Location and Candidate Gene Analysis of Rice Clustered Spikelets Gene OsCL6

doi:10.16819/j.1001-7216.2021.0604

Abstract

Abstract:

【Objective】The mapping and candidate gene analysis of rice clustered spikelet genes help clone the functional genes for clustered spikelet caused by shortening of the branch length in the process of panicle development. 【Method】A stable clustered spikelet mutant cl6 was obtained through the space mutation breeding technique with Yuenongsimiao, a good quality rice cultivar in Guangdong Province as material. F₁ and F₂ mapping populations were constructed by crossing cl6 with Yuejinyinzhan. The clustered spikelet gene was mapped and candidate genes were predicted and evaluated by combining with transcriptome sequencing. 【Result】Genetic analysis showed that the trait was controlled by a pair of semi-dominant gene. The gene was mapped to an interval about 416 kb on chromosome 6 by Bulked Segregant Analysis(BSA). Furthermore, OsFBK16 was selected as the best candidate gene through expression profiling analysis, RNA-seq, gene sequence differences analysis and qRT-PCR verification. A 9 bp insertion mutation in the 5'-UTR region of this gene suggests that it may regulate transcription or translation process through secondary structural changes and participating in the differentiation of stems during the development of young panicle of rice. 【Conclusion】It will lay a theoretical foundation for analyzing the shortening mechanism of secondary branches and spikelet peduncle length.

Key words: space mutation, spikelet cluster, gene mapping, transcriptome sequencing, candidate gene

摘要：

【目的】通过对水稻小穗簇生基因的定位与候选基因分析,为进一步克隆幼穗发育过程中缩短枝梗长度造成小穗簇生的功能基因奠定基础。【方法】以航天诱变育种技术处理常规优质稻品种粤农丝苗获得一个稳定遗传的小穗簇生突变体cl6为试验材料,与粤金银占构建F₁、F₂作图群体,对簇生基因进行定位,结合转录组测序对候选基因进行预测与评价。【结果】遗传分析结果表明,突变体cl6的簇生性状由非完全显性单基因控制,混合分组分析法将该基因定位于第6染色体上约416 kb的区间。进一步通过表达谱分析、转录组测序技术、基因序列差异性分析和qRT-PCR验证等筛选出OsFBK16为最佳候选基因,其5′-UTR区域发生9个碱基的插入突变,暗示该基因可能通过二级结构改变调控转录或翻译水平,参与水稻幼穗发育过程中枝梗的分化。【结论】本研究结果为解析水稻二次枝梗和小穗梗缩短机制奠定一定理论基础。

关键词: 航天诱变, 小穗簇生, 基因定位, 转录组测序, 候选基因

Wei LIU, Zhanhua LU, Dongbai LU, Xiaofei WANG, Shiguang WANG, Jia XUE, Xiuying HE. Location and Candidate Gene Analysis of Rice Clustered Spikelets Gene OsCL6[J]. Chinese Journal OF Rice Science, 2021, 35(3): 238-248.

刘维, 陆展华, 卢东柏, 王晓飞, 王石光, 薛皦, 何秀英. 水稻小穗簇生基因OsCL6的定位及候选基因分析[J]. 中国水稻科学, 2021, 35(3): 238-248.

Figures/Tables 6

Fig. 1. Phenotypes of Yuenongsimiao(WT) and cl6.

Fig. 2. Gene mapping of OsCL6.

Table 1 Eleven highly expressed genes in young panicle development.

基因登录号Gene ID	基因注释Gene annotation	备注Remark
LOC_Os06g39260	溶质载体家族35成员B1 Solute carrier family 35 member B1, putative, expressed	OsUGT41^[42]
LOC_Os06g39344	烯醇辅酶A水合酶/异构酶家族基因Enoyl-CoA hydratase/isomerase family protein, putative
LOC_Os06g39370	OsFBK16-含F盒和Kelch结构域的蛋白质OsFBK16-F-box domain and kelch repeat containing protein
LOC_Os06g39480	含SPOC结构域的蛋白质SPOC domain containing protein, putative, expressed
LOC_Os06g39600	蛋白磷酸酶2C蛋白Protein phosphatase 2C, putative, expressed
LOC_Os06g39640	PINHEAD, putative, expressed	OsPNH1^[43]
LOC_Os06g39680	转座子蛋白 Transposon protein, putative, unclassified
LOC_Os06g39750	3-酮酰基-coA合酶3-ketoacyl-CoA synthase, putative, expressed	WSL1^[44]
LOC_Os06g39760	WD结构域,含G-β重复结构域的蛋白质WD domain, G-beta repeat domain containing protein
LOC_Os06g39870	26S蛋白酶调节亚基8 26S protease regulatory subunit 8, putative
LOC_Os06g39880	细胞色素P450 72A1 Cytochrome P450 72A1, putative, expressed	CYP734A4^[45,46]

Fig. 3. Patterns of dominant expression of candidate genes in young panicles. 1, Embryo and radicle after germination; 2, Seed at 72 h after imbibition; 3, Root of seedling with 2 tillers; 4, Shoot of seedling with 2 tillers; 5, Leaf and root at 3-leaf stage; 6, Leaf at stage Ⅲ of young panicle differentiation; 7, Leaf, at 4-5-cm young panicle stage; 8, Flag leaf, 5 days before heading; 9, Flag leaf, 14 days before heading; 10, Sheath, at stage Ⅲ of panicle differentiation; 11, Sheath, at 4-5-cm young panicle stage; 12, Stem, 5 days before heading; 13, Hull, one day before flowering; 14, Stem, heading stage; 15, Young panicle at stage Ⅲ of panicle differentiation; 16, Young panicle stage Ⅳ of young panicle differentiation; 17, Young panicle at stage V of panicle differentiation; 18, Panicle at 4-5-cm young panicle stage; 19, Panicle, heading stage; 20, Stamen, one day before flowering; 21, Spikelet, 3 days after pollination; 22, Endosperm, 7 days after pollination; 23, Endosperm, 14 days after pollination; 24, Endosperm, 21 days after pollination.

Fig. 4. Candidate gene OsFKB16 validation. A, qRT-PCR analysis expression difference of candidate gene OsFKB16; B, Results of OsFKB16 promoter sequencing; C, OsFKB16 promoter co-separation validation. WT, Yuenongsimiao.

Fig. 5. Partial analysis results of transcriptome sequencing of the wild type and its mutant. A, Cluster map of differentially expressed genes, log2(FPKM+1); B, Enrichment scatter map of differentially expressed gene KEGG pathway; C, Expression difference of some genes related to GA anabolism and signaling pathway.

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