Islam Mohammad Rafiqul, Naveed Shahzad Amir, Zhang Yue, Li Zhikang, Zhao Xiuqin, Fiaz Sajid, Zhang Fan, Wu Zhichao, Hu Zhiqing, Fu Binying, Shi Yingyao, Shah Shahid Masood, Xu Jianlong, Wang Wensheng
Institute of Crop Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing, China.
College of Agronomy, Anhui Agricultural University, Hefei, China.
Front Genet. 2022 Feb 23;13:822516. doi: 10.3389/fgene.2022.822516. eCollection 2022.
Multiple stress tolerance at the seed germination stage is crucial for better crop establishment in the direct-seeded rice ecosystem. Therefore, identifying rice genes/quantitative trait loci (QTLs) associated with salinity and anaerobic tolerance at the germination stage is a prerequisite for adaptive breeding. Here, we studied 498 highly diverse rice accessions () and (), and six traits that are highly associated with salinity and anaerobic tolerance at germination stage were measured. A high-density 2.8M Single Nucleotide Polymorphisms (SNP) genotype map generated from the 3,000 Rice Genomes Project (3KRGP) was used for mapping through a genome-wide association study. In total, 99 loci harboring 117 QTLs were detected in different populations, 54, 21, and 42 of which were associated with anaerobic, salinity, and combined (anaerobic and salinity) stress tolerance. Nineteen QTLs were close to the reported loci for abiotic stress tolerance, whereas two regions on chromosome 4 (// and /) and one region on chromosome 10 () were associated with anaerobic and salinity related traits. Further haplotype analysis detected 25 promising candidates genes significantly associated with the target traits. Two known genes ( and ) significantly associated with grain yield and its related traits under saline and anaerobic stress conditions were identified. In this study, we identified the genes involved in auxin efflux (Os09g0491740) and transportation (Os01g0976100), whereas we identified multistress responses gene (Os01g0974200) and a major gene (Os09g0369400) involved in anaerobic germination and coleoptile elongation on chromosome 9. These promising candidates provide valuable resources for validating potential salt and anaerobic tolerance genes and will facilitate direct-seeded rice breeding for salt and anaerobic tolerance through marker-assisted selection or gene editing.
种子萌发期的多重胁迫耐受性对于直播水稻生态系统中更好地建立作物群体至关重要。因此，鉴定与萌发期耐盐性和厌氧耐受性相关的水稻基因/数量性状位点（QTL）是适应性育种的先决条件。在此，我们研究了498份高度多样化的水稻种质（品种1和品种2），并测定了与萌发期耐盐性和厌氧耐受性高度相关的六个性状。利用从3000份水稻基因组计划（3KRGP）生成的高密度280万个单核苷酸多态性（SNP）基因型图谱，通过全基因组关联研究进行定位。在不同群体中总共检测到99个位点，包含117个QTL，其中54个、21个和42个分别与厌氧、盐度以及组合（厌氧和盐度）胁迫耐受性相关。19个QTL与报道的非生物胁迫耐受性位点相近，而第4染色体上的两个区域（品种1/品种2和品种3/品种4）以及第10染色体上的一个区域（品种5）与厌氧和盐度相关性状有关。进一步的单倍型分析检测到25个与目标性状显著相关的有前景的候选基因。鉴定出两个在盐胁迫和厌氧胁迫条件下与籽粒产量及其相关性状显著相关的已知基因（基因1和基因2）。在本研究中，我们鉴定出参与生长素外排（Os09g0491740）和运输（Os01g0976100）的基因，而我们在第9染色体上鉴定出参与厌氧萌发和胚芽鞘伸长的多重胁迫响应基因（Os01g0974200）和一个主基因（Os09g0369400）。这些有前景的候选基因提供了宝贵的资源，用于验证潜在的耐盐和厌氧耐受性基因，并将通过标记辅助选择或基因编辑促进直播水稻耐盐和厌氧耐受性的育种。
