Table_10_A Multi-Omics Approach for Rapid Identification of Large Genomic Lesions at the Wheat Dense Spike (wds) Locus.xlsx

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.

最优穗型可为籽粒发育与产量提升提供有利的结构基础。然而，目前已克隆的调控小麦穗型的基因数量极为有限。本研究通过对普通小麦地方品种黄方柱进行钴-60（60Co）诱变处理，获得了一份小麦密穗突变体（wds），该突变体的穗长与粒长均显著缩短。穗长缩短的成因在于穗轴细胞的纵向数目与长度均发生了缩减。为鉴定wds突变体的致变基因组位点，本研究采用多组学策略开展分析。通过外显子捕获测序（Exome Capture Sequencing, ECS），我们在wds突变体中鉴定到两个大片段缺失区域：分别为6BL染色体上的6BL.1（334.8~424.3 Mb）与6BL.2（579.4~717.8 Mb）。RNA测序（RNA-seq）分析证实，上述两个区域内的基因均丧失了转录表达活性。随后我们发现，6BL.2位点与已报道的穗长数量性状位点（quantitative trait locus, QTL）qSL6B.2存在重叠。该缺失区域共包含499个基因，其中两个基因的表达量与长穗种质材料呈正相关，而与短穗种质材料无显著相关性。其中一个基因为TraesCS6B01G334600，它是水稻油菜素甾醇（Brassinosteroids, BR）通路基因OsBUL1的高度同源基因，参与调控细胞大小与数目。对幼穗的进一步转录组分析显示，差异表达基因中显著富集了激素相关基因，进一步佐证TraesCS6B01G334600为该突变体的候选功能基因。本研究建立了一种快速定位小麦大片段基因组缺失相关遗传位点的研究策略，同时为后续小麦相关研究提供了宝贵的实验资源。