利用BSA-seq发掘棉花适宜机采的果枝长度相关QTL
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摘要
【目的】将群体分离分析法与下一代测序技术相结合,定位与棉花果枝长度关联的数量性状位点。【方法】以Ⅰ式果枝品系苏机棉125和Ⅱ式果枝品种泗抗1号为亲本,构建棉花F2分离群体。根据F2群体单株中部果枝节间平均长度,选择极端性状单株分为2组,构建DNA混池。再对2个混池进行重测序,分析2个混池之间的单核苷酸多态性和插入缺失突变,并利用欧式距离法关联与果枝节间长度相关的数量性状位点。【结果】利用测序获得的单核苷酸多态性位点数据,在A3染色体上定位到1个与果枝节间长度关联的区域,区间范围为0.8 Mbp;利用测序获得的缺失突变位点数据,也在A3染色体上定位到1个关联区域,区间范围为1.09 Mbp;2个关联区域互相重合,重合区间为0.77 Mbp。【结论】本研究中Ⅰ式果枝相关基因被定位在A3染色体上,说明棉花Ⅰ式果枝和〇式果枝的差异是因为遗传位点和模式的不同,而不是同一基因的剂量效应。
[Objective] This study aims to identify quantitative trait loci(QTLs) associated with cotton fruit branch length by using the combination of bulked-segregant analysis(BSA) and next-generation sequencing(NGS) method. [Method] In this study, the cotton F2 segregating population was developed with the short branch line Sujimian 125 and long-branch variety Sikang 1 as cross parents. According to the average internode length of fruit branches in middle, extreme individuals in F2 population were divided into two groups to generate the bulked DNA samples. The whole-genome resequencing of two DNA bulks was applied to analyze the single nucleotide polymorphism(SNP) and insertion-deletion(InDel) between two groups, and the fruit branch internode length related QTLs were detected using Euclidean distance(ED). [Result] With SNP data obtained from sequencing,a 0.8 Mbp range associated region on chromosome A3 was identified; with InDel data obtained from sequencing, a 1.09 Mbp range associated region on chromosome A3 was identified. Two regions overlapped, and the overlapped range was 0.77 Mbp.[Conclusion] This result suggested that the difference between I-type fruit branch and zero-type was due to different genetic locus and pattern rather than dosage effect of the same gene.
[Objective] This study aims to identify quantitative trait loci(QTLs) associated with cotton fruit branch length by using the combination of bulked-segregant analysis(BSA) and next-generation sequencing(NGS) method. [Method] In this study, the cotton F2 segregating population was developed with the short branch line Sujimian 125 and long-branch variety Sikang 1 as cross parents. According to the average internode length of fruit branches in middle, extreme individuals in F2 population were divided into two groups to generate the bulked DNA samples. The whole-genome resequencing of two DNA bulks was applied to analyze the single nucleotide polymorphism(SNP) and insertion-deletion(InDel) between two groups, and the fruit branch internode length related QTLs were detected using Euclidean distance(ED). [Result] With SNP data obtained from sequencing,a 0.8 Mbp range associated region on chromosome A3 was identified; with InDel data obtained from sequencing, a 1.09 Mbp range associated region on chromosome A3 was identified. Two regions overlapped, and the overlapped range was 0.77 Mbp.[Conclusion] This result suggested that the difference between I-type fruit branch and zero-type was due to different genetic locus and pattern rather than dosage effect of the same gene.
引文
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[8]张云辉,张所兵,林静,等.利用BSA法检测水稻条纹叶枯病高效应抗性位点[J].华北农学报, 2014, 29(2):85-88.Zhang Y H, Zhang S B, Lin J, et al. Detection of high effect site for resistance to rice stripe virus by BSA[J]. Acta Agriculturae Boreali-Sinica, 2014, 29(2):85-88.
[9] Korol A, Frenkel Z, Cohen L, et al. Fractioned DNA pooling:a new cost-effective strategy for fine mapping of quantitative trait loci[J]. Genetics, 2007, 176(4):2611-2623.
[10] Mansur L M, Orf J, Lark K G. Determining the linkage of quantitative trait loci to RFLP markers using extreme phenotypes of recombinant inbreds of soybean(Glycine max L. Merr.)[J].Theoretical and Applied Genetics, 1993, 86(8):914-918.
[11] Darvasi A, Soller M. Selective DNA pooling for determination of linkage between a molecular marker and a quantitative trait locus[J]. Genetics, 1994, 138(4):1365-1373.
[12] Takagi H, Abe A, Yoshida K, et al. QTL-seq:rapid mapping of quantitative trait loci in rice by whole genome resequencing of DNA from two bulked populations[J]. Plant Journal for Cell&Molecular Biology, 2013, 74(1):174-183.
[13] Trick M, Adamski N M, Mugford S G, et al. Combining SNP discovery from next-generation sequencing data with bulked segregant analysis(BSA)to fine-map genes in polyploid wheat[J]. BMC Plant Biology, 2012, 12(1):14. https://doi.org/10.1186/1471-2229-12-14
[14] Mokry M, Nijman I J, Dijken A V, et al. Identification of factors required for meristem function in Arabidopsis using a novel next generation sequencing fast forward genetics approach[J]. BMC Genomics, 2011, 12(1):256. https://doi.org/10.1186/1471-2164-12-256
[15] Wei Q Z, Fu W Y, Wang Y Z, et al. Rapid identification of fruit length loci in cucumber(Cucumis sativus L.)using next-generation sequencing(NGS)-based QTL analysis[J]. Scientific Reports, 2016, 6:27496. https://doi.org/10.1038/srep27496
[16] Song J, Li Z, Liu Z X, et al. Next-generation sequencing from bulked-segregant analysis accelerates the simultaneous identification of two qualitative genes in soybean[J]. Frontiers in Plant Science, 2017, 8:919. https://doi.org/10.3389/fpls.2017.00919
[17]狄佳春,陈旭升,赵亮.陆地棉短果枝的遗传与育种利用研究[J].中国棉花, 2014, 41(11):5-7.Di J C, Chen X S, Zhao L. Genetic research and breeding evaluation on short branch trait of Gossypium hirsutum L.[J]. China Cotton, 2014, 41(11):5-7.
[18]翟腾飞.棉花短果枝基因cl的精细定位[D].重庆:西南大学,2015.Zhai T F. Fine mapping of short fruiting branch gene cl in cotton[D]. Chongqing:Southwest University, 2015.
[19] Si Z F, Liu H, Zhu J K, et al. Mutation of SELF-PRUNING homologs in cotton promotes short-branching plant architecture[J]. Journal of Experimental Botany, 2018, 69(10):2543-2553.
[20]陈立昶,吉守银,孙宝林,等.泗抗1号棉花新品种[J].中国棉花, 2006, 33(8):24-25.Chen L C, Ji S Y, Sun B L, et al. New cotton variety sikang-1[J]. China Cotton, 2006, 33(8):24-25.
[21]杜雄明,周忠丽.棉花种质资源描述规范和数据标准[M].北京:中国农业出版社, 2005:11-14.Du X M, Zhou Z L. Specification and data standard for description of cotton germplasm resources[M]. Beijing:China Agriculture Press, 2005:11-14.
[22] 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.
[23] Deng Y, Jianqi L I, Songfeng W U, et al. Integrated nr database in protein annotation system and its localization[J]. Computer Engineering, 2006, 32(5):71-72.
[24] Hill J T, Demarest B L, Bisgrove B W, et al. MMAPPR:mutation mapping analysis pipeline for pooled RNA-seq[J]. Genome Research, 2013, 23(4):687-697.
[25]杜雄明.棉花果枝类型划分的统一化[J].中国棉花, 1996, 23(4):19.Du X M. The unification of cotton branch classification[J]. China Cotton, 1996, 23(4):19.
[26]刘杰.棉花零式果枝性状候选基因功能的初步分析[D].阿拉尔:塔里木大学, 2017.Liu J. Preliminary analysis of function for candidate nulliplex-branch gene in cotton[D]. Alar:Tarim University, 2017.
[2]齐海坤,严根土,王宁,等.株型育种在机采棉应用中的研究进展[J].中国农业信息, 2016, 2(2):75-77.Qi H K, Yan G T, Wang N, et al. Progress of plant type breeding used in mechanical harvest[J]. China Agricultural Information,2016, 2(2):75-77.
[3]尹国,张玉娟,韩秋成,等.浅析发展机采棉存在的几个问题和对策[J].棉花科学, 2015, 37(1):10-12.Yin G, Zhang Y J, Han Q C, et al. Several problems and countermeasures abo ut the development of machine-packed cotton[J].Cotton Sciences, 2015, 37(1):10-12.
[4]宋敏.新疆棉花主栽品种机采特性的分析[D].乌鲁木齐:新疆农业大学, 2015.Song M. Analysis to the characteristics of mining machine of main cotton varieties in Xinjiang[D]. Urumqi:Xinjiang Agricultural University, 2015.
[5]肖松华,吴巧娟,刘剑光,等.棉花机采品种理想株型模式研究[J].江西农业学报, 2010, 22(8):1-4.Xiao S H, Wu Q J, Liu J G, et al. Study on ideaI plant type of cotton cultivar for mechanical cultivation and harvest[J]. Acta Agriculturae Jiangxi, 2010, 22(8):1-4.
[6] Michelmore R W, Paran I, Kesseli R. Identification of markers linked to disease-resistance genes by bulked segregant analysis:a rapid method to detect markers in specific genomic regions by using segregating populations[J]. Proceedings of the National Academy of Sciences USA, 1991, 88(21):9828-9832.
[7]方宣钧,吴为人,唐纪良.作物DNA标记辅助育种[M].北京:科学出版社, 2001:60-61.Fang X J, Wu W R, Tang J L. Crop DNA marker assisted breeding[M]. Beijing:Science Press, 2001:60-61.
[8]张云辉,张所兵,林静,等.利用BSA法检测水稻条纹叶枯病高效应抗性位点[J].华北农学报, 2014, 29(2):85-88.Zhang Y H, Zhang S B, Lin J, et al. Detection of high effect site for resistance to rice stripe virus by BSA[J]. Acta Agriculturae Boreali-Sinica, 2014, 29(2):85-88.
[9] Korol A, Frenkel Z, Cohen L, et al. Fractioned DNA pooling:a new cost-effective strategy for fine mapping of quantitative trait loci[J]. Genetics, 2007, 176(4):2611-2623.
[10] Mansur L M, Orf J, Lark K G. Determining the linkage of quantitative trait loci to RFLP markers using extreme phenotypes of recombinant inbreds of soybean(Glycine max L. Merr.)[J].Theoretical and Applied Genetics, 1993, 86(8):914-918.
[11] Darvasi A, Soller M. Selective DNA pooling for determination of linkage between a molecular marker and a quantitative trait locus[J]. Genetics, 1994, 138(4):1365-1373.
[12] Takagi H, Abe A, Yoshida K, et al. QTL-seq:rapid mapping of quantitative trait loci in rice by whole genome resequencing of DNA from two bulked populations[J]. Plant Journal for Cell&Molecular Biology, 2013, 74(1):174-183.
[13] Trick M, Adamski N M, Mugford S G, et al. Combining SNP discovery from next-generation sequencing data with bulked segregant analysis(BSA)to fine-map genes in polyploid wheat[J]. BMC Plant Biology, 2012, 12(1):14. https://doi.org/10.1186/1471-2229-12-14
[14] Mokry M, Nijman I J, Dijken A V, et al. Identification of factors required for meristem function in Arabidopsis using a novel next generation sequencing fast forward genetics approach[J]. BMC Genomics, 2011, 12(1):256. https://doi.org/10.1186/1471-2164-12-256
[15] Wei Q Z, Fu W Y, Wang Y Z, et al. Rapid identification of fruit length loci in cucumber(Cucumis sativus L.)using next-generation sequencing(NGS)-based QTL analysis[J]. Scientific Reports, 2016, 6:27496. https://doi.org/10.1038/srep27496
[16] Song J, Li Z, Liu Z X, et al. Next-generation sequencing from bulked-segregant analysis accelerates the simultaneous identification of two qualitative genes in soybean[J]. Frontiers in Plant Science, 2017, 8:919. https://doi.org/10.3389/fpls.2017.00919
[17]狄佳春,陈旭升,赵亮.陆地棉短果枝的遗传与育种利用研究[J].中国棉花, 2014, 41(11):5-7.Di J C, Chen X S, Zhao L. Genetic research and breeding evaluation on short branch trait of Gossypium hirsutum L.[J]. China Cotton, 2014, 41(11):5-7.
[18]翟腾飞.棉花短果枝基因cl的精细定位[D].重庆:西南大学,2015.Zhai T F. Fine mapping of short fruiting branch gene cl in cotton[D]. Chongqing:Southwest University, 2015.
[19] Si Z F, Liu H, Zhu J K, et al. Mutation of SELF-PRUNING homologs in cotton promotes short-branching plant architecture[J]. Journal of Experimental Botany, 2018, 69(10):2543-2553.
[20]陈立昶,吉守银,孙宝林,等.泗抗1号棉花新品种[J].中国棉花, 2006, 33(8):24-25.Chen L C, Ji S Y, Sun B L, et al. New cotton variety sikang-1[J]. China Cotton, 2006, 33(8):24-25.
[21]杜雄明,周忠丽.棉花种质资源描述规范和数据标准[M].北京:中国农业出版社, 2005:11-14.Du X M, Zhou Z L. Specification and data standard for description of cotton germplasm resources[M]. Beijing:China Agriculture Press, 2005:11-14.
[22] 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.
[23] Deng Y, Jianqi L I, Songfeng W U, et al. Integrated nr database in protein annotation system and its localization[J]. Computer Engineering, 2006, 32(5):71-72.
[24] Hill J T, Demarest B L, Bisgrove B W, et al. MMAPPR:mutation mapping analysis pipeline for pooled RNA-seq[J]. Genome Research, 2013, 23(4):687-697.
[25]杜雄明.棉花果枝类型划分的统一化[J].中国棉花, 1996, 23(4):19.Du X M. The unification of cotton branch classification[J]. China Cotton, 1996, 23(4):19.
[26]刘杰.棉花零式果枝性状候选基因功能的初步分析[D].阿拉尔:塔里木大学, 2017.Liu J. Preliminary analysis of function for candidate nulliplex-branch gene in cotton[D]. Alar:Tarim University, 2017.
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