基于CAPS标记的甜瓜单果重相关性状QTL分析
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摘要
【目的】基于甜瓜全基因组重测序技术,挖掘SNP位点并开发CAPS标记,构建遗传连锁图谱。初步为甜瓜单果重相关性状进行QTL定位,为甜瓜单果重相关基因挖掘奠定理论基础。【方法】选取栽培甜瓜品系M4-130为母本,野生甜瓜品系X207为父本,构建F2:3群体材料。对甜瓜果实单果重、果实长宽、果肉厚度、果形指数及可溶性固形物含量等性状进行相关性分析。对亲本材料进行20×深度重测序,利用BWA、SAMTools、VCFTools等软件在全基因组范围内挖掘双亲SNP位点,利用SNP2CAPS软件结合甜瓜基因组上的限制性内切酶酶切位点开发CAPS标记,建立遗传连锁图谱。最后采用复合区间作图法对甜瓜果实单果重、果实长宽、果肉厚度、果形指数及可溶性固形物含量进行QTL分析。【结果】单果重与果实长度、果实宽度及果肉厚度呈显著相关。开发得到可利用CAPS标记185个,构建一张包含12个连锁群的遗传连锁图谱,覆盖总长度为1 600.45 cM,标记间的平均遗传距离8.65 cM。定位发现与单果重相关QTL位点7个(FW3.1、FW4.1、FW5.1、FW6.1、FW8.1、FW8.2、FW11.1),与果实长度相关QTL位点7个(FL2.1、FL3.1、FL4.1、FL5.1、FL6.1、FL8.1、FL11.1),与果实宽度相关QTL位点5个(FWID3.1、FWID4.1、FWID8.1、FWID10.1、FWID11.1),与果肉厚度相关QTL位点2个(FT6.1、FT11.1),与果形指数相关QTL位点1个(FS2.1),与可溶性固形含量相关QTL位点2个(SS6.1、SS12.1)。【结论】获得了24个QTL位点。确定了一个主效QTL位点FW8.1,贡献率高达25.8774%,LOD值为16.8746。发现单果重与果实长度、果实宽度及果肉厚度密切相关,定位区间相同或相邻,紧密集中在3、4、5、6、8、11染色体上。
【Objective】 In our study, based on melon genome-wide resequencing technology, SNP loci were explored and CAPS markers were developed to construct a genetic linkage map. The preliminary QTL analysis of traits related to single fruit weight in melon was carried out, which laid a theoretical foundation for the detection of genes related to single fruit weight traits in melon.【Method】F2:3 population materials were constructed from X207 and M4-130. The cultivated melon accession M4-130 was selected as female parent and wild melon accession X207 as male parent. Correlation analysis was carried out for fruit traits,including single fruit weight, fruit length, fruit width, pulp thickness, fruit shape index and soluble solids content in melon fruit.Parents were resequenced at 20× depth. SNP loci between parents were extracted in the whole genome by the use of BWA,SAMTools, VCFTools and other software. CAPS markers were developed by using SNP2 CAPS software and combined with restriction endonuclease digestion sites in melon genome for genetic linkage map construction. Finally, QTLs of single fruit weight,fruit length, fruit width, pulp thickness, fruit shape index and soluble solids content in melon fruit were analyzed by composite interval mapping.【Result】In this experiment, single fruit weight significantly correlated with fruit length, fruit width and pulp thickness. 185 CAPS markers were developed and subsequently used for genetic linkage map construction. The genetic linkage map contained 12 linkage groups covering a total length of 1 600.45 cM and average distance of 8.65 cM. 7 QTLs(FW3.1, FW4.1,FW5.1, FW6.1, FW8.1, FW8.2 and FW11.1) were related to the single fruit weight. 7 QTLs(FL2.1, FL3.1, FL4.1, FL5.1, FL6.1,FL8.1 and FL11.1) were related to fruit length. 5 QTLs(FWID3.1, FWID4.1, FWID8.1, FWID10.1 and FWID11.1) were related to fruit width. 2 QTLs(FT6.1 and FT11.1) were related to pulp thickness. 1 QTLs(FS2.1) was related to fruit shape index. 2 QTLs(SS6.1 and SS12.1) were related to soluble solids content.【Conclusion】Twenty-three QTLs in total were identified. A major QTL FW8.1 was identified with phenotypic variance contribution rate of 25.8774% and the LOD value was 16.8746. It was also found that single fruit weight was closely related to fruit length, fruit width and pulp thickness. Location intervals were same or adjacent,closely concentrated on chromosomes 3, 4, 5, 6, 8 and 11.
【Objective】 In our study, based on melon genome-wide resequencing technology, SNP loci were explored and CAPS markers were developed to construct a genetic linkage map. The preliminary QTL analysis of traits related to single fruit weight in melon was carried out, which laid a theoretical foundation for the detection of genes related to single fruit weight traits in melon.【Method】F2:3 population materials were constructed from X207 and M4-130. The cultivated melon accession M4-130 was selected as female parent and wild melon accession X207 as male parent. Correlation analysis was carried out for fruit traits,including single fruit weight, fruit length, fruit width, pulp thickness, fruit shape index and soluble solids content in melon fruit.Parents were resequenced at 20× depth. SNP loci between parents were extracted in the whole genome by the use of BWA,SAMTools, VCFTools and other software. CAPS markers were developed by using SNP2 CAPS software and combined with restriction endonuclease digestion sites in melon genome for genetic linkage map construction. Finally, QTLs of single fruit weight,fruit length, fruit width, pulp thickness, fruit shape index and soluble solids content in melon fruit were analyzed by composite interval mapping.【Result】In this experiment, single fruit weight significantly correlated with fruit length, fruit width and pulp thickness. 185 CAPS markers were developed and subsequently used for genetic linkage map construction. The genetic linkage map contained 12 linkage groups covering a total length of 1 600.45 cM and average distance of 8.65 cM. 7 QTLs(FW3.1, FW4.1,FW5.1, FW6.1, FW8.1, FW8.2 and FW11.1) were related to the single fruit weight. 7 QTLs(FL2.1, FL3.1, FL4.1, FL5.1, FL6.1,FL8.1 and FL11.1) were related to fruit length. 5 QTLs(FWID3.1, FWID4.1, FWID8.1, FWID10.1 and FWID11.1) were related to fruit width. 2 QTLs(FT6.1 and FT11.1) were related to pulp thickness. 1 QTLs(FS2.1) was related to fruit shape index. 2 QTLs(SS6.1 and SS12.1) were related to soluble solids content.【Conclusion】Twenty-three QTLs in total were identified. A major QTL FW8.1 was identified with phenotypic variance contribution rate of 25.8774% and the LOD value was 16.8746. It was also found that single fruit weight was closely related to fruit length, fruit width and pulp thickness. Location intervals were same or adjacent,closely concentrated on chromosomes 3, 4, 5, 6, 8 and 11.
引文
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[2]DANTAS D D C,MEDIROS J F,FREIRE A G.Produ??o e qualidade do meloeiro cultivado com filmes plásticos em respostasàlamina de irriga??o.Revista Ciência Agron?mica,2011,42(3):652-661.
[3]董玉梅,王崇启,赵西,肖守华,陈伟,孙建磊,焦自高.不同嫁接方式对厚皮甜瓜植株生长及果实性状的影响.中国瓜菜,2017,30(9):34-37.DONG Y M,WANG C Q,ZHAO X,XIAO S H,CHEN W,SUN J L,JIAO Z G.Influences of different grafting methods on the plant growth and fruit characters of muskmelon.Zhongguo Gua-cai,2017,30(9):34-37.(in Chinese)
[4]于翠香,韩忠才,王占海,张海燕,杨贵春.甜瓜果实性状遗传规律的研究进展.东北农业科学,2016,41(3):91-94.YU C X,HAN Z C,WANG Z H,ZHANG H Y,YANG G C.Advance of studies on genetic law of melon fruit characters.Journal of Northeast Agricultural Sciences,2016,41(3):91-94.(in Chinese)
[5]陈克农,张红卓,袁丽伟,盛云燕.甜瓜果形指数的F2代遗传研究.北方园艺,2016(19):1-2.CHEN K N,ZHANG H Z,YUAN L W,SHENG Y Y.Genetic inheritance analysis on melon index in F2 generation.Northern Horticulture,2016(19):1-2.(in Chinese)
[6]张宁.甜瓜远缘群体果实主要性状遗传分析及遗传图谱构建[D].杨凌:西北农林科技大学,2014.ZHANG N.Genetic analysis of main fruit traits and construction of the genetic linkage map for interspecific population of melon[D].Yangling:Northwest A&F University,2014.(in Chinese)
[7]BAUDRACCO-ARNAS S,PITRAT M.A genetic map of melon(Cucumis melo L.)with RFLP,RAPD,isozyme,disease resistance and morphological markers.Theoretical and Applied Genetics,1996,93(1/2):57-64.
[8]PéRIN C,HAGEN L,De CONTO V,KATZIR N,DANIN-POLEG Y,PORTNOY V,BAUDRACCO-ARNAS S,CHADOEUF J,DOGIMONT C,PITRAT M.A reference map of Cucumis melo based on two recombinant inbred line populations.Theoretical and Applied Genetics,2002,104(6):1017-1034.
[9]CUEVAS H E,STAUB J E,SIMON P W,ZALAPA J E.A consensus linkage map identifies genomic regions controlling fruit maturity and beta-carotene associated flesh color in melon(Cucumis melo L.).Theoretical and Applied Genetics,2009,119(4):741-756.
[10]FUKINO N,OHARA T,SUGIYAMA M,KUBO N,HIRAI M,SAKATA Y,MATSUMOTO S.Mapping of a gene that confers short lateral branching(slb)in melon(Cucumis melo L.).Euphytica,2012,187:133-143.
[11]ZALAPA J E,STAUB J E,MCCREIGHT J D,CHUNG S M,CUEVAS H.Detection of QTL for yield-related traits using recombinant inbred lines derived from exotic and elite US Western Shipping melon germplasm.Theoretical&Applied Genetics,2007,114(7):1185-1201.
[12]RAMAMURTHY R K,WATERS B M.Identification of fruit quality and morphology QTLs in melon(Cucumis melo)using a population derived from flexuosus and cantalupensis botanical groups.Euphytica,2015,204(1):163-177.
[13]DIAZ A,MARTIN-HERNANDEZ A M,DOLCET-SANJUAN R,GARCES-CLAVER A,ALVAREZ J M,GARCIA-MAS J,PICO B,MONFORTE J.Quantitative trait loci analysis of melon(Cucumis melo L.)domestication related traits.Theoretical and Applied Genetics,2017,130(9):1837-1857.
[14]马双武,刘君璞.甜瓜种质资源描述规范和数据标准.北京:中国农业出版社,2006.MA S W,LIU J P.Descriptors and Data Standard for Melon(Cucumis melo L.).Beijing:China Agriculture Press,2006.(in Chinese)
[15]LUAN F S,DELANNAY I,STAUB J E.Chinese melon(Cucumis melo L.)diversity analyses provide strategies for germplasm curation,genetic improvement,and evidentiary support of domestication patterns.Euphytica,2008,164(2):445-461.
[16]THIEL T,KOTA R,GROSSE I,STEIN N,GRANER A.SNP2CAPS:A SNP and INDEL analysis tool for CAPS marker development.Nucleic Acids Research,2004,32(1):e5.
[17]束永俊,李勇,吴娜拉胡,柏锡,才华,纪巍,朱延明.大豆EST-SNP的挖掘、鉴定及其CAPS标记的开发.作物学报,2010,36(4):574-579.SHU Y J,LI Y,WU N L H,BAI X,CAI H,JI W,ZHU Y M.Mining and identification of SNP from EST sequences and convertion of CAPS markers in soybean.Acta Agronomica Sinica,2010,36(4):574-579.(in Chinese)
[18]SANDLIN K,PROTHRO J,HEESACKER A,KHALILIAN N,OKASHAH R,XIANG W W,BACHLAVA E,CALDWELL D G,MTAYLOR C A,SEYMOUR D K,WHITE V,CHAN E,TOLLA G,WHITE C,SAFRAN D,GRAHAM E,KNAPP S,MCGREGOR C.Comparative mapping in watermelon[Citrullus lanatus(Thunb.)Matsum.et Nakai].Tag Theoretical&Applied Genetics Theoretische Und Anbewandte Genetik,2012,125(8):1603-1618.
[19]SEBASTIAN P,SCHAEFER H,TELFORD I R H,RENNER S S.Cucumber(Cucumis sativus)and melon(C.melo)have numerous wild relatives in Asia and Australia,and the sister species of melon is from Australia.Proceeding of National Academy of Sciences of the United States of America,2010,107(32):14269-14273.
[20]MICHEL P.Phenotypic diversity in wild and cultivated melons(Cucumis melo L).Plant Biotechnology,2013,30(3):273-278.
[21]GANAL M W,ALTMANN T.RODER M S.SNP identification in crop plants.Current Opinion in Plant Biology,2009,12(2):211-217.
[22]周慧文,卢丙洋,马鸿艳,高鹏,栾非时,高启帆,齐国安.西瓜种子大小形状相关QTL分析.园艺学报,2016,43(4):715-723.ZHOU H W,LU B Y,MA H Y,GAO P,LUAN F S,GAO Q F,QI G A.QTL mapping of watermelon seed traits.Acta Horticulturae Sinica,2016,43(4):715-723.(in Chinese)
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