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

作物学报 ›› 2023, Vol. 49 ›› Issue (1): 119-128.doi: 10.3724/SP.J.1006.2023.12089

• 作物遗传育种·种质资源·分子遗传学 • 上一篇下一篇

利用高密度Bin遗传图谱定位水稻抽穗期QTL

赵凌(), 梁文化, 赵春芳, 魏晓东, 周丽慧, 姚姝, 王才林, 张亚东()

江苏省农业科学院粮食作物研究所 / 国家水稻改良中心南京分中心 / 国家耐盐碱水稻技术创新中心华东中心 / 江苏省优质水稻工程技术研究中心, 江苏南京 210014

收稿日期:2021-12-28 接受日期:2022-05-05 出版日期:2023-01-12 网络出版日期:2022-05-13
通讯作者: 张亚东
作者简介:E-mail: zhaoling@jaas.ac.cn
基金资助:
江苏省重点研发计划项目(BE2019375)

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

ZHAO Ling(), LIANG Wen-Hua, ZHAO Chun-Fang, WEI Xiao-Dong, ZHOU Li-Hui, YAO Shu, WANG Cai-Lin, ZHANG Ya-Dong()

Institute of Food Crops, Jiangsu Academy of Agricultural Sciences / Nanjing Branch of China National Center for Rice Improvement / East China Branch of National Center of Technology Innovation for Saline-Alkali Tolerant Rice / Jiangsu High Quality Rice Research & Development Center, Nanjing 210014, Jiangsu, China

Received:2021-12-28 Accepted:2022-05-05 Published:2023-01-12 Published online:2022-05-13
Contact: ZHANG Ya-Dong
Supported by:
Jiangsu Science and Technology Development Program(BE2019375)

摘要/Abstract

摘要：

挖掘新的控制水稻抽穗期相关位点和候选基因, 对抽穗期的遗传机制研究和品种改良具有重要的意义。利用抽穗期存在明显差异的粳稻TD70和籼稻Kasalath杂交衍生的包含186个家系的重组自交系群体, 构建了基于深度重测序的高密度Bin遗传图谱, 图谱共包含12,328个Bin标记。RIL群体及亲本2018年和2021年正季种植于江苏省南京市江苏省农业科学院。以家系从播种到抽穗所经历的天数作为抽穗期表型值, 使用IciMapping软件3.4版的完备区间作图法, 对控制水稻抽穗期的QTL进行鉴定。2年共检测到15个抽穗期的QTL, 分布在3号、6号、7号、8号、10号和12号染色体上, LOD值为2.58~10.68, 其中7个QTL和已知抽穗期QTL的位置存在重叠或者部分重叠。共有4个QTL在2年均检测到, 表现出较强的稳定性。对2年重复鉴定到的4个QTL区间进行基因功能注释和亲本间序列分析, 共发现7个注释有功能, 且在2个亲本间编码区存在非同义突变的基因。根据候选基因SNP的类型对RIL群体家系进行基因等位型分类和效应分析, 发现4个基因其不同等位型的RIL家系在抽穗期上存在显著或者极显著差异, 推测可能为候选基因, 可用于后续水稻抽穗期的分子机制研究。

关键词: 水稻, 重组自交系, 高密度Bin图谱, 抽穗期, QTL

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

赵凌, 梁文化, 赵春芳, 魏晓东, 周丽慧, 姚姝, 王才林, 张亚东. 利用高密度Bin遗传图谱定位水稻抽穗期QTL[J]. 作物学报, 2023, 49(1): 119-128.

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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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

利用高密度Bin遗传图谱定位水稻抽穗期QTL

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

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