水稻RIL群体高密度遗传图谱的构建及苗期耐热性QTL定位

doi:10.3864/j.issn.0578-1752.2022.22.001

中国农业科学 ›› 2022, Vol. 55 ›› Issue (22): 4327-4341.doi: 10.3864/j.issn.0578-1752.2022.22.001

• 作物遗传育种·种质资源·分子遗传学 • 上一篇下一篇

水稻RIL群体高密度遗传图谱的构建及苗期耐热性QTL定位

刘进^1,²(),胡佳晓¹,马小定²,陈武¹,勒思¹,Jo Sumin³,崔迪²,周慧颖¹,张立娜¹,Shin Dongjin³,黎毛毛¹,韩龙植²(),余丽琴¹()

¹江西省农业科学院水稻研究所/江西省农作物种质资源研究中心，中国南昌 330200
²中国农业科学院作物科学研究所，中国北京 100081
³韩国农村振兴厅粮食科学院南部作物部，韩国密阳 627-803

收稿日期:2022-07-04 接受日期:2022-08-12 出版日期:2022-11-16 发布日期:2022-12-14
通讯作者: 韩龙植,余丽琴
作者简介:刘进，E-mail：riceliujin@163.com。
基金资助:
国家重点研发计划(2021YFD1200500);国家重点研发计划(2021YFD1200501-7);江西现代农业科研协同创新专项(JXXTCXQN202205);江西现代农业科研协同创新专项(JXXTCX202101)

Construction of High Density Genetic Map for RIL Population and QTL Analysis of Heat Tolerance at Seedling Stage in Rice (Oryza sativa L.)

LIU Jin^1,²(),HU JiaXiao¹,MA XiaoDing²,CHEN Wu¹,LE Si¹,JO Sumin³,CUI Di²,ZHOU HuiYing¹,ZHANG LiNa¹,SHIN Dongjin³,LI MaoMao¹,HAN LongZhi²(),YU LiQin¹()

¹Rice Research Institute, Jiangxi Academy of Agricultural Sciences/Research Center of Jiangxi Crop Germplasm Resources, Nanchang 330200, China
²Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
³Department of Southern Area Crop Science, National Institute of Crop Science, Rural Development Administration, Milyang 627-803, South Korea

Received:2022-07-04 Accepted:2022-08-12 Online:2022-11-16 Published:2022-12-14
Contact: LongZhi HAN,LiQin YU

摘要/Abstract

摘要：

【目的】 随着全球气候变暖，高温严重威胁粮食安全，发掘耐热基因资源是培育耐高温新品种和消除高温危害最直接的绿色生态途径，也是阐明耐热生理生化和分子遗传机理的基础。【方法】 构建苗期耐热性鉴定评价方法，以热敏感品种周南稻和强耐热品种赣早籼58号杂交衍生的重组自交系（recombinant inbred lines，RIL）群体为研究材料，利用高通量测序技术对亲本和RIL群体进行全基因组测序；依据171个家系的基因型数据，利用滑动窗口法将SNP信息转换成Bin基因型，预测染色体上的重组断点，构建RIL群体高密度BinMap遗传图谱，结合耐热表型数据，运用QTL IciMapping软件完备复合区间ICIM的作图方法，进行高温胁迫下幼苗存活率和耐热等级QTL分析。【结果】 构建了一张包含3 321个Bin标记高密度遗传图谱，各染色体Bin标记数为159—400个，标记间平均物理距离为106 kb；利用逐步高温胁迫方式鉴定亲本和RIL家系幼苗耐热表型，高温胁迫下，幼苗存活率和耐热等级存在极显著负相关性，且幼苗存活率与籼型基因频率存在显著正相关性，籼型基因频率越高，耐热性越好，RIL群体表型性状呈现双峰连续分布，苗期耐热性可能受少数几个主效QTL调控；共检测到12个苗期耐热性相关的QTL，其中，调控幼苗存活率和耐热等级的QTL分别有8和4个，幼苗存活率和耐热等级相关QTL存在遗传重叠现象，形成调控耐热性的主效QTL簇qHTS2、qHTS7和qHTS8，三者在调控苗期高温抗逆中具有重要作用，其中，qHTS7为新发现主效QTL，对增强苗期耐热性具有较强的功效。【结论】 构建了一张包含3 321个Bin标记的高密度分子遗传图谱，解析了耐热品种赣早籼58号苗期耐热基因，鉴定出3个苗期耐热调控关键QTL簇，发掘了一个新主效QTL簇qHTS7，基于高密度遗传图谱高效获取目标区段及候选基因，筛选出8个苗期耐热性调控的关键目标基因。

关键词: 水稻, 高密度图谱, 苗期, 耐热性, QTL定位

Abstract:

【Objective】 With global warming, high temperature has an increasing impact on food crop safe. Excavation of heat tolerance gene resources is the most direct green ecological method to cultivate new varieties of heat resistance and eliminate the harm of high temperature, which also the basis for clarifying the physiological, biochemical and molecular genetic mechanism of heat tolerance.【Method】Establishing the identification and evaluation method of heat tolerance at seedling stage, a set of RIL populations was structured from the extreme heat-tolerance Ganzaoxian58(GZX58) and heat-sensitive Junambyeo (JNB), and then the high density genetic map was constructed using genotyping by resequencing technology. To converting SNP information into Bin genotype of the RIL population using sliding window method, which predicting the recombination breakpoints on the chromosomes, finally a high density BinMap genetic map was constructed. Based on the genotype and phenotype data of the 171 lines, QTL mapping of the high temperature seedling survival rate (HTSR) and heat tolerance class (HTC) was performed by ICIM method of the QTL IciMapping software.【Result】A high-density genetic map containing 3 321 Bin markers was constructed, the number of Bin markers for each chromosome between 159 and 400, the average physical distance two markers was about to 106 kb; heat tolerance of the parents and RIL populations was identified by stepwise heat stress at seedlings stage, there have a significant negative correlation between HTSR and HTC, in addition, there has a significant positive correlation between HTSR and indica gene frequency (Fi), which the higher of the Fi, the heat tolerance is better; the bi-modal continuous distribution of phenotype traits from the RIL population showed that the heat tolerance is regulated by few major QTL. A total of 12 QTL controlling with heat tolerance at seedling stage, there have 8 and 4 QTL regulating for HTSR and HTC, respectively. There has a significant genetic overlap from HTSR and HTC, qHTS2, qHTS7 and qHTS8, three major QTL cluster play an important role in regulating the heat tolerance at seedling stage. Among these QTL, qHTS7 was a novel major QTL cluster, which has a strong effect on enhancing the heat resistance at seedling stage. 【Conclusion】 We constructed a high density genetic linkage map containing 3 321 Bin markers, which be used to analyzed the heat tolerance gene from the GZX58 at seedling stage, there have three key QTL cluster identified associated with the heat tolerance, a novel QTL cluster qHTS7 was discovered, efficient acquisition of target segments and candidate genes based on high-density genetic mapping, eight key candidate genes were selected by bioinformatics for regulation of the heat tolerance.

Key words: rice, high-density genetic map, seedling stage, heat tolerance, QTL mapping

刘进,胡佳晓,马小定,陈武,勒思,Jo Sumin,崔迪,周慧颖,张立娜,Shin Dongjin,黎毛毛,韩龙植,余丽琴. 水稻RIL群体高密度遗传图谱的构建及苗期耐热性QTL定位[J]. 中国农业科学, 2022, 55(22): 4327-4341.

LIU Jin,HU JiaXiao,MA XiaoDing,CHEN Wu,LE Si,JO Sumin,CUI Di,ZHOU HuiYing,ZHANG LiNa,SHIN Dongjin,LI MaoMao,HAN LongZhi,YU LiQin. Construction of High Density Genetic Map for RIL Population and QTL Analysis of Heat Tolerance at Seedling Stage in Rice (Oryza sativa L.)[J]. Scientia Agricultura Sinica, 2022, 55(22): 4327-4341.

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图/表 11

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主效QTL簇定位区间关键候选基因分析"

编号 Number	候选基因 Candidate gene	基因功能 Gene function
ORF2-1	Os02g0801700	锌指蛋白，BED型预测结构域 Zinc finger, BED-type predicted domain containing protein
ORF2-2	Os02g0802700*	单半乳糖基二酰基甘油合酶，调控植物生长发育 Monogalactosyldiacylglycerol synthase, plant growth and development
ORF2-3	Os02g0804500*	热休克蛋白Hsp40，含有DnaJ结构域蛋白 Heat shock protein, Hsp40, DnaJ domain containing protein
ORF2-4	Os02g0804900*	核糖核苷酸还原酶，叶绿体生物合成 Ribonucleotide reductase, chloroplast biogenesis
ORF2-5	Os02g0805100	生长素反应蛋白IAA12 Auxin-responsive protein IAA12
ORF2-6	Os02g0806400	锌指家族蛋白 Zine finger family protein
ORF7-1	Os07g0138200*	NAC转录因子，ABA诱导的叶片衰老和分蘖 NAC transcription factor, ABA-induced leaf senescence and tillering
ORF7-2	Os07g0138400	CCCH型锌指蛋白，调控耐旱性 CCCH-type zinc finger protein, drought tolerance
ORF7-3	Os07g0139000	预测的含锌指 CCCH 结构域蛋白48 Putative zinc finger CCCH domain-containing protein 48
ORF7-4	Os07g0141500	含有SWIM型结构域锌指蛋白 Zinc finger, SWIM-type domain containing protein
ORF7-5	Os07g0143200*	光敏色素互作 bHLH 因子，冷诱导OsPIF14可变剪接体，光力信号传导 Phytochrome-interacting bHLH factor, cold-induced alternative splicing variant of OsPIF14, cross-talk between light and stress signaling
ORF7-6	Os07g0148900	特色光系统I蛋白 Photosystem I protein-like protein
ORF7-7	Os07g0150500	含C3HC结构域的锌指蛋白 Zinc finger, C3HC-like domain containing protein
ORF7-8	Os07g0152000*	转录因子，调控耐冷性 Transcription factor, cold tolerance
ORF8-1	Os08g0191100*	乌头酸酶，参与热激响应 Aconitase, response to heat stress
ORF8-2	Os08g0191200	叶绿体发育、叶绿素代谢和细胞分裂调节 Regulation of chloroplast development, chlorophyll metabolism and cell division
ORF8-3	Os08g0191900	低温条件下调控叶绿体发育 Regulation of chloroplast development under low-temperature condition
ORF8-4	Os08g0191700*	乙二醛酶I，非生物逆境应激反应 Glyoxalase I, abiotic stress response
ORF8-5	Os08g0196700	核因子Y转录因子，干旱胁迫耐受性 Nuclear Factor Y transcription factor, drought stress tolerance
ORF8-6	Os08g0198100	锌指蛋白，BED型预测结构域 Zinc finger, BED-type predicted domain containing protein
ORF8-7	Os08g0199300	特异G蛋白，参与植物防御及耐盐胁迫反应 Unconventional G protein, plant defense response, salinity stress tolerance
ORF8-8	Os08g0200600*	NAC转录因子，调控耐旱性 NAC transcription factor, negative regulation of drought tolerance

表4

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图7

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耐热等级 HTC	热胁迫症状 Heat stress phenotype	耐热性 Heat tolerance
1	植株叶片、根系无损害症状，生长势较好，高温胁迫幼苗存活率高于80% The plant leaves and roots showed no damage symptoms, the growth potential was good, and then heat stress seedling survival rate was higher than 80%	强耐热 Extreme heat tolerance
3	部分植株叶片卷曲、黄化失绿，根系受损变黄，高温胁迫幼苗存活率明显下降 The leaves of some plants were curled, yellowing and lost green, the roots were damaged and turned yellow, and then heat stress seedling survival rate have a significantly decreased	耐热 Heat tolerance
5	植株整株或部分叶片黄化、枯死，生长受抑，高温胁迫幼苗存活率低于50% The whole or part of the plant leaves were yellowing and dead, the growth was inhibited, and then heat stress seedling survival rate was less than 50%	中抗 Moderate resistance
7	植株叶片和茎秆脱水、生长停止，幼苗枯死或新叶死亡，高温胁迫幼苗存活率较低 Plant leaves and stalks were dehydrated, growth stopped, and then seedlings died or new leaves died, which heat stress seedling survival rate was lower	热敏感 Heat sensitive
9	幼苗植株全部枯死或接近死亡，高温胁迫幼苗存活率低于10% All seedling plants died or were nearly death, and then heat stress seedlings survival rate was less than 10%	极端热敏感 Extreme heat sensitive

染色体 Chr.	Bin标记数 Bin marker	遗传图距 Distance (cM)	标记间平均遗传距离 Average distance (cM)	最大遗传距离 Max gap (cM)
Chr.1	306	160.62	0.52	3.29
Chr.2	332	115.86	0.35	3.11
Chr.3	400	152.91	0.38	3.34
Chr.4	325	155.75	0.48	3.44
Chr.5	342	141.71	0.41	3.62
Chr.6	192	99.60	0.52	4.77
Chr.7	190	147.96	0.78	4.18
Chr.8	255	142.60	0.56	3.97
Chr.9	225	160.73	0.71	3.79
Chr.10	332	154.57	0.47	5.42
Chr.11	263	155.00	0.59	4.18
Chr.12	159	115.78	0.73	3.80
总计Total	3321	1703.09	0.51	5.42

性状 Trait	位点 Locus	标记 Marker	LOD值 LOD value	贡献率 PVE (%)	加性效应 Additive effect	物理位置及距离 Position(bp) and distance (kb)
幼苗存活率 HTSR	qHTSR2	Block4364-4396	3.89	5.25	6.33	34029923—34439386 (409)
	qHTSR3	Block4512-4513	2.95	7.20	9.44	2137—105390 (103)
	qHTSR4	Block6417-6435	2.89	5.80	4.99	4868070—5212956 (345)
	qHTSR6	Block9309-9325	2.68	5.25	6.33	1814778—1992782 (178)
	qHTSR7	Block11026-11067	4.55	15.89	-17.86	2023438—2912508 (889)
	qHTSR8	Block12594-12597	2.67	6.31	8.34	5289371—5860658 (571)
	qHTSR9	Block14481-14488	2.52	6.72	-9.10	22679210—22800304 (121)
	qHTSR12	Block18068-18081	3.22	8.51	3.53	3003771—3304029 (300)
耐热等级 HTC	qHTC2.1	Block3098-3136	3.39	8.52	0.66	9969848—10850583 (880)
	qHTC2.2	Block4364-4396	3.44	9.93	1.55	34029923—34439386 (409)
	qHTC7	Block11026-11067	6.52	18.88	-2.56	2023438—2912508 (889)
	qHTC8	Block12456-12597	3.67	7.80	0.88	5289371—5860658 (571)

水稻RIL群体高密度遗传图谱的构建及苗期耐热性QTL定位

Construction of High Density Genetic Map for RIL Population and QTL Analysis of Heat Tolerance at Seedling Stage in Rice (Oryza sativa L.)

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