西瓜遗传图谱构建和基因定位研究进展
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摘要
西瓜是一种在世界范围内广泛种植的园艺作物,中国是世界上最大的西瓜生产国和消费国,对西瓜遗传育种的研究具有重要意义。遗传图谱是进行基因定位、图位克隆、分子标记辅助育种的重要工具,并为分子生物学的深入研究提供了基础。近年来,随着高通量测序技术和分子标记的发展,西瓜遗传图谱研究取得了很大进展,基于不同遗传背景的西瓜遗传图谱陆续发表,极大地促进了西瓜基因组学和分子遗传育种的发展。笔者总结了近年来国内外西瓜遗传图谱构建和基因定位的研究进展及应用,并探讨了目前西瓜遗传图谱构建方面存在的主要问题及今后的研究趋势。
Watermelon is a horticultural crop widely cultivated around the world. China is the largest producer and consumer of watermelon. The genetic breeding research of watermelon is of great significance. Genetic map is an important tool for gene mapping, map cloning, molecular marker-assisted breeding, and provides a basis for further research in molecular biology. In recent years, with the development of high-throughput sequencing technology and molecular markers,the research on watermelon genetic map has made great progress. Many genetic maps based on different genetic background have been constructed, which greatly promoted the development of watermelon genomics. This paper reviewed the research progress and application of watermelon genetic map construction and gene mapping in recent years,and discussed the main problems and future research trends of watermelon genetic map construction.
Watermelon is a horticultural crop widely cultivated around the world. China is the largest producer and consumer of watermelon. The genetic breeding research of watermelon is of great significance. Genetic map is an important tool for gene mapping, map cloning, molecular marker-assisted breeding, and provides a basis for further research in molecular biology. In recent years, with the development of high-throughput sequencing technology and molecular markers,the research on watermelon genetic map has made great progress. Many genetic maps based on different genetic background have been constructed, which greatly promoted the development of watermelon genomics. This paper reviewed the research progress and application of watermelon genetic map construction and gene mapping in recent years,and discussed the main problems and future research trends of watermelon genetic map construction.
引文
[1]刘文革,何楠,赵胜杰,等.我国西瓜品种选育研究进展[J].中国瓜菜,2016,29(1):1-7.
[2]刘树兵,王洪刚,孔令让,等.高等植物的遗传作图[J].山东农业大学学报,1999,30(1):74-79.
[3]BOHN M,KHAIRALLAH M,GONZáLEZ-DE-LEóN D,et al.QTL mapping in tropical maize:I.Genomic regions affecting leaf feeding resistance to sugarcane borer and other traits[J].Crop Science,1996,36(5):1352-1361.
[4]SHANG J,LI N,LI N,et al.Construction of a high-density genetic map for watermelon(Citrullus lanatus L.)based on large-scale SNP discovery by specific length amplified fragment sequencing(SLAF-seq)[J].Scientia Horticulturae,2016,203:38-46.
[5]NAVOT N,ZAMIR D.Linkage relationships of 19 protein coding genes in watermelon[J].Theoretical and applied genetics,1986,72(2):274-278.
[6]HASHIZUME T,SHIMAMOTO I,HARUSHIMA Y,et al.Construction of a linkage map for watermelon(Citrullus lanatus(Thunb.)Matsum&Nakai)using random amplified polymorphic DNA(RAPD)[J].Euphytica,1996,90(3):265-273.
[7]REN Y,MCGREGOR C,ZHANG Y,et al.An integrated genetic map based on four mapping populations and quantitative trait loci associated with economically important traits in watermelon(Citrullus lanatus)[J].BMC plant biology,2014,14(1):33.
[8]ZHANG R,XU Y,YI K,et al.A genetic linkage map for watermelon derived from recombinant inbred lines[J].Journal of the American Society for Horticultural Science,2004,129(2):237-243.
[9]范敏,许勇,张海英,等.西瓜果实性状QTL定位及其遗传效应分析[J].遗传学报,2000,27(10):902-910.
[10]HAWKINS L K,DANE F,KUBISIAK T L,et al.Linkage mapping in a watermelon population segregating for fusarium wilt resistance[J].Journal of the American Society for Horticultural Science,2001,126(3):344-350.
[11]LEVI A,THOMAS C E,ZHANG X,et al.A genetic linkage map for watermelon based on randomly amplified polymorphic DNA markers[J].Journal of the American Society for Horticultural Science,2001,126(6):730-737.
[12]LEVI A,THOMAS C,JOOBEUR T,et al.A genetic linkage map for watermelon derived from a testcross population:(Citrullus lanatus var.citroides×C.lanatus var.lanatus)×Citrullus colocynthis[J].Theoretical and Applied Genetics,2002,105(4):555-563.
[13]张仁兵,易克,许勇,等.用重组自交系构建西瓜分子遗传图谱[J].分子植物育种,2003(4):481-489.
[14]HASHIZUME T,SHIMAMOTO I,HIRAI M.Construction of a linkage map and QTL analysis of horticultural traits for watermelon[Citrullus lanatus(THUNB.)MATSUM&NAKAI]using RAPD,RFLP and ISSR markers[J].Theoretical and Applied Genetics,2003,106(5):779-785.
[15]易克,徐向利,卢向阳,等.利用SSR和ISSR标记技术构建西瓜分子遗传图谱[J].湖南农业大学学报(自然科学版),2003,29(4):333-337.
[16]易克,许勇,卢向阳,等.西瓜重组自交系群体的AFLP分子图谱构建[J].园艺学报,2004,31(1):53-58.
[17]LEVI A,THOMAS C,TREBITSH T,et al.An extended linkage map for watermelon based on SRAP,AFLP,SSR,ISSR,and RAPD markers[J].Journal of the American Society for Horticultural Science,2006,131(3):393-402.
[18]邹明学.西瓜EST-SSR标记的开发及遗传图谱的构建与整合[D].北京:首都师范大学,2007.
[19]刘莉,焦定量,郭敏,等.西瓜遗传图谱构建及其强雌性状定位研究[J].果树学报,2010,27(1):50-56.
[20]REN Y,ZHAO H,KOU Q,et al.A high resolution genetic map anchoring scaffolds of the sequenced watermelon genome[J].PLoS One,2012,7(1):e29453.
[21]NIMMAKAYALA P,ABBURI V L,BHANDARY A,et al.Use of VeraCode 384-plex assays for watermelon diversity analysis and integrated genetic map of watermelon with single nucleotide polymorphisms and simple sequence repeats[J].Molecular Breeding,2014,34(2):537-548.
[22]REN R,RAY R,LI P,et al.Construction of a high-density DArTseq SNP-based genetic map and identification of genomic regions with segregation distortion in a genetic population derived from a cross between feral and cultivated-type watermelon[J].Molecular Genetics and Genomics,2015,290(4):1457-1470.
[23]LIU S,GAO P,ZHU Q,et al.Development of cleaved amplified polymorphic sequence markers and a CAPS-based genetic linkage map in watermelon(Citrullus lanatus[Thunb.]Matsum.and Nakai)constructed using whole-genome re-sequencing data[J].Breeding Science,2016,66(2):244-259.
[24]CHENG Y,LUAN F,WANG X,et al.Construction of a genetic linkage map of watermelon(Citrullus lanatus)using CAPS and SSR markers and QTL analysis for fruit quality traits[J].Scientia Horticulturae,2016,202:25-31.
[25]迟莹莹,高鹏,朱子成,等.基于CAPS标记的西瓜果实与种子相关性状QTL分析[J].中国农业科学,2017,50(7):1282-1293.
[26]ZHANG Z,ZHANG Y,SUN L,et al.Construction of a genetic map for Citrullus lanatus based on CAPS markers and mapping of three qualitative traits[J].Scientia Horticulturae,2018,233:532-538.
[27]LI B,LU X,DOU J,et al.Construction of a high-density genetic map and mapping of fruit traits in watermelon(Citrullus lanatus L.)based on whole-genome resequencing[J].International Journal of Molecular Sciences,2018,19(10):3268.
[28]GUO S,ZHANG J,SUN H,et al.The draft genome of watermelon(Citrullus lanatus)and resequencing of 20 diverse accessions[J].Nature Genetics,2013,45(1):51-82.
[29]SANDLIN K,PROTHRO J,HEESACKER A,et al.Comparative mapping in watermelon[Citrullus lanatus(Thunb.)Matsum.et Nakai][J].Theoretical and Applied Genetics,2012,125(8):1603-1618.
[30]LAMBEL S,LANINI B,VIVODA E,et al.A major QTL associated with Fusarium oxysporum race 1 resistance identified in genetic populations derived from closely related watermelon lines using selective genotyping and genotyping-by-sequencing for SNP discovery[J].Theoretical and Applied Genetics,2014,127(10):2105-2115.
[31]GUO S,SUN H,ZHANG H,et al.Comparative transcriptome analysis of cultivated and wild watermelon during fruit development[J].PloS One,2015,10(6):e0130267.
[32]REN Y,GUO S,ZHANG J,et al.A tonoplast sugar transporter underlies a sugar accumulation QTL in watermelon[J].Plant Physiology,2018,176(1):836-850.
[33]PARK S W,KIM K T,KANG S C,et al.Rapid and practical molecular marker development for rind traits in watermelon[J].Horticulture,Environment,and Biotechnology,2016,57(4):385-391.
[34]DOU J,LU X,ALI A,et al.Genetic mapping reveals a marker for yellow skin in watermelon(Citrullus lanatus L.)[J].PLoSOne,2018,13(9):e0200617.
[35]袁平丽,刘文革,路绪强,等.不同倍性西瓜果实发育过程中番茄红素含量动态[J].果树学报,2012,29(5):890-894.
[36]ZHAO W E,LV P,GU H.Studies on carotenoids in watermelon flesh[J].Agricultural Sciences,2013,4(7):13-20.
[37]BANG H,KIM S,LESKOVAR D,et al.Development of a codominant CAPS marker for allelic selection between canary yellow and red watermelon based on SNP in lycopeneβ-cyclase(LCYB)gene[J].Molecular Breeding,2007,20(1):63-72.
[38]ZHANG J,GUO S,REN Y,et al.High-level expression of a novel chromoplast phosphate transporter ClPHT4;2 is required for flesh color development in watermelon[J].New Phytologist,2017,213(3):1208-1221.
[39]WEETMAN L M.Inheritance and correlation of shape size,and color in the watermelon[J].Iowa Agriculture and Home Economics Experiment Station,1937,20(228):1.
[40]DOU J,ZHAO S,LU X,et al.Genetic mapping reveals a candidate gene(ClFS1)for fruit shape in watermelon(Citrullus lanatus L.)[J].Theoretical and Applied Genetics,2018,131(4):947-958.
[41]PROTHRO J,ABDEL-HALEEM H,BACHLAVA E,et al.Quantitative trait loci associated with sex expression in an inter-subspecific watermelon population[J].Journal of the American Society for Horticultural Science,2013,138(2):125-130.
[42]DONG W,WU D,LI G,et al.Next-generation sequencing from bulked segregant analysis identifies a dwarfism gene in watermelon[J].Scientific Reports,2018,8(1):2908.
[43]WEI C,CHEN X,WANG Z,et al.Genetic mapping of the LOBED LEAF 1(ClLL1)gene to a 127.6-kb region in watermelon(Citrullus lanatus L.)[J].PloS One,2017,12(7):e0180741.
[44]高磊,赵胜杰,路绪强,等.利用SSR标记对西瓜果肉硬度性状的连锁分析[J].植物遗传资源学报,2016,17(5):866-870.
[45]GAO L,ZHAO S,LU X,et al.Comparative transcriptome analysis reveals key genes potentially related to soluble sugar and organic acid accumulation in watermelon[J].PloS One,2018,13(1):e0190096.
[2]刘树兵,王洪刚,孔令让,等.高等植物的遗传作图[J].山东农业大学学报,1999,30(1):74-79.
[3]BOHN M,KHAIRALLAH M,GONZáLEZ-DE-LEóN D,et al.QTL mapping in tropical maize:I.Genomic regions affecting leaf feeding resistance to sugarcane borer and other traits[J].Crop Science,1996,36(5):1352-1361.
[4]SHANG J,LI N,LI N,et al.Construction of a high-density genetic map for watermelon(Citrullus lanatus L.)based on large-scale SNP discovery by specific length amplified fragment sequencing(SLAF-seq)[J].Scientia Horticulturae,2016,203:38-46.
[5]NAVOT N,ZAMIR D.Linkage relationships of 19 protein coding genes in watermelon[J].Theoretical and applied genetics,1986,72(2):274-278.
[6]HASHIZUME T,SHIMAMOTO I,HARUSHIMA Y,et al.Construction of a linkage map for watermelon(Citrullus lanatus(Thunb.)Matsum&Nakai)using random amplified polymorphic DNA(RAPD)[J].Euphytica,1996,90(3):265-273.
[7]REN Y,MCGREGOR C,ZHANG Y,et al.An integrated genetic map based on four mapping populations and quantitative trait loci associated with economically important traits in watermelon(Citrullus lanatus)[J].BMC plant biology,2014,14(1):33.
[8]ZHANG R,XU Y,YI K,et al.A genetic linkage map for watermelon derived from recombinant inbred lines[J].Journal of the American Society for Horticultural Science,2004,129(2):237-243.
[9]范敏,许勇,张海英,等.西瓜果实性状QTL定位及其遗传效应分析[J].遗传学报,2000,27(10):902-910.
[10]HAWKINS L K,DANE F,KUBISIAK T L,et al.Linkage mapping in a watermelon population segregating for fusarium wilt resistance[J].Journal of the American Society for Horticultural Science,2001,126(3):344-350.
[11]LEVI A,THOMAS C E,ZHANG X,et al.A genetic linkage map for watermelon based on randomly amplified polymorphic DNA markers[J].Journal of the American Society for Horticultural Science,2001,126(6):730-737.
[12]LEVI A,THOMAS C,JOOBEUR T,et al.A genetic linkage map for watermelon derived from a testcross population:(Citrullus lanatus var.citroides×C.lanatus var.lanatus)×Citrullus colocynthis[J].Theoretical and Applied Genetics,2002,105(4):555-563.
[13]张仁兵,易克,许勇,等.用重组自交系构建西瓜分子遗传图谱[J].分子植物育种,2003(4):481-489.
[14]HASHIZUME T,SHIMAMOTO I,HIRAI M.Construction of a linkage map and QTL analysis of horticultural traits for watermelon[Citrullus lanatus(THUNB.)MATSUM&NAKAI]using RAPD,RFLP and ISSR markers[J].Theoretical and Applied Genetics,2003,106(5):779-785.
[15]易克,徐向利,卢向阳,等.利用SSR和ISSR标记技术构建西瓜分子遗传图谱[J].湖南农业大学学报(自然科学版),2003,29(4):333-337.
[16]易克,许勇,卢向阳,等.西瓜重组自交系群体的AFLP分子图谱构建[J].园艺学报,2004,31(1):53-58.
[17]LEVI A,THOMAS C,TREBITSH T,et al.An extended linkage map for watermelon based on SRAP,AFLP,SSR,ISSR,and RAPD markers[J].Journal of the American Society for Horticultural Science,2006,131(3):393-402.
[18]邹明学.西瓜EST-SSR标记的开发及遗传图谱的构建与整合[D].北京:首都师范大学,2007.
[19]刘莉,焦定量,郭敏,等.西瓜遗传图谱构建及其强雌性状定位研究[J].果树学报,2010,27(1):50-56.
[20]REN Y,ZHAO H,KOU Q,et al.A high resolution genetic map anchoring scaffolds of the sequenced watermelon genome[J].PLoS One,2012,7(1):e29453.
[21]NIMMAKAYALA P,ABBURI V L,BHANDARY A,et al.Use of VeraCode 384-plex assays for watermelon diversity analysis and integrated genetic map of watermelon with single nucleotide polymorphisms and simple sequence repeats[J].Molecular Breeding,2014,34(2):537-548.
[22]REN R,RAY R,LI P,et al.Construction of a high-density DArTseq SNP-based genetic map and identification of genomic regions with segregation distortion in a genetic population derived from a cross between feral and cultivated-type watermelon[J].Molecular Genetics and Genomics,2015,290(4):1457-1470.
[23]LIU S,GAO P,ZHU Q,et al.Development of cleaved amplified polymorphic sequence markers and a CAPS-based genetic linkage map in watermelon(Citrullus lanatus[Thunb.]Matsum.and Nakai)constructed using whole-genome re-sequencing data[J].Breeding Science,2016,66(2):244-259.
[24]CHENG Y,LUAN F,WANG X,et al.Construction of a genetic linkage map of watermelon(Citrullus lanatus)using CAPS and SSR markers and QTL analysis for fruit quality traits[J].Scientia Horticulturae,2016,202:25-31.
[25]迟莹莹,高鹏,朱子成,等.基于CAPS标记的西瓜果实与种子相关性状QTL分析[J].中国农业科学,2017,50(7):1282-1293.
[26]ZHANG Z,ZHANG Y,SUN L,et al.Construction of a genetic map for Citrullus lanatus based on CAPS markers and mapping of three qualitative traits[J].Scientia Horticulturae,2018,233:532-538.
[27]LI B,LU X,DOU J,et al.Construction of a high-density genetic map and mapping of fruit traits in watermelon(Citrullus lanatus L.)based on whole-genome resequencing[J].International Journal of Molecular Sciences,2018,19(10):3268.
[28]GUO S,ZHANG J,SUN H,et al.The draft genome of watermelon(Citrullus lanatus)and resequencing of 20 diverse accessions[J].Nature Genetics,2013,45(1):51-82.
[29]SANDLIN K,PROTHRO J,HEESACKER A,et al.Comparative mapping in watermelon[Citrullus lanatus(Thunb.)Matsum.et Nakai][J].Theoretical and Applied Genetics,2012,125(8):1603-1618.
[30]LAMBEL S,LANINI B,VIVODA E,et al.A major QTL associated with Fusarium oxysporum race 1 resistance identified in genetic populations derived from closely related watermelon lines using selective genotyping and genotyping-by-sequencing for SNP discovery[J].Theoretical and Applied Genetics,2014,127(10):2105-2115.
[31]GUO S,SUN H,ZHANG H,et al.Comparative transcriptome analysis of cultivated and wild watermelon during fruit development[J].PloS One,2015,10(6):e0130267.
[32]REN Y,GUO S,ZHANG J,et al.A tonoplast sugar transporter underlies a sugar accumulation QTL in watermelon[J].Plant Physiology,2018,176(1):836-850.
[33]PARK S W,KIM K T,KANG S C,et al.Rapid and practical molecular marker development for rind traits in watermelon[J].Horticulture,Environment,and Biotechnology,2016,57(4):385-391.
[34]DOU J,LU X,ALI A,et al.Genetic mapping reveals a marker for yellow skin in watermelon(Citrullus lanatus L.)[J].PLoSOne,2018,13(9):e0200617.
[35]袁平丽,刘文革,路绪强,等.不同倍性西瓜果实发育过程中番茄红素含量动态[J].果树学报,2012,29(5):890-894.
[36]ZHAO W E,LV P,GU H.Studies on carotenoids in watermelon flesh[J].Agricultural Sciences,2013,4(7):13-20.
[37]BANG H,KIM S,LESKOVAR D,et al.Development of a codominant CAPS marker for allelic selection between canary yellow and red watermelon based on SNP in lycopeneβ-cyclase(LCYB)gene[J].Molecular Breeding,2007,20(1):63-72.
[38]ZHANG J,GUO S,REN Y,et al.High-level expression of a novel chromoplast phosphate transporter ClPHT4;2 is required for flesh color development in watermelon[J].New Phytologist,2017,213(3):1208-1221.
[39]WEETMAN L M.Inheritance and correlation of shape size,and color in the watermelon[J].Iowa Agriculture and Home Economics Experiment Station,1937,20(228):1.
[40]DOU J,ZHAO S,LU X,et al.Genetic mapping reveals a candidate gene(ClFS1)for fruit shape in watermelon(Citrullus lanatus L.)[J].Theoretical and Applied Genetics,2018,131(4):947-958.
[41]PROTHRO J,ABDEL-HALEEM H,BACHLAVA E,et al.Quantitative trait loci associated with sex expression in an inter-subspecific watermelon population[J].Journal of the American Society for Horticultural Science,2013,138(2):125-130.
[42]DONG W,WU D,LI G,et al.Next-generation sequencing from bulked segregant analysis identifies a dwarfism gene in watermelon[J].Scientific Reports,2018,8(1):2908.
[43]WEI C,CHEN X,WANG Z,et al.Genetic mapping of the LOBED LEAF 1(ClLL1)gene to a 127.6-kb region in watermelon(Citrullus lanatus L.)[J].PloS One,2017,12(7):e0180741.
[44]高磊,赵胜杰,路绪强,等.利用SSR标记对西瓜果肉硬度性状的连锁分析[J].植物遗传资源学报,2016,17(5):866-870.
[45]GAO L,ZHAO S,LU X,et al.Comparative transcriptome analysis reveals key genes potentially related to soluble sugar and organic acid accumulation in watermelon[J].PloS One,2018,13(1):e0190096.