基于高密度遗传图谱定位栽培种花生主茎高、第一侧枝长和分枝数的QTL研究（英文）
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摘要
目前关于花生株型的遗传机制了解不深。本研究利用来源于花育28和P76杂交构建的重组自交系群体(RIL),构建高密度遗传连锁图谱,对控制花生主茎高(MSH)、第一侧枝长(FBL)和分枝数(BN)的数量性状位点(QTL)进行定位分析。该图谱包含2266个SNP和68个SSR,总遗传距离为2586.37cM。相邻标记间平均间距为2.25cM。研究发现MSH分别与BN(r=0.354)、FBL(r=0.854)高度相关。QTL分析检测到18个加性QTL位点(4个与MSH相关,5个与FBL相关,9个与BN相关),分布于10个染色体。大多数QTL位点只在一个环境下检测到,其中主茎高相关位点qMSHA01.1,第一侧枝长相关位点qFBLA01.2,分枝数相关位点qBNB07.1和qBNB07.2在两个环境下均能检测到。另外,针对MSH、FBL、BN,共有24对上位性QTL被检测到,表型变异解释率均低于10%。以上结果将为花生株型相关基因的图位克隆和分子标记设计育种提供重要的基础。
The genetic basis for plant architecture traits in peanut(Arachis hypogaea L.)is poorly understood.This study characterized quantitative trait loci(QTLs)underlying peanut main stem height(MSH),first branch length(FBL)and branch number(BN),using a high-density genetic linkage map in a recombinant inbred line(RIL)population derived from Huayu28 and P76.The map consists of 2266 SNPs and 68 SSRs covering agenetic distance of 2586.37 cM.The average distance between adjacent markers was 2.25 cM.A positive correlation was found between MSH and BN(r=0.354),FBL(r=0.854).QTL analysis showed 18 additive QTLs(four MSH,five FBL,and nine BN)mapped to 10 chromosomes.While most QTLs were identified in only one environment,qMSHA01.1 for MSH,qFBLA01.2 for FBL,qBNB07.1 and qBNB07.2 for BN were in two environments.Besides,24 pairs of epistatic QTLs were identified for MSH,FBL,and BN;all of which accounted for phenotypic variation explained(PVE)less than 10%.These results provide a foundation for fine mapping and cloning of genes affecting plant architecture and the design of molecular breeding in peanut.
The genetic basis for plant architecture traits in peanut(Arachis hypogaea L.)is poorly understood.This study characterized quantitative trait loci(QTLs)underlying peanut main stem height(MSH),first branch length(FBL)and branch number(BN),using a high-density genetic linkage map in a recombinant inbred line(RIL)population derived from Huayu28 and P76.The map consists of 2266 SNPs and 68 SSRs covering agenetic distance of 2586.37 cM.The average distance between adjacent markers was 2.25 cM.A positive correlation was found between MSH and BN(r=0.354),FBL(r=0.854).QTL analysis showed 18 additive QTLs(four MSH,five FBL,and nine BN)mapped to 10 chromosomes.While most QTLs were identified in only one environment,qMSHA01.1 for MSH,qFBLA01.2 for FBL,qBNB07.1 and qBNB07.2 for BN were in two environments.Besides,24 pairs of epistatic QTLs were identified for MSH,FBL,and BN;all of which accounted for phenotypic variation explained(PVE)less than 10%.These results provide a foundation for fine mapping and cloning of genes affecting plant architecture and the design of molecular breeding in peanut.
引文
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[24]YANG C Y.QTL analysis for height of main stem and number of branches in peanut(Arachis hypogaea L.)[D].Wuhan:South-Central University for Nationalities,2015.
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[27]LIU D,MA C,HONG W,et al.Construction and analysis of high-density linkage map using highthroughput sequencing data[J].PLoS One,2014,9(6):e98855.
[28]WU Y,BHAT P R,CLOSE T J,et al.Efficient and accurate construction of genetic linkage maps from the minimum spanning tree of a graph[J].PLoS Genetics,2008,4(10):e1000212.
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[32]ZHANG J,SONG Q,CREGAN P B,et al.Genome-wide association study for flowering time,maturity dates and plant height in early maturing soybean(Glycine max)germplasm[J].BMC Genomics,2015,16(1):217.
[33]KATO K,MIURA H,SAWADA S.Mapping QTLs controlling grain yield and its components on chromosome 5Aof wheat[J].Theoretical and Applied Genetics,2000,101(7):1114-112.
[2]CHEN Y N,REN X,ZHENG Y L,et al.Genetic mapping of yield traits using RIL population derived from Fuchuan Dahuasheng and ICG6375of peanut(Arachis hypogaea L.)[J].Molecular Breeding,2017,37(2):17.
[3]LI Y,LI L,ZHANG X,et al.QTL mapping and marker analysis of main stem height and the first lateral branch length in peanut(Arachis hypogaea L.)[J].Euphytica,2017,213(2):57.
[4]JIANG H F,HUANG L,REN X P,et al.Diversity characterization and association analysis of agronomic traits in a Chinese peanut(Arachis hypogaea L.)mini-core collection[J].Journal of Integrative Plant Biology,2014,56(2):159-169.
[5]TORADA A,KOIKE M,MOCHIDA K,et al.SSR-based linkage map with new markers using an intraspecific population of common wheat[J].Theoretical and Applied Genetics,2006,112(6):1042-1051.
[6]PANDEY M K,WANG M L,QIAO L,et al.Identification of QTLs associated with oil content and mapping FAD2genes and their relative contribution to oil quality in peanut(Arachis hypogaea L.)[J].BMCGenetics,2014,15(1):133.
[7]WANG M L,KHERA P,PANDEY M K,et al.Genetic mapping of QTLs controlling fatty acids provided insights into the genetic control of fatty acid synthesis pathway in peanut(Arachis hypogaea L.)[J].PLoS One,2015,10(4):e0119454.
[8]HERSELMAN L,THWAITES R,KIMMINS F M,et al.Identification and mapping of AFLP markers linked to peanut(Arachis hypogaea L.)resistance to the aphid vector of groundnut rosette disease[J].Theoretical and Applied Genetics,2004,109(7):1426-1433.
[9]KHEDIKAR Y P,GOWDA M V,SARVAMAN-GALA C,et al.A QTL study on late leaf spot and rust revealed one major QTL for molecular breeding for rust resistance in groundnut(Arachis hypogaea L.)[J].Theoretical and Applied Genetics,2010,121(5):971-984.
[10]KHERA P,PANDEY M K,WANG H,et al.Mapping quantitative trait loci of resistance to tomato spotted wilt virus and leaf spots in a recombinant inbred line population of peanut(Arachis hypogaea L.)from SunOleic 97R and NC94022[J].PLoSOne,2016,11(7):e0158452.
[11]PANDEY M K,WANG H,KHERA P,et al.Genetic dissection of novel QTLs for resistance to leaf spots and tomato spotted wilt virus in peanut(Arachis hypogaea L.)[J].Frontiers in Plant Science,2017,8:25.
[12]SUJAY V,GOWDA M V,PANDEY M K,et al.Quantitative trait locus analysis and construction of consensus genetic map for foliar disease resistance based on two recombinant inbred line populations in cultivated groundnut(Arachis hypogaea L.)[J].Molecular Breeding,2012,30(2):773-788.
[13]TSENG Y C,TILLMAN B L,PENG Z,et al.I-dentification of major QTLs underlying tomato spotted wilt virus resistance in peanut cultivar FloridaEP(TM)'113'[J].BMC Genetics,2016,17(1):128.
[14]VARSHNEY R K,PANDEY M K,JANILA P,et al.Marker-assisted introgression of a QTL region to improve rust resistance in three elite and popular varieties of peanut(Arachis hypogaea L.)[J].Theoretical and Applied Genetics,2014,127(8):1771-1781.
[15]ZHAO Y,ZHANG C,CHE H,et al.QTL mapping for bacterial wilt resistance in peanut(Arachis hypogaea L.)[J].Molecular Breeding,2016,36(2):13.
[16]RAVI K,VADEZ V,ISOBE S,et al.Identification of several small main-effect QTLs and a large number of epistatic QTLs for drought tolerance related traits in groundnut(Arachis hypogaea L.)[J].Theoretical and Applied Genetics,2011,122(6):1119-1132.
[17]VARSHNEY R K,BERTIOLI D J,MORETZ-SOHN M C,et al.The first SSR-based genetic linkage map for cultivated groundnut(Arachis hypogaea L.)[J].Theoretical and Applied Genetics,2009,118(4):729-739.
[18]CHEN W,JIAO Y,CHENG L,et al.Quantitative trait locus analysis for pod-and kernel-related traits in the cultivated peanut(Arachis hypogaea L.)[J].BMC Genetics,2016,17(1):25.
[19]CHENG L,TANG M,REN X,et al.Construction of genetic map and QTL analysis for mainstem height and total branch number in peanut(Arachis hypogaea L.)[J].Acta Agronomica Sinica,2015,41(6):979-987.
[20]FONCEKA D,TOSSIM H A,RIVALLAN R,et al.Construction of chromosome segment substitution lines in peanut(Arachis hypogaea L.)using a wild synthetic and QTL mapping for plant morphology[J].PLoS One,2012,7(11):e48642.
[21]HUANG L,HE H,CHEN W,et al.Quantitative trait locus analysis of agronomic and quality-related traits in cultivated peanut(Arachis hypogaea L.).Theoretical and Applied Genetics,2015,128(6):1103-1115.
[22]LUO H,REN X,LI Z,et al.Co-localization of major quantitative trait loci for pod size and weight to a3.7cM interval on chromosome A05in cultivated peanut(Arachis hypogaea L.)[J].BMC Genomics,2017,18(1):58.
[23]SHIRASAWA K,KOILKONDA P,AOKI K,et al.In silico polymorphism analysis for the development of simple sequence repeat and transposon markers and construction of linkage map in cultivated peanut[J].BMC Plant Biology,2012,12(1):80.
[24]YANG C Y.QTL analysis for height of main stem and number of branches in peanut(Arachis hypogaea L.)[D].Wuhan:South-Central University for Nationalities,2015.
[25]HUANG L,REN X,WU B,et al.Development and deployment of a high-density linkage map identified quantitative trait loci for plant height in peanut(Arachis hypogaea L.)[J].Scientific Reports,2016,6:39478.
[26]SUN X,LIU D,ZHANG X,et al.SLAF-seq:an efficient method of large-scale de novo SNP discovery and genotyping using high-throughput sequencing[J].PLoS One,2013,8(3):e58700.
[27]LIU D,MA C,HONG W,et al.Construction and analysis of high-density linkage map using highthroughput sequencing data[J].PLoS One,2014,9(6):e98855.
[28]WU Y,BHAT P R,CLOSE T J,et al.Efficient and accurate construction of genetic linkage maps from the minimum spanning tree of a graph[J].PLoS Genetics,2008,4(10):e1000212.
[29]VAN OS H,STAM P,VISSER R G,et al.SMOOTH:a statistical method for successful removal of genotyping errors from high-density genetic linkage data[J].Theoretical and Applied Genetics,2005,112(1):187-194.
[30]KOSAMBI D D.The estimation of map distances from recombination values[J].Annals of Human Genetics,1943,12(1):172-175.
[31]PEIFFER J A,ROMAY M C,GORE M A,et al.The genetic architecture of maize height[J].Genetics,2014,196(4):1337-1356.
[32]ZHANG J,SONG Q,CREGAN P B,et al.Genome-wide association study for flowering time,maturity dates and plant height in early maturing soybean(Glycine max)germplasm[J].BMC Genomics,2015,16(1):217.
[33]KATO K,MIURA H,SAWADA S.Mapping QTLs controlling grain yield and its components on chromosome 5Aof wheat[J].Theoretical and Applied Genetics,2000,101(7):1114-112.
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