domesticated oats and wild oats. Using the STRUCTURE software at K = 2, PCoA, and UPGMA, a distinct genetic structure was displayed in the dataset. Despite variations in ploidy levels and genomes, A. sterilis and A. vaviloviana were determined to be more closely linked, whereas A. abyssinica and A. fatua demonstrated a close association. This research delivers valuable insights for scientists and can be employed in oat breeding programs to improve future oat yield and productivity.

Development of a next generation SNP genotyping array for wheat

High-throughput genotyping arrays have provided a cost-effective, reliable and interoperable system for genotyping hexaploid wheat and its relatives. Existing, highly cited arrays including our 35K Wheat Breeder's array and the Illumina 90K array were designed based on a limited amount of varietal sequence diversity and with imperfect knowledge of SNP positions. Recent progress in wheat sequencing has given us access to a vast pool of SNP diversity, whilst technological improvements have allowed us to fit significantly more probes onto a 384-well format Axiom array than previously possible. Here we describe a novel Axiom genotyping array, the 'Triticum aestivum Next Generation' array (TaNG), largely derived from whole genome skim sequencing of 204 elite wheat lines and 111 wheat landraces taken from the Watkins 'Core Collection'. We used a novel haplotype optimization approach to select SNPs with the highest combined varietal discrimination and a design iteration step to test and replace SNPs which failed to convert to reliable markers. The final design with 43 372 SNPs contains a combination of haplotype-optimized novel SNPs and legacy cross-platform markers. We show that this design has an improved distribution of SNPs compared to previous arrays and can be used to generate genetic maps with a significantly higher number of distinct bins than our previous array. We also demonstrate the improved performance of TaNGv1.1 for Genome-wide association studies (GWAS) and its utility for Copy Number Variation (CNV) analysis. The array is commercially available with supporting marker annotations and initial genotyping results freely available.

Evaluation of stripe rust resistance and genome-wide association study in wheat varieties derived from the International Center for Agricultural Research in the Dry Areas

159 wheat varieties obtained from ICARDA, CYR32, CYR33 and CYR34 were used to evaluate the stripe rust resistance in this study. Seedling resistance was carried out in the green house at the two-leaf stage. Adult-plant resistance was carried out between 2022 and 2023 in Xining and Guide, respectively. A total of 24,151 high-quality SNP loci were obtained from a 55K SNP chip data. Genome-wide association study was carried out between SNP loci and stripe rust resistance. Seedling resistance screening revealed that 91.8% (146) of wheat varieties were resistant to CYR32 and CYR33, while only 49.7% (79) of wheat varieties were resistant to CYR34. Adult-plant resistance showed 153 (96.2%) germplasms represented resistance in 2022, while only 85 (53.4%) showed resistance in 2023. An association study using the 55K SNP chip data results combined with disease ratings of 159 materials at both the seedling and adult stages discovered 593 loci related to stripe rust resistance (P ≤ 0.0001). These loci exhibited contribution rates ranging from 11.1% to 18.7%. Among them, 71 were significantly related to resistance against CYR32 at the seedling stage, with a contribution rate of 12.7%-17.2%. Constituting the vast majority, 518 loci distributed across 21 chromosomes were significantly related to CYR33 at the seedling stage, with a contribution rate of 12.6%-18.7%. Fewer loci were found to be associated with disease resistance in adult plants. In E1 environment, a sole locus was detected on chromosome 2B with a contribution rate of 14.4%. In E2 environment, however, exhibited three loci across chromosomes 2B, 4A, and 7B with contribution rates ranging from 11.1% to 16.9%. A total of 68 multi-effect loci were significantly related to resistance against both CYR32 and CYR33 at the seedling stage, and one stable locus was significantly associated with stripe rust resistance at the adult plant stage.

Using ddRADseq to assess the genetic diversity of in-farm and gene bank cacao resources in the Baracoa region, eastern Cuba, for use and conservation purposes

The Baracoa region, eastern Cuba, hosts around 80 % of the country cacao (Theobroma cacao L.) plantations. Cacao plants in farms are diverse in origin and propagation, with grafted and hybrid plants being the more common ones. Less frequent are plants from cuttings, TSH progeny, and traditional Cuban cacao. A national cacao gene bank is also present in Baracoa, with 282 accessions either prospected in Cuba or introduced from other countries. A breeding program associated with the gene bank started in the 1990s based on agro-morphological descriptors. The genetic diversity of cacao resources in Baracoa has been poorly described, except for traditional Cuban cacao, affecting the proper development of the breeding program and the cacao planting policies in the region. To assess the population structure and genetic diversity of cacao resources in Baracoa region, we genotyped plants from both cacao gene bank (CG) and cacao farms (CF) applying a new ddRADseq protocol for cacao. After data processing, two SNPs datasets containing 11,425 and 6,481 high-quality SNPs were generated with 238 CG and 135 CF plants, respectively. SNPs were unevenly distributed along the 10 cacao chromosomes and laid mainly in noncoding regions of the genome. Population structure analysis with these SNP datasets identified seven and four genetic groups in CG and CF samples, respectively. Clustering using UPGMA and principal component analysis mostly agree with population structure results. Amelonado was the predominant cacao ancestry, accounting for 49.22 % (CG) and 57.73 % (CF) of the total. Criollo, Contamana, Iquitos, and Nanay ancestries were detected in both CG and CF samples, while Nacional and Marañon backgrounds were only identified in CG. Genetic differentiation among CG (FST ranging from 0.071 to 0.407) was higher than among CF genetic groups (FST: 0.093-0.282). Genetic diversity parameters showed similar values for CG and CF samples. The CG and CF genetic groups with the lowest genetic diversity parameters had the highest proportion of Amelonado ancestry. These results should contribute to reinforcing the ongoing breeding program and updating the planting policies on cacao farms, with an impact on the social and economic life of the region.

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.

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 analysis of tan spot disease resistance in durum wheat accessions from Tunisia

Background: Tunisia harbors a rich collection of unexploited durum wheat landraces (Triticum durum ssp. durum) that have been gradually replaced by elite cultivars since the 1970s. These landraces represent an important potential source for broadening the genetic background of elite durum wheat cultivars and for the introgression of novel genes for key traits, including disease resistance, into these cultivars. Methods: In this study, single nucleotide polymorphism (SNP) markers were used to investigate the genetic diversity and population structure of a core collection of 235 durum wheat accessions consisting mainly of landraces. The high phenotypic and genetic diversity of the fungal pathogen Pyrenophora tritici-repentis (cause of tan spot disease of wheat) in Tunisia allowed the assessment of the accessions for tan spot resistance at the adult plant stage under field conditions over three cropping seasons. A genome-wide association study (GWAS) was performed using a 90k SNP array. Results: Bayesian population structure analysis with 9191 polymorphic SNP markers classified the accessions into two groups, where groups 1 and 2 included 49.79% and 31.49% of the accessions, respectively, while the remaining 18.72% were admixtures. Principal coordinate analysis, the unweighted pair group method with arithmetic mean and the neighbor-joining method clustered the accessions into three to five groups. Analysis of molecular variance indicated that 76% of the genetic variation was among individuals and 23% was between individuals. Genome-wide association analyses identified 26 SNPs associated with tan spot resistance and explained between 8.1% to 20.2% of the phenotypic variation. The SNPs were located on chromosomes 1B (1 SNP), 2B (4 SNPs), 3A (2 SNPs), 3B (2 SNPs), 4A (2 SNPs), 4B (1 SNP), 5A (2 SNPs), 5B (4 SNPs), 6A (5 SNPs), 6B (2 SNPs), and 7B (1 SNP). Four markers, one on each of chromosomes 1B, and 5A, and two on 5B, coincided with previously reported SNPs for tan spot resistance, while the remaining SNPs were either novel markers or closely related to previously reported SNPs. Eight durum wheat accessions were identified as possible novel sources of tan spot resistance that could be introgressed into elite cultivars. Conclusion: The results highlighted the significance of chromosomes 2B, 5B, and 6A as genomic regions associated with tan spot resistance.

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.

Exploiting genetic and genomic resources to enhance productivity and abiotic stress adaptation of underutilized pulses

Underutilized pulses and their wild relatives are typically stress tolerant and their seeds are packed with protein, fibers, minerals, vitamins, and phytochemicals. The consumption of such nutritionally dense legumes together with cereal-based food may promote global food and nutritional security. However, such species are deficient in a few or several desirable domestication traits thereby reducing their agronomic value, requiring further genetic enhancement for developing productive, nutritionally dense, and climate resilient cultivars. This review article considers 13 underutilized pulses and focuses on their germplasm holdings, diversity, crop-wild-crop gene flow, genome sequencing, syntenic relationships, the potential for breeding and transgenic manipulation, and the genetics of agronomic and stress tolerance traits. Recent progress has shown the potential for crop improvement and food security, for example, the genetic basis of stem determinacy and fragrance in moth bean and rice bean, multiple abiotic stress tolerant traits in horse gram and tepary bean, bruchid resistance in lima bean, low neurotoxin in grass pea, and photoperiod induced flowering and anthocyanin accumulation in adzuki bean have been investigated. Advances in introgression breeding to develop elite genetic stocks of grass pea with low β-ODAP (neurotoxin compound), resistance to Mungbean yellow mosaic India virus in black gram using rice bean, and abiotic stress adaptation in common bean, using genes from tepary bean have been carried out. This highlights their potential in wider breeding programs to introduce such traits in locally adapted cultivars. The potential of de-domestication or feralization in the evolution of new variants in these crops are also highlighted.

Identification of Novel QTLs/Defense Genes in Spring Wheat Germplasm Panel for Seedling and Adult Plant Resistance to Stem Rust and Their Validation Through KASP Marker Assays

Stem rust is one of the major diseases threatening wheat production globally. To identify novel resistance quantitative trait loci (QTLs), we performed 35K Axiom Array SNP genotyping assays on an association mapping panel of 400 germplasm accessions, including Indian landraces, in conjunction with phenotyping for stem rust at seedling and adult plant stages. Association analyses using three genome wide association study (GWAS) models (CMLM, MLMM, and FarmCPU) revealed 20 reliable QTLs for seedling and adult plant resistance. Among these 20 QTLs, five QTLs were found consistent with three models, i.e., four QTLs on chromosome 2AL, 2BL, 2DL, and 3BL for seedling resistance and one QTL on chromosome 7DS for adult plant resistance. Further, we identified a total of 21 potential candidate genes underlying QTLs using gene ontology analysis, including a leucine rich repeat receptor (LRR) and P-loop nucleoside triphosphate hydrolase, which have a role in pathogen recognition and disease resistance. Furthermore, four QTLs (Qsr.nbpgr-3B_11, QSr.nbpgr-6AS_11, QSr.nbpgr-2AL_117-6, and QSr.nbpgr-7BS_APR) were validated through KASP located on chromosomes 3B, 6A, 2A, and 7B. Out of these QTLs, QSr.nbpgr-7BS_APR was identified as a novel QTL for stem rust resistance which has been found effective in both seedling as well as the adult plant stages. Identified novel genomic regions and validated QTLs have the potential to be deployed in wheat improvement programs to develop disease resistant varieties for stem rust and can diversify the genetic basis of resistance.

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.

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.

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.

Elucidating the Genetic Relationships on the Original Old Sicilian Triticum Spp. Collection by SNP Genotyping

Several Triticum species spread in cultivation in Sicily and neighboring regions over the centuries, which led to the establishment of a large genetic diversity. Many ancient varieties were widely cultivated until the beginning of the last century before being replaced by modern varieties. Recently, they have been reintroduced in cultivation in Sicily. Here, the genetic diversity of 115 and 11 accessions from Sicily and Calabria, respectively, belonging to Triticum species was evaluated using a high-density SNP array. Einkorn, emmer, and spelta wheat genotypes were used as outgroups for species and subspecies; five modern varieties of durum and bread wheat were used as references. A principal coordinates analysis (PCoA) and an unweighted pair group method with arithmetic mean (UPGMA) showed four distinct groups among Triticum species and T. turgidum subspecies. The population structure analysis distinguished five gene pools, among which three appeared private to the T. aestivum, T. turgidum subsp. Turgidum, and 'Timilia' group. The principal component analysis (PCA) displayed a bio-morphological trait relationship of a subset (110) of ancient wheat varieties and their wide variability within the T. turgidum subsp. durum subgroups. A discriminant analysis of principal components (DAPC) and phylogenetic analyses applied to the four durum wheat subgroups revealed that the improved varieties harbored a different gene pool compared to the most ancient varieties. The 'Russello' and 'Russello Ibleo' groups were distinguished; both displayed higher genetic variability compared to the 'Timilia' group accessions. This research represents a comprehensive approach to fingerprinting the old wheat Sicilian germplasm, which is useful in avoiding commercial fraud and sustaining the cultivation of landraces and ancient varieties.

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.

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.

Multi-locus genome-wide association studies (ML-GWAS) reveal novel genomic regions associated with seedling and adult plant stage leaf rust resistance in bread wheat (Triticum aestivum L.)

Leaf rust is one of the important diseases limiting global wheat production and productivity. To identify quantitative trait nucleotides (QTNs) or genomic regions associated with seedling and adult plant leaf rust resistance, multilocus genome-wide association studies (ML-GWAS) were performed on a panel of 400 diverse wheat genotypes using 35 K single-nucleotide polymorphism (SNP) genotyping assays and trait data of leaf rust resistance. Association analyses using six multi-locus GWAS models revealed a set of 201 significantly associated QTNs for seedling and 65 QTNs for adult plant resistance (APR), explaining 1.98-31.72% of the phenotypic variation for leaf rust. Among these QTNs, 51 reliable QTNs for seedling and 15 QTNs for APR were consistently detected in at least two GWAS models and were considered reliable QTNs. Three genomic regions were pleiotropic, each controlling two to three pathotype-specific seedling resistances to leaf rust. We also identified candidate genes, such as leucine-rich repeat receptor-like (LRR) protein kinases, P-loop containing nucleoside triphosphate hydrolase and serine-threonine/tyrosine-protein kinases (STPK), which have a role in pathogen recognition and disease resistance linked to the significantly associated genomic regions. The QTNs identified in this study can prove useful in wheat molecular breeding programs aimed at enhancing resistance to leaf rust and developing next-generation leaf rust-resistant varieties.

GWAS to Identify Novel QTNs for WSCs Accumulation in Wheat Peduncle Under Different Water Regimes

Water-soluble carbohydrates (WSCs) play a vital role in water stress avoidance and buffering wheat grain yield. However, the genetic architecture of stem WSCs' accumulation is partially understood, and few candidate genes are known. This study utilizes the compressed mixed linear model-based genome wide association study (GWAS) and heuristic post GWAS analyses to identify causative quantitative trait nucleotides (QTNs) and candidate genes for stem WSCs' content at 15 days after anthesis under different water regimes (irrigated, rainfed, and drought). Glucose, fructose, sucrose, fructans, total non-structural carbohydrates (the sum of individual sugars), total WSCs (anthrone based) quantified in the peduncle of 301 bread wheat genotypes under multiple environments (E01-E08) pertaining different water regimes, and 14,571 SNPs from "35K Axiom Wheat Breeders" Array were used for analysis. As a result, 570 significant nucleotide trait associations were identified on all chromosomes except for 4D, of which 163 were considered stable. A total of 112 quantitative trait nucleotide regions (QNRs) were identified of which 47 were presumable novel. QNRs qWSC-3B.2 and qWSC-7A.2 were identified as the hotspots. Post GWAS integration of multiple data resources prioritized 208 putative candidate genes delimited into 64 QNRs, which can be critical in understanding the genetic architecture of stem WSCs accumulation in wheat under optimum and water-stressed environments. At least 19 stable QTNs were found associated with 24 prioritized candidate genes. Clusters of fructans metabolic genes reported in the QNRs qWSC-4A.2 and qWSC-7A.2. These genes can be utilized to bring an optimum combination of various fructans metabolic genes to improve the accumulation and remobilization of stem WSCs and water stress tolerance. These results will further strengthen wheat breeding programs targeting sustainable wheat production under limited water conditions.

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.

Elucidating SNP-based genetic diversity and population structure of advanced breeding lines of bread wheat (Triticum aestivum L.)

Genetic diversity and population structure information are crucial for enhancing traits of interest and the development of superlative varieties for commercialization. The present study elucidated the population structure and genetic diversity of 141 advanced wheat breeding lines using single nucleotide polymorphism markers. A total of 14,563 high-quality identified genotyping-by-sequencing (GBS) markers were distributed covering 13.9 GB wheat genome, with a minimum of 1,026 SNPs on the homoeologous group four and a maximum of 2,838 SNPs on group seven. The average minor allele frequency was found 0.233, although the average polymorphism information content (PIC) and heterozygosity were 0.201 and 0.015, respectively. Principal component analyses (PCA) and population structure identified two major groups (sub-populations) based on SNPs information. The results indicated a substantial gene flow/exchange with many migrants (Nm = 86.428) and a considerable genetic diversity (number of different alleles, Na = 1.977; the number of effective alleles, Ne = 1.519; and Shannon's information index, I = 0.477) within the population, illustrating a good source for wheat improvement. The average PIC of 0.201 demonstrates moderate genetic diversity of the present evaluated advanced breeding panel. Analysis of molecular variance (AMOVA) detected 1% and 99% variance between and within subgroups. It is indicative of excessive gene traffic (less genetic differentiation) among the populations. These conclusions deliver important information with the potential to contribute new beneficial alleles using genome-wide association studies (GWAS) and marker-assisted selection to enhance genetic gain in South Asian wheat breeding programs.

Highly Accurate Chip-Based Resequencing of SARS-CoV-2 Clinical Samples

SARS-CoV-2 has infected over 128 million people worldwide, and until a vaccine is developed and widely disseminated, vigilant testing and contact tracing are the most effective ways to slow the spread of COVID-19. Typical clinical testing only confirms the presence or absence of the virus, but rather, a simple and rapid testing procedure that sequences the entire genome would be impactful and allow for tracing the spread of the virus and variants, as well as the appearance of new variants. However, traditional short read sequencing methods are time consuming and expensive. Herein, we describe a tiled genome array that we developed for rapid and inexpensive full viral genome resequencing, and we have applied our SARS-CoV-2-specific genome tiling array to rapidly and accurately resequence the viral genome from eight clinical samples. We have resequenced eight samples acquired from patients in Wyoming that tested positive for SARS-CoV-2. We were ultimately able to sequence over 95% of the genome of each sample with greater than 99.9% average accuracy.

Impact of different numbers of microsatellite markers on population genetic results using SLAF-seq data for Rhododendron species

Microsatellites (simple sequence repeats, SSRs) are co-dominant nuclear markers that are widely used in population genetic studies. Population genetic parameters from different studies might be significantly influenced by differences in marker number. In our study, 265 sequences with polymorphic microsatellites were obtained from SLAF-seq data. Then, subpopulations containing different numbers (5, 6, 7,…, 15, 20, 25, 30, 35, 40) of markers were genotyped 10 times to investigate the impact of marker numbers on population genetic diversity results. Our results show that genotyping with less than 11 or 12 microsatellite markers lead to significant deviations in the population genetic diversity or genetic structure results. In order to provide markers for population genetic and conservation studies for Rhododendron, 26 SSR primers were designed and validated in three species.

Evaluation of genetic structure in European wheat cultivars and advanced breeding lines using high-density genotyping-by-sequencing approach

BACKGROUND

The genetic diversity and gene pool characteristics must be clarified for efficient genome-wide association studies, genomic selection, and hybrid breeding. The aim of this study was to evaluate the genetic structure of 509 wheat accessions representing registered varieties and advanced breeding lines via the high-density genotyping-by-sequencing approach.

RESULTS

More than 30% of 13,499 SNP markers representing 2162 clusters were mapped to genes, whereas 22.50% of 26,369 silicoDArT markers overlapped with coding sequences and were linked in 3527 blocks. Regarding hexaploidy, perfect sequence matches following BLAST searches were not sufficient for the unequivocal mapping to unique loci. Moreover, allelic variations in homeologous loci interfered with heterozygosity calculations for some markers. Analyses of the major genetic changes over the last 27 years revealed the selection pressure on orthologs of the gibberellin biosynthesis-related GA2 gene and the senescence-associated SAG12 gene. A core collection representing the wheat population was generated for preserving germplasm and optimizing breeding programs.

CONCLUSIONS

Our results confirmed considerable differences among wheat subgenomes A, B and D, with D characterized by the lowest diversity but the highest LD. They revealed genomic regions that have been targeted by breeding.

Forensic features and genetic structure of 20 autosomal STR loci in the Han population of Ningde City, Southeastern China

BACKGROUND

Short tandem repeat (STR) loci are widely used in forensic medicine and population genetics.

AIM

To profile 20 autosomal STR loci using the SureID^® 21 G Human STR Identification Kit.

SUBJECTS AND METHODS

Samples were obtained from 1412 unrelated Chinese Han individuals from Ningde City, Southeastern China and 20 autosomal STR loci were profiled using the SureID^® 21 G Human STR Identification Kit.

RESULTS

A total of 261 alleles were observed among 1412 unrelated individuals and the corresponding allelic frequencies ranged from 0.5464 to 0.0004. The combined power of discrimination and exclusion of the 20 autosomal STR loci were 0.99999999999999999922 and 0.999999340285752, respectively. There was no significant deviation from Hardy-Weinberg equilibrium (HWE) and minimal departure from linkage equilibrium (LE) for two pairwise combinations of loci after sequential Bonferroni correction. In the population comparison, phylogenetic analysis was performed between the Han population and other relevant populations on the basis of the shared autosomal STR genotyping. Moreover, the neighbor-joining tree and principal component analysis were analysed based on the Nei's standard genetic distance.

CONCLUSION

The population comparison revealed that the structure of the Ningde Han population was similar to the structure of southern Han populations in China and was significantly different to the other Chinese ethnic groups, such as Kyrgyz, Uzbek, Kazakh, Uyghur, Manchu from Xinjiang and Mongols.

Genome-Wide Association Studies in Diverse Spring Wheat Panel for Stripe, Stem, and Leaf Rust Resistance

Among several important wheat foliar diseases, Stripe rust (YR), Leaf rust (LR), and Stem rust (SR) have always been an issue of concern to the farmers and wheat breeders. Evolution of virulent pathotypes of these rusts has posed frequent threats to an epidemic. Pyramiding rust-resistant genes are the most economical and environment-friendly approach in postponing this inevitable threat. To achieve durable long term resistance against the three rusts, an attempt in this study was made searching for novel sources of resistant alleles in a panel of 483 spring wheat genotypes. This is a unique and comprehensive study where evaluation of a diverse panel comprising wheat germplasm from various categories and adapted to different wheat agro-climatic zones was challenged with 18 pathotypes of the three rusts with simultaneous screening in field conditions. The panel was genotyped using 35K SNP array and evaluated for each rust at two locations for two consecutive crop seasons. High heritability estimates of disease response were observed between environments for each rust type. A significant effect of population structure in the panel was visible in the disease response. Using a compressed mixed linear model approach, 25 genomic regions were found associated with resistance for at least two rusts. Out of these, seven were associated with all the three rusts on chromosome groups 1 and 6 along with 2B. For resistance against YR, LR, and SR, there were 16, 18, and 27 QTL (quantitative trait loci) identified respectively, associated at least in two out of four environments. Several of these regions got annotated with resistance associated genes viz. NB-LRR, E3-ubiquitin protein ligase, ABC transporter protein, etc. Alien introgressed (on 1B and 3D) and pleiotropic (on 7D) resistance genes were captured in seedling and adult plant disease responses, respectively. The present study demonstrates the use of genome-wide association for identification of a large number of favorable alleles for leaf, stripe, and stem rust resistance for broadening the genetic base. Quick conversion of these QTL into user-friendly markers will accelerate the deployment of these resistance loci in wheat breeding programs.

Genotyping-by-Sequencing Derived Single Nucleotide Polymorphisms Provide the First Well-Resolved Phylogeny for the Genus Triticum (Poaceae)

Wheat (Triticum spp.) has been an important staple food crop for mankind since the beginning of agriculture. The genus Triticum L. is composed of diploid, tetraploid, and hexaploid species, majority of which have not yet been discriminated clearly, and hence their phylogeny and classification remain unresolved. Genotyping-by-sequencing (GBS) is an easy and affordable method that allows us to generate genome-wide single nucleotide polymorphism (SNP) markers. In this study, we used GBS to obtain SNPs covering all seven chromosomes from 283 accessions of Triticum-related genera. After filtering low-quality and redundant SNPs based on haplotype information, the GBS assay provided 14,188 high-quality SNPs that were distributed across the A (71%), B (26%), and D (2.4%) genomes. Cluster analysis and discriminant analysis of principal components (DAPC) allowed us to distinguish six distinct groups that matched well with Triticum species complexity. We constructed a Bayesian phylogenetic tree using 14,188 SNPs, in which 17 Triticum species and subspecies were discriminated. Dendrogram analysis revealed that the polyploid wheat species could be divided into groups according to the presence of A, B, D, and G genomes with strong nodal support and provided new insight into the evolution of spelt wheat. A total of 2,692 species-specific SNPs were identified to discriminate the common (T. aestivum) and durum (T. turgidum) wheat cultivar and landraces. In principal component analysis grouping, the two wheat species formed individual clusters and the SNPs were able to distinguish up to nine groups of 10 subspecies. This study demonstrated that GBS-derived SNPs could be used efficiently in genebank management to classify Triticum species and subspecies that are very difficult to distinguish by their morphological characters.