Genetic diversity, population structure and linkage disequilibrium in Nordic spring barley (Hordeum vulgare L. subsp. vulgare)

Abstract

Genetic diversity, population structure and genome-wide linkage disequilibrium (LD) was estimated in Nordic spring barley (Hordeum vulgare L. subsp. vulgare) by genotyping 180 breeding lines with 48 SSR markers and 7842 high-confidence SNPs using the Illumina Infinium 9K assay. In total 6208 SNPs were polymorphic and selected for further statistical analysis. A Mantel test revealed a strong positive correlation with a Pearson's correlation coefficient (r) of 0.86, between the estimates of genetic distances based on SSR and SNP data. Population structure analysis identified two groups with a clear ancestry and one group with an admixed ancestry. The groups were primarily separated based on row-type and geographical origin. Average LD for the whole population decayed below a critical level of r 2 = 0.20 within a range of 0-4 cM. To avoid confounding effects of the strong population structure, LD decay for the different groups was analysed separately and ranged from 0 to 12 cM. A slower LD decay was found within the two-rowed lines compared to the six-rowed lines and the two-rowed lines originating from the northern part, which could be the result of strong selection for malting quality and yield in the southern part. No large difference in genetic diversity was observed between population sub-groups, but differences at certain chromosomal regions were evident.

A Novel QTL for Powdery Mildew Resistance in Nordic Spring Barley (Hordeum vulgare L. ssp. vulgare) Revealed by Genome-Wide Association Study

“…The genotyping based on the SSR markers resulted in 234 scorable loci and an average PIC value of 0.46. More detailed information regarding the genotyping, as well as results from the comparison of the two marker systems, can be found in Bengtsson et al (2017) .…”

“…Out of the 169 lines, 124 lines were two-rowed and 45 six-rowed. Further description of the lines can be found in Bengtsson et al (2017) .…”

“…DNA was extracted from 2 weeks old seedlings, using a CTAB (Cetyl Trimethyl Ammonium Bromide) method as described earlier by Orabi et al (2014) . The spring barley panel was genotyped using 48 SSR markers evenly distributed over all chromosomes and the barley iSelect SNP chip based on the Illumina Infinium 9K assay as described in Bengtsson et al (2017) . The SNP genotyping of the lines were outsourced to Trait Genetics (Gatersleben, Germany).…”

“…Analyses of population structure based on a Bayesian clustering approach (STRUCTURE v.2.3.4, Pritchard et al, 2000 ), linkage disequilibrium (allele frequency correlation, r 2 ) estimates between the SNP marker pairs using the full matrix option (Tassel 3.0 software 1 ) and LD decay within this spring barley panel were performed and reported by Bengtsson et al (2017) .…”

“…The power of the GWAS lies in the degree of LD between the marker allele and the functional disease resistance allele. In cultivated barley, LD between markers has been found to be extensive, from 1 cM to beyond 10 cM ( Kraakman et al, 2004 ; Caldwell et al, 2006 ; Malysheva-Otto et al, 2006 ; Rostoks et al, 2006 ; Comadran et al, 2011 ; Bengtsson et al, 2017 ). Compared to wild barley ( H. vulgare ssp.…”