Status and Prospects of Association Mapping in Plants
- C. Zhu and J. Yu, Dep. of Agronomy, Kansas State University, 2004 Throckmorton Hall, Manhattan, KS 66506; M. Gore, Dep. of Plant Breeding and Genetics, Cornell University, Ithaca, NY 14853; Edward S. Buckler, USDA-ARS and Institute for Genomic Diversity, Cornell University, Ithaca, NY 14853. Mention of trade names or commercial products in this publication is solely for the purpose of providing specific information and does not imply recommendation or endorsement by the USDA.
Abstract
There is tremendous interest in using association mapping to identify genes responsible for quantitative variation of complex traits with agricultural and evolutionary importance. Recent advances in genomic technology, impetus to exploit natural diversity, and development of robust statistical analysis methods make association mapping appealing and affordable to plant research programs. Association mapping identifies quantitative trait loci (QTLs) by examining the marker-trait associations that can be attributed to the strength of linkage disequilibrium between markers and functional polymorphisms across a set of diverse germplasm. General understanding of association mapping has increased significantly since its debut in plants. We have seen a more concerted effort in assembling various association-mapping populations and initiating experiments through either candidate-gene or genome-wide approaches in different plant species. In this review, we describe the current status of association mapping in plants and outline opportunities and challenges in complex trait dissection and genomics-assisted crop improvement.
- AB-QTL, advanced backcross QTL
- AFLP, amplified fragment length polymorphism
- GC, genomic control
- IL, introgression library
- K, kinship matrix
- lcyE, lycopene epsilon cyclase
- LD, linkage disequilibrium
- NAM, nested association mapping
- oligo, oligonucleotide
- PCA, principal component analysis
- Q, population structure
- QTDT, quantitative transmission disequilibrium test
- QTLs, quantitative trait loci
- RAPD, random amplified polymorphic DNA
- RILs, recombinant inbred lines
- SA, structured association
- SBE, single base extension
- SFP, single feature polymorphism
- SNPs, single nucleotide polymorphisms
- SSRs, simple sequence repeats
Footnotes
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↵ * Corresponding author (jyu{at}ksu.edu).
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- Received February 11, 2008.
- Accepted July 16, 2008.
- Copyright © 2008 Crop Science Society of America
