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

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 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 (<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.

Fig. 1.

Distribution of minor allele frequencies for 522 lines (A) and 305 lines (B) at 2,052 SNP loci and distribution of allele frequency for B73 alleles at the 93 SNP loci with minor allele frequency <0.05 in 305 maize lines (C).

Fig. 2.

Q–Q plots for SNP markers significantly associated with ASI under WW and WS conditions using 522 maize lines. (A) Single SNP–based analysis. (B) Haplotype-based analysis using 386 haplotype loci.