Genome-wide association study and candidate gene analysis of alkalinity tolerance in japonica rice germplasm at the seedling stage
Genome-wide association study and candidate gene analysis of alkalinity tolerance in japonica rice germplasm at the seedling stage
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苗期粳稻种质耐碱性全基因组关联研究及候选基因分析
DOI：
10.1186/s12284-019-0285-y
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发表时间：
2019-04-11
期刊：
影响因子：
5.5
通讯作者：
Zou, Detang
中科院分区：
文献类型：
--
作者：
Li, Ning;Zheng, Hongliang;Zou, Detang
背景：盐碱胁迫是限制水稻生产的主要因素之一。碱性盐胁迫对水稻生长的伤害比中性盐胁迫严重。目前，可供水稻育种者利用以提高耐碱性的遗传资源（数量性状位点（QTL）和基因）有限。本研究以295个粳稻品种的788，396个单核苷酸多态性（SNPs）基因型数据为基础，对水稻苗期的耐碱性进行了评估，并进行了全基因组关联研究（GWAS）。结果：以耐碱性评分（SAT）、地上部Na+和K+浓度（SNC和SKC）以及地上部Na+/K+比值（SNK）为指标，对水稻苗期的耐碱性进行了评估。根据群体结构分析，将粳稻群体划分为3个亚群。连锁不平衡（LD）分析表明，LD衰减发生在109.77 kb处，在12条染色体上的LD衰减在13.79 kb和415.77 kb之间变化，此时两两平方相关系数（r2）下降到最大值的一半。通过全基因组关联分析，共检测到8个与SAT、SNC和SNK显著相关的QTL。在第3染色体15.0Mb处，选择了一个与SAT、SNC和SNK相关的QTL，该QTL可解释13.36~13.64%的表型变异。基于LD衰减、基因本体（GO）富集、RNA测序数据和定量实时PCR（qRT-PCR）分析来筛选候选基因。此外，序列分析显示，一个7-bp的插入/缺失（indel）的差异在水稻品种之间的耐碱性和碱敏感的LOC_0s03g26210（OsIRO 3）。结论：OsIRO 3基因可能是一个与粳稻耐碱性相关的新基因。本研究为水稻耐碱性改良提供了资源，并为利用分子标记辅助选择（MAS）选育耐碱性水稻新品种提供了验证。
Background:Salinity-alkalinity stress is one of the major factors limiting rice production. The damage caused by alkaline salt stress to rice growth is more severe than that caused by neutral salt stress. At present, the genetic resources (quantitative trait loci (QTLs) and genes) that can be used by rice breeders to improve alkalinity tolerance are limited. Here, we assessed the alkalinity tolerance of rice at the seedling stage and performed a genome-wide association study (GWAS) based on genotypic data including 788,396 single-nucleotide polymorphisms (SNPs) developed by re-sequencing 295 japonica rice varieties.Results:We used the score of alkalinity tolerance (SAT), the concentrations of Na+and K+in the shoots (SNC and SKC, respectively) and the Na+/K+ratio of shoots (SNK) as indices to assess alkalinity tolerance at the seedling stage in rice. Based on population structure analysis, the japonica rice panel was divided into three subgroups. Linkage disequilibrium (LD) analysis showed that LD decay occurred at 109.77 kb for the whole genome and varied between 13.79 kb and 415.77 kb across the 12 chromosomes, at which point the pairwise squared correlation coefficient (r2) decreased to half of its maximum value. A total of eight QTLs significantly associated with the SAT, SNC and SNK were identified by genome-wide association mapping. A common QTL associated with the SAT, SNC and SNK on chromosome 3 at the position of 15.0 Mb, which explaining 13.36~13.64% of phenotypic variation, was selected for further analysis. The candidate genes were filtered based on LD decay, Gene Ontology (GO) enrichment, RNA sequencing data, and quantitative real-time PCR (qRT-PCR) analysis. Moreover, sequence analysis revealed one 7-bp insertion/deletion (indel) difference in LOC_Os03g26210 (OsIRO3) between the alkalinity-tolerant and alkalinity-sensitive rice varieties. OsIRO3 encodes a bHLH-type transcription factor and has been shown to be a negative regulator of the Fe-deficiency response in rice.Conclusion:Based on these results, OsIRO3 maybe a novel functional gene associated with alkalinity tolerance in japonica rice. This study provides resources for improving alkalinity tolerance in rice, and the functional molecular marker could be verified to breed new rice varieties with alkalinity tolerance via marker-assisted selection (MAS).