利用高密度Bin遗传图谱定位水稻抽穗期QTL

doi:10.3724/SP.J.1006.2023.12089

Abstract

Abstract:

Identification of new loci and genes related to heading date is very important for the genetic mechanism research and molecular improvement in rice. A recombinant inbred lines (RILs) was developed by crossing the japonica rice TD70 and the indica rice Kasalath with obvious difference in heading date. A high-density genetic linkage map with 12,328 recombination Bin markers was constructed based on the re-sequencing data of parents and RILs. The RILs and two parents were planted at the Jiangsu Academy of Agricultural Sciences, in Nanjing in 2018 and 2021. QTLs that controlled the heading date were analyzed by IciMappingv3.4 software with inclusive compound interval mapping method. 15 QTLs related to heading date of rice were detected, distributed on chromosome 3, 6, 7, 8, 10, and 12 in two years. The phenotype variation explained (PVE) and LOD value of single QTL ranged from 3.29%-14.73% and 2.58-10.68, respectively. Among them, seven QTLs were found to locate in the same interval or adjacent to previously QTLs, and four QTLs were detected in two years indicating their genetic stability. According to the annotation and sequences analysis of genes located in the region of repeatable QTLs, we found that seven annotated genes had non-synonymous mutations in the coding regions between TD70 and Kasalath. Based on the mutations in the coding regions, the haplotypes of seven genes were identified in RIL population. The heading date of RILs had significant difference between the RILs with different haplotype of four genes, indicating that they might be the candidate genes for heading date. These results could be useful for subsequent functional studies and molecular marker assisted breeding of heading date.

Key words: rice (Oryza sativa L.), recombinant inbred lines, high-density bin map, heading date, QTLs

ZHAO Ling, LIANG Wen-Hua, ZHAO Chun-Fang, WEI Xiao-Dong, ZHOU Li-Hui, YAO Shu, WANG Cai-Lin, ZHANG Ya-Dong. Mapping of QTLs for heading date of rice with high-density bin genetic map[J].Acta Agronomica Sinica, 2023, 49(1): 119-128.

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References 40

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年份Year	亲本Parents (d)		重组自交系RIL population
年份Year	TD70	Kasalath	平均值Average (d)	变异范围 Range	变异系数 CV (%)	峰度 Kurtosis	偏度 Skewness
2018	106	84	98.6	85-117	5.23	-0.73	0.28
2021	99	89	96.5	84-111	7.55	0.08	0.14

年份Year	QTL	染色体Chr.	标记区间 Marker interval	置信区间 Confidence interval (Mb)	LOD	贡献率 PVE (%)	加性效应 Additive effect
2018	qHD3	3	RBN2916-RBN2917	21.75-21.81	2.58	3.29	1.41
	qHD6.1	6	RBN5492-RBN5493	1.80-1.85	10.68	14.73	2.98
	qHD6.2	6	RBN5834-RBN5835	10.93-11.07	3.15	4.65	-2.58
	qHD7.1^*	7	RBN7031-RBN7032	14.50-14.54	6.02	11.77	2.66
	qHD7.2	7	RBN7535-RBN7536	28.65-28.71	3.73	4.77	-1.70
	qHD8^*	8	RBN7647-RBN7648	1.73-1.82	3.11	3.97	1.56
	qHD10.1^*	10	RBN9497-RBN9498	3.15-3.20	4.89	6.30	2.40
	qHD10.2^*	10	RBN9520-RBN9521	3.61-3.71	6.01	10.19	2.36
2021	qHD7.1^*	7	RBN7031-RBN7032	14.50-14.54	8.21	12.58	1.81
	qHD7.3	7	RBN6705-RBN6706	4.47-4.52	7.84	11.80	1.74
	qHD7.4	7	RBN7524-RBN7525	28.35-28.37	6.27	9.66	-1.58
	qHD8^*	8	RBN7647-RBN7648	1.73-1.82	3.15	3.92	1.01
	qHD10.1^*	10	RBN9497-RBN9498	3.15-3.20	4.95	6.52	1.32
	qHD10.2^*	10	RBN9520-RBN9521	3.61-3.71	4.06	6.24	1.53
	qHD12	12	RBN12280-RBN12281	26.21-26.27	3.06	4.47	1.07

QTL	染色体 Chr.	物理图谱区间Interval (Mb)	基因 Gene name	基因功能注释 Gene annotation
qHD7.1	7	14.50-14.54	Os07g0434500	SNF2家族蛋白 Snf2 family protein
			Os07g0434700^*	甲硫氨酸氨基肽酶家族成员 Methionine aminopeptidase family protein
			Os07g0435100	26S蛋白酶体非ATP酶调节亚基8 26S proteasome non-ATPase regulatory subunit 8
			Os07g0435300	光系统I反应中心亚基IV A, 叶绿体前体 Photosystem I reaction center subunit IV A, chloroplast precursor
			Os07g0435400	WD结构域, G-β重复结构域蛋白 WD domain, G-beta repeat domain containing protein
qHD8	8	1.73-1.82	Os08g0130900^*	半乳糖基转移酶家族 Galactosyltransferase family
			Os08g0131000	五肽 Pentatricopeptide
			Os08g0131100^*	细胞色素P450羟化酶 Cytochrome P450 hydroxylase
			Os08g0131200	蛋白酶抑制剂, 种子储存, LTP家族蛋白前体 Protease inhibitor, seed storage, LTP family protein precursor
			Os08g0131300^*	3-磷酸甘油酰基转移酶 Glycerol-3-phosphate acyltransferase
qHD10.1	10	3.15-3.20	Os10g0152000^*	OsWAK类受体蛋白激酶 OsWAK receptor-like protein kinase
qHD10.2	10	3.61-3.71	Os10g0157200	丝裂原活化蛋白激酶15 Mitogen-activated protein kinase 15
			Os10g0157400^*	钙依赖性蛋白激酶12 Calcium-dependent protein kinase 12
			Os10g0158400^*	查尔酮合酶 Chalcone synthase

QTL	本研究This study		已发表的相关位点/基因 Known QTLs or genes
QTL	染色体Chr.	物理位置 Position (Mb)	定位群体或已克隆基因 Populations or known gene	物理位置 Position (Mb)	参考文献 Reference
qHD3	3	21.75-21.81	Caiapo/O. rufipogon BC₂F₂	19.41-22.34	29
qHD6.1	6	1.80-1.85	Nipponbare/Kasalath BC₃F₂ NIL	1.64-3.08	30
qHD6.2	6	10.93-11.07	Nipponbare/Kasalath BC₃F₂ NIL	6.82-11.68	30
			V20A/IRGC 105491 BC₂	10.05-27.25	31
qHD7.1	7	14.50-14.54	Zhenshan 97/Ming 63 F_2:3	7.23-16.87	32
qHD7.3	7	4.47-4.52	IR64/Azucena DH	4.57-6.78	33
			Sasanishiki/Habataki BCIL	4.57-9.10	34
qHD7.4	7	28.35-28.37	IR64/Azucena DH	28.41-29.46	30
			Gui630/Taiwanjing DH	27.78-29.26	35
			OsCOL13	28.18	16, 36
qHD12	12	26.21-26.27	IR64/Azucena DH	24.85-27.49	30
qHD12	12	26.21-26.27	Lemont/Teqing RIL	26.11-26.99	37, 38

Mapping of QTLs for heading date of rice with high-density bin genetic map

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