小麦SSR和SNP标记在Taichung29×白芒麦重组自交系群体中的偏分离分析
|
摘要
为明确小麦SSR和SNP标记在Taichung29×白芒麦重组自交系群体中的偏分离现象及产生原因,提高遗传图谱构建的质量,以我国小麦农家品种白芒麦与感病品种Taichung29杂交构建的包含181个F8代重组自交系(recombinant inbred line,RIL)为试验材料,利用筛选得到的110个SSR标记和6 859个SNPs多态性标记进行偏分离分析。结果显示,共有1 069个标记位点表现出偏分离,占标记总数的15.3%。其中,683个标记偏向于白芒麦,占偏分离标记数的63.9%;386个标记偏向于Taichung29,占偏分离标记数的36.1%。偏分离位点在染色体上分布大多数是成簇出现,有76.3%的偏分离标记形成偏分离热点区域(segregation distortion region,SDR),共检测到了74个SDR,分布在15条染色体上,其中B染色体组包含有最多的SDR,偏分离方向为白芒麦。抗病亲本白芒麦和感病亲本Taichung29的基因型在RIL群体中分布比例为1.03∶1.00,接近1∶1的理论比例,标记在RIL群体整体分离比基本平衡,显示出偏分离主要是由遗传因素引起。
The analyses of segregation distortion phenomenon and reasons in the Taichung29 × baimangmai recombinant inbred wheat lines by using SSR and SNP markers are helpful for improving the quality of the genetic map. By using a population consisting of 181 F8 recombinant inbred lines(RIL) derived from a common wheat variety Taichung29 crossed by a landrace Baimangmai, segregation distortion analysis was performed with the 110 SSRs and 6859 SNPs polymorphic markers developed for the population. The results showed that a total of 1 069 marker loci showed segregation distortion, accounting for15.3% of the total marker number of the wheat genetic maps, of which 683 markers(63.9% of the segregation distortion total markers) distributed on wheat genomes distorted to parent Baimangmai, and 386 markers(36.1% of the segregation distortion total ones) distorted to parent Taichung29. Meanwhile, segregation distortion regions usually distributed as clusters. Among the segregation distortion markers,76.3% formed segregation distortion regions(SDRs), and a total of 74 SDRs were detected, scattering on15 chromosomes. Most SDRs lay on genome B, genetically distorted to parent Baimangmai. The distribution proportion of the resistant parent baimangmai and susceptible parent Taichung29 genotypes in RIL population was 1.03:1.00, close to the theoretical ratio of 1∶1, and the overall separation ratio was basically balanced, showing that segregation was mainly caused by genetic factors.
The analyses of segregation distortion phenomenon and reasons in the Taichung29 × baimangmai recombinant inbred wheat lines by using SSR and SNP markers are helpful for improving the quality of the genetic map. By using a population consisting of 181 F8 recombinant inbred lines(RIL) derived from a common wheat variety Taichung29 crossed by a landrace Baimangmai, segregation distortion analysis was performed with the 110 SSRs and 6859 SNPs polymorphic markers developed for the population. The results showed that a total of 1 069 marker loci showed segregation distortion, accounting for15.3% of the total marker number of the wheat genetic maps, of which 683 markers(63.9% of the segregation distortion total markers) distributed on wheat genomes distorted to parent Baimangmai, and 386 markers(36.1% of the segregation distortion total ones) distorted to parent Taichung29. Meanwhile, segregation distortion regions usually distributed as clusters. Among the segregation distortion markers,76.3% formed segregation distortion regions(SDRs), and a total of 74 SDRs were detected, scattering on15 chromosomes. Most SDRs lay on genome B, genetically distorted to parent Baimangmai. The distribution proportion of the resistant parent baimangmai and susceptible parent Taichung29 genotypes in RIL population was 1.03:1.00, close to the theoretical ratio of 1∶1, and the overall separation ratio was basically balanced, showing that segregation was mainly caused by genetic factors.
引文
Allen AM,Winfield MO,Burridge AJ,Downie RC,Benbow HR,Barker GL,Wilkinson PA,Coghill J,Waterfall C,Davassi A,et al.2017.Characterization of a wheat breeders’array suitable for high-throughput SNP genotyping of global accessions of hexaploid bread wheat(Triticum aestivum).Plant Biotechnology Journal,15(3):390-401
An M.2012.Construction of molecular genetic linkage map and QTLmapping analysis of flag leaf traits associated with drought tolerance in wheat(Triticum aestivum L).Master Thesis.Lanzhou:Gansu Agricultural University(in Chinese)[安梅.2012.小麦分子遗传连锁图谱构建及旗叶相关抗旱性状QTL定位分析.硕士学位论文.兰州:甘肃农业大学]
Cavanagh CR,Chao S,Wang S,Huang BE,Stephen S,Kiani S,Forrest K,Saintenac C,Brownguedira GL,Akhunova A.2013.Genome-wide comparative diversity uncovers multiple targets of selection for improvement in hexaploid wheat landraces and cultivars.Proceedings of the National Academy of Science,110(20):8057
Ching A,Caldwell KS,Jung M,Dolan M,Smith OS,Tingey S,Morgante M,Rafalski AJ.2002.SNP frequency,haplotype structure and linkage disequilibrium in elite maize inbred lines.BMC Genetics,3(1):1-14
Cloutier S,Cappadocia M,Landry BS.1997.Analysis of RFLP mapping inaccuracy in Brassica napus L.Theoretical and Applied Genetics,95(1):83-91
Faris JD,Laddomada B,Gill BS.1998.Molecular mapping of segregation distortion loci in Aegilops tauschii.Genetics,149:319-327
Hoskins RA,Phan AC,Naeemuddin M,Mapa FA,Ruddy DA,Ryan JJ,Young LM,Wells T,Kopczynski C,Ellis MC.2001.Single nucleotide polymorphism markers for genetic mapping in Drosophila melanogaster.Genome Research,11(6):1100-1113
Jelena VE.2008.An impact of environment on segregation ratio of qualitative traits in maize.Genetika,40(2):145-156
Jia JZ.1997.Advances in molecular markers of Wheat.Biotechnology Bulletin,(2):1-5(in Chinese)[贾继增.1997.小麦分子标记研究进展.生物技术通报,(2):1-5]
Konishi T,Yano Y,Abe K.1992.Geographic distribution of alleles at the Ga2 locus for segregation distortion in barley.Theoretical&Applied Genetics,85(4):419-422
Lander ES.1996.The new genomics:global views of biology.Science,274(5287):536-539
Li HH,Zhang LY,Wang JK.2010.Analysis and answers to frequently asked questions in quantitative trait locus mapping.Acta Agronomica Sinica,36(6):918-931(in Chinese)[李慧慧,张鲁燕,王建康.2010.数量性状基因定位研究中若干常见问题的分析与解答.作物学报,36(6):918-931]
Liu F,Wu XL,Chen SY.2000.Segregation distortion of molecular markers in recombinant inbred population in soybean.Journal of Genetics and Genomics,27(10):883-887(in Chinese)[刘峰,吴晓雷,陈受宜.2000.大豆分子标记在RIL群体中的偏分离分析.Journal of Genetics and Genomics,27(10):883-887]
Liu HY,Cui JT,Gao YM.2009.Progress of segregation distortion.Journal of Plant Genetic Resources,10(4):613-617(in Chinese)[刘海燕,崔金腾,高用明.2009.遗传群体偏分离研究进展.植物遗传资源学报,10(4):613-617]
Lorieux M,Goffinet B,Perrier X,de León DG,Lanaud C.1995.Maximum-likelihood models for mapping genetic markers showing segregation distortion.1.backcross populations.Theoretical and Applied Genetics,90(1):73-80
Lu H,Romero-Severson J,Bernardo R.2002.Chromosomal regions associated with segregation distortion in maize.Theoretical&Applied Genetics,105(4):622-628
Nakagahara M.1972.Genetic mechanism on the distorted segregation of marker genes belonging to the eleventh linkage group in cultivated rice.Japanese Journal of Breeding,22(4):232-238
Peng Y,Liang YS,Wang SQ,Wu FQ,Li SC,Deng QM,Li P.2006.Analysis of segregation distortion of SSR markers in RI population of rice.Molecular Plant Breeding,4(6):786-790(in Chinese)[彭勇,梁永书,王世全,吴发强,李双成,邓其明,李平.2006.水稻SSR标记在RI群体的偏分离分析.分子植物育种,4(6):786-790]
Rafalski JA.2002.Novel genetic mapping tools in plants:SNPs and LD-based approaches.Plant Science,162(3):329-333
Rogers SO,Bendich AJ.1985.Extraction of DNA from milligram amounts of fresh,herbarium and mummified plant tissues.Plant Molecular Biology,5(2):69-76
Somers DJ,Isaac P,Edwards K.2004.A high-density microsatellite consensus map for bread wheat(Triticum aestivum L.).Theoretical&Applied Genetics,109(6):1105-1114
Wang HL,Liu HX,Wang N,Zhao P,Li CL,Wang ZH.2014.Genetic analysis of segregation of SNP and SSR markers in wheat RILpopulation from the cross Heyne×Lakin.Journal of Triticease Crops,34(9):1205-1209(in Chinese)[王慧兰,刘红侠,王娜,赵朋,李春莲,王中华.2014.SNP和SSR标记在小麦Heyne×Lakin重组自交系群体中的偏分离分析.麦类作物学报,34(9):1205-1209]
Wang JK,Li HH,Zhang LY.2014.Genetic mapping and breeding design.Beijing:Science Press,pp.258-266(in Chinese)[王建康,李慧慧,张鲁燕.2014.基因定位与育种设计.北京:科学出版社,pp.258-266]
Wang S,Wong D,Forrest K,Allen A,Chao S,Huang BE,Maccaferri M,Salvi S,Milner SG,Cattivelli L,et al.2014.Characterization of polyploid wheat genomic diversity using a high-density 90000single nucleotide polymorphism array.Plant Biotechnology Journal,12(6):787-796
Xu Y,Zhu L,Xiao J,Huang N,Mc Couch SR.1997.Chromosomal regions associated with segregation distortion of molecular markers in F2,backcross,doubled haploid,and recombinant inbred populations in rice(Oryza sativa L.).Molecular&General Genetics:Mgg,253(5):535
Yamagishi M,Takeuchi Y,Tanaka I,Kono I,Murai K,Yano M.2010.Segregation distortion in F2,and doubled haploid populations of temperate japonica,rice.Journal of Genetics,89(2):237-241
Zeng YC,Li J,Yang YM,Liao J,Peng ZS,Tang YL,Yang WY.2007.Segregation distortion in the recombinant inbred lines of Chuanyu12×Syn780 by SSR markers.Southwest China Journal of Agricultural Sciences,20(2):230-233(in Chinese)[曾云超,李俊,杨玉敏,廖杰,彭正松,汤永禄,杨武云.2007.利用SSR标记分析川育12×人工合成小麦Syn780重组自交系群体中的偏分离现象.西南农业学报,20(2):230-233]
Zhang F,Wan XQ,Pan GT.2006.Genetic analysis of segregation distortion of molecular markers in maize F2population.Acta Agronomica Sinica,32(9):1391-1396(in English)[张帆,万雪琴,潘光堂.2006.玉米F2群体分子标记偏分离的遗传分析.作物学报,32(9):1391-1396]
Zhang WJ,Yuan HM,Chen DS,Wang XL,Kang L,He JS.2015.Advances in studies on physiological and biochemical indexes and QTL for drought resistance in wheat.Agricultural Research in the Arid Areas,33(6):139-148(in Chinese)[张维军,袁汉民,陈东升,王小亮,亢玲,何进尚.2015.小麦抗旱性生理生化机制及QTL研究进展.干旱地区农业研究,33(6):139-148]
Zhao P,Li TT,Zhang YY,Wang N,Li CL,Wang ZH.2014.Detection of wheat chromosome segregation distortion region using SNPmarkers and RIL population of Ning 7840/Clark.Journal of Triticease Crops,34(11):1453-1458(in Chinese)[赵朋,李婷婷,张芸芸,王娜,李春莲,王中华.2014.利用SNP标记和宁7840×Clark重组自交系(RIL)群体检测小麦染色体偏分离区域.麦类作物学报,34(11):1453-1458]
An M.2012.Construction of molecular genetic linkage map and QTLmapping analysis of flag leaf traits associated with drought tolerance in wheat(Triticum aestivum L).Master Thesis.Lanzhou:Gansu Agricultural University(in Chinese)[安梅.2012.小麦分子遗传连锁图谱构建及旗叶相关抗旱性状QTL定位分析.硕士学位论文.兰州:甘肃农业大学]
Cavanagh CR,Chao S,Wang S,Huang BE,Stephen S,Kiani S,Forrest K,Saintenac C,Brownguedira GL,Akhunova A.2013.Genome-wide comparative diversity uncovers multiple targets of selection for improvement in hexaploid wheat landraces and cultivars.Proceedings of the National Academy of Science,110(20):8057
Ching A,Caldwell KS,Jung M,Dolan M,Smith OS,Tingey S,Morgante M,Rafalski AJ.2002.SNP frequency,haplotype structure and linkage disequilibrium in elite maize inbred lines.BMC Genetics,3(1):1-14
Cloutier S,Cappadocia M,Landry BS.1997.Analysis of RFLP mapping inaccuracy in Brassica napus L.Theoretical and Applied Genetics,95(1):83-91
Faris JD,Laddomada B,Gill BS.1998.Molecular mapping of segregation distortion loci in Aegilops tauschii.Genetics,149:319-327
Hoskins RA,Phan AC,Naeemuddin M,Mapa FA,Ruddy DA,Ryan JJ,Young LM,Wells T,Kopczynski C,Ellis MC.2001.Single nucleotide polymorphism markers for genetic mapping in Drosophila melanogaster.Genome Research,11(6):1100-1113
Jelena VE.2008.An impact of environment on segregation ratio of qualitative traits in maize.Genetika,40(2):145-156
Jia JZ.1997.Advances in molecular markers of Wheat.Biotechnology Bulletin,(2):1-5(in Chinese)[贾继增.1997.小麦分子标记研究进展.生物技术通报,(2):1-5]
Konishi T,Yano Y,Abe K.1992.Geographic distribution of alleles at the Ga2 locus for segregation distortion in barley.Theoretical&Applied Genetics,85(4):419-422
Lander ES.1996.The new genomics:global views of biology.Science,274(5287):536-539
Li HH,Zhang LY,Wang JK.2010.Analysis and answers to frequently asked questions in quantitative trait locus mapping.Acta Agronomica Sinica,36(6):918-931(in Chinese)[李慧慧,张鲁燕,王建康.2010.数量性状基因定位研究中若干常见问题的分析与解答.作物学报,36(6):918-931]
Liu F,Wu XL,Chen SY.2000.Segregation distortion of molecular markers in recombinant inbred population in soybean.Journal of Genetics and Genomics,27(10):883-887(in Chinese)[刘峰,吴晓雷,陈受宜.2000.大豆分子标记在RIL群体中的偏分离分析.Journal of Genetics and Genomics,27(10):883-887]
Liu HY,Cui JT,Gao YM.2009.Progress of segregation distortion.Journal of Plant Genetic Resources,10(4):613-617(in Chinese)[刘海燕,崔金腾,高用明.2009.遗传群体偏分离研究进展.植物遗传资源学报,10(4):613-617]
Lorieux M,Goffinet B,Perrier X,de León DG,Lanaud C.1995.Maximum-likelihood models for mapping genetic markers showing segregation distortion.1.backcross populations.Theoretical and Applied Genetics,90(1):73-80
Lu H,Romero-Severson J,Bernardo R.2002.Chromosomal regions associated with segregation distortion in maize.Theoretical&Applied Genetics,105(4):622-628
Nakagahara M.1972.Genetic mechanism on the distorted segregation of marker genes belonging to the eleventh linkage group in cultivated rice.Japanese Journal of Breeding,22(4):232-238
Peng Y,Liang YS,Wang SQ,Wu FQ,Li SC,Deng QM,Li P.2006.Analysis of segregation distortion of SSR markers in RI population of rice.Molecular Plant Breeding,4(6):786-790(in Chinese)[彭勇,梁永书,王世全,吴发强,李双成,邓其明,李平.2006.水稻SSR标记在RI群体的偏分离分析.分子植物育种,4(6):786-790]
Rafalski JA.2002.Novel genetic mapping tools in plants:SNPs and LD-based approaches.Plant Science,162(3):329-333
Rogers SO,Bendich AJ.1985.Extraction of DNA from milligram amounts of fresh,herbarium and mummified plant tissues.Plant Molecular Biology,5(2):69-76
Somers DJ,Isaac P,Edwards K.2004.A high-density microsatellite consensus map for bread wheat(Triticum aestivum L.).Theoretical&Applied Genetics,109(6):1105-1114
Wang HL,Liu HX,Wang N,Zhao P,Li CL,Wang ZH.2014.Genetic analysis of segregation of SNP and SSR markers in wheat RILpopulation from the cross Heyne×Lakin.Journal of Triticease Crops,34(9):1205-1209(in Chinese)[王慧兰,刘红侠,王娜,赵朋,李春莲,王中华.2014.SNP和SSR标记在小麦Heyne×Lakin重组自交系群体中的偏分离分析.麦类作物学报,34(9):1205-1209]
Wang JK,Li HH,Zhang LY.2014.Genetic mapping and breeding design.Beijing:Science Press,pp.258-266(in Chinese)[王建康,李慧慧,张鲁燕.2014.基因定位与育种设计.北京:科学出版社,pp.258-266]
Wang S,Wong D,Forrest K,Allen A,Chao S,Huang BE,Maccaferri M,Salvi S,Milner SG,Cattivelli L,et al.2014.Characterization of polyploid wheat genomic diversity using a high-density 90000single nucleotide polymorphism array.Plant Biotechnology Journal,12(6):787-796
Xu Y,Zhu L,Xiao J,Huang N,Mc Couch SR.1997.Chromosomal regions associated with segregation distortion of molecular markers in F2,backcross,doubled haploid,and recombinant inbred populations in rice(Oryza sativa L.).Molecular&General Genetics:Mgg,253(5):535
Yamagishi M,Takeuchi Y,Tanaka I,Kono I,Murai K,Yano M.2010.Segregation distortion in F2,and doubled haploid populations of temperate japonica,rice.Journal of Genetics,89(2):237-241
Zeng YC,Li J,Yang YM,Liao J,Peng ZS,Tang YL,Yang WY.2007.Segregation distortion in the recombinant inbred lines of Chuanyu12×Syn780 by SSR markers.Southwest China Journal of Agricultural Sciences,20(2):230-233(in Chinese)[曾云超,李俊,杨玉敏,廖杰,彭正松,汤永禄,杨武云.2007.利用SSR标记分析川育12×人工合成小麦Syn780重组自交系群体中的偏分离现象.西南农业学报,20(2):230-233]
Zhang F,Wan XQ,Pan GT.2006.Genetic analysis of segregation distortion of molecular markers in maize F2population.Acta Agronomica Sinica,32(9):1391-1396(in English)[张帆,万雪琴,潘光堂.2006.玉米F2群体分子标记偏分离的遗传分析.作物学报,32(9):1391-1396]
Zhang WJ,Yuan HM,Chen DS,Wang XL,Kang L,He JS.2015.Advances in studies on physiological and biochemical indexes and QTL for drought resistance in wheat.Agricultural Research in the Arid Areas,33(6):139-148(in Chinese)[张维军,袁汉民,陈东升,王小亮,亢玲,何进尚.2015.小麦抗旱性生理生化机制及QTL研究进展.干旱地区农业研究,33(6):139-148]
Zhao P,Li TT,Zhang YY,Wang N,Li CL,Wang ZH.2014.Detection of wheat chromosome segregation distortion region using SNPmarkers and RIL population of Ning 7840/Clark.Journal of Triticease Crops,34(11):1453-1458(in Chinese)[赵朋,李婷婷,张芸芸,王娜,李春莲,王中华.2014.利用SNP标记和宁7840×Clark重组自交系(RIL)群体检测小麦染色体偏分离区域.麦类作物学报,34(11):1453-1458]