简化基因组测序技术研究进展
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摘要
随着高通量测序技术的快速发展,简化基因组测序技术作为一种高效标记开发技术得到了广泛应用.现代简化基因组测序技术主要划分成简化代表库、特异性位点扩增片段测序技术以及基于限制性酶切的简化基因组测序技术,针对此3种类型的技术,综述其在群体遗传学、遗传图谱构建及数量性状位点定位等方面的研究进展.
With the rapid development of high-throughput sequencing technology,reduced-representation sequencing has been widely used as an efficient marker development technique in various research areas.Modern reduced-representation sequencing technique can be divided into reduced-representation libraries,specific length amplification fragment sequencing and restriction-site associated DNA sequencing.The research progress of those three types was summarized in population genetics,linkage map construction and quantitative trait locus mapping.
With the rapid development of high-throughput sequencing technology,reduced-representation sequencing has been widely used as an efficient marker development technique in various research areas.Modern reduced-representation sequencing technique can be divided into reduced-representation libraries,specific length amplification fragment sequencing and restriction-site associated DNA sequencing.The research progress of those three types was summarized in population genetics,linkage map construction and quantitative trait locus mapping.
引文
[1]黎裕,李英慧,杨庆文,等.基于基因组学的作物种质资源研究:现状与展望[J].中国农业科学,2015,48(17):3333.
[2]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.
[3]党少飞,王占林,张得芳,等.枸杞基因组微卫星特征分析[J].西北林学院学报,2016,31(1):97.
[4] Zhan Aibin,MacIsaac H J.Rare biosphere exploration using high-throughput sequencing:research progress and perspectives[J].Conserv Genet,2015,16(3):513.
[5]秦楠,栗东芳,杨瑞馥.高通量测序技术及其在微生物学研究中的应用[J].微生物学报,2011,51(4):445.
[6]许艳蕊,方志军,卢晓平,等.基于高通量测序技术分析使它隆对玉米土壤细菌多样性的影响[J].微生物学报,2017,57(7):985.
[7] Liu Yang,Wang Ronghuan,Li Yinhu,et al.High-throughput sequencing-based analysis of the composition and diversity of endophytic bacterial community in seeds of“Beijing”hybrid maize planted in China[J].Plant Growth Regul,2017,81(2):317.
[8] Massart S,Chiumenti M,De Jonghe K,et al.Virus detection by high-throughput sequencing of small RNAs:large scale performance testing of sequence analysis strategies[J].Phytopathol,2018,DOI:10.1094/PHYTO-02-18-0067-R.
[9]李杨,陈涛,赵学明.微生物基因组简化的研究进展[J].生命科学,2011,23(9):838.
[10]梅楚刚,王洪程,昝林森,等.基于高通量测序的动物基因组研究进展[J].西北农林科技大学学报(自然科学版),2016,44(3):43.
[11]汪文强,赵生国,马利青,等.动物基因组学重测序的应用研究进展[J].畜牧兽医学报,2016,47(10):1947.
[12]段修军,董飚,孙国波,等.基于酶切的简化基因组测序在水禽品种进化关系研究中的应用[J].西北农业学报,2015,24(1):13.
[13] 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 Res,2007,17(2):240.
[14]陈小明,李佳凯,王志勇,等.基于简化基因组测序的大黄鱼耐高温性状全基因组关联分析[J].水生生物学报,2017,41(4):735.
[15]夏照华,何建行.宏基因组测序在传染性疾病中的研究进展[J].中国微生态学杂志,2017,29(2):245.
[16] Winger B M,Hosner P A,Bravo G A,et al.Inferring speciation history in the Andes with reduced-representation sequence data:an example in the bay-backed antpittas(Aves;Grallariidae;Grallaria hypoleuca s.l.)[J].Mol Ecol,2015,24(24):6256.
[17] van Tassell C P,Smith T P L,Matukumalli L K,et al.SNP discovery and allele frequency estimation by deep sequencing of reduced representation libraries[J].Nat Meth,2008,5(3):247.
[18] Sun Zhifu,Baheti S,Middha S,et al.SAAP-RRBS:streamlined analysis and annotation pipeline for reduced representation bisulfite sequencing[J].Bioinformat,2012,28(16):2180.
[19] Guo Hongshan,Zhu Ping,Wu Xinglong,et al.Single-cell methylome landscapes of mouse embryonic stem cells and early embryos analyzed using reduced representation bisulfite sequencing[J].Genome Res,2013,23(12):2126.
[20] Wang Xuefeng,Yu Xiaoqing,Zhu Wei,et al.A trimming-and-retrieving alignment scheme for reduced representation bisulfite sequencing[J].Bioinformat,2015,31(12):2040.
[21] Blhed I,K9nigsson H,Ericsson G,et al.Discovery of SNPs for individual identification by reduced representation sequencing of moose(Alces alces)[J].PLoS One,2018,13(5):e0197364.
[22] Onyango M G,Aitken N C,Jack C,et al.Genotyping of whole genome amplified reduced representation libraries reveals a cryptic population of Culicoides brevitarsis in the Northern Territory,Australia[J].BMC Genomics,2016,17:769.
[23] Zuo Xiaolu,Shi Chun,Austin R S,et al.Genome-wide single nucleotide polymorphism and insertion-deletion discovery through next-generation sequencing of reduced representation libraries in common bean[J].Mol Breed,2014,33(4):769.
[24] Guo Gangang,Dondup D,Zhang Lisha,et al.Identification of SNPs in barley(Hordeum vulgare L.)by deep sequencing of six reduced representation libraries[J].Crop J,2014,2(6):419.
[25] Conner J,Sapkota S,Deschamps S,et al.Targeted sequencing of a complex locus within a polyploid genome using reduced representation libraries[J].Mol Breed,2016,36(5):60.
[26] Kerstens H H D,Crooijmans R P M A,Veenendaal A,et al.Large scale single nucleotide polymorphism discovery in unsequenced genomes using second generation high throughput sequencing technology:applied to turkey[J].BMC Genomics,2009,10(1):1.
[27] van Orsouw N J,Hogers R C J,Janssen A,et al.Complexity reduction of polymorphic sequences(CRoPSTM):a novel approach for large-scale polymorphism discovery in complex genomes[J].PLoS One,2007,2(11):e1172.
[28] Mammadov J A,Chen Wei,Ren Ruihua,et al.Development of highly polymorphic SNP markers from the complexity reduced portion of maize[Zea may L.]genome for use in marker-assisted breeding[J].Theor Appl Genet,2010,121(3):577.
[29] Gompert Z,Forister M L,Fordyce J A,et al.Bayesian analysis of molecular variance in pyrosequences quantifies population genetic structure across the genome of Lycaeides butterflies[J].Mol Ecol,2010,19(12):2455.
[30] De bacher M,Bonants P,Pedley K F,et al.Genetic relationships in an international collection of Puccinia horiana isolates based on newly identified molecular markers and demonstration of recombination[J].Phytopathol,2013,103(11):1169.
[31] Wang Li,Sun Jihua,Wu Honglong,et al.Systematic assessment of reduced representation bisulfite sequencing to human blood samples:apromising method for large-sample-scale epigenomic studies[J].J Biotechnol,2012,157(1):1.
[32] Ashktorab H,Daremipouran M,Rahi H,et al.Abstract 4247:identification of new hypermethylated candidate genes in colorectal cancer using reduced representation bisulfite next generation sequencing[J].Canc Res,2013,73(8):4247.
[33] Sun Xiaowen,Liu Dongyuan,Zhang Xiaofeng,et al.SLAF-seq:an efficient method of large-scale denovo SNP discovery and genotyping using high-throughput sequencing[J].PLoS One,2013,8(3):e58700.
[34] Chen Wei,Yao Jinbo,Chu Li,et al.The development of specific SNP markers for chromosome 14in cotton using nextgeneration sequencing[J].Plant Breed,2014,133(2):256.
[35]苏文瑾,赵宁,雷剑,等.基于SLAF-seq技术的甘薯SNP位点开发[J].中国农业科学,2016,49(1):27.
[36] Su Wenjin,Wang Lianjun,Lei Jian,et al.Genome-wide assessment of population structure and genetic diversity and development of a core germplasm set for sweet potato based on specific length amplified fragment(SLAF)sequencing[J].PLoS One,2017,12(2):e0172066.
[37] Cai Changfu,Cheng Fangyun,Wu Jing,et al.The first high-density genetic map construction in tree peony(Paeonia Sect.Moutan)using genotyping by specific-locus amplified fragment sequencing[J].PLoS One,2015,10(5):e0128584.
[38] Ma Jianjian,Huang Long,Ma Chunlei,et al.Large-scale SNP discovery and genotyping for constructing a high-density genetic map of tea plant using specific-locus amplified fragment sequencing(SLAF-seq)[J].PLoS One,2015,10(6):e0128798.
[39] Zhu Yufeng,Yin Yanfei,Yang Keqiang,et al.Construction of a high-density genetic map using specific length amplified fragment markers and identification of a quantitative trait locus for anthracnose resistance in walnut(Juglans regia L.)[J].BMC Genomics,2015,16(1):1.
[40]陈士强,秦树文,黄泽峰,等.基于SLAF-seq技术开发长穗偃麦草染色体特异分子标记[J].作物学报,2013,39(4):727.
[41] Liang Danna,Chen Minyang Qi Xiaohua,et al.QTL mapping by SLAF-seq and expression analysis of candidate genes for aphid resistance in cucumber[J].Fron Plant Sci,2016,7:1000.
[42] Wang Jiahui,Su kai,Guo Yinshan,et al.Construction of a high-density genetic map for grape using specific length amplified fragment(SLAF)sequencing[J].PLoS One,2017,12(7):e0181728.
[43] Liu Tian,Guo Linin,Pan Yuling,et al.Construction of the first highdensity genetic linkage map of Salvia miltiorrhiza using specifc length amplifed fragment(SLAF)sequencing[J].Sci Rep,2016,6:24070.
[44] Zhang Jian,Yuan Huwei,Li Min,et al.A high-density genetic map of tetraploid Salix matsudana using specific length amplified fragment sequencing(SLAF-seq)[J].PLoS One,2016,11(6):e0157777.
[45] 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 Biol,2016,16:79.
[46] Xia Chao,Chen Lili,Rong Tingzhao,et al.Identification of a new maize inflorescence meristem mutant and association analysis using SLAF-seq method[J].Euphyt,2015,202(1):35.
[47] Zhang Yanxin,Wang Linhai,Xin Huaigen,et al.Construction of a high-density genetic map for sesame based on large scale marker development by specific length amplified fragment(SLAF)sequencing[J].BMC Plant Biol,2013,13(1):141.
[48] Qi Zhaoming,Huang Long,Zhu Rongsheng,et al.A high-density genetic map for soybean based on specific length amplified fragment sequencing[J].PLoS One,2014,9(8):e104871.
[49] Wang Zhihui,Huai Dongxin,Zhang Zhaohua,et al.Development of a high-density genetic map based on specific length amplified fragment sequencing and its application in quantitative trait loci analysis for yield-related traits in cultivated peanut[J].Front Plant Sci,2018,9:827.
[50] Chen Shen,Wang Wenjuan,Su Jing,et al.Rapid identification of rice blast resistance gene by specific length amplified fragment sequencing[J].Biotechnol Biotec Eq,2016,30(3):462.
[51] Etter P D,Bassham S,Hohenlohe P A,et al.SNP discovery and genotyping for evolutionary genetics using RAD sequencing[J].Methods Mol Biol,2011,772:157.
[52] Harvey M G,Smith B T,Glenn T C,et al.Sequence capture versus restriction site associated DNA sequencing for shallow systematics[J].Syst Biol,2016,65(5):910.
[53] Gamble T,Coryell J,Ezaz T,et al.Restriction site-associated DNA sequencing(RAD-seq)reveals an extraordinary number of transitions among gecko sex-determining systems[J].Mol Biol Evol,2015,32(5):1296.
[54] Zhang Dafeng,Xia Tao,Dang Shaofei,et al.Investigation of Chinese wolfberry(Lyciumspp.)germplasm by restriction site-associated DNA sequencing(RAD-seq)[J/OL].Biochem Genet,2018.[2018-08-30].https://doi.org/10.1007/s10528-018-9861-x.
[55] Bian Li,Liu Changlin,Liu Gang,et al.SNP discovery in spotted halibut(Verasper variegatus)using restriction site-associated DNA sequencing(RAD-seq)[J].Conserv Genet Resour,2018,10(3):409.
[56] Barchi L,Lanteri S,Portis E,et al.Identification of SNP and SSR markers in eggplant using RAD tag sequencing[J].BMC Genomics,2011,12:304.
[57] Xu Xiao,Dong Guixin,Hu Xuesong,et al.The genetic basis of white tigers[J].Curr Biol,2013,23(11):1031.
[58] Houston R D,Davey J W,Bishop S C,et al.Characterisation of QTL-linked and genome-wide restriction site-associated DNA(RAD)markers in farmed Atlantic salmon[J].BMC Genomics,2012,13(1):244.
[59] Yang Guoqian,Chen Yunmei,Wang Jinpeng,et al.Development of a universal and simplified ddRAD library preparation approach for SNP discovery and genotyping in angiosperm plants[J].Plant Meth,2016,12:39.
[60] Poland J A,Brown P J,Sorrells M E,et al.Development of high-density genetic maps for barley and wheat using a novel two-enzyme genotyping-by-sequencing approach[J].PLoS One,2012,7(2):e32253.
[61] Watanabe S,Tsukamoto C,Oshita T,et al.Identification of quantitative trait loci for flowering time by a combination of restriction site-associated DNA sequencing and bulked segregant analysis in soybean[J].Breed Sci,2017,67:277.
[62] Wang Shi,Meyer E,McKay J K,et al.2b-RAD:a simple and flexible method for genome-wide genotyping[J].Nat Methods,2012,9(8):808.
[2]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.
[3]党少飞,王占林,张得芳,等.枸杞基因组微卫星特征分析[J].西北林学院学报,2016,31(1):97.
[4] Zhan Aibin,MacIsaac H J.Rare biosphere exploration using high-throughput sequencing:research progress and perspectives[J].Conserv Genet,2015,16(3):513.
[5]秦楠,栗东芳,杨瑞馥.高通量测序技术及其在微生物学研究中的应用[J].微生物学报,2011,51(4):445.
[6]许艳蕊,方志军,卢晓平,等.基于高通量测序技术分析使它隆对玉米土壤细菌多样性的影响[J].微生物学报,2017,57(7):985.
[7] Liu Yang,Wang Ronghuan,Li Yinhu,et al.High-throughput sequencing-based analysis of the composition and diversity of endophytic bacterial community in seeds of“Beijing”hybrid maize planted in China[J].Plant Growth Regul,2017,81(2):317.
[8] Massart S,Chiumenti M,De Jonghe K,et al.Virus detection by high-throughput sequencing of small RNAs:large scale performance testing of sequence analysis strategies[J].Phytopathol,2018,DOI:10.1094/PHYTO-02-18-0067-R.
[9]李杨,陈涛,赵学明.微生物基因组简化的研究进展[J].生命科学,2011,23(9):838.
[10]梅楚刚,王洪程,昝林森,等.基于高通量测序的动物基因组研究进展[J].西北农林科技大学学报(自然科学版),2016,44(3):43.
[11]汪文强,赵生国,马利青,等.动物基因组学重测序的应用研究进展[J].畜牧兽医学报,2016,47(10):1947.
[12]段修军,董飚,孙国波,等.基于酶切的简化基因组测序在水禽品种进化关系研究中的应用[J].西北农业学报,2015,24(1):13.
[13] 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 Res,2007,17(2):240.
[14]陈小明,李佳凯,王志勇,等.基于简化基因组测序的大黄鱼耐高温性状全基因组关联分析[J].水生生物学报,2017,41(4):735.
[15]夏照华,何建行.宏基因组测序在传染性疾病中的研究进展[J].中国微生态学杂志,2017,29(2):245.
[16] Winger B M,Hosner P A,Bravo G A,et al.Inferring speciation history in the Andes with reduced-representation sequence data:an example in the bay-backed antpittas(Aves;Grallariidae;Grallaria hypoleuca s.l.)[J].Mol Ecol,2015,24(24):6256.
[17] van Tassell C P,Smith T P L,Matukumalli L K,et al.SNP discovery and allele frequency estimation by deep sequencing of reduced representation libraries[J].Nat Meth,2008,5(3):247.
[18] Sun Zhifu,Baheti S,Middha S,et al.SAAP-RRBS:streamlined analysis and annotation pipeline for reduced representation bisulfite sequencing[J].Bioinformat,2012,28(16):2180.
[19] Guo Hongshan,Zhu Ping,Wu Xinglong,et al.Single-cell methylome landscapes of mouse embryonic stem cells and early embryos analyzed using reduced representation bisulfite sequencing[J].Genome Res,2013,23(12):2126.
[20] Wang Xuefeng,Yu Xiaoqing,Zhu Wei,et al.A trimming-and-retrieving alignment scheme for reduced representation bisulfite sequencing[J].Bioinformat,2015,31(12):2040.
[21] Blhed I,K9nigsson H,Ericsson G,et al.Discovery of SNPs for individual identification by reduced representation sequencing of moose(Alces alces)[J].PLoS One,2018,13(5):e0197364.
[22] Onyango M G,Aitken N C,Jack C,et al.Genotyping of whole genome amplified reduced representation libraries reveals a cryptic population of Culicoides brevitarsis in the Northern Territory,Australia[J].BMC Genomics,2016,17:769.
[23] Zuo Xiaolu,Shi Chun,Austin R S,et al.Genome-wide single nucleotide polymorphism and insertion-deletion discovery through next-generation sequencing of reduced representation libraries in common bean[J].Mol Breed,2014,33(4):769.
[24] Guo Gangang,Dondup D,Zhang Lisha,et al.Identification of SNPs in barley(Hordeum vulgare L.)by deep sequencing of six reduced representation libraries[J].Crop J,2014,2(6):419.
[25] Conner J,Sapkota S,Deschamps S,et al.Targeted sequencing of a complex locus within a polyploid genome using reduced representation libraries[J].Mol Breed,2016,36(5):60.
[26] Kerstens H H D,Crooijmans R P M A,Veenendaal A,et al.Large scale single nucleotide polymorphism discovery in unsequenced genomes using second generation high throughput sequencing technology:applied to turkey[J].BMC Genomics,2009,10(1):1.
[27] van Orsouw N J,Hogers R C J,Janssen A,et al.Complexity reduction of polymorphic sequences(CRoPSTM):a novel approach for large-scale polymorphism discovery in complex genomes[J].PLoS One,2007,2(11):e1172.
[28] Mammadov J A,Chen Wei,Ren Ruihua,et al.Development of highly polymorphic SNP markers from the complexity reduced portion of maize[Zea may L.]genome for use in marker-assisted breeding[J].Theor Appl Genet,2010,121(3):577.
[29] Gompert Z,Forister M L,Fordyce J A,et al.Bayesian analysis of molecular variance in pyrosequences quantifies population genetic structure across the genome of Lycaeides butterflies[J].Mol Ecol,2010,19(12):2455.
[30] De bacher M,Bonants P,Pedley K F,et al.Genetic relationships in an international collection of Puccinia horiana isolates based on newly identified molecular markers and demonstration of recombination[J].Phytopathol,2013,103(11):1169.
[31] Wang Li,Sun Jihua,Wu Honglong,et al.Systematic assessment of reduced representation bisulfite sequencing to human blood samples:apromising method for large-sample-scale epigenomic studies[J].J Biotechnol,2012,157(1):1.
[32] Ashktorab H,Daremipouran M,Rahi H,et al.Abstract 4247:identification of new hypermethylated candidate genes in colorectal cancer using reduced representation bisulfite next generation sequencing[J].Canc Res,2013,73(8):4247.
[33] Sun Xiaowen,Liu Dongyuan,Zhang Xiaofeng,et al.SLAF-seq:an efficient method of large-scale denovo SNP discovery and genotyping using high-throughput sequencing[J].PLoS One,2013,8(3):e58700.
[34] Chen Wei,Yao Jinbo,Chu Li,et al.The development of specific SNP markers for chromosome 14in cotton using nextgeneration sequencing[J].Plant Breed,2014,133(2):256.
[35]苏文瑾,赵宁,雷剑,等.基于SLAF-seq技术的甘薯SNP位点开发[J].中国农业科学,2016,49(1):27.
[36] Su Wenjin,Wang Lianjun,Lei Jian,et al.Genome-wide assessment of population structure and genetic diversity and development of a core germplasm set for sweet potato based on specific length amplified fragment(SLAF)sequencing[J].PLoS One,2017,12(2):e0172066.
[37] Cai Changfu,Cheng Fangyun,Wu Jing,et al.The first high-density genetic map construction in tree peony(Paeonia Sect.Moutan)using genotyping by specific-locus amplified fragment sequencing[J].PLoS One,2015,10(5):e0128584.
[38] Ma Jianjian,Huang Long,Ma Chunlei,et al.Large-scale SNP discovery and genotyping for constructing a high-density genetic map of tea plant using specific-locus amplified fragment sequencing(SLAF-seq)[J].PLoS One,2015,10(6):e0128798.
[39] Zhu Yufeng,Yin Yanfei,Yang Keqiang,et al.Construction of a high-density genetic map using specific length amplified fragment markers and identification of a quantitative trait locus for anthracnose resistance in walnut(Juglans regia L.)[J].BMC Genomics,2015,16(1):1.
[40]陈士强,秦树文,黄泽峰,等.基于SLAF-seq技术开发长穗偃麦草染色体特异分子标记[J].作物学报,2013,39(4):727.
[41] Liang Danna,Chen Minyang Qi Xiaohua,et al.QTL mapping by SLAF-seq and expression analysis of candidate genes for aphid resistance in cucumber[J].Fron Plant Sci,2016,7:1000.
[42] Wang Jiahui,Su kai,Guo Yinshan,et al.Construction of a high-density genetic map for grape using specific length amplified fragment(SLAF)sequencing[J].PLoS One,2017,12(7):e0181728.
[43] Liu Tian,Guo Linin,Pan Yuling,et al.Construction of the first highdensity genetic linkage map of Salvia miltiorrhiza using specifc length amplifed fragment(SLAF)sequencing[J].Sci Rep,2016,6:24070.
[44] Zhang Jian,Yuan Huwei,Li Min,et al.A high-density genetic map of tetraploid Salix matsudana using specific length amplified fragment sequencing(SLAF-seq)[J].PLoS One,2016,11(6):e0157777.
[45] 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 Biol,2016,16:79.
[46] Xia Chao,Chen Lili,Rong Tingzhao,et al.Identification of a new maize inflorescence meristem mutant and association analysis using SLAF-seq method[J].Euphyt,2015,202(1):35.
[47] Zhang Yanxin,Wang Linhai,Xin Huaigen,et al.Construction of a high-density genetic map for sesame based on large scale marker development by specific length amplified fragment(SLAF)sequencing[J].BMC Plant Biol,2013,13(1):141.
[48] Qi Zhaoming,Huang Long,Zhu Rongsheng,et al.A high-density genetic map for soybean based on specific length amplified fragment sequencing[J].PLoS One,2014,9(8):e104871.
[49] Wang Zhihui,Huai Dongxin,Zhang Zhaohua,et al.Development of a high-density genetic map based on specific length amplified fragment sequencing and its application in quantitative trait loci analysis for yield-related traits in cultivated peanut[J].Front Plant Sci,2018,9:827.
[50] Chen Shen,Wang Wenjuan,Su Jing,et al.Rapid identification of rice blast resistance gene by specific length amplified fragment sequencing[J].Biotechnol Biotec Eq,2016,30(3):462.
[51] Etter P D,Bassham S,Hohenlohe P A,et al.SNP discovery and genotyping for evolutionary genetics using RAD sequencing[J].Methods Mol Biol,2011,772:157.
[52] Harvey M G,Smith B T,Glenn T C,et al.Sequence capture versus restriction site associated DNA sequencing for shallow systematics[J].Syst Biol,2016,65(5):910.
[53] Gamble T,Coryell J,Ezaz T,et al.Restriction site-associated DNA sequencing(RAD-seq)reveals an extraordinary number of transitions among gecko sex-determining systems[J].Mol Biol Evol,2015,32(5):1296.
[54] Zhang Dafeng,Xia Tao,Dang Shaofei,et al.Investigation of Chinese wolfberry(Lyciumspp.)germplasm by restriction site-associated DNA sequencing(RAD-seq)[J/OL].Biochem Genet,2018.[2018-08-30].https://doi.org/10.1007/s10528-018-9861-x.
[55] Bian Li,Liu Changlin,Liu Gang,et al.SNP discovery in spotted halibut(Verasper variegatus)using restriction site-associated DNA sequencing(RAD-seq)[J].Conserv Genet Resour,2018,10(3):409.
[56] Barchi L,Lanteri S,Portis E,et al.Identification of SNP and SSR markers in eggplant using RAD tag sequencing[J].BMC Genomics,2011,12:304.
[57] Xu Xiao,Dong Guixin,Hu Xuesong,et al.The genetic basis of white tigers[J].Curr Biol,2013,23(11):1031.
[58] Houston R D,Davey J W,Bishop S C,et al.Characterisation of QTL-linked and genome-wide restriction site-associated DNA(RAD)markers in farmed Atlantic salmon[J].BMC Genomics,2012,13(1):244.
[59] Yang Guoqian,Chen Yunmei,Wang Jinpeng,et al.Development of a universal and simplified ddRAD library preparation approach for SNP discovery and genotyping in angiosperm plants[J].Plant Meth,2016,12:39.
[60] Poland J A,Brown P J,Sorrells M E,et al.Development of high-density genetic maps for barley and wheat using a novel two-enzyme genotyping-by-sequencing approach[J].PLoS One,2012,7(2):e32253.
[61] Watanabe S,Tsukamoto C,Oshita T,et al.Identification of quantitative trait loci for flowering time by a combination of restriction site-associated DNA sequencing and bulked segregant analysis in soybean[J].Breed Sci,2017,67:277.
[62] Wang Shi,Meyer E,McKay J K,et al.2b-RAD:a simple and flexible method for genome-wide genotyping[J].Nat Methods,2012,9(8):808.