A Multi-Omics Approach for Rapid Identification of Large Genomic Lesions at the Wheat Dense Spike (wds) Locus.
A Multi-Omics Approach for Rapid Identification of Large Genomic Lesions at the Wheat Dense Spike (wds) Locus.
复制标题
DOI：
10.3389/fpls.2022.850302
复制
发表时间：
2022
影响因子：
5.6
通讯作者：
Li, Aili
中科院分区：
文献类型：
--
作者：
Wang, Zhenyu;Tao, Shu;Liu, Shaoshuai;Jia, Meiling;Cui, Dada;Sun, Guoliang;Deng, Zhongyin;Wang, Fang;Kong, Xingchen;Fu, Mingxue;Che, Yuqing;Liao, Ruyi;Li, Tao;Geng, Shuaifeng;Mao, Long;Li, Aili
最佳的穗结构为籽粒发育和产量提高提供了有利的结构。然而，克隆到小麦穗结构之下的基因数量极其有限。在这里，我们获得了由 60Co 处理普通小麦地方品种黄芳珠诱导的小麦密集穗突变体 (wds)，该突变体表现出穗和粒长度显着缩短。穗长度缩短是由于轴细胞数量和长度的纵向减少造成的。我们采用多组学方法来鉴定 wds 突变体背后的基因组位点。我们进行了外显子组捕获测序（ECS）并在 wds 突变体中鉴定了两个大的缺失片段，分别命名为 6BL.1（334.8∼424.3 Mb）和 6BL.2（579.4∼717.8 Mb）。 RNA-seq 分析证实位于这些区域的基因失去了 RNA 表达。然后我们发现 6BL.2 基因座与已知的穗长 QTL qSL6B.2 重叠。总共有 499 个基因位于删除区域内，其中两个被发现与长穗种质呈正相关，但与短穗种质无关。其中之一 TraesCS6B01G334600 是水稻 OsBUL1 基因的良好匹配同源物，在油菜素类固醇 (BR) 途径中发挥作用，被确定参与细胞大小和数量调节。对幼穗的进一步转录组分析表明，激素相关基因在差异表达基因中富集，支持 TraesCS6B01G334600 作为候选基因。我们的工作提供了一种快速定位小麦中具有大基因组损伤的遗传位点的策略，并为未来的小麦研究提供了有用的资源。
Optimal spike architecture provides a favorable structure for grain development and yield improvement. However, the number of genes cloned to underlie wheat spike architecture is extremely limited. Here, we obtained a wheat dense spike mutant (wds) induced by 60Co treatment of a common wheat landrace Huangfangzhu that exhibited significantly reduced spike and grain lengths. The shortened spike length was caused by longitudinal reduction in number and length of rachis cells. We adopted a multi-omics approach to identify the genomic locus underlying the wds mutant. We performed Exome Capture Sequencing (ECS) and identified two large deletion segments, named 6BL.1 at 334.8∼424.3 Mb and 6BL.2, 579.4∼717.8 Mb in the wds mutant. RNA-seq analysis confirmed that genes located in these regions lost their RNA expression. We then found that the 6BL.2 locus was overlapping with a known spike length QTL, qSL6B.2. Totally, 499 genes were located within the deleted region and two of them were found to be positively correlated with long spike accessions but not the ones with short spike. One of them, TraesCS6B01G334600, a well-matched homolog of the rice OsBUL1 gene that works in the Brassinosteroids (BR) pathway, was identified to be involved in cell size and number regulation. Further transcriptome analysis of young spikes showed that hormone-related genes were enriched among differentially expressed genes, supporting TraesCS6B01G334600 as a candidate gene. Our work provides a strategy to rapid locate genetic loci with large genomic lesions in wheat and useful resources for future wheat study.
登录
查看更多内容
DOI：
10.1093/bioinformatics/btu638
发表时间：
2015-01-15
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Anders S;Pyl PT;Huber W
通讯作者：
Huber W
影响因子：
14.9
作者：
Ritchie ME;Phipson B;Wu D;Hu Y;Law CW;Shi W;Smyth GK
通讯作者：
Smyth GK
DOI：
10.1007/s00438-017-1401-6
发表时间：
2018-04
期刊：
Molecular genetics and genomics : MGG
影响因子：
--
作者：
Mo Y;Howell T;Vasquez-Gross H;de Haro LA;Dubcovsky J;Pearce S
通讯作者：
Pearce S
影响因子：
16.6
作者：
Cai, Qiang;Yuan, Zheng;Zhang, Dabing
通讯作者：
Zhang, Dabing
影响因子：
27.5
作者：
Pang, Yunlong;Liu, Chunxia;Liu, Shubing
通讯作者：
Liu, Shubing