Joint linkage–linkage disequilibrium mapping is a powerful approach to detecting quantitative trait loci underlying drought tolerance in maize

Yanli, Lu and Shihuang, Zhang and Trushar, Shah and Chuanxiao, Xie and Zhuanfang, Hao and Xinhai, Li and Farkhari, Md and Jean-Marcel, Ribaut and Moju, Cao and Tingzhao, Rong and Yunbi, Xu (2010) Joint linkage–linkage disequilibrium mapping is a powerful approach to detecting quantitative trait loci underlying drought tolerance in maize. Proceedings of the National Academy of Sciences of the United States of America (PNAS) ISSN 1091-6490, 1. pp. 1-6.

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Abstract

This paper describes two joint linkage–linkage disequilibrium (LD) mapping approaches: parallel mapping (independent linkage and LD analysis) and integrated mapping (datasets analyzed in combination). These approaches were achieved using 2,052 single nucleotide polymorphism (SNP) markers, including 659 SNPs developed from drought-response candidate genes, screened across three recombinant inbred line (RIL) populations and 305 diverse inbred lines, with anthesis-silking interval (ASI), an important trait for maize drought tolerance, as the target trait. Mapping efficiency was improved significantly due to increased population size and allele diversity and balanced allele frequencies. Integrated mapping identified 18 additional quantitative trait loci (QTL) not detected by parallel mapping. The use of haplotypes improved mapping efficiency, with the sum of phenotypic variation explained (PVE) increasing from 5.4% to 23.3% for single SNPbased analysis. Integrated mapping with haplotype further improved the mapping efficiency, and the most significant QTL had a PVE of up to 34.7%. Normal allele frequencies for 113 of 277 (40.8%) SNPs with minor allele frequency (<5%) in 305 lines were recovered in three RIL populations, three of which were significantly associated with ASI. The candidate genes identified by two significant haplotype loci included one for a SET domain protein involved in the control of flowering time and the other encoding aldo/keto reductase associated with detoxification pathways that contribute to cellular damage due to environmental stress. Joint linkage–LD mapping is a powerful approach for detecting QTL underlying complex traits, including drought tolerance.

Item Type:	Article
Divisions:	UNSPECIFIED
CRP:	UNSPECIFIED
Agro Tags:	<h1>Unable to Generate Tags new17.pdf</h1>
Subjects:	Others > Maize
Depositing User:	Library ICRISAT
Date Deposited:	12 Aug 2011 08:20
Last Modified:	12 Aug 2011 08:20
URI:	http://oar.icrisat.org/id/eprint/164
Official URL:	http://dx.doi.org/10.1073/pnas.1006105107
Projects:	UNSPECIFIED
Funders:	UNSPECIFIED
Acknowledgement:	UNSPECIFIED
Links:	Author

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