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.anthesis-silking interval | drought resistance | haplotype loci | integrated quantitative trait locus mapping
Large-scale selective genotyping and high-throughput analysis are two important strategies for low-cost and high-effective genetic mapping. In this study, selective genotyping was applied to four maize F 2 populations. Thirty plants were selected from each of the two tails of the original F 2 populations to represent extreme resistant and susceptible plants to root lodging, and genotyped individually with 1536 single nucleotide polymorphisms (SNPs). A quantitative trait locus (QTL) was declared when at least three closely linked SNPs showed significant allele frequency difference between the two tails. Nine QTL were identified for root lodging across the four populations, which were located on chromosomes 2, 4, 5, 7, 8 and 10 and one of them was shared between two populations. A total of 20 segregation distortion regions (SDRs) were identified across the four populations, one of which was co-localized with a QTL on chromosome 4. The tightly linked SNPs identified in this study can be used for marker-assisted selection for root lodging. Selective genotyping, when combined with pooled DNA analysis, can be used to develop strategies for high-throughput genetic mapping for all crops.
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