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

doi:10.11983/CBB22259

Abstract

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

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[J]. Chinese Bulletin of Botany, 2023, 58(3): 394-403.

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URL: https://www.chinbullbotany.com/EN/10.11983/CBB22259

https://www.chinbullbotany.com/EN/Y2023/V58/I3/394

Figures/Tables 8

References 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