Genetic Locus Mining and Candidate Gene Analysis of Antioxidant Traits in Rice

doi:10.11983/CBB24065

Abstract

Abstract: Rice (Oryza sativa) is one of the most important food crops in the world. Improving its antioxidant ability and stress resistance is an important way to ensure high and stable yields. In this study, we used the indica rice HZ and the japonica rice Nekken2 as parents and the 120 recombinant inbred line population constructed from them as experimental materials to determine the hydroxyl radical scavenging rate, total phenol content, flavonoid content, and anthocyanin content in sword leaves, glume shells and grains of parents and their progeny at three stages: the tillering stage, the grain filling stage and the maturity stage. Additionally, a total of 62 QTLs related to rice antioxidant damage were identified on the basis of the constructed high-density genetic map for QTL mapping, with an LOD value of up to 4.36. A quantitative analysis of candidate genes related to antioxidant damage ability in these regions revealed that thirteen candidate genes, including LOC_Os06g01850, LOC_Os12g07820, LOC_Os12g07830, and LOC_Os03g60509 were significantly differentially expressed between the two parents at different growth stages. A multitude of QTLs associated with antioxidant damage resistance in rice were identified, providing a foundation for further mapping and cloning of related genes and the development of new rice varieties with increased resistance and nutritional value.

Key words: rice, antioxidant ability, genetic map, QTL mapping

Lian Jinjin, Tang Luyao, Zhang Yinuo, Zheng Jiaxing, Zhu Chaoyu, Ye Yuhan, Wang Yuexing, Shang Wennan, Fu Zhenghao, Xu Xinxuan, Wu Richeng, Lu Mei, Wang Changchun, Rao Yuchun. Genetic Locus Mining and Candidate Gene Analysis of Antioxidant Traits in Rice[J]. Chinese Bulletin of Botany, 2024, 59(5): 738-751.

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URL: https://www.chinbullbotany.com/EN/10.11983/CBB24065

https://www.chinbullbotany.com/EN/Y2024/V59/I5/738

Figures/Tables 7

References 40

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Physiological traits	Gene name	Forward primer (5'-3')	Reverse primer (5′-3′)
	OsActin	TGGCATCTCAGCACATTCC	TGCACAATGGATGGGTCAGA
Hydroxyl radical scavenging rate	LOC_Os06g01850	ACATGGTCTTCAGCACCGAG	CTTTGCCTACTGGTCCGGTT
	LOC_Os06g48000	TTCAACCTCGACCAGCTCAC	GGAGGTTCTGGTAGAAGGCG
	LOC_Os06g48020	GTTGTGACGCGTCGATCATG	CCGCTCTGGTAGACGGATTC
Total phenolic content	LOC_Os04g45210	AGCTGGTCAAGACGTTCCAG	GAAGTAGACCATCTCGCCGG
	LOC_Os12g07820	GTTCGGTTAGGGTGGCATGA	CATTGTTCAGGGGCAGCAAC
	LOC_Os12g07830	CCTCTCCCCTCCCTTCTCTC	GTCATGCCACCCTAACCGAA
Flavonoid content	LOC_Os05g12190	GACCTCAAGCTGGCATCACT	CCCAAACAGTCCATGACCGA
	LOC_Os05g12210	ATGCCCTCCCTTGAAACTCG	TCACGGTTGTTCTCGGTGAG
	LOC_Os05g12240	GGCCTCAACCCTTCTGTCTC	AGGACCATCTCAAACAGCGG
	LOC_Os05g45120	CTCATGGTGGAGGACATGGG	CAACAGGAACTCGGCAAACG
	LOC_Os12g16260	TGATACGCAACTTCTACACTGCT	AGATGGCTCAGGTTGGTTGG
Anthocyanin content	LOC_Os03g60509	TGTGTTCCGTGTCAGTGGAG	CAGGATCATCGTCACCCTCG
Anthocyanin content	LOC_Os03g62480	CCATCCCCGCCTACTTCTTC	ATCGAAGCTGTTCACGAGCA

Physiological traits	Gene name	Forward primer (5'-3')	Reverse primer (5′-3′)
	OsActin	TGGCATCTCAGCACATTCC	TGCACAATGGATGGGTCAGA
Hydroxyl radical scavenging rate	LOC_Os06g01850	ACATGGTCTTCAGCACCGAG	CTTTGCCTACTGGTCCGGTT
	LOC_Os06g48000	TTCAACCTCGACCAGCTCAC	GGAGGTTCTGGTAGAAGGCG
	LOC_Os06g48020	GTTGTGACGCGTCGATCATG	CCGCTCTGGTAGACGGATTC
Total phenolic content	LOC_Os04g45210	AGCTGGTCAAGACGTTCCAG	GAAGTAGACCATCTCGCCGG
	LOC_Os12g07820	GTTCGGTTAGGGTGGCATGA	CATTGTTCAGGGGCAGCAAC
	LOC_Os12g07830	CCTCTCCCCTCCCTTCTCTC	GTCATGCCACCCTAACCGAA
Flavonoid content	LOC_Os05g12190	GACCTCAAGCTGGCATCACT	CCCAAACAGTCCATGACCGA
	LOC_Os05g12210	ATGCCCTCCCTTGAAACTCG	TCACGGTTGTTCTCGGTGAG
	LOC_Os05g12240	GGCCTCAACCCTTCTGTCTC	AGGACCATCTCAAACAGCGG
	LOC_Os05g45120	CTCATGGTGGAGGACATGGG	CAACAGGAACTCGGCAAACG
	LOC_Os12g16260	TGATACGCAACTTCTACACTGCT	AGATGGCTCAGGTTGGTTGG
Anthocyanin content	LOC_Os03g60509	TGTGTTCCGTGTCAGTGGAG	CAGGATCATCGTCACCCTCG
Anthocyanin content	LOC_Os03g62480	CCATCCCCGCCTACTTCTTC	ATCGAAGCTGTTCACGAGCA

Physiological traits	QTL	Chromosome	Physical distance (bp)	Position of support (cM)	Limit of detection
Hydroxyl radical scavenging rate	qHRSR1.1	1	2556386-2834929	10.96-12.15	2.14
	qHRSR2.1	2	3467582-4955784	14.87-21.24	4.36
	qHRSR2.2	2	5098574-6084984	21.86-26.08	3.37
	qHRSR2.3	2	27009300-27239796	115.78-116.77	2.75
	qHRSR2.4	2	28427871-28664694	121.86-122.88	2.21
	qHRSR3.1	3	12723031-12925845	54.54-55.41	2.22
	qHRSR3.2	3	29949770-30321190	128.39-129.98	2.31
	qHRSR4.1	4	23316226-23991142	99.95-102.84	3.35
	qHRSR4.2	4	23680403-239113 17	101.51-102.50	2.00
	qHRSR4.3	4	24725621-25022230	105.99-107.26	2.29
	qHRSR5.1	5	26927610-27082669	115.43-116.10	2.30
	qHRSR6.1	6	33441-781344	0.14-3.35	2.50
	qHRSR6.2	6	26490081-27333693	113.56-117.17	2.24
	qHRSR6.3	6	28674720-29130039	123.31-124.87	2.62
	qHRSR8.1	8	1092742-2649021	4.68-11.36	2.97
	qHRSR8.2	8	11086291-11153903	47.52-47.81	2.22
	qHRSR8.3	8	14983464-15034055	64.23-64.45	2.36
	qHRSR8.4	8	21388530-22202508	91.69-95.18	2.44
Total phenolic content	qTPC1.1	1	7667525-8235815	32.87-35.30	2.23
	qTPC3.1	3	15484683-16021103	66.38-68.68	3.07
	qTPC3.2	3	16899768-17721978	72.45-75.97	3.58
	qTPC3.3	3	25032115-25648379	107.31-109.95	2.50
	qTPC4.1	4	26377931-27479589	113.07-117.80	2.44
	qTPC12.1	12	2689107-3043767	11.53-13.05	2.52
	qTPC12.2	12	3933801-4462301	16.86-19.13	2.08
	qTPC12.3	12	11398960-11895586	48.86-50.99	2.00
	qTPC12.4	12	13100229-14071703	56.16-60.32	2.00
	qTPC12.5	12	14215593-15112427	60.94-64.78	2.11
	qTPC12.6	12	16682032-1680484	71.51-72.19	2.47
Flavonoid content	qFC1.1	1	26148806-27178896	112.09-116.50	2.42
	qFC1.2	1	27178896-27631674	116.50-118.45	2.03
	qFC1.3	1	37113012-37638053	159.09-161.34	2.12
	qFC1.4	1	38157798-38395992	163.57-164.59	2.35
	qFC2.1	2	21915215-22231364	93.94-95.30	2.30
	qFC4.1	4	17472715-19028032	74.90-81.57	3.67
	qFC4.2	4	19642144-19986484	84.20-85.68	2.70
	qFC4.3	4	22019563-23235126	94.39-99.60	3.74
	qFC4.4	4	26377931-26619819	113.07-114.11	2.87
	qFC5.1	5	5206830-6439595	22.32-27.60	4.03
	qFC5.2	5	6673100-7059585	28.61-30.26	4.12
	qFC5.3	5	12422042-12794190	53.25-54.85	2.04
	qFC5.4	5	26189817-26927610	112.27-115.43	2.59
	qFC6.1	6	5187517-6015262	22.24-25.79	3.28
	qFC6.2	6	6069227-6560451	26.02-28.12	2.68
	qFC6.3	6	21068005-21507916	90.31-92.20	2.16
	qFC6.4	6	27961504-28384769	119.86-121.68	2.51
	qFC9.1	9	13119644-13620974	56.24-58.39	2.07
	qFC10.1	10	21806620-22080253	93.48-94.65	2.02
	qFC12.1	12	2351235-2689107	10.08-11.53	2.56
	qFC12.2	12	4462301-6224960	19.13-26.68	2.95
	qFC12.3	12	7508660-9990803	32.19-42.83	3.74
	qFC12.4	12	11398960-14215593	48.86-60.94	3.04
	qFC12.5	12	17056555-17574928	73.12-75.34	2.19
	qFC12.6	12	23839134-24088353	102.19-103.26	2.39
Anthocyanin content	qAC2.1	2	35599368-35902152	152.60-153.90	2.42
	qAC3.1	3	31965505-32493480	137.03-138.32	2.25
	qAC3.2	3	33386000-34509821	143.12-147.93	3.23
	qAC3.3	3	35314343-35646346	151.38-152.81	2.30
	qAC5.1	5	22147125-22524107	94.94-96.55	2.88
	qAC11.1	11	9832804-10200412	42.15-43.73	2.28
	qAC12.1	12	927518-2689107	3.98-11.53	2.31
	qAC12.2	12	23013674-23469132	98.65-100.61	2.50

Physiological traits	QTL	Chromosome	Physical distance (bp)	Position of support (cM)	Limit of detection
Hydroxyl radical scavenging rate	qHRSR1.1	1	2556386-2834929	10.96-12.15	2.14
	qHRSR2.1	2	3467582-4955784	14.87-21.24	4.36
	qHRSR2.2	2	5098574-6084984	21.86-26.08	3.37
	qHRSR2.3	2	27009300-27239796	115.78-116.77	2.75
	qHRSR2.4	2	28427871-28664694	121.86-122.88	2.21
	qHRSR3.1	3	12723031-12925845	54.54-55.41	2.22
	qHRSR3.2	3	29949770-30321190	128.39-129.98	2.31
	qHRSR4.1	4	23316226-23991142	99.95-102.84	3.35
	qHRSR4.2	4	23680403-239113 17	101.51-102.50	2.00
	qHRSR4.3	4	24725621-25022230	105.99-107.26	2.29
	qHRSR5.1	5	26927610-27082669	115.43-116.10	2.30
	qHRSR6.1	6	33441-781344	0.14-3.35	2.50
	qHRSR6.2	6	26490081-27333693	113.56-117.17	2.24
	qHRSR6.3	6	28674720-29130039	123.31-124.87	2.62
	qHRSR8.1	8	1092742-2649021	4.68-11.36	2.97
	qHRSR8.2	8	11086291-11153903	47.52-47.81	2.22
	qHRSR8.3	8	14983464-15034055	64.23-64.45	2.36
	qHRSR8.4	8	21388530-22202508	91.69-95.18	2.44
Total phenolic content	qTPC1.1	1	7667525-8235815	32.87-35.30	2.23
	qTPC3.1	3	15484683-16021103	66.38-68.68	3.07
	qTPC3.2	3	16899768-17721978	72.45-75.97	3.58
	qTPC3.3	3	25032115-25648379	107.31-109.95	2.50
	qTPC4.1	4	26377931-27479589	113.07-117.80	2.44
	qTPC12.1	12	2689107-3043767	11.53-13.05	2.52
	qTPC12.2	12	3933801-4462301	16.86-19.13	2.08
	qTPC12.3	12	11398960-11895586	48.86-50.99	2.00
	qTPC12.4	12	13100229-14071703	56.16-60.32	2.00
	qTPC12.5	12	14215593-15112427	60.94-64.78	2.11
	qTPC12.6	12	16682032-1680484	71.51-72.19	2.47
Flavonoid content	qFC1.1	1	26148806-27178896	112.09-116.50	2.42
	qFC1.2	1	27178896-27631674	116.50-118.45	2.03
	qFC1.3	1	37113012-37638053	159.09-161.34	2.12
	qFC1.4	1	38157798-38395992	163.57-164.59	2.35
	qFC2.1	2	21915215-22231364	93.94-95.30	2.30
	qFC4.1	4	17472715-19028032	74.90-81.57	3.67
	qFC4.2	4	19642144-19986484	84.20-85.68	2.70
	qFC4.3	4	22019563-23235126	94.39-99.60	3.74
	qFC4.4	4	26377931-26619819	113.07-114.11	2.87
	qFC5.1	5	5206830-6439595	22.32-27.60	4.03
	qFC5.2	5	6673100-7059585	28.61-30.26	4.12
	qFC5.3	5	12422042-12794190	53.25-54.85	2.04
	qFC5.4	5	26189817-26927610	112.27-115.43	2.59
	qFC6.1	6	5187517-6015262	22.24-25.79	3.28
	qFC6.2	6	6069227-6560451	26.02-28.12	2.68
	qFC6.3	6	21068005-21507916	90.31-92.20	2.16
	qFC6.4	6	27961504-28384769	119.86-121.68	2.51
	qFC9.1	9	13119644-13620974	56.24-58.39	2.07
	qFC10.1	10	21806620-22080253	93.48-94.65	2.02
	qFC12.1	12	2351235-2689107	10.08-11.53	2.56
	qFC12.2	12	4462301-6224960	19.13-26.68	2.95
	qFC12.3	12	7508660-9990803	32.19-42.83	3.74
	qFC12.4	12	11398960-14215593	48.86-60.94	3.04
	qFC12.5	12	17056555-17574928	73.12-75.34	2.19
	qFC12.6	12	23839134-24088353	102.19-103.26	2.39
Anthocyanin content	qAC2.1	2	35599368-35902152	152.60-153.90	2.42
	qAC3.1	3	31965505-32493480	137.03-138.32	2.25
	qAC3.2	3	33386000-34509821	143.12-147.93	3.23
	qAC3.3	3	35314343-35646346	151.38-152.81	2.30
	qAC5.1	5	22147125-22524107	94.94-96.55	2.88
	qAC11.1	11	9832804-10200412	42.15-43.73	2.28
	qAC12.1	12	927518-2689107	3.98-11.53	2.31
	qAC12.2	12	23013674-23469132	98.65-100.61	2.50

Antioxidant physiological indicators	Gene ID	QTL locus	Functional annotation	Gene name
Hydroxyl radical scavenging rate	LOC_Os06g01850	qHRSR6.1	Leaf-type ferredoxin-NADP⁺oxidoreductase	OsLFNR2 (Da et al., 2023)
	LOC_Os06g48000	qHRSR6.3	Peroxidase precursor
	LOC_Os06g48020	qHRSR6.3	Peroxidase precursor
Total phenolic content	LOC_Os04g45210	qTPC4.1	Peroxisomal biogenesis factor 11
	LOC_Os12g07820	qTPC12.2	Ascorbate peroxidase gene	OsAPx6 (Chou et al., 2012)
	LOC_Os12g07830	qTPC12.2	Ascorbate peroxidase gene	OsAPx5 (Hong et al., 2007)
Flavonoid content	LOC_Os05g12190	qFC5.2	Chalcone synthase
	LOC_Os05g12210	qFC5.2	Chalcone synthase
	LOC_Os05g12240	qFC5.2	Chalcone synthase
	LOC_Os05g45120	qFC5.4	Anthocyanidin 5,3-O-glucosyltransferase
	LOC_Os12g16260	qFC12.3	Isoflavone reductase
Anthocyanin content	LOC_Os03g60509	qAC3.2	Chalcone isomerase gene	OsCHI (Lam et al., 2022)
Anthocyanin content	LOC_Os03g62480	qAC3.3	UV-B-responsive glycosyltransferase; flavonoid 7-O-glycosyltransferase