Comparative LD mapping using single SNPs and haplotypes identifies QTL for plant height and biomass as secondary traits of drought tolerance in maize

Lu, Y and et al, . (2012) Comparative LD mapping using single SNPs and haplotypes identifies QTL for plant height and biomass as secondary traits of drought tolerance in maize. Molecular Breeding, 30 (1). pp. 407-418. ISSN 1572-9788

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Abstract

Drought often delays developmental events so that plant height and above-ground biomass are reduced, resulting in yield loss due to inadequate photosynthate. In this study, plant height and biomass measured by the Normalized Difference Vegetation Index (NDVI) were used as criteria for drought tolerance. A total of 305 lines representing temperate, tropical and subtropical maize germplasm were genotyped using two single nucleotide polymorphism (SNP) chips each containing 1536 markers, from which 2052 informative SNPs and 386 haplotypes each constructed with two or more SNPs were used for linkage disequilibrium (LD) or association mapping. Single SNP- and haplotype-based LD mapping identified two significant SNPs and three haplotype loci [a total of four quantitative trait loci (QTL)] for plantheight under well-watered and water-stressed conditions. For biomass, 32 SNPs and 12 haplotype loci (30 QTL) were identified using NDVIs measured at seven stages under the two water regimes. Some significant SNP and haplotype loci for NDVI were shared by different stages. Comparing significant loci identified by single SNP- and haplotype-based LD mapping, we found that six out of the 14 chromosomal regions defined by haplotype loci each included at least one significant SNP for the same trait. Significant SNP haplotype loci explained much higher phenotypic variation than individual SNPs. Moreover, we found that two significant SNPs (two QTL) and one haplotype locus were shared by plant height and NDVI. The results indicate the power of comparative LD mapping using single SNPs and SNP haplotypes with QTL shared by plant height and biomass as secondary traits for drought tolerance in maize.

Item Type: Article
Divisions: UNSPECIFIED
CRP: UNSPECIFIED
Uncontrolled Keywords: Maize, Drought tolerance, Secondary traits, Plant height, Biomass, Single nucleotide polymorphism (SNP), Haplotype, LD mapping, Association mapping
Subjects: Others > Maize
Depositing User: Mr Sanat Kumar Behera
Date Deposited: 16 Feb 2012 10:27
Last Modified: 18 Feb 2013 04:13
URI: http://oar.icrisat.org/id/eprint/5514
Official URL: http://dx.doi.org/10.1007/s11032-011-9631-5
Projects: UNSPECIFIED
Funders: Rockefeller Foundation, Bill and Melinda Gates Foundation, Generation Challenge Programme, European Community, National High Technology Research and Development Program of China, National Basic Research Program of China
Acknowledgement: The SNP chips used in this study were developed through a collaborative project between Cornell University (Ed Buckler and Tim Setter) and CIMMYT (Marilyn Warburton and Jianbing Yan).Maize drought tolerance work was funded by the Rockefeller Foundation, Bill and Melinda Gates Foundation, Generation Challenge Programme, European Community, National High Technology Research and Development Program of China (No. 2009AA10AA03-2) and National Basic Research Program of China (No.2007CB108900
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