Population structure, genetic diversity and linkage disequilibrium in elite winter wheat assessed with SNP and SSR markers

Abstract

Modern genomics approaches rely on the availability of high-throughput and high-density genotyping platforms. A major breakthrough in wheat genotyping was the development of an SNP array. In this study, we used a diverse panel of 172 elite European winter wheat lines to evaluate the utility of the SNP array for genomic analyses in wheat germplasm derived from breeding programs. We investigated population structure and genetic relatedness and found that the results obtained with SNP and SSR markers differ. This suggests that additional research is required to determine the optimum approach for the investigation of population structure and kinship. Our analysis of linkage disequilibrium (LD) showed that LD decays within approximately 5-10 cM. Moreover, we found that LD is variable along chromosomes. Our results suggest that the number of SNPs needs to be increased further to obtain a higher coverage of the chromosomes. Taken together, SNPs can be a valuable tool for genomics approaches and for a knowledge-based improvement of wheat.

Development of 107 SSR markers from whole genome shotgun sequences of Chinese bayberry (Myrica rubra) and their application in seedling identification

“…SSRs from genome and transcriptome sequences have been widely used for genetic diversity analysis and map construction (Emanuelli et al, 2013;Frascaroli et al, 2013;Würschum et al, 2013). In our study, the mean value of PIC (0.63) was less than that (0.67) previously reported for genomic-SSRs (Jiao et al, 2012), but significantly higher than the figure (0.44) for EST-SSRs (Zhang et al, 2012).…”

Potential and limits to unravel the genetic architecture and predict the variation of Fusarium head blight resistance in European winter wheat (Triticum aestivum L.)

“…The same study also unraveled a sampling bias for the used diversity array technology markers. Würschum et al (2013) compared SNP and SSR markers in wheat and found only low congruency among the genetic relatedness matrices estimated with the two marker types. As genetic relatedness is one of the major forces exploited in genomic selection, substantial differences are expected for the prediction models trained with SNP or SSR markers in wheat.…”

Development and application of a 20K SNP array in potato

“…In the literature only relatively high averages of short range LD values have been reported, for example in crop species such as wheat (Würschum et al 2013)and maize (Yan et al 2009), where average initial LD of r 2 = 0.32 and r 2 = 0.24 respectively were observed, in (Wang et al 2013) even averages of r 2 = 0.5 are observed. We observed a lower average r 2 for short range LD in our data (r 2 is between 0.19 and 0.22).…”

“…In many studies a restriction on the MAF is applied, where a 5% cutoff is most commonly used (Zhao et al 2011;Delourme et al 2013;Esteras et al 2013;Wang et al 2013;Würschum et al 2013;Adetunji et al 2014;Li et al 2014). In some cases a 10% (Hyten et al 2007;Comadran et al 2011) or even a 20% cut-off (Branca et al 2011) is used.…”