Maize Research Institute, Sichuan Agricultural University, Ya'an 625014, China.
Proc Natl Acad Sci U S A. 2010 Nov 9;107(45):19585-90. doi: 10.1073/pnas.1006105107. Epub 2010 Oct 25.
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.
本文描述了两种联合连锁-连锁不平衡（LD）映射方法：并行映射（独立连锁和 LD 分析）和综合映射（组合分析数据集）。这些方法使用了 2052 个单核苷酸多态性（SNP）标记，包括从耐旱候选基因中开发的 659 个 SNP，在三个重组自交系（RIL）群体和 305 个不同的自交系中进行了筛选，以开花-吐丝间隔（ASI）为目标性状，这是玉米耐旱性的一个重要性状。由于群体规模的增加和等位基因多样性的提高以及等位基因频率的平衡，映射效率显著提高。综合映射鉴定了 18 个额外的数量性状位点（QTL），这些 QTL在并行映射中未被检测到。使用单倍型提高了映射效率，基于单个 SNP 的分析中表型变异解释（PVE）的总和从 5.4%增加到 23.3%。单倍型的综合映射进一步提高了映射效率，最显著的 QTL 的 PVE 高达 34.7%。在三个 RIL 群体中，305 个系中少数等位基因频率（<5%）的 277 个（40.8%）SNP 的正常等位基因频率得到恢复，其中三个与 ASI 显著相关。通过两个显著单倍型位点鉴定的候选基因包括一个参与控制开花时间的 SET 结构域蛋白，另一个编码醛酮还原酶，与解毒途径相关，这些途径导致细胞因环境压力而受损。联合连锁 LD 映射是一种用于检测复杂性状（包括耐旱性）下 QTL 的强大方法。
