QTL Analysis of Rice Cold Tolerance at Germination and Bud Stage Utilizing Indica-Japonica RIL Population

doi:10.7668/hbnxb.20192749

Abstract

Abstract:

To map QTLs that control cold tolerance at germination and bud stages,to explore the genetic mechanism,a recombinant inbred line(RIL)population was used as experimental material.The RIL population contained 189 lines derived from the cross between Caidao,a japonica rice variety that had strong cold tolerance and was adopted as the female parent,and WD,a indica rice variety that had weak cold tolerance and was used as the male parent.The QTLs that control cold tolerance at germination and bud stage were mapped between four phenotypic indexes and 978 Bin markers by IciMapping 4.2.The four phenotypic indexes included relative germination rate,average germination days,seedling rate and cold tolerance level.The results showed that two pairs of epistatic QTLs related to cold tolerance at bud stage were mapped.The LOD scores were 5.70 and 5.55 and the phenotypic contribution rates were 13.22% and 39.87%,respectively.In addition,five and five QTLs that were related to cold tolerance at germination and bud stage were mapped,respectively.These QTLs were located on chromosomes 1,3,5 and 8.The LOD score and phenotypic contribution rate of these QTLs ranged from 2.55 to 7.07 and from 6.41% to 17.17%,respectively.qLTG3 had the highest phenotypic contribution rate among the five germination stage QTLs and was also related to cold tolerance at germination stage.qCTP1-2 had the maximum of phenotypic contribution rate among the five bud stage QTLs.qCTB1,qCTP1-2 and qLTG8 had not been reported.The QTLs and epistatic QTLs detected will provide a reference for the genetic research and improvement of cold tolerance in rice.

Key words: Rice, Germination stage, Bud stage, Cold tolerance, QTL

CHEN Ziqi, WANG Weiping, ZHAO Hongqiang, WANG Hao, HAN Xiao, YANG Luomiao, XIN Wei, LIU Hualong, ZHENG Hongliang, WANG Jingguo. QTL Analysis of Rice Cold Tolerance at Germination and Bud Stage Utilizing Indica-Japonica RIL Population[J]. Acta Agriculturae Boreali-Sinica, 2022, 37(1): 50-57. doi: 10.7668/hbnxb.20192749.

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References 46

[1]	Jiang L,Xun M M,Wang J K,Wan J M.QTL analysis of cold tolerance at seedling stage in rice(Oryza sativa L.)using recombination inbred lines[J].Journal of Cereal Science,2008,48(1):173-179.doi:10.1016/j.jcs.2007.08.013.
[2]	刘次桃,王威,毛毕刚,储成才.水稻耐低温逆境研究:分子生理机制及育种展望[J].遗传,2018,40(3):171-185.doi:10.16288/j.yczz.18-007.
	Liu C T,Wang W,Mao B G,Chu C C.Cold stress tolerance in rice:Physiological changes,molecular mechanism,and future prospects[J].Hereditas,2018,40(3):171-185.
[3]	来永才,张喜娟,罗锡文,孟英,张凤鸣,朱琳,董国忠,曾山,王在满,唐傲,章秀福,殷延勃,董文军,刘猷红,姚翊涵,王丹英.寒地水稻直播栽培技术研究与应用[C]//中国作物学会:2019年中国作物学会学术年会论文摘要集,2019:1.doi:10.26914/c.cnkihy.2019.016013.
	Lai Y C,Zhang X J,Luo X W,Meng Y,Zhang F M,Zhu L,Dong G Z,Zeng S,Wang Z M,Tang A,Zhang X F,Yin Y B,Dong W J,Liu Y H,Yao Y H,Wang D Y.Research and application of direct seeding cultivation technology of rice in cold area[C]//China Crop Society:Abstracts of 2019 annual academic meeting of China crop Society,2019:1.
[4]	赵正武,李仕贵,黄文章,雷树凡.水稻不同低温敏感期的耐冷性研究进展及前景[J].西南农业学报,2006,19(2):330-335.doi:10.3969/j.issn.1001-4829.2006.02.037.
	Zhao Z W,Li S G,Huang W Z,Lei S F.Development and foreground of cold tolerance in different low temperature sensitive stage of rice[J].Southwest China Journal of Agricultural Sciences,2006,19(2):330-335.
[5]	郭丽颖,耿艳秋,金峰,宋微,邵玺文.寒地水稻低温冷害防御栽培技术研究进展[J].作物杂志,2017(4):7-14.doi:10.16035/j.issn.1001-7283.2017.04.002.
	Guo L Y,Geng Y Q,Jin F,Song W,Shao X W.Research advances about low temperature,cold damage defense cultivation techniques of rice in cold region of China[J].Crops,2017(4):7-14.
[6]	赵海新. 水直播与移栽对水稻穗部性状及籽粒形态的影响[J].黑龙江农业科学,2021(6):13-19.doi:10.11942/j.issn1002-2767.2021.06.0013.
	Zhao H X.Effects of direct seeding and transplanting on panicle traits and grain morphology of rice[J].Heilongjiang Agricultural Sciences,2021(6):13-19.
[7]	Iwata N,Shinada H,Kiuchi H,Sato T,Fujino K.Mapping of QTLs controlling seedling establishment using a direct seeding method in rice[J].Breeding Science,2010,60(4):353-360.doi:10.1270/jsbbs.60.353.
[8]	侯名语.水稻低温、低氧发芽力的QTL定位[D].南京:南京农业大学,2003.doi:10.7666/d.Y605176.
	Hou M Y.The QTL mapping of low temperature germinability and anoxia germinability in rice(Oryza Sativa L.)[D].Nanjing:Nanjing Agricultural University,2003.
[9]	Schläppi M R,Jackson A K,Eizenga G C,Wang A J,Chu C C,Shi Y,Shimoyama N,Boykin D L.Assessment of five chilling tolerance traits and GWAS mapping in rice using the USDA mini-core collection[J].Frontiers in Plant Science,2017,8:957.doi:10.3389/fpls.2017.00957.
[10]	姜旋,李辰昱,毛婷.水稻低温发芽性QTL的分子标记定位[J].武汉植物学研究,2005,23(3):216-220.doi:10.3969/j.issn.2095-0837.2005.03.003.
	Jiang X,Li C Y,Mao T.Mapping of QTL controlling low-temperature germinability in rice[J].Journal of Wuhan Botanical Research,2005,23(3):216-220.
[11]	纪素兰,江玲,王益华,刘世家,刘喜,翟虎渠,吉村醇,万建民.水稻种子耐低温发芽力的QTL定位及上位性分析[J].作物学报,2008,34(4):551-556.doi:10.3321/j.issn:0496-3490.2008.04.003.
	Ji S L,Jiang L,Wang Y H,Liu S J,Liu X,Zhai H Q,Yoshimura A,Wan J M.QTL and epistasis for low temperature germinability in rice[J].Acta Agronomica Sinica,2008,34(4):551-556.
[12]	张所兵,张云辉,林静,陈海元,汪迎节,朱晓妹,宋春凤,方先文.利用重组自交系定位水稻种子耐低温发芽QTL[J].分子植物育种,2021,19(14):4690-4695.doi:10.13271/j.mpb.019.004690.
	Zhang S B,Zhang Y H,Lin J,Chen H Y,Wang Y J,Zhu X M,Song C F,Fang X W.QTL involved in low-temperature tolerance at the germination stage by recombination inbred lines in rice[J].Molecular Plant Breeding,2021,19(14):4690-4695.
[13]	姚晓云,熊运华,黄永萍,吴延寿,杨平,刘进,尹建华.低温环境下水稻种子活力QTL鉴定[J].江西农业大学学报(自然科学版),2020,42(4):633-640.doi:10.13836/j.jjau.2020073.
	Yao X Y,Xiong Y H,Huang Y P,Wu Y S,Yang P,Liu J,Yin J H.QTL mapping for rice seed vigor under low temperature environment[J].Acta Agriculturae Universitatis Jiangxiensis(Natural Sciences Edition),2020,42(4):633-640.
[14]	滕胜,曾大力,钱前,国广泰史,黄大年,朱立煌.低温条件下水稻发芽力QTL的定位分析[J].科学通报,2001,46(13):1104-1108.doi:10.3321/j.issn:0023-074X.2001.13.012.
	Teng S,Zeng D L,Qian Q,Guo G T S,Huang D N,Zhu L H.QTL mapping analysis of rice germination ability under low temperature[J].Chinese Science Bulletin,2001,46(13):1104-1108.
[15]	朱金燕,刘楠,王军,周勇,范方军,李文奇,王芳权,许扬,仲维功,梁国华,杨杰.利用染色体单片段代换系定位水稻低温发芽率QTL[J].扬州大学学报(农业与生命科学版),2017,38(4):74-80.doi:10.16872/j.cnki.1671-4652.2017.04.014.
	Zhu J Y,Liu N,Wang J,Zhou Y,Fan F J,Li W Q,Wang F Q,Xu Y,Zhong W G,Liang G H,Yang J.Identification of quantitative trait loci for low temperature germination rate with single segment substituted lines in rice[J].Journal of Yangzhou University (Agricultural and Life Science Edition),2017,38(4):74-80.
[16]	Zhang M C,Ye J,Xu Q,Feng Y,Yuan X P,Yu H Y,Wang Y P,Wei X H,Yang Y L.Genome-wide association study of cold tolerance of Chinese indica rice varieties at the bud burst stage[J].Plant Cell Reports,2018,37(3):529-539.doi:10.1007/s00299-017-2247-4.
[17]	张露霞.水稻芽期耐冷性QTL定位与分析[D].南京:南京农业大学,2006.doi:10.7666/d.Y1078646.
	Zhang L X.Detection and analysis of QTL for cold tolerance at the bud bursting period in rice(Oryza Sativa L.)[D].Nanjing:Nanjing Agricultural University,2006.
[18]	Baruah A R,Ishigo-Oka N,Adachi M,Oguma Y,Tokizono Y,Onishi K,Sano Y.Cold tolerance at the early growth stage in wild and cultivated rice[J].Euphytica,2009,165(3):459-470.doi:10.1007/s10681-008-9753-y.
[19]	李太贵. 在低温下筛选水稻不同生长期耐寒品种的室内方法[J].国外农业技术,1981(4):18-21.
	Li T G.Indoor method for screening cold-tolerant varie-ties of rice in different growth stages at low temperature[J].Foreign Agricultural Technology,1981(4):18-21.
[20]	Wang X,Zou B H,Shao Q L,Cui Y M,Lu S,Zhang Y,Huang Q S,Huang J,Hua J.Natural variation reveals that OsSAP16 controls low-temperature germination in rice[J].Journal of Experimental Botany,2018,69(3):413-421.doi:10.1093/jxb/erx413.
[21]	周志彬,张元明,Robert S N,Liliya D.温度和光照对3种雀麦属(Bromus)植物种子萌发的影响[J].中国沙漠,2013,33(4):1048-1053.doi:10.7522/j.issn.1000-694X.2013.00148.
	Zhou Z B,Zhang Y M,Robert S N,Liliya D.Effects of temperature and light on seed germination of three Bromus species[J].Journal of Desert Research,2013,33(4):1048-1053.
[22]	韩龙植,魏兴华.水稻种质资源描述规范和数据标准[S].北京:中国农业出版社,2006.
	Han L Z,Wei X H.Specification and data standard for description of rice germplasm resources[S].Beijing:China Agricultural Press,2006.
[23]	姜树坤,王立志,杨贤莉,李波,母伟杰,董世晨,车韦才,李忠杰,迟力勇,李明贤,张喜娟,姜辉,李锐,赵茜,李文华.基于高密度SNP遗传图谱的粳稻芽期耐低温QTL鉴定[J].作物学报,2020,46(8):1174-1184.doi:10.3724/SP.J.1006.2020.92066.
	Jiang S K,Wang L Z,Yang X L,Li B,Mu W J,Dong S C,Che W C,Li Z J,Chi L Y,Li M X,Zhang X J,Jiang H,Li R,Zhao Q,Li W H.Detection of QTLs controlling cold tolerance at bud bursting stage by using a high-density SNP linkage map in Japonica rice[J].Acta Agronomica Sinica,2020,46(8):1174-1184.
[24]	McCouch S R,Cho Y G,Yano M,Paul E,Blinstrub M,Morishima H,et al.Report on QTL nomenclature[J].Rice Genet Newsl,1997,14:11-13.
[25]	Fujino K,Sekiguchi H,Matsuda Y,Sugimoto K,Ono K,Yano M.Molecular identification of a major quantitative trait locus,qLTG3-1,controlling low-temperature germinability in rice[J].PNAS,2008,105(34):12623-12628.doi:10.1073/pnas.0805303105.
[26]	任永梅.籼粳稻重组自交系耐冷性鉴定与QTL分析[D].沈阳:沈阳农业大学,2020.doi:10.27327/d.cnki.gshnu.2020.000261.
	Ren Y M.cold tolerance identification and QTL analysis of indica and japonica recombinant inbred lines[D].Shenyang:Shenyang Agricultural University,2020.
[27]	Li L F,Liu X,Xie K,Wang Y H,Liu F,Lin Q Y,Wang W Y,Yang C Y,Lu B Y,Liu S J,Chen L M,Jiang L,Wan J M.qLTG-9,a stable quantitative trait locus for low-temperature germination in rice(Oryza sativa L.)[J].Theoretical and Applied Genetics,2013,126(9):2313-2322.doi:10.1007/s00122-013-2137-2.
[28]	Xie L X,Tan Z W,Zhou Y,Xu R B,Feng L B,Xing Y Z,Qi X Q.Identification and fine mapping of quantitative trait loci for seed vigor in germination and seedling establishment in rice[J]. Journal of Integrative Plant Biology,2014,56(8):749-759.doi:10.1111/jipb.12190.
[29]	Andaya V C,Tai T H.Fine mapping of the qCTS4 locus associated with seedling cold tolerance in rice(Oryza sativa L.)[J].Molecular Breeding,2007,20(4):349-358.doi:10.1007/s11032-007-9096-8.
[30]	Koseki M,Kitazawa N,Yonebayashi S,Maehara Y,Wang Z X,Minobe Y.Identification and fine mapping of a major quantitative trait locus originating from wild rice,controlling cold tolerance at the seedling stage[J].Molecular Genetics and Genomics,2010,284(1):45-54.doi:10.1007/s00438-010-0548-1.
[31]	Kim S M,Suh J P,Lee C K,Lee J H,Kim Y G,Jena K K.QTL mapping and development of candidate gene-derived DNA markers associated with seedling cold tolerance in rice(Oryza sativa L.)[J].Molecular Genetics and Genomics,2014,289(3):333-343.doi:10.1007/s00438-014-0813-9.
[32]	Xiao N,Huang W N,Li A H,Gao Y,Li Y H,Pan C H,Ji H J,Zhang X X,Dai Y,Dai Z Y,Chen J M.Fine mapping of the qLOP2 and qPSR2-1 loci associated with chilling stress tolerance of wild rice seedlings[J].Theoretical and Applied Genetics,2015,128(1):173-185.doi:10.1007/s00122-014-2420-x.
[33]	Endo T,Chiba B,Wagatsuma K,Saeki K,Ando T,Shomura A,Mizubayashi T,Ueda T,Yamamoto T,Nishio T.Detection of QTLs for cold tolerance of rice cultivar Kuchum' and effect of QTL pyramiding[J].Theoretical and Applied Genetics,2016,129(3):631-640.doi:10.1007/s00122-015-2654-2.
[34]	Zhou L,Zeng Y W,Zheng W W,Tang B,Yang S M,Zhang H L,Li J J,Li Z C.Fine mapping a QTL qCTB7 for cold tolerance at the booting stage on rice chromosome 7 using a near-isogenic line[J].Theoretical and Applied Genetics,2010,121(5):895-905.doi:10.1007/s00122-010-1358-x.
[35]	Kuroki M,Saito K,Matsuba S,Yokogami N,Shimizu H,Ando I,Sato Y.A quantitative trait locus for cold tolerance at the booting stage on rice chromosome 8[J].Theoretical and Applied Genetics,2007,115(5):593-600.doi:10.1007/s00122-007-0589-y.
[36]	Zhu Y J,Chen K,Mi X F,Chen T X,Ali J,Ye G Y,Xu J L,Li Z K.Identification and fine mapping of a stably expressed QTL for cold tolerance at the booting stage using an interconnected breeding population in rice[J].PLoS One,2015,10(12):e0145704.doi:10.1371/journal.pone.0145704.
[37]	Li J L,Pan Y H,Guo H F,Zhou L,Yang S M,Zhang Z Y,Yang J Z,Zhang H L,Li J J,Zeng Y W,Li Z C.Fine mapping of QTL qCTB10-2 that confers cold tolerance at the booting stage in rice[J].Theoretical and Applied Genetics,2018,131(1):157-166.doi:10.1007/s00122-017-2992-3.
[38]	Xiao N,Huang W N,Zhang X X,Gao Y,Li A H,Dai Y,Yu L,Liu G Q,Pan C H,Li Y H,Dai Z Y,Chen J M.Fine mapping of qRC10-2,a quantitative trait locus for cold tolerance of rice roots at seedling and mature stages[J].PLoS One,2014,9(5):e96046.doi:10.1371/journal.pone.0096046.
[39]	Wang Z F,Wang F H,Zhou R,Wang J F,Zhang H S.Identification of quantitative trait loci for cold tolerance during the germination and seedling stages in rice(Oryza sativa L.)[J].Euphytica,2011,181(3):405-413.doi:10.1007/s10681-011-0469-z.
[40]	Zhang Z H,Qu X S,Wan S,Chen L H,Zhu Y G.Comparison of QTL controlling seedling vigour under different temperature conditions using recombinant inbred lines in rice(Oryza sativa)[J].Annals of Botany,2005,95(3):423-429.doi:10.1093/aob/mci039.
[41]	王棋,范淑秀,郭江华,陈兆赫,梁银培,刘振宇,殷业超,王嘉宇.利用籼粳交RIL群体对水稻发芽期和苗期耐冷性的QTL分析[J].华北农学报,2019,34(1):83-88.doi:10.7668/hbnxb.201751291.
	Wang Q,Fan S X,Guo J H,Chen Z H,Liang Y P,Liu Z Y,Yin Y C,Wang J Y.QTL analysis of cold tolerance at germination and seedling stages of rice[J].Acta Agriculturae Boreali-Sinica,2019,34(1):83-88.
[42]	Fujino K,Matsuda Y.Genome-wide analysis of genes targeted by qLTG3-1 controlling low-temperature germinability in rice[J].Plant Molecular Biology,2009,72(1/2):137-152.doi:10.1007/s11103-009-9559-x.
[43]	詹庆才,曾曙珍,熊伏星,齐藤浩二,加藤明.水稻苗期耐冷性QTLs的分子定位[J].湖南农业大学学报(自然科学版),2003,29(1):7-11.doi:10.3321/j.issn:1007-1032.2003.01.002.
	Zhan Q C,Zeng S Z,Xiong F X,Koji S,Akira K.Molecular mapping of QTLs for seedling cold tolerance in rice[J].Journal of Hunan Agricultural University (Natural Sciences),2003,29(1):7-11.
[44]	Jiang L,Liu S J,Hou M Y,Tang J Y,Chen L M,Zhai H Q,Wan J M.Analysis of QTLs for seed low temperature germinability and anoxia germinability in rice(Oryza sativa L.)[J]. Field Crops Research,2006,98(1):68-75.doi:10.1016/j.fcr.2005.12.015.
[45]	潘招远.水稻种子低温发芽力QTL定位及qLTGR3-1的精细定位与转录组分析[D].广州:华南农业大学,2018.
	Pan Z Y.Mapping of QTLs controlling seed low temperature germinability and fine mapping and transcriptome analysis of qLTGR3-1 in rice[D].Guangzhou:South China Agricultural University,2018.
[46]	周勇,朱孝波,袁华,郑英,钦鹏,魏应海,王玉平,黄世君,李仕贵.水稻单片段代换系芽期和苗期耐冷性分析及耐冷性QTL鉴定[J].中国水稻科学,2013,27(4):381-388.doi:10.3969/j.issn.1001-7216.2013.04.007.
	Zhou Y,Zhu X B,Yuan H,Zheng Y,Qin P,Wei Y H,Wang Y P,Huang S J,Li S G.Characterization of cold tolerance and identification of cold tolerance QTLs for rice single segment substitution lines at plumule and seedling stages[J].Chinese Journal of Rice Science,2013,27(4):381-388.

级别 Level	秧苗恢复状态 Seedling recovery state
0	恢复后幼芽死亡
1	恢复后幼芽尚未死亡,但发育停止
2	恢复后发育非常缓慢,叶色淡
3	恢复后发育较慢,叶色较淡
4	恢复后能够正常生长,叶色较深

级别 Level	秧苗恢复状态 Seedling recovery state
0	恢复后幼芽死亡
1	恢复后幼芽尚未死亡,但发育停止
2	恢复后发育非常缓慢,叶色淡
3	恢复后发育较慢,叶色较淡
4	恢复后能够正常生长,叶色较深

染色体 Chromosome	染色体长度 /cM Chromosome length	标记数/个 Number of marker	标记间平均距离 /cM Mean distance between adjacent Bins
1	308.99	120	2.57
2	269.94	86	3.14
3	245.66	57	4.31
4	201.55	98	2.06
5	164.41	84	1.96
6	127.90	60	2.13
7	183.46	54	3.40
8	218.24	90	2.42
9	159.53	49	3.26
10	163.25	74	2.21
11	229.56	140	1.64
12	192.84	66	2.92

染色体 Chromosome	染色体长度 /cM Chromosome length	标记数/个 Number of marker	标记间平均距离 /cM Mean distance between adjacent Bins
1	308.99	120	2.57
2	269.94	86	3.14
3	245.66	57	4.31
4	201.55	98	2.06
5	164.41	84	1.96
6	127.90	60	2.13
7	183.46	54	3.40
8	218.24	90	2.42
9	159.53	49	3.26
10	163.25	74	2.21
11	229.56	140	1.64
12	192.84	66	2.92

时期 Period	性状 Trait	亲本Parents		重组自交系RIL population
时期 Period	性状 Trait	彩稻Caidao	WD	平均值±标准差 Means±s	变幅 Range	变异系数/% CV	偏度 Kurtosis	峰度 Skewness
发芽期	相对发芽率/%	90.82±1.29a	41.60±4.39b	59.16±14.07	3.49~95.45	23.78	-0.36	-0.93
Germination stage	平均发芽天数/d	11.21±0.47b	14.61±0.30a	13.21±3.59	8.00~15.67	27.18	-0.99	1.46
芽期	成苗率/%	75.00±2.55a	40.00±4.11b	68.44±22.60	10.00~100.00	33.02	-0.84	-0.16
Bud stage	耐冷级别	2.25±0.17a	1.00±0.09b	2.08±0.68	0.45~3.39	32.69	-0.45	-0.63

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