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离子束诱变体水稻JD-1的表型及基因组变异分析
敬银钦1, 高方远2, 刘利平2, 苏相文2, 任明鑫2, 陆贤军2, 吕建群2, 金文杰3, 胡运高1, 任鄄胜2, 任光俊2
0
(1.西南科技大学;2.四川省农业科学院作物研究所;3.中国科学院近代物理研究所)
摘要:
辐射诱变是作物种质创新的有效途径之一。本研究利用碳离子束诱变‘津稻565’,获得穗下垂及穗部其他性状发生变异的突变体,命名为‘JD-1’。对突变体及野生型的主要农艺性状进行调察,结果表明JD-1的主穗颈穗弯曲度、着粒数和着粒密度都较‘津稻565’极显著增加,增幅分别为305.90%、66.86%和47.79%;其主穗穗长、实粒数和二次枝梗数显著性增加,增幅分别为12.11%、63.06%和74.19%,而千粒重显著性降低11.54%。基因组序列比对表明,在突变体JD-1和野生型‘津稻565’之间有18639个单核苷酸多态性位点(SNP,single nucleotide polymorphism),转换/颠换比值为2.34;有3428个小片段插入缺失(InDel,insertion-deletion)。这些突变表现为成簇分布,主要发生在第5和第11染色体上,占比分别为25.19%和22.98%。在基因结构变异中,基因间区的变异数占比较高,为45.22%;剪切位点的变异数占比较低,为0.08%。变异基因GO注释表明,参与细胞生理过程的变异基因数较多。变异基因中与株高、千粒重、穗长、二次枝梗数相关的已克隆基因有16个;根据变异位点设计了16个已克隆基因的分子标记,有12个SNP标记和9个InDel标记在9个基因上鉴定出多态性。该研究创制出新的水稻种质资源并发掘出与产量性状相关基因的等位变异。
关键词:  水稻  碳离子束  全基因组重测序  等位变异  分子标记
DOI:10.13430/j.cnki.jpgr. 20210219001
投稿时间:2021-02-19修订日期:2021-05-07
基金项目:国家重点研发计划“七大农作物育种”重点专项(2017YFD0100200);现代农业产业技术体系建设专项资金(CARS-01-08)、;四川省水稻育种攻关(2016NYZ0028-3);四川省创新能力提升工程项目(2016ZYPZ-011)
Phenotype and Genome Variation Analysis of Ion-beam Induced Mutant Rice JD-1
JING Yin-qin1, GAO Fang-yuan2, LIU Li-ping2, SU Xiang-wen2, REN Ming-xin2, LU Xian-jun2, LYU Jian-qun2, JIN Wen-jie3, HU Yun-gao1, REN Juan-sheng2, REN Guang-jun2
(1.Southwest University of Science and Technology;2.Crop Research Institute Sichuan Academy of Agricultural Science;3.Institute of Modern Physics,Chinese Academy of Sciences)
Abstract:
Mutation induced by irradiation is one of the efficient ways to innovate crop germplasm resources. In this study, a drooping-panicled mutant rice with other variations in the panicle, named JD-1, was derived from ‘Jindao 565’ by carbon ion beam irradiation. Compared with the agronomic traits of the wild type ‘Jindao 565’, JD-1 had a highly significant (P<0.01) increase in neck-panicle curvature, number and density of main panicle grains by 305.90%, 66.86% and 47.79%, respectively. In addition, panicle length, number of main panicle filled grains and number of main panicle secondary branches increased significantly (P<0.05) by 12.11%, 63.06% and 74.19%, respectively, but the 1000-grain weight significantly decreased by 11.54%. The whole genome sequence alignment revealed the existence of 18639 single nucleotide polymorphisms (SNPs) with a conversion/transversion ratio of 2.34, and of 3428 insertion-deletions (InDels), between ‘Jindao 565’ and JD-1, which were distributed in clusters and mainly located on chromosomes 5 and 11, accounting for 25.19% and 22.98%, respectively. Through the structural analysis of mutated genes, the mutations occurred in intergenetic regions had the maximum proportion of 45.22%, while those detected in splicing hold the minimum proportion of 0.08%. GO functional analysis of the mutated genes revealed that most of them were involved in cell physiological process. The sixteen genes related to plant height, 1000-grain weight, panicle length and secondary branches were identified from the cloned genes which were mutated in JD-1. The molecular markers for these genes were further designed based on the mutation sites, and the twelve SNP markers and the nine InDel markers were proved to be polymorphic in nine genes between ‘Jindao 565’ and JD-1. This study created a new rice germplasm and explored the allelic variation related to yield trait in rice.
Key words:  rice  carbon ion beam  whole-genome resequencing  allelic variation  molecular marker

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