QTL Mapping of Candidate Genes for Heading Date in Rice

doi:10.11983/CBB22114

Abstract

Abstract: The heading date is an important trait that determines the yield and quality of rice, and plays an important role in the process of rice breeding, seed production, introduction and domestication. In this study, F₁ was obtained by a cross between Nekken2 (Oryza sativa subsp. japonica cv. ‘Nekken2’) and Huazhan (O. sativa subsp. indica cv. ‘HZ’), and 120 recombination inbred lines (RILs) were obtained through successive multi-generational selfing. The population of RILs was used as experimental material. Under the condition of conventional water and fertilizer management, the time of heading stage of 120 lines was analyzed. Using the high-density genetic map constructed by this population, the QTLs for the heading date was mapped and analyzed. A total of 11 QTLs were detected on chromosomes 1, 3, 4, 5, 6, 8, and 12, respectively, and one of the LOD values was as high as 5.75. By analyzing the candidate genes in the QTLs interval, the related genes that may affect the heading date were screened out, and real-time quantitative PCR was used for gene expression analysis. The expression levels of six genes, LOC_Os03g03070, LOC_Os03g50310, LOC_Os03g55389, LOC_Os04g55510, LOC_Os08g07740, and LOC_Os08g01670 significantly different between parents, and the expression of LOC_Os03g50310 in Nekken2 was 3.6 times higher than that in HZ. In addition, the sequencing analysis showed that there were 4 differences in the 5'UTR, CDS region and 3'UTR of the candidate gene LOC_Os03g50310 between the parents, of which the single nucleotide polymorphisms (SNP) difference in the CDS region caused a single amino acid change. This study provides new clues for further cloning of heading date-related genes and cultivar selection by mining the QTL loci related to heading date in rice.

Key words: rice, heading date, QTL mapping, candidate genes, single nucleotide polymorphisms (SNP)

Wei Heping, Lu Tao, Jia Qiwei, Deng Fei, Zhu Hao, Qi Zehua, Wang Yuxi, Ye Hanfei, Yin Wenjing, Fang Yuan, Mu Dan, Rao Yuchun. QTL Mapping of Candidate Genes for Heading Date in Rice[J]. Chinese Bulletin of Botany, 2022, 57(5): 588-595.

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URL: https://www.chinbullbotany.com/EN/10.11983/CBB22114

https://www.chinbullbotany.com/EN/Y2022/V57/I5/588

Figures/Tables 8

References 32

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Primer name	Forward primer (5′-3′)	Reverse primer (5′-3′)
OsActin	TGGCATCTCAGCACATTCC	TGCACAATGGATGGGTCAGA
LOC_Os03g50310	AGCAGCAGATCGAGCAGAAG	CTTCTCGTCGTCCAAGAAGC
LOC_Os03g55389	TGTCAAGCCCCACAATGTTA	AAGGCTCCACATGTCCAAAG
LOC_Os03g57940	AGCACCGAAGCAGTAAAGGA	AAGCAACCATATGGGCAGAC
LOC_Os03g03070	AAAAGCTGACGCTGATGGTT	TCCTTCCCCTGATGCTAATG
LOC_Os04g55510	GTGGCCTAAGGATTGGTGAA	TGAGAGCAGCCACCATGTAG
LOC_Os08g07740	GGAAGAGCTATGGGCACTTG	CGACTCCTTGGAGATCTTGG
LOC_Os08g01420	GACAGGTCTAGCGAGCAACC	GGCACAGTTCGTTTCGGTAT
LOC_Os08g01670	GATGGGGCAGCAGGACTAC	GATGCAGGAGAGGAGGTGAG

Primer name	Forward primer (5′-3′)	Reverse primer (5′-3′)
OsActin	TGGCATCTCAGCACATTCC	TGCACAATGGATGGGTCAGA
LOC_Os03g50310	AGCAGCAGATCGAGCAGAAG	CTTCTCGTCGTCCAAGAAGC
LOC_Os03g55389	TGTCAAGCCCCACAATGTTA	AAGGCTCCACATGTCCAAAG
LOC_Os03g57940	AGCACCGAAGCAGTAAAGGA	AAGCAACCATATGGGCAGAC
LOC_Os03g03070	AAAAGCTGACGCTGATGGTT	TCCTTCCCCTGATGCTAATG
LOC_Os04g55510	GTGGCCTAAGGATTGGTGAA	TGAGAGCAGCCACCATGTAG
LOC_Os08g07740	GGAAGAGCTATGGGCACTTG	CGACTCCTTGGAGATCTTGG
LOC_Os08g01420	GACAGGTCTAGCGAGCAACC	GGCACAGTTCGTTTCGGTAT
LOC_Os08g01670	GATGGGGCAGCAGGACTAC	GATGCAGGAGAGGAGGTGAG

QTL	Chromosome	Physical distance (bp)	Position of support (cM)	Likelihood of odd (LOD)
qhd-1	1	25257953-25481977	108.27-109.23	3.75
qhd-3	3	13767411-14882947	54.53-63.79	3.82
qhd-4	3	15628988-15779451	66.72-67.64	3.09
qhd-5	3	17197291-17357469	73.72-74.40	3.33
qhd-6	3	28536151-33494350	122.32-143.58	4.87
qhd-7	4	2572479-3906500	11.02-16.74	3.17
qhd-8	4	31066905-34944379	133.17-149.79	5.75
qhd-9	5	26262798-26850392	112.58-115.10	3.14
qhd-10	6	4227455-4659759	18.12-19.97	3.97
qhd-11	8	3480879-4936569	18.12-19.97	5.06
qhd-12	12	26219257-27272729	112.39-116.97	3.98

QTL	Chromosome	Physical distance (bp)	Position of support (cM)	Likelihood of odd (LOD)
qhd-1	1	25257953-25481977	108.27-109.23	3.75
qhd-3	3	13767411-14882947	54.53-63.79	3.82
qhd-4	3	15628988-15779451	66.72-67.64	3.09
qhd-5	3	17197291-17357469	73.72-74.40	3.33
qhd-6	3	28536151-33494350	122.32-143.58	4.87
qhd-7	4	2572479-3906500	11.02-16.74	3.17
qhd-8	4	31066905-34944379	133.17-149.79	5.75
qhd-9	5	26262798-26850392	112.58-115.10	3.14
qhd-10	6	4227455-4659759	18.12-19.97	3.97
qhd-11	8	3480879-4936569	18.12-19.97	5.06
qhd-12	12	26219257-27272729	112.39-116.97	3.98

Chromosome	Gene name	Function
3	LOC_Os03g50310	Regulation of rice blast resistance through salicylic acid and ethylene signaling pathways, mediating heading stage
3	LOC_Os03g55389	Delaying flowering time by inhibiting the expression of FT-like genes
3	LOC_Os03g57940	Negative regulation of gibberellin signaling by phosphorylating the DELLA protein SLR1
3	LOC_Os03g03070	Involved in the regulation of adventitious root formation in rice by regulating auxin transport
4	LOC_Os04g55510	Mediates ubiquitination to degrade Hd1 through a 26S proteasome-mediated pathway
8	LOC_Os08g07740	Controlling the yield, plant height and heading date of rice
8	LOC_Os08g01420	Induction of rice heading by inhibiting Ghd7
8	LOC_Os08g01670	Regulation of pectin methyl esterification levels