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

Shamseldeen Eltaher,Ahmed A Nower,Vikas Belamkar,Khaled F M Salem,Jesse Poland,Hamdy A Emara,Ahmed Sallam,Peter S Baenziger

doi:10.3389/fgene.2018.00076

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.

Highlights

Wheat (Triticum aestivum L.) is a staple cereal crop for people worldwide
DNA markers are extensively used in various genetic analyses including genetic diversity, evolutionary origin, genome wide association mapping, fingerprinting, and breeding applications
The lowest and highest number of single nucleotide polymorphism (SNPs) identified per chromosome in each genome ranged from 700 (Chr. 5A) to 1575 (Chr. 2A), 706 (Chr. 6B) to 2,370 (Chr. 3B), and 319 (Chr.3D) to 1,220 (Chr. 5D) (Figure 1B)

Summary

Introduction

Wheat (Triticum aestivum L.) is a staple cereal crop for people worldwide. Bread wheat is an allohexaploid with three distinct genomes (AABBDD) (Dubcovsky and Dvorak, 2007; Shewry, 2009; Matsuoka, 2011). The haploid DNA content of bread wheat genome is relatively larger than Arabidopsis thaliana, Genetic Diversity in Nebraska Winter Wheat (∼100 times), Oryza sativa L. New techniques for genotyping using next-generation sequencing (NGS) have been developed in the large genome species as an useful method to produce high-density genome wide markers with low cost per-sample (Elshire et al, 2011). Genotyping-by-sequencing (GBS) uses the benefits of restriction enzymes to reduce the complexity of a large genome, (Poland J. et al, 2012). Poland J. et al (2012) developed a GBS protocol that uses two restriction enzymes (PstI/MspI) to greatly reduce genome complexity and create more homogeneous libraries for sequencing than the one enzyme protocol (Elshire et al, 2011). The GBS method has many advantages including low cost, easy sample handling, and fewer purification steps (Davey et al, 2011)

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