Population Structure, Linkage Disequilibrium, and Genetic Diversity in Soft Winter Wheat Enriched for Fusarium Head Blight Resistance

Abstract

The occurrence of epidemics of Fusarium head blight (FHB), caused by Fusarium graminearum Schwabe, in U.S. winter wheat (Triticum aestivum L.) during the past two decades led to signifi cant emphasis on development of resistant cultivars. Understanding the genetic diversity, population structure (PS), and linkage disequilibrium (LD) in winter wheat in the eastern United States is important for marker-assisted breeding and association analysis in this germplasm. Lines selected from collaborative FHB screening nurseries were genotyped with simple sequence repeat (SSR), sequence tagged site (STS), and Diversity Array Technology (DArT) markers to assess LD, genetic diversity, and PS. The genomewide average of LD decay to r 2 < 0.2 was 9.9 cM and moderate levels of LD (r 2 > 0.2) were generally constrained to markers less than 5 cM apart. Although the lines evaluated were targeted to distinct production zones of the eastern winter wheat region, cluster and principal component analyses did not detect separation of lines into subpopulations. The short, intense breeding history for scab resistance may have localized effects on LD. Lack of subgroups within our population could be due to intercrossing among common resistant parents and indicate frequent admixture and germplasm exchange among U.S. winter wheat programs focused on development of FHB resistant cultivars.

Genetic Diversity, Linkage Disequilibrium, and Genome Evolution in Soft Winter Wheat

“…The HP lines were selected to represent the potential diversity and partial breeding history of the eastern U.S. SW wheat from 1808 to 2005. An analysis of diversity has been recently conducted in eastern U.S. SW germplasm using only lines with short breeding history (Benson et al, 2012). (Horvath et al, 2009).…”

“…Linkage disequilibrium between markers with assigned genetic locations (Benson et al, 2012;Cavanagh et al, 2013) and map distances was calculated as r 2 using the software package TASSEL 3.0 (www.maizegenetics.net, verified 20 May 2014). The expected LD decay with genetic distance was estimated by the nonlinear regression method (Hill and Weir, 1988).…”

“…Similarly, Chao et al (2007) reported significant genetic differentiation between SWW and SRW wheat classes (Wright's fixation index, Fst = 0.171, p < 0.0001), and a gene diversity score of 0.66 among U.S. SW germplasm. More recently, Benson et al (2012) used DArTs in a set of 251 Eastern U.S. SW lines that have been tested for resistance to scab (caused by the fungus Fusarium graminearum) and reported no clear population stratification and an average genome-wide LD decay of 9.9 cM (generally constrained to a distance <5 cM when analyzed in each chromosome). They reported moderated population differentiation (Fst = 0.188) across four subpopulations and LD decay to r 2 = 0.2 over 1 cM on chromosome 2D and decayed over 5 cM on the centromeric region of chromosome 5A.…”

Using DArT Markers to Monitor Genetic Diversity throughout Selection: A Case Study in Nebraska's Winter Wheat Breeding Nurseries

“…In previous studies, the mean PIC value for DArT markers in wheat was 0.31 ( Jing et al, 2009;Benson et al, 2012). Given that DArT markers are dominant, the maximum PIC value was 0.5.…”

“…Molecular markers such as DArT, amplified fragment length polymorphism (AFLP), simple sequence repeat (SSR), or single nucleotide polymorphism (SNP) have been applied to study genetic diversity in several crops (Trick et al, 2012;Benson et al, 2012;Matthies et al, 2012). The usefulness of molecular markers in characterizing the genetic diversity among different lines depends on the number of marker alleles it has and their corresponding relative frequencies, which is defined as the polymorphism information content (PIC) (Shete et al, 2000).…”