棉花重组自交系铃重性状的QTL定位
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摘要
【目的】铃重是构成棉花产量的基本因子之一。本研究旨在定位铃重QTL(Quantitative trait loci),为分析铃重遗传组成提供参考。【方法】以中棉所36和海陆渐渗系G2005组配的137个RILs (Recombinant inbred lines)家系为作图群体,利用RAD-seq(Restriction-site associated DNA sequencing)技术及SSR(Simple sequence repeat)标记,构建遗传连锁图谱,并对5个环境下的铃重进行QTL分析。【结果】构建了包含26个连锁群、6 434个标记、总长为4 071.98 cM、标记间平均距离为0.63 cM的遗传图谱。采用WinQTLCart 2.5软件的复合区间作图法进行QTL定位,共得到32个铃重QTL,分布于15条染色体,单个位点解释的表型变异率为4.46%~15.84%;qBW-A4-1、qBW-A4-2、qBW-A5-2、qBW-D9-1和qBW-D9-2能够在2个环境中检测到,解释5.07%~15.84%的表型变异率。【结论】本研究定位的主效QTL可用于分析铃重遗传机理。
[Objective] The aim of this study was to explore the quantitative trait locus(QTL) related to the boll weight.[Method]A single seed descended population of 137 recombinant inbred lines(RILs) was developed from the cross of upland cotton(Gossypium hirsutum L.) CCRI 36 and G2005,an introgression inbred line introgressed from G.barbadense.Using restriction-site associated DNA sequencing(RAD-seq),a genetic linkage map composed of 6 434 makers,including 6 295 single nucleotide polymorphisms(SNP) and 139 simple sequence repeat(SSR) markers,was developed from the RILs population.[Result] This map spanned 4 071.98 cM with an average distance of 0.63 cM between adjacent markers.QTL mapping was performed by using boll weight data of five environments through Win QTLCart 2.5 software.Thirty-two QTL,with 4.46%-15.84%explained phenotypic variation related boll weight,were detected and found distributing on 15 chromosomes.qBW-A4-1,qBW-A4-2,qBW-A5-2,qBW-D9-1,and qBW-D9-2 were detected in two environments,which explained 5.07%-15.84% of the phenotypic variation.[Conclusion] Major QTLs detected in this study will provide an important reference for analysis of the genetic mechanism of boll weight.
[Objective] The aim of this study was to explore the quantitative trait locus(QTL) related to the boll weight.[Method]A single seed descended population of 137 recombinant inbred lines(RILs) was developed from the cross of upland cotton(Gossypium hirsutum L.) CCRI 36 and G2005,an introgression inbred line introgressed from G.barbadense.Using restriction-site associated DNA sequencing(RAD-seq),a genetic linkage map composed of 6 434 makers,including 6 295 single nucleotide polymorphisms(SNP) and 139 simple sequence repeat(SSR) markers,was developed from the RILs population.[Result] This map spanned 4 071.98 cM with an average distance of 0.63 cM between adjacent markers.QTL mapping was performed by using boll weight data of five environments through Win QTLCart 2.5 software.Thirty-two QTL,with 4.46%-15.84%explained phenotypic variation related boll weight,were detected and found distributing on 15 chromosomes.qBW-A4-1,qBW-A4-2,qBW-A5-2,qBW-D9-1,and qBW-D9-2 were detected in two environments,which explained 5.07%-15.84% of the phenotypic variation.[Conclusion] Major QTLs detected in this study will provide an important reference for analysis of the genetic mechanism of boll weight.
引文
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[16]Paterson A H,Brubaker C L,Wendel J F.A rapid method for extraction of cotton(Gossypium spp.)genomic DNA suitable for RFLP or PCR analysis[J].Plant Molecular Biology Reporter,1993,11(2):122-127.
[17]Willing E M,Hoffmann M,Klein J D,et al.Paired-end RAD-seq for de novo assembly and marker design without available reference[J].Bioinformatics,2011,27(16):2187-2193.
[18]Miller M R,Dunham J P,Amores A,et al.Rapid and cost-effective polymorphism identification and genotyping using restriction site associated DNA(RAD)markers[J].Genome Research,2007,17(2):240-248.
[19]Liu Dongyuan,Ma Chouxian,Hong Weiguo,et al.Construction and analysis of high-density linkage map using high-throughput sequencing data[J].PLoS One,2014,9(6):e98855.https://doi.org/10.1371/journal.pone.0098855.
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[21]Mc Couch S R,Chen Xiuli,Panaud O,et al.Microsatellite marker development,mapping and applications in rice genetics and breeding[J].Plant Molecular Biology,1997,35(1/2):89-99.
[22]Zhang Tianzhen,Hu Yan,Jiang Wenkai,et al.Sequencing of allotetraploid cotton(Gossypium hirsutum L.acc.TM-1)provides a resource for fiber improvement[J].Nature Biotechnology,2015,33(5):531-537.
[23]贾晓昀.陆地棉种内高密度遗传图谱构建及重要农艺性状QTL定位[D].杨凌:西北农林科技大学,2017.Jia Xiaoyun.Inter-specific high-density genetic map construction and major agronomic traits QTL mapping for upland cotton(Gossypium hirsutum L.)[D].Yangling:Northwest A&F U-niversity,2017.
[24]Jia Xiaoyun,Pang Chaoyou,Wei Hengling,et al.High-density linkage map construction and QTL analysis for earliness-related traits in Gossypium hirsutum L.[J].BMC Genomics,2016,17(1):909.https://doi.org/10.1186/s12864-016-3269-y.
[25]Wang Hantao,Jin Xin,Zhang Beibei,et al.Enrichment of an intraspecific genetic map of upland cotton by developing markers using parental RAD sequencing[J].DNA Research,2015,22(2):147-160.
[26]Wang Hantao,Huang Cong,Guo Huanle,et al.QTL mapping for fiber and yield traits in upland cotton under multiple environments[J].PLoS One,2015,10(6):e130742.https://doi.org/10.1371/journal.pone.0130742.
[27]徐云碧.分子植物育种[M].北京:科学出版社,2014:132.Xu Yunbi.Molecular Plant Breeding[M].Beijing:Science Press,2014:132.
[28]郑巨云,George O,Khan M K R,等.毛棉苗期抗旱性状的QTL定位[J].棉花学报,2017,29(1):29-39.Zheng Juyun,George O,Khan M K R,et al.Mapping QTLs for traits related to drought tolerance at the seedling stage in an inter-specific[J].Cotton Science,2017,29(1):29-39.https://doi.org/10.11963/issn.1002-7807.201701004
[29]Nielsen R,Paul J S,Albrechtsen A,et al.Genotype and SNPcalling from next-generation sequencing data[J].Nature Reviews Genetics,2011,12(6):443-451.
[30]Lorenzo B,Sergio L,Ezio P,et al.Identification of SNP and SSR markers in eggplant using RAD tag sequencing[J].BMCGenomics,2011,12(1):1-9.
[31]Blenda A,Fang D D,Rami J F,et al.A high density consensus genetic map of tetraploid cotton that integrates multiple component maps through molecular marker redundancy check[J].PLoSOne,2012,7(9):e45739.https://doi.org/10.1371/journal.pone.0045739.
[32]Liang Zhao,LüYuanda,Cai Caiping,et al.Toward allotetraploid cotton genome assembly:integration of a high-density molecular genetic linkage map with DNA sequence information[J].BMC Genomics,2012,13(1):539.https://doi.org/10.1186/1471-2164-13-539.
[33]Tanksley S D,Nelson J C.Advanced backcross QTL analysis:a method for the simultaneous discovery and transfer of valuable QTLs from unadapted germplasm into elite breeding lines[J].Theoretical and Applied Genetics,1996,92(2):191-203.
[34]Jiang Chunxiao,Wright R J,El-Zik K M,et al.Polyploid formation created unique avenues for response to selection in Gossypium(cotton)[J].Proceedings of the National Academy of Sciences of the United States of America,1998,95(8):4419-4424.
[35]Yu Jing,Kohel R J,Smith C W.The construction of a tetraploid cotton genome wide comprehensive reference map[J].Genomics,2010,95(4):230-240.
[36]Wang Kai,Song Xianliang,Han Zhiguo,et al.Complete assignment of the chromosomes of Gossypium hirsutum L.by translocation and fluorescence in situ hybridization mapping[J].Theoretical and Applied Genetics,2006,113(1):73-80.
[2]董合忠,毛树春,张旺锋,等.棉花优化成铃栽培理论及其新发展[J].中国农业科学,2014,47(3):441-445.Dong Hezhong,Mao Shuchun,Zhang Wangfeng,et al.On boll-setting optimization theory for cotton cultivation and its new development[J].Scientia Agricultura Sinica,2014,47(3):441-445.
[3]Fedak G.Molecular aids for integration of alien chromatin through wide crosses[J].Genome,1999,42(42):584-591.
[4]邓琳,余小刚,姜朵,等.棉花分子育种研究进展[J].山东农业科学,2017,49(5):144-150.Deng Lin,Yu Xiaogang,Jiang Duo,et al.Research progress of cotton molecular breeding[J].Shandong Agricultural Sciences,2017,49(5):144-150.
[5]Wang Yonghong,Xue Yongbiao,Li Jiayang.Towards molecular breeding and improvement of rice in China[J].Trends in Plant Science,2005,10(12):610-614.
[6]程式华,庄杰云,曹立勇,等.超级杂交稻分子育种研究[J].中国水稻科学,2004,18(5):377-383.Cheng Shihua,Zhuang Jieyun,Cao Liyong,et al.Molecular breeding for super rice hybrids[J].Chinese Journal of Rice Science,2004,18(5):377-383.
[7]李成奇,郭旺珍,马晓玲,等.陆地棉衣分差异群体产量及产量构成因素的QTL标记和定位[J].棉花学报,2008,20(3):163-169.Li Chengqi,Guo Wangzhen,Ma Xiaoling,et al.Tagging and mapping of QTL for yield and its components in upland cotton(Gossypium hirsutum L.)population with varied lint percentage[J].Cotton Science,2008,20(3):163-169.
[8]王婷.陆地棉铃重相关性状的QTL定位分析[D].南京:南京农业大学,2013.Wang Ting.QTL mapping for traits related to boll weight in upland cotton(Gossypium hirsutum L.)[D].Nanjing:Nanjing A-gricultural University,2013.
[9]Wu Jiaxiang,Gutierrez O A,Jenkins J N,et al.Quantitative analysis and QTL mapping for agronomic and fiber traits in an RIpopulation of upland cotton[J].Euphytica,2009,165(2):231-245.
[10]Wang Baohua,Guo Wangzhen,Zhu Xiefeng,et al.QTL mapping of yield and yield components for elite hybrid derived-RILs in upland cotton[J].Journal of Genetics and Genomics,2007,34(1):35-45.
[11]Zhang Shuwen,Feng Liuchun,Xing Luting,et al.New QTLs for lint percentage and boll weight mined in introgression lines from two feral landraces into Gossypium hirsutum acc TM-1[J].Plant Breeding,2016,135(1):90-101.
[12]Fan Liping,Wang Liping,Wang Xinyi,et al.A high-density genetic map of extra-long staple cotton(Gossypium barbadense)constructed using genotyping-by sequencing based single nucleotide polymorphic markers and identification of fiber traits-related QTL in a recombinant inbred line population[J].BMC Genomics2018,19:489.https://doi.org/10.1186/s12864-018-4890-8.
[13]Yu Jiwen,Zhang Ke,Li Shuaiyang,et al.Mapping quantitative trait loci for lint yield and fiber quality across environments in a Gossypium hirsutum×Gossypium barbadense backcross inbred line population[J].Theoretical and Applied Genetics,2013,126(1):275-287.
[14]Zhang Zhen,Shang Haihong,Shi Yuzhen,et al.Construction of a high-density genetic map by specific locus amplified fragment sequencing(SLAF-seq)and its application to quantitative trait loci(QTL)analysis for boll weight in upland cotton(Gossypium hirsutum.)[J].BMC Plant Biology,2016,16(1):79.https://doi.org/10.1186/s12870-016-0741-4.
[15]杨继龙.利用RILs进行棉花早熟和纤维品质性状的QTL定位研究[D].武汉:华中农业大学,2013.Yang Jilong.QTL location of earliness and fiber quality in cotton using RILs[D].Wuhan:Huazhong Agricultural University,2013.
[16]Paterson A H,Brubaker C L,Wendel J F.A rapid method for extraction of cotton(Gossypium spp.)genomic DNA suitable for RFLP or PCR analysis[J].Plant Molecular Biology Reporter,1993,11(2):122-127.
[17]Willing E M,Hoffmann M,Klein J D,et al.Paired-end RAD-seq for de novo assembly and marker design without available reference[J].Bioinformatics,2011,27(16):2187-2193.
[18]Miller M R,Dunham J P,Amores A,et al.Rapid and cost-effective polymorphism identification and genotyping using restriction site associated DNA(RAD)markers[J].Genome Research,2007,17(2):240-248.
[19]Liu Dongyuan,Ma Chouxian,Hong Weiguo,et al.Construction and analysis of high-density linkage map using high-throughput sequencing data[J].PLoS One,2014,9(6):e98855.https://doi.org/10.1371/journal.pone.0098855.
[20]Zeng Zhaobang.Precision mapping of quantitative trait loci[J].Genetics,1994,136(4):1457-1468.
[21]Mc Couch S R,Chen Xiuli,Panaud O,et al.Microsatellite marker development,mapping and applications in rice genetics and breeding[J].Plant Molecular Biology,1997,35(1/2):89-99.
[22]Zhang Tianzhen,Hu Yan,Jiang Wenkai,et al.Sequencing of allotetraploid cotton(Gossypium hirsutum L.acc.TM-1)provides a resource for fiber improvement[J].Nature Biotechnology,2015,33(5):531-537.
[23]贾晓昀.陆地棉种内高密度遗传图谱构建及重要农艺性状QTL定位[D].杨凌:西北农林科技大学,2017.Jia Xiaoyun.Inter-specific high-density genetic map construction and major agronomic traits QTL mapping for upland cotton(Gossypium hirsutum L.)[D].Yangling:Northwest A&F U-niversity,2017.
[24]Jia Xiaoyun,Pang Chaoyou,Wei Hengling,et al.High-density linkage map construction and QTL analysis for earliness-related traits in Gossypium hirsutum L.[J].BMC Genomics,2016,17(1):909.https://doi.org/10.1186/s12864-016-3269-y.
[25]Wang Hantao,Jin Xin,Zhang Beibei,et al.Enrichment of an intraspecific genetic map of upland cotton by developing markers using parental RAD sequencing[J].DNA Research,2015,22(2):147-160.
[26]Wang Hantao,Huang Cong,Guo Huanle,et al.QTL mapping for fiber and yield traits in upland cotton under multiple environments[J].PLoS One,2015,10(6):e130742.https://doi.org/10.1371/journal.pone.0130742.
[27]徐云碧.分子植物育种[M].北京:科学出版社,2014:132.Xu Yunbi.Molecular Plant Breeding[M].Beijing:Science Press,2014:132.
[28]郑巨云,George O,Khan M K R,等.毛棉苗期抗旱性状的QTL定位[J].棉花学报,2017,29(1):29-39.Zheng Juyun,George O,Khan M K R,et al.Mapping QTLs for traits related to drought tolerance at the seedling stage in an inter-specific[J].Cotton Science,2017,29(1):29-39.https://doi.org/10.11963/issn.1002-7807.201701004
[29]Nielsen R,Paul J S,Albrechtsen A,et al.Genotype and SNPcalling from next-generation sequencing data[J].Nature Reviews Genetics,2011,12(6):443-451.
[30]Lorenzo B,Sergio L,Ezio P,et al.Identification of SNP and SSR markers in eggplant using RAD tag sequencing[J].BMCGenomics,2011,12(1):1-9.
[31]Blenda A,Fang D D,Rami J F,et al.A high density consensus genetic map of tetraploid cotton that integrates multiple component maps through molecular marker redundancy check[J].PLoSOne,2012,7(9):e45739.https://doi.org/10.1371/journal.pone.0045739.
[32]Liang Zhao,LüYuanda,Cai Caiping,et al.Toward allotetraploid cotton genome assembly:integration of a high-density molecular genetic linkage map with DNA sequence information[J].BMC Genomics,2012,13(1):539.https://doi.org/10.1186/1471-2164-13-539.
[33]Tanksley S D,Nelson J C.Advanced backcross QTL analysis:a method for the simultaneous discovery and transfer of valuable QTLs from unadapted germplasm into elite breeding lines[J].Theoretical and Applied Genetics,1996,92(2):191-203.
[34]Jiang Chunxiao,Wright R J,El-Zik K M,et al.Polyploid formation created unique avenues for response to selection in Gossypium(cotton)[J].Proceedings of the National Academy of Sciences of the United States of America,1998,95(8):4419-4424.
[35]Yu Jing,Kohel R J,Smith C W.The construction of a tetraploid cotton genome wide comprehensive reference map[J].Genomics,2010,95(4):230-240.
[36]Wang Kai,Song Xianliang,Han Zhiguo,et al.Complete assignment of the chromosomes of Gossypium hirsutum L.by translocation and fluorescence in situ hybridization mapping[J].Theoretical and Applied Genetics,2006,113(1):73-80.