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About the Authors:
Anthony Becker
Affiliation: Donald Danforth Plant Sciences Center, St. Louis, Missouri, United States of America
Dai-Yin Chao
Affiliation: Center for Plant Environmental Stress Physiology, Purdue University, West Lafayette, Indiana, United States of America
Xu Zhang
Affiliation: Department of Genetics, University of Chicago, Chicago, Illinois, United States of America
David E. Salt
Affiliation: Center for Plant Environmental Stress Physiology, Purdue University, West Lafayette, Indiana, United States of America
Ivan Baxter
* E-mail: [email protected]
Affiliations Donald Danforth Plant Sciences Center, St. Louis, Missouri, United States of America, Plant Genetics Research Unit, United States Department of Agriculture-Agricutlural Research Service, St. Louis, Missouri, United States of America
Introduction
Mapping the causal allele or alleles for a particular trait is one of the most common methods for learning about the genetic processes underlying biological function. One method to rapidly identify markers in a genomic region linked to a phenotype is Bulk Segregant Analysis (BSA) [1]. BSA partitions a population from a single cross into two pools, or bulks, according to a single trait, so that each bulk contains individuals corresponding to a particular phenotype or specific section of a phenotypic range. The method uses marker measurements of pooled genomic DNA samples from each bulk to measure correlation between marker and phenotype and thereby designate a probable location for the gene basedon that correlation. BSA was first combined with microarray genotyping in yeast using arrays designed for measuring mRNA expression [2]. The technique allows for the parallel interrogation of thousands of single feature polymorphisms (SFPs), i.e. differences in the binding intensity to a particular oligonucleotide probe between two different samples of genomic DNA. Later studies showed the potential of BSA combined with SFP genotyping arrays in successfully mapping genes to mutant phenotypes in more complex genomes, such as Arabidopsis [3], [4] and the technique has been used to map mutants in several species [5]–[10].
The microarray genotyping approach was later extended to BSA-based investigations of quantitative traits where the pools were selected from the extreme ends of phenotypes in a continuously variable population. This process, called eXtreme Array Mapping (XAM), has successfully mapped Quantitative Trait Loci (QTL) in Arabidopsis and offers a time-efficient and cost-effective method of discovering new QTL [11]. However, SFP marker approaches require multiple parental...