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

Abstract

The availability of information on the genetic diversity and population structure in wheat (Triticum aestivum L.) breeding lines will help wheat breeders to better use their genetic resources and manage genetic variation in their breeding program. The recent advances in sequencing technology provide the opportunity to identify tens or hundreds of thousands of single nucleotide polymorphism (SNPs) in large genome species (e.g., wheat). These SNPs can be utilized for understanding genetic diversity and performing genome wide association studies (GWAS) for complex traits. In this study, the genetic diversity and population structure were investigated in a set of 230 genotypes (F3:6) derived from various crosses as a prerequisite for GWAS and genomic selection. Genotyping-by-sequencing provided 25,566 high-quality SNPs. The polymorphism information content (PIC) across chromosomes ranged from 0.09 to 0.37 with an average of 0.23. The distribution of SNPs markers on the 21 chromosomes ranged from 319 on chromosome 3D to 2,370 on chromosome 3B. The analysis of population structure revealed three subpopulations (G1, G2, and G3). Analysis of molecular variance identified 8% variance among and 92% within subpopulations. Of the three subpopulations, G2 had the highest level of genetic diversity based on three genetic diversity indices: Shannon’s information index (I) = 0.494, diversity index (h) = 0.328 and unbiased diversity index (uh) = 0.331, while G3 had lowest level of genetic diversity (I = 0.348, h = 0.226 and uh = 0.236). This high genetic diversity identified among the subpopulations can be used to develop new wheat cultivars.

GWAS revealed a novel resistance locus on chromosome 4D for the quarantine disease Karnal bunt in diverse wheat pre-breeding germplasm

“…www.nature.com/scientificreports www.nature.com/scientificreports/ in wheat contains comparatively fewer polymorphic markers than the A and B genomes due to low recombination attributed to its evolutionary and domestication history. Consistent with previous findings, the B genome contains a greater number of polymorphisms than the A and D genomes, which is attributed to a greater number of effective recombination events in the B genome [24][25][26] . The average number of SNPs per chromosome was 304, and the value ranged from 147 (4B) to 500 (7D) ( Supplementary Fig.…”

Wheat tandem kinases provide insights on disease‐resistance gene flow and host–parasite co‐evolution

“…Population genetic studies are essential for understanding the evolution of wheat under natural hybridization, allopolyploid speciation, natural selection, domestication, and other factors (Fahima et al ., , ; Novoselović et al ., ; Perez‐Lara et al ., ; Wang et al ., ; Eltaher et al ., ). Studies that are based on large amounts of high‐throughput genetic markers are preferable as they are aiming to characterize the general pattern of gene flow between and within populations.…”

“…The characterization of population genetic structure provides important information contributing to a better understanding of spacial distribution, adaptation, and evolution of natural plant populations. In wheat, diverse technologies that are based on randomly distributed markers were used for genotyping both natural WEW populations and domesticated wheat collections, such as RAPDs (Fahima et al ., ), microsatellites (Fahima et al ., ; Wang et al, 2017) DArTs (Novoselović et al ., ), and SNPs (GBS, Eltaher et al ., ; 90K SNP array, Perez‐Lara et al ., ). Various studies have been conducted also based on sequence variation of a single gene in WEW populations and cultivated wheat collections aimed to understand the evolutionary processes that shaped the allelic variation, structure and function of pivotal genes, including the NAM‐B1 ( Gpc‐B1 ) high grain protein and mineral content gene (Lundström et al ., ), the Pm3 powdery mildew resistance gene (Yahiaoui et al ., ), the Lr10 leaf rust‐resistance gene (Sela et al ., ), and the WKS stripe rust‐resistance genes (Huang et al ., ).…”

Genome‐wide association studies on the phyllosphere microbiome: Embracing complexity in host–microbe interactions

“…As more diverse genomes are included in a panel and LD decreases, a denser set of SNPs will be necessary to ensure that all the relevant variants in the genome fall within the LD block of a marker. High‐density SNP panels already exist for a variety of plant species (Bayer et al ., ; Shirasawa et al ., ; Eltaher et al ., ).…”