Institute of Crop Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing, China.
Beijing Vegetable Research Center, Beijing Academy of Agricultural and Forestry Sciences, Beijing, China.
PLoS One. 2018 Jun 12;13(6):e0198589. doi: 10.1371/journal.pone.0198589. eCollection 2018.
Aluminum (Al) stress is becoming the major limiting factor in crop production in acidic soils. Rice has been reported as the most Al-tolerant crop and the capacity of Al toxicity tolerance is generally evaluated by comparing root growth under Al stress. Here, we performed an association mapping of Al toxicity tolerance using a core collection of 211 indica rice accessions with 700 K high quality SNP data. A total of 21 putative QTL affecting shoot height (SH), root length (RL), shoot fresh weight (SFW), shoot dry weight (SDW), root dry weight (RDW) and shoot water content (SWC) were identified at seedling stage, including three QTL detected only under control condition, eight detected only under Al stress condition, ten simultaneously detected in both control and Al stress conditions, and seven were identified by stress tolerance index of their corresponding traits. Total of 21 candidate genes for 7 important QTL regions associated with Al toxicity tolerance were identified based on combined haplotype analysis and functional annotation, and the most likely candidate gene(s) for each important QTL were also discussed. Also a candidate gene Nrat1 on chromosome 2 was further fine-mapped using BSA-seq and linkage analysis in the F2 population derived from the cross of Al tolerant accession CC105 and super susceptible accession CC180. A new non-synonymous SNP variation was observed at Nrat1 between CC105 and CC180, which resulted in an amino-acid substitution from Ala (A) in CC105 to Asp (D) in CC180. Haplotype analysis of Nrat1 using 327 3K RGP accessions indicated that minor allele variations in aus and indica subpopulations decreased Al toxicity tolerance in rice. The candidate genes identified in this study provide valuable information for improvement of Al toxicity tolerance in rice. Our research indicated that minor alleles are important for QTL mapping and its application in rice breeding when natural gene resources are used.
铝（Al）胁迫正在成为酸性土壤中作物生产的主要限制因素。水稻被报道为最耐 Al 的作物，Al 毒性耐性的能力通常通过比较 Al 胁迫下的根生长来评估。在这里，我们使用 211 份籼稻核心种质资源进行了 Al 毒性耐性的关联作图，该资源具有 700 K 高质量 SNP 数据。在幼苗期共鉴定出 21 个影响株高（SH）、根长（RL）、地上部鲜重（SFW）、地上部干重（SDW）、根干重（RDW）和地上部含水量（SWC）的假定 QTL，其中 3 个 QTL 仅在对照条件下检测到，8 个 QTL 仅在 Al 胁迫条件下检测到，10 个 QTL 同时在对照和 Al 胁迫条件下检测到，7 个 QTL 通过其对应性状的胁迫耐性指数来鉴定。基于组合单倍型分析和功能注释，共鉴定出与 Al 毒性耐性相关的 7 个重要 QTL 区域的 21 个候选基因，还讨论了每个重要 QTL 的最可能候选基因。还使用来自 Al 耐受系 CC105 和超敏系 CC180 的杂交 F2 群体的 BSA-seq 和连锁分析，对第 2 号染色体上与 Al 毒性耐性相关的 Nrat1 重要 QTL 进行了精细定位。在 CC105 和 CC180 之间观察到 Nrat1 上的一个新非同义 SNP 变异，导致丙氨酸（A）突变为天冬氨酸（D）。使用 327 3K RGP 系对 Nrat1 进行的单倍型分析表明，籼稻和粳稻亚群中的次要等位基因变异降低了水稻的 Al 毒性耐性。本研究鉴定的候选基因为提高水稻的 Al 毒性耐性提供了有价值的信息。我们的研究表明，在利用自然基因资源进行 QTL 作图及其在水稻育种中的应用时，次要等位基因对 QTL 作图及其应用很重要。
