Abstract
Association mapping enables the detection of marker-trait associations in unstructured populations by taking advantage of historical linkage disequilibrium (LD) that exists between a marker and the true causative polymorphism of the trait phenotype. Our first objective was to understand the pattern of LD decay in the diploid alfalfa genome. We used 89 highly polymorphic SSR loci in 374 unimproved diploid alfalfa (Medicago sativa L.) genotypes from 120 accessions to infer chromosome-wide patterns of LD. We also sequenced four lignin biosynthesis candidate genes (caffeoyl-CoA 3-O-methyltransferase (CCoAoMT), ferulate-5-hydroxylase (F5H), caffeic acid-O-methyltransferase (COMT), and phenylalanine amonialyase (PAL 1)) to identify single nucleotide polymorphisms (SNPs) and infer within gene estimates of LD. As the second objective of this study, we conducted association mapping for cell wall components and agronomic traits using the SSR markers and SNPs from the four candidate genes. We found very little LD among SSR markers implying limited value for genomewide association studies. In contrast, within gene LD decayed within 300 bp below an r 2 of 0.2 in three of four candidate genes. We identified one SSR and two highly significant SNPs associated with biomass yield. Based on our results, focusing association mapping on candidate gene sequences will be necessary until a dense set of genome-wide markers is available for alfalfa.Electronic supplementary materialThe online version of this article (doi:10.1007/s00122-012-1854-2) contains supplementary material, which is available to authorized users.
Highlights
Linking DNA polymorphism to trait phenotypic variation is an increasingly important tool for plant breeding programs (Lande and Thompson 1990)
We evaluated neutral detergent Wber (NDF), acid detergent Wber (ADF) acid detergent lignin (ADL), and total nonstructural carbohydrate (TNC) composition, glucose, xylose, arabinose, total aboveground biomass yield, and regrowth after harvest in 2007 and 2008
We evaluated four genes in the lignin biosynthetic pathway as candidate loci associated with stem composition: caVeoyl-CoA 3-O-methyltransferase (CCoAoMT), ferulate-5-hydroxylase (F5H), caVeic acid-Omethyltransferase (COMT), and phenylalanine ammonialyase (PAL 1)
Summary
Linking DNA polymorphism to trait phenotypic variation is an increasingly important tool for plant breeding programs (Lande and Thompson 1990). Segregating populations of a particular cross have been used to identify marker-trait associations (e.g., Stuber et al 1999). Association mapping has shown promise for trait mapping due to the increased access to abundant molecular markers in many crops (Stich et al 2005). Association mapping takes advantage of the fact that historical recombination within a population has decreased linkage disequilibrium (LD) to short chromosomal intervals, enabling potentially statistically strong and robust marker-trait associations to be detected (Jannink and Walsh 2002). In association mapping, existing allele variation within an entire population can be more eYciently represented because mapping is conducted directly in breeding populations (Hirschhorn and Daly 2005; Remington et al 2001). The precision of locating a QTL is much higher in association panels compared to biparental
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