水稻叶绿素含量QTL定位与候选基因表达分析

doi:10.11983/CBB22259

植物学报 ›› 2023, Vol. 58 ›› Issue (3): 394-403.DOI: 10.11983/CBB22259

水稻叶绿素含量QTL定位与候选基因表达分析

金佳怡¹, 罗怿婷¹, 杨惠敏¹, 芦涛¹, 叶涵斐¹, 谢继毅¹, 王珂欣¹, 陈芊羽¹, 方媛¹, 王跃星²(), 饶玉春¹()

¹浙江师范大学生命科学学院, 金华 321004
²中国水稻研究所, 水稻生物学国家重点实验室, 杭州 310006

收稿日期:2022-11-08 接受日期:2023-02-09 出版日期:2023-05-01 发布日期:2023-05-17
通讯作者: *E-mail: wangyuexing@caas.cn; ryc@zjnu.cn
基金资助:
浙江省自然科学基金重点项目(LZ23C130003);国家级大学生创新创业训练计划(202210345029);浙江省大学生科技创新活动计划暨新苗人才计划(2022R404A005)

QTL Mapping and Expression Analysis on Candidate Genes Related to Chlorophyll Content in Rice

Jiayi Jin¹, Yiting Luo¹, Huimin Yang¹, Tao Lu¹, Hanfei Ye¹, Jiyi Xie¹, Kexin Wang¹, Qianyu Chen¹, Yuan Fang¹, Yuexing Wang²(), Yuchun Rao¹()

¹College of Life Sciences, Zhejiang Normal University, Jinhua 321004, China
²State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, China

Received:2022-11-08 Accepted:2023-02-09 Online:2023-05-01 Published:2023-05-17
Contact: *E-mail: wangyuexing@caas.cn; ryc@zjnu.cn

摘要/Abstract

摘要： 水稻(Oryza sativa)是我国主要粮食作物之一。提高水稻叶片叶绿素含量, 进而提高其光合作用效率是实现高产稳产的重要途径之一。该研究以父系籼稻品种华占(HZ)、母系粳稻品种热研2号(Nekken2)及其构建的120个重组自交系(RILs)为实验材料, 在分蘖期和成熟期分别对亲本及其后代剑叶的叶绿素含量(SPAD值)进行测定, 同时基于已构建的高密度遗传连锁图谱进行QTL定位。结果共挖掘到20个与叶绿素含量相关的QTLs (分蘖期7个, 成熟期13个), LOD值最高达4.77。利用qRT-PCR方法检测QTL区间内与叶绿素含量相关的候选基因的表达, 发现LOC_Os06g11780、LOC_Os06g12360、LOC_Os06g39716、LOC_Os08g42610、LOC_Os02g18500、LOC_Os03g21240、LOC_Os03g21400、LOC_Os03g21780、LOC_Os03g30950及LOC_Os03g40550基因的表达量在双亲间差异显著。结合基因表达量及亲本叶绿素表型数据, 推测LOC_Os06g11780、LOC_Os06g12360和LOC_Os08g42610的高表达极大地提高了水稻叶绿素含量, 进而有效提高植物光合产能。研究结果为筛选和培育高光能利用效率的水稻新品种提供了有利的遗传资源, 并为揭示水稻叶绿素含量的动态变化规律及分子调控机制奠定了重要基础。

关键词: 候选基因, 叶绿素含量, 遗传图谱, 水稻, 光合作用, QTL定位

Abstract: Rice (Oryza sativa) is one of a major food crops in China. Increasing chlorophyll content in rice leaves and thus promoting its photosynthetic efficiency is one of the most important ways to obtain high and stable yields. In this study, 120 recombinant inbred lines (RILs) were constructed from the paternal indica rice HZ and the maternal japonica rice Nekken2 and they were used as experimental materials. We measured the flag leaf chlorophyll content (SPAD) of the parents and their progeny at the tillering and maturing stages. Meanwhile, the quantitative trait locus (QTL) mapping was carried out based on the high-density genetic map. Twenty QTLs related to chlorophyll content (7 at tillering stage and 13 at maturity stage) were identified, with the highest LOD score of 4.77. The expression of candidate genes associated with chlorophyll content within these QTL regions was analyzed by qRT-PCR, which showed that LOC_Os06g11780, LOC_Os06g12360, LOC_Os06g39716, LOC_Os08g42610, LOC_Os02g18500, LOC_Os03g21240, LOC_Os03g21400, LOC_Os03g21780, LOC_Os03g30950, and LOC_Os03g40550 were significantly different between the parents. Combining the gene expression and parental chlorophyll phenotype data, we think that the high expression of LOC_ Os06g11780, LOC_Os06g12360 and LOC_Os08g42610 might greatly enhance the chlorophyll content of rice, which in turn effectively promoted the photosynthetic productivity of the plants. The results provide favorable genetic resources for screening and breeding new rice varieties for efficient light energy utilization, and lay an important foundation for revealing the dynamic change pattern and the molecular regulation mechanism of chlorophyll content in rice.

Key words: candidate genes, chlorophyll content, genetic map, Oryza sativa (rice), photosynthesis, QTL mapping

金佳怡, 罗怿婷, 杨惠敏, 芦涛, 叶涵斐, 谢继毅, 王珂欣, 陈芊羽, 方媛, 王跃星, 饶玉春. 水稻叶绿素含量QTL定位与候选基因表达分析. 植物学报, 2023, 58(3): 394-403.

Jiayi Jin, Yiting Luo, Huimin Yang, Tao Lu, Hanfei Ye, Jiyi Xie, Kexin Wang, Qianyu Chen, Yuan Fang, Yuexing Wang, Yuchun Rao. QTL Mapping and Expression Analysis on Candidate Genes Related to Chlorophyll Content in Rice. Chinese Bulletin of Botany, 2023, 58(3): 394-403.

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图/表 8

参考文献 34

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Primer name	Sequence (5′-3′)
LOC_Os06g11780-F-qrt	TGTTGGTCCCTGAAAACTCC
LOC_Os06g11780-R-qrt	TCAAGCAAATTCACCCATGA
LOC_Os06g12360-F-qrt	ATGCAAAAAGGAGAGGCTGA
LOC_Os06g12360-R-qrt	ATGCCGATCAGGAATCTCAC
LOC_Os06g39650-F-qrt	GTGCTCTTCAACCAGTGCAA
LOC_Os06g39650-R-qrt	AGATTGGCACAGCATGTCAG
LOC_Os06g39716-F-qrt	CAACCTTTTCGTAGGCATCC
LOC_Os06g39716-R-qrt	TTGAAATTGACTGGGCTTGA
LOC_Os08g42610-F-qrt	GCTCGCACACTGAAAACAAA
LOC_Os08g42610-R-qrt	ATGGGATAGGCCCCAAATAG
LOC_Os02g18500-F-qrt	AGGAGGAGGTGTTGGGAACT
LOC_Os02g18500-R-qrt	ATGCAGTTGTTGATGGCGTA
LOC_Os03g21240-F-qrt	TATGCCTTTGCACCAGAGTG
LOC_Os03g21240-R-qrt	CAGCATTCGACGACTGAGAA
LOC_Os03g21400-F-qrt	AGGAAAGCGGAGAAGAAAGG
LOC_Os03g21400-R-qrt	TTAGACACCAGGCAGCTGTG
LOC_Os03g21780-F-qrt	CTCCCTTCCACTCCTCCTTC
LOC_Os03g21780-R-qrt	CTTCTCCTCCTCGACACCAG
LOC_Os03g30950-F-qrt	TCTTCTTCTCCATGGCCTGT
LOC_Os03g30950-R-qrt	AGCAGGGAAGGAAGTCGTG
LOC_Os03g40550-F-qrt	CTTTGCTCCCTGCCTTGTAG
LOC_Os03g40550-R-qrt	CACGTCTCGGAGCTCTTTTC

Primer name	Sequence (5′-3′)
LOC_Os06g11780-F-qrt	TGTTGGTCCCTGAAAACTCC
LOC_Os06g11780-R-qrt	TCAAGCAAATTCACCCATGA
LOC_Os06g12360-F-qrt	ATGCAAAAAGGAGAGGCTGA
LOC_Os06g12360-R-qrt	ATGCCGATCAGGAATCTCAC
LOC_Os06g39650-F-qrt	GTGCTCTTCAACCAGTGCAA
LOC_Os06g39650-R-qrt	AGATTGGCACAGCATGTCAG
LOC_Os06g39716-F-qrt	CAACCTTTTCGTAGGCATCC
LOC_Os06g39716-R-qrt	TTGAAATTGACTGGGCTTGA
LOC_Os08g42610-F-qrt	GCTCGCACACTGAAAACAAA
LOC_Os08g42610-R-qrt	ATGGGATAGGCCCCAAATAG
LOC_Os02g18500-F-qrt	AGGAGGAGGTGTTGGGAACT
LOC_Os02g18500-R-qrt	ATGCAGTTGTTGATGGCGTA
LOC_Os03g21240-F-qrt	TATGCCTTTGCACCAGAGTG
LOC_Os03g21240-R-qrt	CAGCATTCGACGACTGAGAA
LOC_Os03g21400-F-qrt	AGGAAAGCGGAGAAGAAAGG
LOC_Os03g21400-R-qrt	TTAGACACCAGGCAGCTGTG
LOC_Os03g21780-F-qrt	CTCCCTTCCACTCCTCCTTC
LOC_Os03g21780-R-qrt	CTTCTCCTCCTCGACACCAG
LOC_Os03g30950-F-qrt	TCTTCTTCTCCATGGCCTGT
LOC_Os03g30950-R-qrt	AGCAGGGAAGGAAGTCGTG
LOC_Os03g40550-F-qrt	CTTTGCTCCCTGCCTTGTAG
LOC_Os03g40550-R-qrt	CACGTCTCGGAGCTCTTTTC

Trait	QTL	Chromosome	Physical distance (bp)	Position of support (cM)	Likelihood of odd (LOD)
Chlorophyll content at tillering stage	qFLCC6.1	6	6015262-6720585	25.79-28.81	3.13
	qFLCC6.2	6	22337450-23745958	95.75-101.79	2.92
	qFLCC6.3	6	24051716-24198880	103.10-103.73	2.13
	qFLCC6.4	6	25991018-26126806	111.42-111.99	2.12
	qFLCC8.1	8	26687999-27132649	114.40-116.31	2.50
	qFLCC8.2	8	27513012-27730624	117.94-118.87	2.28
	qFLCC9.1	9	20982305-21030827	89.95-90.15	2.09
Chlorophyll content at maturing stage	qFLCC1.1	1	2407127-2649258	10.32-11.36	2.63
	qFLCC2.1	2	10729809-10871055	45.99-46.60	2.01
	qFLCC3.1	3	8989609-9140871	38.54-39.18	2.00
	qFLCC3.2	3	11602077-12505077	49.73-53.61	4.77
	qFLCC3.3	3	17425033-18170152	74.70-77.90	2.38
	qFLCC3.4	3	19142858-20859360	82.06-89.42	2.29
	qFLCC3.5	3	22349012-22880743	95.80-98.08	2.59
	qFLCC3.6	3	23094070-24507431	98.99-105.06	3.25
	qFLCC4.1	4	867957-1087636	3.72-4.66	2.40
	qFLCC4.2	4	2647701-3012559	11.35-12.91	2.30
	qFLCC4.3	4	6230638-6599549	26.71-28.29	2.46
	qFLCC7.1	7	9758981-9899583	41.83-42.68	2.45
	qFLCC11.1	11	3100542-3229790	13.29-13.85	2.27

Trait	QTL	Chromosome	Physical distance (bp)	Position of support (cM)	Likelihood of odd (LOD)
Chlorophyll content at tillering stage	qFLCC6.1	6	6015262-6720585	25.79-28.81	3.13
	qFLCC6.2	6	22337450-23745958	95.75-101.79	2.92
	qFLCC6.3	6	24051716-24198880	103.10-103.73	2.13
	qFLCC6.4	6	25991018-26126806	111.42-111.99	2.12
	qFLCC8.1	8	26687999-27132649	114.40-116.31	2.50
	qFLCC8.2	8	27513012-27730624	117.94-118.87	2.28
	qFLCC9.1	9	20982305-21030827	89.95-90.15	2.09
Chlorophyll content at maturing stage	qFLCC1.1	1	2407127-2649258	10.32-11.36	2.63
	qFLCC2.1	2	10729809-10871055	45.99-46.60	2.01
	qFLCC3.1	3	8989609-9140871	38.54-39.18	2.00
	qFLCC3.2	3	11602077-12505077	49.73-53.61	4.77
	qFLCC3.3	3	17425033-18170152	74.70-77.90	2.38
	qFLCC3.4	3	19142858-20859360	82.06-89.42	2.29
	qFLCC3.5	3	22349012-22880743	95.80-98.08	2.59
	qFLCC3.6	3	23094070-24507431	98.99-105.06	3.25
	qFLCC4.1	4	867957-1087636	3.72-4.66	2.40
	qFLCC4.2	4	2647701-3012559	11.35-12.91	2.30
	qFLCC4.3	4	6230638-6599549	26.71-28.29	2.46
	qFLCC7.1	7	9758981-9899583	41.83-42.68	2.45
	qFLCC11.1	11	3100542-3229790	13.29-13.85	2.27

Chromosome	QTL locus	Gene ID	Functional annotation	Reference
6	qFLCC6.1	LOC_Os06g11780	MYB family transcription factor, putative, expressed
6	qFLCC6.1	LOC_Os06g12360	Pentatricopeptide, putative, expressed
6	qFLCC6.2	LOC_Os06g39650	Pentatricopeptide repeat protein	Jiang et al., 2014
6	qFLCC6.2	LOC_Os06g39716	Chloroplast 30S ribosomal protein S18, putative, expressed
8	qFLCC8.1	LOC_Os08g42610	Pentatricopeptide, putative, expressed

水稻叶绿素含量QTL定位与候选基因表达分析

QTL Mapping and Expression Analysis on Candidate Genes Related to Chlorophyll Content in Rice

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Chromosome	QTL locus	Gene ID	Functional annotation	Reference
2	qFLCC2.1	LOC_Os02g18500	Chlorophyllase-2, chloroplast precursor, putative
3	qFLCC3.2	LOC_Os03g21240	Transcription factor with a MYB domain; PHOSPHATE RESPONSE 1	Guo et al., 2015
3	qFLCC3.2	LOC_Os03g21400	Cytochrome P450 gene; gibberellin 13-oxidase
3	qFLCC3.2	LOC_Os03g21780	Pentatricopeptide repeat domain containing protein, putative, expressed
3	qFLCC3.3	LOC_Os03g30950	Acyl-desaturase, chloroplast precursor, putative, expressed
3	qFLCC3.5	LOC_Os03g40550	pfkB-type carbohydrate kinase family protein

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