甜瓜果面茸毛、果面瘤以及果面沟全基因组关联分析
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摘要
为寻找调控果面茸毛、果面沟以及果面瘤表型变异的位点,调查200份甜瓜种质在2017年和2018年的表型,并对这200份种质进行全基因组重测序,利用全基因组关联分析的方法对其进行关联。结果在3号染色体上找到了一个与果面茸毛显著相关的SNP;在11号染色体上找到了2个与果面沟显著相关的SNP,在5号、7号和11号染色体上各找到了一个与果面沟深显著相关的SNP;在12条染色体上均找到了与果面瘤显著相关的SNP,所有与果面瘤显著相关的SNP标记中有8个标记显著性远远高于其他标记。进一步对果面茸毛的1个显著SNP,果面沟的5个显著SNP和果面瘤的8个SNP进行了基因注释,共计找到了146个基因。研究结果有助于甜瓜果面茸毛、果面瘤以及果面沟性状的快速精细定位,也将为甜瓜果实遗传改良提供重要参考依据。
Based on the phenotyping and re-sequencing of 200 melon germplasms, the genome-wide association analysis was used to identify loci associated with fruit villi, fruit sulcus, and fruit surface tumors in melon. These traits were investigated of 200 melon germplasms in 2017 and 2018, and genome-wide resequencing of these 200 germplasms was conducted for SNP detection. As a result, 1 SNP was found on chromosome 3 that was significantly associated with fruit fluff. 2 SNPs were found on chromosome 11 that were significantly associated with the fruit surface ditch. There was only1 SNP was found significantly associated with the fruit surface ditch on the chromosome 5, 7 and 11, respectively. SNPs that were significantly associated with fruit surface tumors were found on all 12 chromosomes. Among of them, 8 SNPs had much higher significantly associated than the other SNPs, therefore those SNPs were used in further study. Totally 14 SNPs were detected associated for fruit villi, fruit sulcus, and fruit surface tumors, and 146 genes flanking these SNP were annotated. The SNPs significantly associated withthese traits will be helpful to quickly and finely locate candidate genes,and will also provide an important reference for the genetic improvement of melon fruit.
Based on the phenotyping and re-sequencing of 200 melon germplasms, the genome-wide association analysis was used to identify loci associated with fruit villi, fruit sulcus, and fruit surface tumors in melon. These traits were investigated of 200 melon germplasms in 2017 and 2018, and genome-wide resequencing of these 200 germplasms was conducted for SNP detection. As a result, 1 SNP was found on chromosome 3 that was significantly associated with fruit fluff. 2 SNPs were found on chromosome 11 that were significantly associated with the fruit surface ditch. There was only1 SNP was found significantly associated with the fruit surface ditch on the chromosome 5, 7 and 11, respectively. SNPs that were significantly associated with fruit surface tumors were found on all 12 chromosomes. Among of them, 8 SNPs had much higher significantly associated than the other SNPs, therefore those SNPs were used in further study. Totally 14 SNPs were detected associated for fruit villi, fruit sulcus, and fruit surface tumors, and 146 genes flanking these SNP were annotated. The SNPs significantly associated withthese traits will be helpful to quickly and finely locate candidate genes,and will also provide an important reference for the genetic improvement of melon fruit.
引文
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[27]王艳玲,许彦宾,李琼,等.基于GWAS发掘甜瓜核心种质果实性状的关联位点[J].农业生物技术学报,2017,25(9):1434-1442.
[2]GARCIA-MAS J,BENJAK A,SANSEVERINO W,et al.The genome of melon(Cucumis melo L.)[J].Proceedings of the National Academy of Sciences of the United States of America,2012,109:11872-11877.
[3]HAREL-BEJI R,TZURI G,PORTNOY V,et al.A genetic map of melon highly enriched with fruit quality QTLs and ESTmarkers,including sugar and carotenoid metabolism genes[J].Theoretical and Applied Genetics,2010,121(3):511-533.
[4]王贤磊,高兴旺,李冠,等.甜瓜遗传图谱的构建及果实与种子QTL分析[J].遗传,2011,33(12):1398-1408.
[5]吕丽华.甜瓜果肉β-胡萝卜素含量的遗传分析及QTL定位[D].北京:中国农业科学院,2012.
[6]杨光华,范荣,杨小锋,等.甜瓜果实颜色3个质量性状基因的定位[J].园艺学报,2014,41(5):898-906.
[7]DíAZ AUROR,BELKACEM Z,MOHAMAED F,et al.Mapping and introgression of QTL involved in fruit shape transgressive segregation into‘Piel de Sapo’melon(Cucucumis melo L.)[J].PLoS ONE,2014,9(8):e104188.
[8]高兴旺,王贤磊,宁雪飞,等.甜瓜掌状裂叶基因pll的精细定位[J].北方园艺,2015(6):98-102.
[9]齐振宇.甜瓜株型和抗白粉病性状的遗传与全基因组关联分析[D].杭州:浙江大学,2015.
[10]矫士琦.甜瓜果实、种子相关性状QTL分析[D].哈尔滨:东北农业大学,2017.
[11]段金凤.甜瓜果实外观特征遗传分析及果皮颜色相关基因的初步定位[D].武汉:华中农业大学,2016.
[12]WANG Y H,WU D H,HUANG J H,et al.Mapping quantitative trait loci for fruit traits and powdery mildew resistance in melon(Cucumis melo)[J].Botanical Studies,2016,57:19.
[13]ARGYRIS J M,DíAZ A,VALENTINO R,et al.QTL Analyses in multiple populations employed for the fine mapping and identification of candidate genes at a locus affecting sugar accumulation in melon(Cucumis melo L.)[J].Frontiers in Plant Science,2017,8:1679.
[14]PEREIRA L,RUGGIERI V,PéREZ S,et al.QTL mapping of melon fruit quality traits using a high-density GBS-based genetic map[J].BMC Plant Biology,2018,18:324.
[15]PALOMARES-RIUS F J,YUSTE-LIBONA F J,VIRUEL M A,et al.Inheritance and QTL mapping of glandular trichomes type idensity in Cucumis melo L.[J].Molecular Breeding,2016,36(9):132.
[16]ZHU H,SUN X,ZHANG Q,et al.GLABROUS(CmGL)encodes a HD-ZIP IV transcription factor playing roles in multicellular trichome initiation in melon[J].Theoretical and Applied Genetics,2017,131(2):1-11.
[17]王学征,邱果,陈克农,等.基于BSA法开发CAPS标记定位甜瓜果面沟相关基因研究[J].东北农业大学学报,2018,49(5):17-23.
[18]CORDER E H,SAUNDERS A M,RISCH N J,et al.Protective effect of apolipoprotein E type 2 allele for late onset alzheimer disease[J].Nature Genetics,1994,7(2):180-184.
[19]唐富福,徐非非,包劲松.全基因组关联分析在水稻遗传育种中的应用[J].核农学报,2012,27(5):598-606.
[20]TIAN F,BRADBURY P J,BROWN P J,et al.Genome-wide association study of leaf architecture in the maize nested association mapping population[J].Nature Genetics,2011,43(2):159-162.
[21]马双武,刘君璞.甜瓜种质资源描述规范和数据标准[M].北京:中国农业出版社,2006.
[22]MCKENNA A,HANNA M,BANKS E,et al.The genome analysis toolkit:a mapreduce framework for analyzing next-generation DNA sequencing data[J].Genome Research,2010,20(9):1297-303.
[23]PRICE A L,PATTERSON N J,PLENGE R M,et al.Principal components analysis corrects for stratification in genome-wide association studies[J].Nature Genetics,2006,38(8):904-909.
[24]YU J,BUCKLER E S.Genetic association mapping and genome organization of maize[J].Current Opinion in Biotechnology,2006,17(2):155-160.
[25]CAO K,ZHOU Z,WANG Q,et al.Genome-wide association study of 12 agronomic traits in peach[J].Nature Communications,2016,7:13246.
[26]NIMMAKAYALA P,TOMASON Y R,ABBURI V L,et al.Genome-wide differentiation of various melon horticultural groups for use in gwas for fruit firmness and construction of a high resolution genetic map[J].Frontiers in Plant Science,2016,7:1437.
[27]王艳玲,许彦宾,李琼,等.基于GWAS发掘甜瓜核心种质果实性状的关联位点[J].农业生物技术学报,2017,25(9):1434-1442.
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