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

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...

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Published in:Proceedings of the National Academy of Sciences - PNAS 2010-11, Vol.107 (45), p.19585-19590
Main Authors: Lu, Yanli, Zhang, Shihuang, Shah, Trushar, Xie, Chuanxiao, Hao, Zhuanfang, Li, Xinhai, Farkhari, Mohammad, Ribaut, Jean-Marcel, Cao, Moju, Rong, Tingzhao, Xu, Yunbi, Zhang, Qifa
Format: Article
Language:English
Subjects:
Acclimatization - genetics
Alcohol Oxidoreductases - genetics
Aldehyde Reductase
Aldo-Keto Reductases
Alleles
Biological Sciences
Cells
Chromosomes
Computational Biology
Corn
Detoxification
Drought resistance
Droughts
Environmental stress
Flowering
Flowers - genetics
Gene frequency
Gene loci
Genetic diversity
Genetic linkage
Genetic loci
Genomics
Genotype & phenotype
Haplotypes
Inbreeding
Joints
Linkage analysis
Linkage Disequilibrium
Phenotype
Phenotypic traits
Plants
Polymorphism
Polymorphism, Single Nucleotide
Population genetics
Population structure
Quantitative Trait Loci
reductase
Single-nucleotide polymorphism
Zea mays
Zea mays - genetics
Zea mays - physiology
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cited_by cdi_FETCH-LOGICAL-c564t-6f87e5868e2cb6f829732903752189a78dcd7fea93c71c725d0e939d12ef10d73
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creator Lu, Yanli
Zhang, Shihuang
Shah, Trushar
Xie, Chuanxiao
Hao, Zhuanfang
Li, Xinhai
Farkhari, Mohammad
Ribaut, Jean-Marcel
Cao, Moju
Rong, Tingzhao
Xu, Yunbi
Zhang, Qifa
description 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 SNP-based 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 (
doi_str_mv 10.1073/pnas.1006105107
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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 SNP-based analysis. Integrated mapping with haplotype further improved the mapping efficiency, and the most significant QTL had a PVE of up to 34.7%. 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Normal allele frequencies for 113 of 277 (40.8%) SNPs with minor allele frequency (&lt;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.</abstract><cop>United States</cop><pub>National Academy of Sciences</pub><pmid>20974948</pmid><doi>10.1073/pnas.1006105107</doi><tpages>6</tpages><oa>free_for_read</oa></addata></record>
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subjects Acclimatization - genetics
Alcohol Oxidoreductases - genetics
Aldehyde Reductase
Aldo-Keto Reductases
Alleles
Biological Sciences
Cells
Chromosomes
Computational Biology
Corn
Detoxification
Drought resistance
Droughts
Environmental stress
Flowering
Flowers - genetics
Gene frequency
Gene loci
Genetic diversity
Genetic linkage
Genetic loci
Genomics
Genotype & phenotype
Haplotypes
Inbreeding
Joints
Linkage analysis
Linkage Disequilibrium
Phenotype
Phenotypic traits
Plants
Polymorphism
Polymorphism, Single Nucleotide
Population genetics
Population structure
Quantitative Trait Loci
reductase
Single-nucleotide polymorphism
Zea mays
Zea mays - genetics
Zea mays - physiology
title Joint linkage–linkage disequilibrium mapping is a powerful approach to detecting quantitative trait loci underlying drought tolerance in maize
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