Genetic diversity of Hemarthria altissima and its related species by EST-SSR and SCoT markers

There is a need for an appropriate evaluation of Hemarthria germplasm resources using genetic analysis. Understanding their genetic background will promote effective development and utilization of its germplasm resources in plant breeding. We examined the genetic diversity and relationships among 46 Hemarthria germplasm resources from four continents. Expressed Sequence Tags-Simple Sequence Repeat (EST-SSR) and Start Codon Targeted (SCoT) markers were used to investigate species Hemarthria altissima (36), Hemarthria compressa (8) and Hemarthria uncinata (2). We selected 19 EST-SSR primers and generated 550 polymorphic (94.7%). Twenty one SCoT primers were selected and amplified to produce 597 bands with 89.4% of polymorphic bands. The Mantel test between EST-SSR and SCoT matrices revealed significant correlations (r = 0.854) and the data from both markers were combined for cluster analysis. The 46 materials were clustered into two main groups by UPGMA clustering with a similarity coefficient ranging from 0.573 to 0.940 and the dendrogram was basically concordant with geographical origins and species. Among the three Hemarthria species, H. altissima was genetically closest to H. compressa while it was not close to H. uncinata. When the utility of the two markers were compared, we found EST-SSR to be more efficient than SCoT in determining the genetic diversity study of Hemarthria species.     

Genetic diversity of common bean (Phaseolus vulgaris L.) ecotypes from Pakistan using Simple Sequence Repeats

Common bean (Phaseolus vulgaris L.) is a legume crop grown all over the world and is a very important food of mountain population of Pakistan for protein intake. The Western Himalayan Mountains are rich in biodiversity including unexplored landraces of the common bean crop. Unfortunately, very little attention has been given to this valuable crop in Pakistan, and it is being exported, majorly from Ethiopia, to meet the country’s requirements. The exploitation, utilization, preservation and multiplication of existing germplasm within the area are very important for sustainable production of the crop and enhancing the nutrition value for the local community in mountain regions. A research study was conducted for evaluation of biological diversity of common bean landraces from Azad Kashmir and Northern areas of Pakistan using morpho-physiological and molecular markers. Thirty-five common bean ecotypes along with one check variety were collected from different altitudes of Azad Kashmir and Northern Pakistan and screened for biological diversity. Morphological characterization revealed high genetic diversity in parameters including stem anthocyanin, growth type, days to flowering, pods/plant and 100 seeds weight. Genomic characterization using SSR markers, for allelic diversity evaluation among germplasm, also provided diverse profile with 83.3% polymorphism in banding pattern. The bulk of gene pool diversity evaluated within bean landraces may help to initiate breeding program for common bean improvement.     

Association mapping of agronomic traits on chromosome 2A of wheat

Association mapping is a method to test the association between molecular markers and quantitative trait loci (QTL) based on linkage disequilibrium (LD). In this study, the collection of 108 wheat germplasm accessions form China were evaluated for their plant heights, spike length, spikelets per spike, grains per spike, thousand kernel weight and spikelets density in 3 years at three locations. And they were genotyped with 85 SSR markers and 40 EST-SSR markers. The population structure was inferred on the basis of unlinked 48 SSR markers and 40 EST-SSR markers. The extent of LD on chromosome 2A was 2.3 cM. Association of 37 SSR loci on chromosomes 2A with six agronomic traits was analysed with a mixed linear model. A total of 14 SSR loci were significantly associated with agronomic traits. Some of the associated markers were located in the QTL region detected in previous linkage mapping analysis. Our results demonstrated that association mapping can enhance QTL information and achieves higher resolution with short LD extent.     

Molecular Diversity and Population Structure of a Worldwide Collection of Cultivated Tetraploid Alfalfa (Medicago sativa subsp. sativa L.) Germplasm as Revealed by Microsatellite Markers

Information on genetic diversity and population structure of a tetraploid alfalfa collection might be valuable in effective use of the genetic resources. A set of 336 worldwide genotypes of tetraploid alfalfa (Medicago sativa subsp. sativa L.) was genotyped using 85 genome-wide distributed SSR markers to reveal the genetic diversity and population structure in the alfalfa. Genetic diversity analysis identified a total of 1056 alleles across 85 marker loci. The average expected heterozygosity and polymorphism information content values were 0.677 and 0.638, respectively, showing high levels of genetic diversity in the cultivated tetraploid alfalfa germplasm. Comparison of genetic characteristics across chromosomes indicated regions of chromosomes 2 and 3 had the highest genetic diversity. A higher genetic diversity was detected in alfalfa landraces than that of wild materials and cultivars. Two populations were identified by the model-based population structure, principal coordinate and neighbor-joining analyses, corresponding to China and other parts of the world. However, lack of strictly correlation between clustering and geographic origins suggested extensive germplasm exchanges of alfalfa germplasm across diverse geographic regions. The quantitative analysis of the genetic diversity and population structure in this study could be useful for genetic and genomic analysis and utilization of the genetic variation in alfalfa breeding.     

Development of new EST-derived SSRs in Salvia miltiorrhiza (Labiatae) in China and preliminary analysis of genetic diversity and population structure

Salvia miltiorrhiza, known as Dan-shen in China, is a well-known and important medicinal herb in Asia. Its root and rhizome has been used to treat cardiovascular diseases in China for centuries. Recently, it had been widely cultivated in China due to a rapid decline in wild resources. However, the germplasm resources of different cultivated regions are extremely variable. Here, new simple sequence repeats (SSRs) from expressed sequence tags (ESTs) were mined to analyze the frequency and distribution of SSRs, assess the validity of developed EST-SSR marker and identify new EST-SSR marker for the preparatory investigation of the population structure in cultivated S. miltiorrhiza. This study showed that 5160 unique ESTs were accumulated from database, 760 SSRs combined with 41 types of SSR motifs were mined. High polymorphism and transferability were presented in newly developed EST-SSR marker. It also showed that cultivated S. miltiorrhiza were mainly divided into three large groups. The results suggested that S. miltiorrhiza may has high abundance of SSRs in transcribed regions of genome and the developed EST-SSR marker may be useful for analysis of genetic diversity and population structure.     

Population structure and association mapping on chromosome 7 using a diverse panel of Chinese germplasm of rice (<Emphasis Type="Italic">Oryza sativa</Emphasis> L.)

The majority of 170 rice accessions used in this study were diverse landraces or varieties from a putative mini-core collection of Chinese germplasm along with some widely used parental lines in genetic analysis or breeding (a few from abroad). The population was genotyped using 84 SSR or InDel markers on chromosome 7 and 48 markers on other chromosomes. The phenotyping of heading date, plant height and panicle length were carried out in different locations for 2 years. Based on morphological characterization, distance-based clustering and model-based estimation of marker data, the population showed a predominant structure with two subpopulations in correspondence with indica and japonica subspecies. The estimation of linkage disequilibrium in 2 Mb windows varied along chromosome 7 and showed parallel changes with inter-subspecies differentiation of marker loci (Fst). Based on the mixed linear model considering population structure and family relatedness [i.e. the (Q + K) model], one to three associated markers (P ≤ 0.0001) per trait per experiment were scanned out on rice chromosome 7. Most significant loci were repeated for the data from both field experiments while two loci were associated with two or three traits. Marker-based allelic effects were shown in a couple of associated markers as examples. The application of association results in breeding program was also discussed. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Application of EST-derived microsatellite markers for analysis of genetic variation in tall fescue and its comparison with morphological markers

Analysis of genetic diversity in germplasm collections is an important component of crop improvement programs. This study was conducted to analyze genetic variation and to classify tall fescue genotypes based on phenotypic evaluation and EST-SSR molecular markers. Twenty-five genotypes were assessed based on phenotypic and 42 EST-SSR molecular markers according to a completely randomized block design with three replications during eight years (2007–2014). Results indicated that the effect of year, genotype and their interaction were significant for all of the measured traits. Both morphological and molecular assessments showed considerable genetic variation among genotypes. The estimates of broad-sense heritability (h²_b) were moderate to high (h²_b = 42.1–78.4) for the traits studied. Based on EST-SRR analysis, a total number of 229 alleles were detected with an average of 4.58 alleles per marker. Average PIC value was 0.49 with a range of 0.014 for NFA140 to 0.95 for NFA047. Phenotypic evaluations and EST-SSR molecular marker classified genotypes into 3 and 7 clusters, respectively which mainly supported geographical origins. The general correspondence was observed between morphological and molecular classification. Therefore, combining the molecular markers with morphological responses could be more beneficial to describe genetic variation and distinguish superior genotypes for future breeding programs.     

Evidence for Introduction Bottleneck and Extensive Inter-Gene Pool (Mesoamerica x Andes) Hybridization in the European Common Bean (Phaseolus vulgaris L.) Germplasm

Common bean diversity within and between Mesoamerican and Andean gene pools was compared in 89 landraces from America and 256 landraces from Europe, to elucidate the effects of bottleneck of introduction and selection for adaptation during the expansion of common bean (Phaseolus vulgaris L.) in Europe. Thirteen highly polymorphic nuclear microsatellite markers (nuSSRs) were used to complement chloroplast microsatellite (cpSSRs) and nuclear markers (phaseolin and Pv-shatterproof1) data from previous studies. To verify the extent of the introduction bottleneck, inter-gene pool hybrids were distinguished from “pure” accessions. Hybrids were identified on the basis of recombination of gene pool specific cpSSR, phaseolin and Pv-shatterproof1 markers with a Bayesian assignments based on nuSSRs, and with STRUCTURE admixture analysis. More hybrids were detected than previously, and their frequency was almost four times larger in Europe (40.2%) than in America (12.3%). The genetic bottleneck following the introduction into Europe was not evidenced in the analysis including all the accessions, but it was significant when estimated only with “pure” accessions, and five times larger for Mesoamerican than for Andean germplasm. The extensive inter-gene pool hybridization generated a large amount of genotypic diversity that mitigated the effects of the bottleneck that occurred when common bean was introduced in Europe. The implication for evolution and the advantages for common bean breeding are discussed.     

DNA based iPBS-retrotransposon markers for investigating the population structure of pea (Pisum sativum) germplasm from Turkey

Retrotransposons have been highly studied in monocots; however retrotransposon diversity in dicot crops has not been well documented. Our objective was to assess the diversity harbored by field pea landraces using retrotranposon markers. In this research, molecular characterization of 104 landraces and 34 field pea breeding lines was assessed using newly developed iPBS-retrotransposon markers. The 12 iPBS-retrotransposon primers generated a total 106 scorable bands, and 81 of these were found to be polymorphic (76.4%), with an average of 6.75 polymorphic fragments per primer. Polymorphism information content (PIC) ranged from 0.33 to 0.84 with an average of 0.61. It was evident that field pea landraces from the same geographical region were often placed in different groups in the neighbor joining analysis, indicating that grouping based on genetic parameters was not closely related to the geographical origin. The population structure was determined by using STRUCTURE software, and three populations at K = 3 and five populations at K = 5 were identified among landraces. The plentiful diversity present in Turkish field pea landraces could be used as genetic resource in designing breeding program, and may also contribute to worldwide pea breeding programs. Our data also suggested a role of iPBS-retrotransposons as ‘a universal marker’ for molecular characterization of pea germplasm.     

Genetic differentiation analysis of African cassava (Manihot esculenta) landraces and elite germplasm using amplified fragment length polymorphism and simple sequence repeat markers

Molecular‐marker‐aided evaluation of germplasm plays an important role in defining the genetic diversity of plant genotypes for genetic and population improvement studies. A collection of African cassava landraces and elite cultivars was analysed for genetic diversity using 20 amplified fragment length polymorphic (AFLP) DNA primer combinations and 50 simple sequence repeat (SSR) markers. Within‐population diversity estimates obtained with both markers were correlated, showing little variation in their fixation index. The amount of within‐population variation was higher for landraces as illustrated by both markers, allowing discrimination among accessions along their geographical origins, with some overlap indicating the pattern of germplasm movement between countries. Elite cultivars were grouped in most cases in agreement with their pedigree and showed a narrow genetic variation. Both SSR and AFLP markers showed some similarity in results for the landraces, although SSR provided better genetic differentiation estimates. Genetic differentiation (Fst) in the landrace population was 0.746 for SSR and 0.656 for AFLP. The molecular variance among cultivars in both populations accounted for up to 83% of the overall variation, while 17% was found within populations. Gene diversity (H_e) estimated within each population varied with an average value of 0.607 for the landraces and 0.594 for the elite lines. Analyses of SSR data using ordination techniques identified additional cluster groups not detected by AFLP and also captured maximum variation within and between both populations. Our results indicate the importance of SSR and AFLP as efficient markers for the analysis of genetic diversity and population structure in cassava. Genetic differentiation analysis of the evaluated populations provides high prospects for identifying diverse parental combinations for the development of segregating populations for genetic studies and the introgression of desirable genes from diverse sources into the existing genetic base.     

Analysis of genetic diversity and population structure in <Emphasis Type="Italic">Capsicum</Emphasis> landraces from North Eastern India using TE-AFLP markers

North eastern (NE) India harbours a precious germplasm repository of Capsicum in the form of various landraces. The present study was undertaken to characterise the extent of genetic variation present in different Capsicum landraces from north eastern India. A set of 171 Capsicum accessions were characterised using three-endonuclease amplified fragment length polymorphism (AFLP) markers. Out of 416 bands obtained from six primer combinations, 254 (61 %) were polymorphic. The pairwise genetic dissimilarity among accessions ranged from 0.03 to 0.97. Cluster analysis based on neighbour joining showed two major clusters. Cluster I contained most of the bhut jolokia accessions whereas cluster II contained all of the Capsicum annuum genotypes. Similar grouping was observed with population STRUCTURE analysis as well as principle coordinate analysis. Analysis of molecular variance (AMOVA) revealed 45 and 54 % variation among and within populations, respectively. This information on population structure analysis and molecular characterisation will be helpful for effective utilisation of this germplasm in Capsicum improvement programs.     

SSR and morphological trait based population structure analysis of 130 diverse flax (Linum usitatissimum L.) accessions

A total of 130 flax accessions of diverse morphotypes and worldwide origin were assessed for genetic diversity and population structure using 11 morphological traits and microsatellite markers (15 gSSRs and 7 EST–SSRs). Analysis performed after classifying these accessions on the basis of plant height, branching pattern, seed size, Indian/foreign origin into six categories called sub-populations viz. fibre type exotic, fibre type indigenous, intermediate type exotic, intermediate type indigenous, linseed type exotic and linseed type indigenous. The study assessed different diversity indices, AMOVA, population structure and included a principal coordinate analysis based on different marker systems. The highest diversity was exhibited by gSSR markers (SI = 0.46; He = 0.31; P = 85.11). AMOVA based on all markers explained significant difference among fibre type, intermediate type and linseed type populations of flax. In terms of variation explained by different markers, EST-SSR markers (12%) better differentiated flax populations compared to morphological (9%) and gSSR (6%) markers at P = 0.01. The maximum Nei's unbiased genetic distance (D = 0.11) was observed between fibre type and linseed type exotic sub-populations based on EST-SSR markers. The combined structure analysis by using all markers grouped Indian fibre type accessions (63.4%) in a separate cluster along with the Indian intermediate type (48.7%), whereas Indian accessions (82.16%) of linseed type constituted an independent cluster. These findings were supported by the results of the principal coordinate analysis. Morphological markers employed in the study found complementary with microsatellite based markers in deciphering genetic diversity and population structure of the flax germplasm.     

Molecular characterization of Greek pepper (Capsicum annuum L) landraces with neutral (ISSR) and gene-based (SCoT and EST-SSR) molecular markers

Thirty landraces were selected from a Gene Bank collection comprising of pepper (Capsicum annuum L.) landraces from across Greece. The genetic variability among the 30 landraces and one commercial greek cultivar, intended for industrial use, was assessed by Inter-Simple Sequence Repeat (ISSR), Start Codon Targeted (SCoT) and Expressed Sequence Tag (EST) - Simple Sequence Repeat (SSR) molecular markers. All genotypes were clearly distinguished in the dendrograms produced, with the ISSR and SCoT dendrograms being the most consistent. Three landraces were grouped together in all dendrogams revealing a possible phylogenetic relationship. Furthermore, EST-SSR markers were combined with High Resolution Melting (HRM) analysis by which the more adequate and confident separation of the landraces was accomplished due to the unique HRM profiles produced. Genotyping the rich Greek pepper germplasm by molecular markers will aid the breeding process towards well adopted Greek pepper cultivars of higher quality and productivity.     

Genetic diversity and population structure of common walnut (<Emphasis Type="Italic">Juglans regia</Emphasis>) in China based on EST-SSRs and the nuclear gene phenylalanine ammonia-lyase (<Emphasis Type="Italic">PAL</Emphasis>)

Common walnut (Juglans regia L.) is an economically important temperate tree species valued for both its nut and wood. We investigated the genetic diversity and population structure of J. regia germplasm from 13 locations in China using 10 markers derived from expressed sequences (EST-SSR) and sequence polymorphisms within the phenylalanine ammonia-lyase (PAL) gene. Analysis of the population genetic structure based on EST-SSRs showed distinct populations in northern versus southern China that were not reflected in the spatial distribution of PAL haplotypes. High levels of population differentiation were probably the result of reproductive isolation and in southern China, hybridization with Juglans sigillata. The results indicate the possible presence of distinct evolutionary lineages of J. regia in the Qinling and Daba Mountains of China and in Yunnan province that may require ecological management if they are to be retained as in situ resources.     

Genetic diversity of switchgrass and its relative species in Panicum genus using molecular markers

Switchgrass (Panicum virgatum), a warm season C4 grass, is a promising crop for bioenergy-dedicated biomass production. Understanding of genetic diversity within Panicum genus will facilitate switchgrass breeding. Genetic relationships of 22 Panicum species from six continents including ninety-one USDA germplasm accessions were investigated by Sequence-Related Amplified Polymorphism (SRAP) and Expressed Sequence Tags-Simple Sequence Repeat (EST-SSR) markers. Eight hundred and twenty-six markers from 28 pairs of SRAP and 25 pairs of EST-SSR Primers were used to differentiate between accessions of a bulk of 25 genotypes. The results showed that there was high genetic diversity found in Panicum species. Most genetic variation was present among the different species and cluster analysis indicated that all the Panicum accessions could be distinguished by SRAP or EST-SSR. Dendrogram results reflected the phylogenetic relationships between Panicum species and Panicum amarum was found to be the closest species to switchgrass. Comparison between molecular markers revealed that SRAP methods were considered more efficient than EST-SSR for screening Panicum accessions.     

Uncovering the genetic diversity of yams (Dioscorea spp.) in China by combining phenotypic trait and molecular marker analyses

Yam is an important edible tuber and root plant worldwide; China as one of the native places of yams has many diverse local resources. The goal of this study was to clarify the genetic diversity of the commonly cultivated yam landraces and the genetic relationship between the main yam species in China. In this study, 26 phenotypic traits of 112 yam accessions from 21 provinces in China were evaluated, and 24 simple sequence repeat (SSR) and 29 sequence‐related amplified polymorphism (SRAP) markers were used for the genetic diversity analysis. Phenotypic traits revealed that Dioscorea opposita had the highest genetic diversity, followed by D. alata, D. persimilis, D. fordii, and D. esculenta. Among the 26 phenotypic traits, the Shannon diversity indexes of leaf shape, petiole color, and stem color were high, and the range in the variation of tuber‐related traits in the underground part was higher than that in the aboveground part. All accessions were divided into six groups by phenotypic trait clustering, which was also supported by principal component analysis (PCA). Molecular marker analysis showed that SSR and SRAP markers had good amplification effects and could effectively and accurately evaluate the genetic variation of yam. The unweighted pair‐group method with arithmetic means analysis based on SSR‐SRAP marker data showed that the 112 accessions were also divided into six groups, similar to the phenotypic trait results. The results of PCA and population structure analysis based on SSR‐SRAP data also produced similar results. In addition, the analysis of the origin and genetic relationship of yam indicated that the species D. opposita may have originated from China. These results demonstrate the genetic diversity and distinctness among the widely cultivated species of Chinese yam and provide a theoretical reference for the classification, breeding, germplasm innovation, utilization, and variety protection of Chinese yam resources.     

Uncovering the dispersion history,adaptive evolution and selection of wheat in China

Wheat was introduced to China approximately 4500 years ago, where it adapted over a span of time to various environments in agro‐ecological growing zones. We investigated 717 Chinese and 14 Iranian/Turkish geographically diverse, locally adapted wheat landraces with 27 933 DArTseq (for 717 landraces) and 312 831 Wheat660K (for a subset of 285 landraces) markers. This study highlights the adaptive evolutionary history of wheat cultivation in China. Environmental stresses and independent selection efforts have resulted in considerable genome‐wide divergence at the population level in Chinese wheat landraces. In total, 148 regions of the wheat genome show signs of selection in at least one geographic area. Our data show adaptive events across geographic areas, from the xeric northwest to the mesic south, along and among homoeologous chromosomes, with fewer variations in the D genome than in the A and B genomes. Multiple variations in interdependent functional genes such as regulatory and metabolic genes controlling germination and flowering time were characterized, showing clear allelic frequency changes corresponding to the dispersion of wheat in China. Population structure and selection data reveal that Chinese wheat spread from the northwestern Caspian Sea region to South China, adapting during its agricultural trajectory to increasingly mesic and warm climatic areas.     

Transferability of Cucurbita SSR markers for genetic diversity assessment of Turkish bottle gourd (Lagenaria siceraria) genetic resources

The genetic diversity present in crop landraces represents a valuable genetic resource for breeding and genetic studies. Bottle gourd (Lagenaria siceraria) landraces in Turkey are highly genetically diverse. However, the limited genomic resources available for this crop hinder the molecular characterization of Turkish bottle gourd germplasm for its adequate conservation and management. Therefore, we evaluated the efficacy of 40 SSR markers from major cucurbit crops (Cucurbita pepo L. and Cucurbita moschata L.) in 30 bottle gourd landraces, together with 16 SRAP primer combinations. In addition, we compared the genetic relationship between bottle gourd and 31 other cucurbit accessions (11 Cucurbita maxima, 3 C. moschata, 5 C. pepo subsp. ovifera, 10 C. pepo and 2 Luffa cylindrica). Twenty-seven Cucurbita SSR markers showed transferability to bottle gourd. SSR markers amplified 59 alleles, in bottle gourd genome with an average of 1.64 alleles per locus. Together, SSR and SRAP markers amplified 453 fragments across the 61 accessions, and clearly discriminated L. siceraria and L. cylindrica from the other cucurbit species. Genetic diversity analysis separated edible cucurbit from ornamentals, while population structure analysis classified L. siceraria in two subpopulations defined by fruit shape, rather than geographical origin. The results indicated that the genomic resources available for Cucurbita species are valuable to study and preserve the genetic diversity of bottle gourd in Turkey.     

Molecular variation among Chinese and global winter faba bean germplasm

A sample of winter faba bean germplasm from China was compared with germplasm from outside China, using AFLP analyses. Both sets of germplasm were obtained from the National Genebank of China, Institute of Crop Sciences (ICS), Chinese Academy of Agricultural Sciences, Beijing, China. A sample of 39 winter type accessions from outside of China and 204 Chinese landraces and varieties (201 winter types and 3 spring types) were characterized with 10 AFLP primers. These detected 266 polymorphic bands. The Chinese germplasm was clearly separated from the rest of the world in principal component analysis and clustering analysis, with the spring types from China showing the greatest separation. Yunnan germplasm, both landraces and commercial varieties, showed the greatest separation among the germplasm of Chinese winter faba bean provinces. The landraces/varieties from Anhui, Zhejiang, Sichuan, Jianxi, Guizhou and Fujian provinces clustered in a central group. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Population structure and linkage disequilibrium in oat (<Emphasis Type="Italic">Avena sativa</Emphasis> L.): implications for genome-wide association studies

The level of population structure and the extent of linkage disequilibrium (LD) can have large impacts on the power, resolution, and design of genome-wide association studies (GWAS) in plants. Until recently, the topics of LD and population structure have not been explored in oat due to the lack of a high-throughput, high-density marker system. The objectives of this research were to survey the level of population structure and the extent of LD in oat germplasm and determine their implications for GWAS. In total, 1,205 lines and 402 diversity array technology (DArT) markers were used to explore population structure. Principal component analysis and model-based cluster analysis of these data indicated that, for the lines used in this study, relatively weak population structure exists. To explore LD decay, map distances of 2,225 linked DArT marker pairs were compared with LD (estimated as r ²). Results showed that LD between linked markers decayed rapidly to r ² = 0.2 for marker pairs with a map distance of 1.0 centi-Morgan (cM). For GWAS, we suggest a minimum of one marker every cM, but higher densities of markers should increase marker-QTL association and therefore detection power. Additionally, it was found that LD was relatively consistent across the majority of germplasm clusters. These findings suggest that GWAS in oat can include germplasm with diverse origins and backgrounds. The results from this research demonstrate the feasibility of GWAS and related analyses in oat.