Patterns of genetic diversity and linkage disequilibrium in a highly structured Hordeum vulgare association-mapping population for the Mediterranean basin
Population structure and genome-wide linkage disequilibrium (LD) were investigated in 192 Hordeum vulgare accessions providing a comprehensive coverage of past and present barley breeding in the Mediterranean basin, using 50 nuclear microsatellite and 1,130 DArT® markers. Both clustering and principal coordinate analyses clearly sub-divided the sample into five distinct groups centred on key ancestors and regions of origin of the germplasm. For given genetic distances, large variation in LD values was observed, ranging from closely linked markers completely at equilibrium to marker pairs at 50 cM separation still showing significant LD. Mean LD values across the whole population sample decayed below r 2 of 0.15 after 3.2 cM. By assaying 1,130 genome-wide DArT® markers, we demonstrated that, after accounting for population substructure, current genome coverage of 1 marker per 1.5 cM except for chromosome 4H with 1 marker per 3.62 cM is sufficient for whole genome association scans. We show, by identifying associations with powdery mildew that map in genomic regions known to have resistance loci, that associations can be detected in strongly stratified samples provided population structure is effectively controlled in the analysis. The population we describe is, therefore, shown to be a valuable resource, which can be used in basic and applied research in barley.
KeywordsLinkage Disequilibrium Powdery Mildew Simple Sequence Repeat Marker Association Mapping Polymorphism Information Content
The above work was funded by the European Union-INCO-MED program (ICA3-CT2002-10026). SCRI received grant in aid from the Scottish Government Rural and Environment Research and Analysis Department.
- Benjamini Y, Hochberg Y (1995) Controlling the false discovery rate: a practical and powerful approach to multiple testing. J R Stat Soc 57:289–300Google Scholar
- Fischbeck G (2002) Contribution of barley to agriculture: a brief overview. In: Slafer GA, Molina-Cano JS, Savin R, Araus JL, Romagosa I (eds) Barley science: recent advances from molecular biology to agronomy of yield and quality. Food Products Press, New York, pp 1–29Google Scholar
- Grando S, von Bothmer R, Ceccarelli S (2001) Genetic diversity of barley: use of locally adapted germplasm to enhance yield and yield stability of barley in dry areas. In: Cooper HD, Spillane C, Hodgkin T (eds) Broadening the genetic base of crop production, pp 351–372Google Scholar
- Heun M (1992) Mapping quantitative powdery mildew resistance of barley using a restriction fragment length polymorphism map. Genome 35:1019–1025Google Scholar
- Park SDE (2001) Trypano tolerance in West African cattle and the population genetic effects of selection. University of Dublin, DublinGoogle Scholar
- Payne RW, Harding SA, Murray DA, Soutar DM, Baird DB et al (2006) GenStat release 9 reference manual. Part 2. Directives. VSN International, Hemel HempsteadGoogle Scholar