Patterns of linkage disequilibrium and association mapping in diploid alfalfa (M. sativa L.)
Open Access
- 5 April 2012
- journal article
- research article
- Published by Springer Science and Business Media LLC in Theoretical and Applied Genetics
- Vol. 125 (3), 577-590
- https://doi.org/10.1007/s00122-012-1854-2
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.Keywords
This publication has 52 references indexed in Scilit:
- A next-generation sequencing method for overcoming the multiple gene copy problem in polyploid phylogenetics, applied to Poa grassesBMC Biology, 2011
- Polymorphisms in monolignol biosynthetic genes are associated with biomass yield and agronomic traits in European maize (Zea mays L.)BMC Plant Biology, 2010
- Association Mapping: Critical Considerations Shift from Genotyping to Experimental DesignPlant Cell, 2009
- DnaSP v5: a software for comprehensive analysis of DNA polymorphism dataBioinformatics, 2009
- Lignin modification improves fermentable sugar yields for biofuel productionNature Biotechnology, 2007
- A unified mixed-model method for association mapping that accounts for multiple levels of relatednessNature Genetics, 2005
- Genome-Wide Association Mapping in Arabidopsis Identifies Previously Known Flowering Time and Pathogen Resistance GenesPLoS Genetics, 2005
- MUSCLE: multiple sequence alignment with high accuracy and high throughputNucleic Acids Research, 2004
- Statistical significance for genomewide studiesProceedings of the National Academy of Sciences of the United States of America, 2003
- A Direct Approach to False Discovery RatesJournal of the Royal Statistical Society Series B: Statistical Methodology, 2002