基于SLAF-seq技术分析甜、糯玉米种质遗传多样性
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摘要
利用简化基因组测序技术SLAF-seq,对国内外引进选育的81份鲜食甜、糯玉米自交系进行遗传多样性分析。结果表明,共获得803 058个SLAF标签,其中,多态性SLAF标签373 764个。通过序列分析,获得169 128个有效单核苷酸(SNP)多态标记,利用这些SNP标记分析和构建了81份鲜食甜、糯玉米资源的群体结构和系统发生树,并将其分为2个群。结果表明,简化基因组测序技术SLAF-seq能高效、低廉地开发出大量SNP标记,是作物种质资源群体遗传分析的有效工具。研究结果为甜玉米不同基因的聚合、温-热种质杂交育种、鲜食甜、糯玉米亚种间杂交育种提供依据,有利于鲜食甜、糯玉米自交系的高效利用、品种选育及杂种优势群的建立。
High-throughput specific locus amplified fragment sequencing(SLAF-seq) technology was employed to identify the genetic diversity of 81 inbred lines include sweet and wax corn. The results indicated that the total of 803 058 SLAF tags and 373 764 polymorphic SLAF tags were obtained. A total of 169 128 single nucleotide polymorphisms(SNPs) were obtained through sequences analysis. Population structure and phylogenetic relationship of 81 germplasms of fresh sweet and wax corn were analyzed using the SNP dataset, the population was significantly divided into two different groups. It suggests that SLAF-seq can be used to develop large-scale SNPs for population genetic analysis, effectively and economically. The results can provide molecular basis for gene pyramiding of sweet corn, hybrid breeding of temperate-tropical mode and sweet-wax type. It is beneficial for promoting effective utilization of sweet corn inbred lines, breeding new cultivars and building of heterotic groups.
High-throughput specific locus amplified fragment sequencing(SLAF-seq) technology was employed to identify the genetic diversity of 81 inbred lines include sweet and wax corn. The results indicated that the total of 803 058 SLAF tags and 373 764 polymorphic SLAF tags were obtained. A total of 169 128 single nucleotide polymorphisms(SNPs) were obtained through sequences analysis. Population structure and phylogenetic relationship of 81 germplasms of fresh sweet and wax corn were analyzed using the SNP dataset, the population was significantly divided into two different groups. It suggests that SLAF-seq can be used to develop large-scale SNPs for population genetic analysis, effectively and economically. The results can provide molecular basis for gene pyramiding of sweet corn, hybrid breeding of temperate-tropical mode and sweet-wax type. It is beneficial for promoting effective utilization of sweet corn inbred lines, breeding new cultivars and building of heterotic groups.
引文
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[21]Li H,Vikram P,Singh R P,et al.A high density GBS map of bread wheat and its application for dissecting complex disease resistance traits[J].BMC Genomics,2015,16:1-15.
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[23]赖国荣，张静，刘函，等.基于GBS构建玉米高密度遗传图谱及营养品质性状QTL定位[J].农业生物技术学报，2017,25(9):1400-1410.Lai G R,Zhang J,Liu H,et al.Construction of high density genetic map via GBS technology and QTL mapping for nutritional quality traits in Maize(Zea mays)[J].Journal of Agricultural Biotechnology,2017,25(9):1400-1410.(in Chinese)
[24]Lu Y,Yan J,Guimar?es C T.Molecular characterization of global maize breeding germplasm based on genome wide single nucleotide polymorphisms[J].Theor Appl Genet.Dec,2009,120(1):93-115.doi:10.1007/s00122-009-1162-7.
[25]Xie C,Zhang S,Li M,et al.Inferring genome ancestry and estimating molecular relatedness among 187 Chinese Maize inbred lines[J].J Genet Genomics,2007,34(8):738-48.
[26]张世煌.商业育种只需要两个杂种优势群[J].种子科技，2014(7):7-8.Zhang S H.Commercial breeding only requires the two heterotic groups[J].Seeds Technology,2014(7):7-8.(in Chinese)
[27]赵旭，方永丰，王汉宁.玉米SSR标记杂优类群划分及群体遗传结构分析[J].核农学报，2013,27(12):1828-1838.Zhao X,Fang Y F,Wang H N.Analysis of population genetic structure of maize by SSR marker and heterotic grouping[J].Journal of Nuclear Agricultural Sciences,2013,27(12):1828-1838.(in Chinese)
[2]Laughnan J R.The effect of the sh2 factor on carbohydrate reserves in the mature endosperm of maize[J].Genetics,1953,38(5):485-499.
[3]曾孟潜，刘雅楠，杨涛兰，等.甜玉米、笋玉米的起源与遗传[J].遗传，1999,21(3):44-45.Zeng M Q,Liu Y N,Yang T L,et al.The evolution and genetics of sweet corn and baby corn[J].Hereditas,1999,21(3):44-45.(in Chinese)
[4]胡建广，王子明，李余良，等.我国甜玉米育种概况与发展方向[J].玉米科学，2004,12(1):12-15.Hu J G,Wang Z M,Li Y L,et al.General situation and development direction of sweet corn breeding in China[J].Journal of Maize Sciences,2004,12(1):12-15.(in Chinese)
[5]赵久然，卢柏山，史亚兴，等.我国糯玉米育种及产业发展动态[J].玉米科学，2016,24(4):67-71.Zhao J R,Lu B S,Shi Y X,et al.Development trends of waxy corn breeding and industry in China[J].Journal of Maize Sciences,2016,24(4):67-71.(in Chinese)
[6]Dodson-Swenson H G,Tracy W F.Endosperm carbohydrate composition and kernel characteristics of shrunken2-intermediate(sh2-i/sh2-i Su1/Su1)and shrunken2-in-termediate-sugary1-reference(sh2-i/sh2-i su1-r/su1-r)in sweet corn[J].Crop Science,2015,55(6):2647-2656.
[7]黄君，冯发强，王青峰，等.54份甜玉米自交系的SSR遗传多样性分析[J].华南农业大学学报，2012,33(1):1-4.Huang J,Feng F Q,Wang Q F,et al.Study on genetic diversity of54 sweet corn inbred lines by SSR markers[J].Journal of South China Agricultural University,2012,33(1):1-4.(in Chinese)
[8]卢柏山，史亚兴，宋伟，等.利用SNP标记划分甜玉米自交系的杂种优势类群[J].玉米科学，2015,23(1):58-62,68.Lu B S,Shi Y X,Song W,et al.Heterotic grouping of sweet corn inbred lines by SNP markers[J].Journal of Maize Sciences,2015,23(1):58-62,68.(in Chinese)
[9]雍洪军，张世煌，张德贵，等.利用SSR荧光标记分析90个糯玉米地方品种的遗传多样性[J].玉米科学，2009,17(1):6-12.Yong H J,Zhang S H,Zhang D G,et al.Analysis of genetic diversity among 90 waxy corn landraces using fluorescent SSR markers[J].Journal of Maize Sciences,2009,17(1):6-12.(in Chinese)
[10]史亚兴，卢柏山，宋伟，等.基于SNP标记技术的糯玉米种质遗传多样性分析[J].华北农学报，2015,30(3):77-82.Shi Y X,Lu B S,Song W,et al.Genetic diversity analysis of waxy corn inbred lines by single nucleotide polymorphism(SNP)markers[J].Acta Agriculturae Boreali-sinica,2015,30(3):77-82.(in Chinese)
[11]Sun X,Liu D Y,Zhang X F,et al.SLAF-seq:an efficient method of large-scale De novo SNP discovery and genotyping using highthroughput sequencing[J].PloS One,2013,8:e58700.
[12]Davey J W,Cezard T,Fuentes-Utrila P,et al.Special features of RAD Sequencing data:implications for genotyping[J].Molecular Ecology,2013,22:3151-3164.
[13]石璇，王茹媛，唐君，等.利用简化基因组技术分析甘薯种间单核苷酸多态性[J].作物学报，2016,42(5):641-647.Shi X,Wang R Y,Tang J,et al.Analysis of interspecific SNPs in sweetpotato using a reduced-representation genotyping technology[J].Acta Agronomica Sinica,2016,42(5):641-647.(in Chinese)
[14]Kozich J J,Westcott S L,Baxter N T,et al.Development of a dualindex sequencing strategy and curation pipeline for analyzing amplicon sequence data on the MiSeqIllumina sequencing platform[J].Applied and Environmental Microbiology,2013,79(17):5112-5120.
[15]Li R Q,Yu C,Li Y R,et al.SOAP2:an improved ultrafast tool for short read alignment[J].Bioinformatics,2009,25(15):1966-1967.
[16]Rafalski A.Applications of single nucleotide polymorphisms in crop genetics[J].Current Opinion in Plant Biology,2002,5(4):94-100.
[17]Jones E S,Sullivan H,Bhattramakki D,et al.A comparison of simple sequence repeat and single nucleotide polymorphism marker technologies for the genotypic analysis of maize(Zea mays L.)[J].Theoretical and Applied Genetics,2007,115:361-371.
[18]Varshney R K,Thiel T,Sretenovic-Rajicic T,et al.Identification and validation of a core set of informative genic SSR and SNP markers for assaying functional diversity in barley[J].Molecular Breeding,2008,22:1-13.
[19]Cabezas J A,Ibanez J,Lijavetzky D,et al.A 48 SNP set for grapevine cultivar identification[J].BMC Plant Biology,2011,11:153.
[20]Paux E,Sourdille P,Mackay I,et al.Sequence-based marker development in wheat:advances and applications to breeding[J].Biotechnology Advances,2012,30(5):1071-1088.
[21]Li H,Vikram P,Singh R P,et al.A high density GBS map of bread wheat and its application for dissecting complex disease resistance traits[J].BMC Genomics,2015,16:1-15.
[22]王洋坤，胡艳，张天真.RAD-seq技术在基因组研究中的现状及展望[J].遗传，2014,36(1):41-49.Wang Y K,Hu Y,Zhang T Z.Current status and perspective of RAD-seq in genomic research[J].Hereditas,2014,36(1):41-49.(in Chinese)
[23]赖国荣，张静，刘函，等.基于GBS构建玉米高密度遗传图谱及营养品质性状QTL定位[J].农业生物技术学报，2017,25(9):1400-1410.Lai G R,Zhang J,Liu H,et al.Construction of high density genetic map via GBS technology and QTL mapping for nutritional quality traits in Maize(Zea mays)[J].Journal of Agricultural Biotechnology,2017,25(9):1400-1410.(in Chinese)
[24]Lu Y,Yan J,Guimar?es C T.Molecular characterization of global maize breeding germplasm based on genome wide single nucleotide polymorphisms[J].Theor Appl Genet.Dec,2009,120(1):93-115.doi:10.1007/s00122-009-1162-7.
[25]Xie C,Zhang S,Li M,et al.Inferring genome ancestry and estimating molecular relatedness among 187 Chinese Maize inbred lines[J].J Genet Genomics,2007,34(8):738-48.
[26]张世煌.商业育种只需要两个杂种优势群[J].种子科技，2014(7):7-8.Zhang S H.Commercial breeding only requires the two heterotic groups[J].Seeds Technology,2014(7):7-8.(in Chinese)
[27]赵旭，方永丰，王汉宁.玉米SSR标记杂优类群划分及群体遗传结构分析[J].核农学报，2013,27(12):1828-1838.Zhao X,Fang Y F,Wang H N.Analysis of population genetic structure of maize by SSR marker and heterotic grouping[J].Journal of Nuclear Agricultural Sciences,2013,27(12):1828-1838.(in Chinese)
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