基于SNP遗传图谱定位甘蓝型油菜分枝角度QTL
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摘要
分枝角度是油菜株型的重要性状,与油菜的耐密植性密切相关。本研究利用油菜分枝角差异显著的育种亲本材料1098B (分枝角小)和R~2 (分枝角大)杂交获得F1,通过小孢子培养获得含163份株系的DH群体。以油菜60K SNP芯片进行DH群体基因分型,构建高密度遗传图谱,并利用QTL Cartographer 2.5对2个环境下油菜顶端分枝角和基部分枝角进行QTL分析。结果表明,构建的高密度遗传图谱覆盖甘蓝型油菜19条染色体,包含9521个多态性SNP标记, 1442个簇(bin),覆盖基因组长度为2544.07 cM,相邻簇(bin)之间平均距离为1.76 cM。在此图谱基础上采用复合区间作图法(CIM),在2个环境下检测到17个分枝角度QTL,分别位于A01、A02、A03、A06、A09、C02、C03、C04、C06和C08染色体上,单个QTL解释的表型变异为6.39%～21.78%。用比较基因组方法与拟南芥分枝角度同源基因区间比对,鉴定出其中6个QTL的12个候选基因。其中位于A03连锁群QTL在2年的试验中被重复检测到,根据物理位置和基因组信息推测VAMP714为分枝角度的候选基因。这些QTL和候选基因将为油菜分枝角度的遗传改良提供有用的信息。
Branch angle is an important agronomic trait of plant architecture. In this study, 163 lines of a DH population derived from a cross between 1019 B(compact type) and R~2(loose type) were genotyped by using 60 K SNP array and a high-density genetic linkage map was constructed with 1442 bins inclusive of 9521 SNP markers to detect quantitative trait loic(QTL) for basal branch angle and top branch angle. The genetic map contained 19 lingkage groups with a total length of 2544.07 cM and an average distance between adjacent bin-markers of 1.76 cM. Totally, 17 QTL for branch angle were detected on chromosomes A01, A02, A03, A06, A09, C02, C03, C04, C06, and C08, respectively. The phenotypic variation accounted by a single locus was from 6.36% to 21.78%. Twelve candidate genes of branch angle were found underlying six QTL by comparing with homologous genes in Arabidopsis. Candidate gene VAMP714 was close to the peak position of A03 QTL confidence interval, which was identified on chromosome A03 in both environments. These QTL and candidate genes provide useful information for the genetic modification of rapeseed branch angle.
Branch angle is an important agronomic trait of plant architecture. In this study, 163 lines of a DH population derived from a cross between 1019 B(compact type) and R~2(loose type) were genotyped by using 60 K SNP array and a high-density genetic linkage map was constructed with 1442 bins inclusive of 9521 SNP markers to detect quantitative trait loic(QTL) for basal branch angle and top branch angle. The genetic map contained 19 lingkage groups with a total length of 2544.07 cM and an average distance between adjacent bin-markers of 1.76 cM. Totally, 17 QTL for branch angle were detected on chromosomes A01, A02, A03, A06, A09, C02, C03, C04, C06, and C08, respectively. The phenotypic variation accounted by a single locus was from 6.36% to 21.78%. Twelve candidate genes of branch angle were found underlying six QTL by comparing with homologous genes in Arabidopsis. Candidate gene VAMP714 was close to the peak position of A03 QTL confidence interval, which was identified on chromosome A03 in both environments. These QTL and candidate genes provide useful information for the genetic modification of rapeseed branch angle.
引文
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[2]Cai G Q,Yang Q Y,Chen H,Yang Q,Zhang C Y,Fan C C,Zhou Y M.Genetic dissection of plant architecture and yield-related traits in Brassica napus.Sci Rep,2016,6:21625.
[3]Wang Y H,Li J Y.Molecular basis of plant architecture.Annu Rev Plant Biol,2008,59:253-279.
[4]Chalhoub B,Denoeud F,Liu S Y,Parkin I A,Tang H B,Wang XY,Chiquet J,Belcram H,Tong C B,Samans B,Corréa M,Da Silva C,Just J,Falentin C,Koh C S,Le Clainche I,Bernard M,Bento P,Noel B,Labadie K,Alberti A,Charles M,Arnaud D,Guo H,Daviaud C,Alamery S,Jabbari K,Zhao M X,Edger P P,Chelaifa H,Tack D,Lassalle G,Mestiri I,Schnel N,Le Paslier MC,Fan G,Renault V,Bayer P E,Golicz A A,Manoli S,Lee T H,Thi V H,Chalabi S,Hu Q,Fan C,Tollenaere R,Lu Y,Battail C,Shen J,Sidebottom C H,Wang X,Canaguier A,Chauveau A,Bérard A,Deniot G,Guan M,Liu Z,Sun F,Lim Y P,Lyons E,Town C D,Bancroft I,Wang X,Meng J,Ma J,Pires J C,King GJ,Brunel D,Delourme R,Renard M,Aury J M,Adams K L,Batley J,Snowdon R J,Tost J,Edwards D,Zhou Y,Hua W,Sharpe AG,Paterson A H,Guan C,Wincker P.Early allopolyploid evolution in the post-Neolithic Brassica napus oilseed genome.Science,2014,345:950-953.
[5]Sun F M,Fan G Y,Hu Q,Zhou Y M,Guan M,Tong C B,Li J N,Du D Z,Qi C K,Jiang L C,Liu W Q,Huang S M,Chen W B,Yu J Y,Mei D S,Meng J L,Zeng P,Shi J Q,Liu K D,Wang X,Wang X F,Long Y,Liang X M,Hu Z Y,Huang G D,Dong C H,Zhang H,Li J,Zhang Y L,Li L W,Shi C C,Wang J H,Lee M S,Guan C Y,Xu X,Liu S Y,Liu X,Chalhoub B,Hua W,Wang H Z.The high-quality genome of Brassica napus cultivar‘ZS11’reveals the introgression history in semi-winter morphotype.Plant J,2017,92:452-468.
[6]Liu L Z,Qu C M,Wittkop B,Yi B,Xiao Y,He Y J,Snowdon R J,Li J N.A high-density SNP map for accurate mapping of seed fibre QTL in Brassica napus L.PLoS One,2013,8:e83052.
[7]Wang N,Li F,Chen B Y,Xu K,Yan G X,Qiao J W,Li J,Gao GZ,Bancroft L,Meng J L,King G,Wu X M.Genome-wide investigation of genetic changes during modern breeding of Brassica napus.Theor Appl Genet,2014,127:1817-1829.
[8]张凤启,刘越英,程晓辉,童超波,董彩华,唐敏强,黄军艳,刘胜毅.利用高密度SNP标记定位甘蓝型油菜株高QTL.中国油料作物学报,2014,36:695-700.Zhang Q F,Liu Y Y,Cheng X H,Tong C B,Dong C H,Tang MQ,Huang J Y,Liu S Y.QTL mapping of plant height using high density SNP markers in Brassica napus.Chin J Oil Crop Sci,2014,36:695-700(in Chinese with English abstract).
[9]Xu L P,Hu K N,Zhang Z Q,Guan C Y,Shen S,Hua W,Li J N,Wen J,Yi B,Shen J X,Ma C Z,Tu J X,Fu T D.Genome-wide association study reveals the genetic architecture of flowering time in rapeseed(Brassica napus L.).DNA Res,2015,23:43-52.
[10]Li F,Chen B Y,Xu K,Gao G Z,Yan G X,Qiao J W,Li J,Li H,Li L X,Xiao X,Zhang T Y,Nishio T,Wu X M.A genome-wide association study of plant height and primary branch number in rapeseed(Brassica napus).Plant Sci,2016,242:169-177.
[11]Liu J,Wang J,Wang H,Wang W X,Zhou R J,Mei D S,Chen HT,Yang J,Raman H,Hu Q.Multigenic control of pod shattering resistance in Chinese rapeseed germplasm revealed by genome-wide association and linkage analyses.Front Plant Sci,2016,7:1058.
[12]Luo X,Ma C Z,Yue Y,Hu K N,Li Y Y,Duan Z Q,Wu M,Tu JX,Shen J X,Yi B,Fu T D.Unravelling the complex trait of harvest index in rapeseed(Brassica napus L.)with association mapping.BMC Genomics,2015,16:379.
[13]Lu K,Peng L,Zhang C,Lu J H,Yang B,Xiao Z C,Liang Y,Xu X F,Qu C M,Zhang K,Liu L Z,Zhu Q L,Fu M L,Yuan X Y,Li J N.Genome-wide association and transcriptome analyses reveal candidate genes underlying yield-determining traits in Brassica napus.Front Plant Sci,2017,8:206.
[14]Liu S,Fan C C,Li J N,Cai G Q,Yang Q Y,Wu J,Yi X Q,Zhang C Y,Zhou Y M.A genome-wide association study reveals novel elite allelic variations in seed oil content of Brassica napus.Theor Appl Genet,2016,129:1203-1215.
[15]Sun C M,Wang B Q,Yan L,Hu K N,Liu S,Zhou Y M,Guan CY,Zhang Z Q,Li J N,Chen S,Wen J,Ma C Z,Tu J X,Shen J X,Fu T D,Yi B.Genome-wide association study provides insight into the genetic control of plant height in rapeseed(Brassica napus L.).Front Plant Sci,2016,7:1102.
[16]Fu Y,Wei D Y,Dong H L,He Y J,Cui Y X,Mei J Q,Wan H F,Li J N,Snowdon R,Friedt W,Li R X,Qian W.Comparative quantitative trait loci for silique length and seed weight in Brassica napus.Sci Rep,2015,5:14407.
[17]汪文祥,胡琼,梅德圣,李云昌,王会,王军,付丽,刘佳.基于图像处理的油菜分枝及角果着生角度测量方法.中国油料作物学报,2015,37:566-570.Wang W X,Hu Q,Mei D S,Li Y C,Wang H,Wang J,Fu L,Liu J.Evaluation of branch and pod angle measurement based on digital images from Brassica napus L.Chin J Oil Crop Sci,2015,37:566-570(in Chinese with English abstract).
[18]Liu J,Wang W,Mei D,Wang H,Fu L,Liu D,Li Y,Hu Q.Characterising variation of branch angle and genome-wide association mapping in rapeseed(Brassica napus L.).Front Plant Sci,2016,7:21.
[19]Sun C,Wang B,Wang X.Genome-wide association study dissecting the genetic architecture underlying the branch angle trait in rapeseed(Brassica napus L.).Sci Rep,2016,6:33673.
[20]Wang H,Cheng H T,Wang W X,Liu J,Hao M Y,Mei D S,Zhou R J,Fu L,Hu Q.Identification of BnaYUCCA6 as a candidate gene for branch angle in Brassica napus by QTL-seq.Sci Rep,2016,6:38493.
[21]Li H G,Zhang L P,Hu J H,Zhang F G,Chen B Y,Xu K,Gao G Z,Li H,Zhang T Y,Li Z Y,Wu X M.Genome-wide association mapping reveals the genetic control underlying branch angle in rapeseed(Brassica napus L.).Front Plant Sci,2017,8:1054.
[22]Shen Y S,Yang Y,Xu E S,Ge X H,Xiang Y,Li Z Y.Novel and major QTL for branch angle detected by using DH population from an exotic introgression in rapeseed(Brassica napus L.).Theor Appl Genet,2018,131:67-78.
[23]张倩.甘蓝型油菜主要株型性状的遗传分析和QTL初步定位.西南大学硕士学位论文,重庆,2013.Zhang Q.Genetic Effects Analysis and QTL Mapping of Major Plant-type Traits in Brassica napus L.MS Thesis of Southwest University,Chongqing,China,2013(in Chinese with English abstract).
[24]汪文祥,胡琼,梅德圣,李云昌,周日金,王会,成洪涛,付丽,刘佳.甘蓝型油菜分枝角度主基因+多基因混合遗传模型及遗传效应.作物学报,2016,42:1103-1111.Wang W X,Hu Q,Mei D S,Li Y C,Zhou R J,Wang H,Cheng HT,Fu L,Liu J.Genetic effects of branch angle using mixture model of major gene plus polygene in Brassica napus L.Acta Agron Sin,2016,42:1103-1111(in Chinese with English abstract).
[25]Wu Y H,Bhat P R,Close T J,Lonardi S.Efficient and accurate construction of genetic linkage maps from the minimum spanning tree of a graph.PLoS Genet,2008,4:e1000212.
[26]Van Ooijen J W.JoinMap version 4.0:software for the calculation of genetic linkage maps in experimental populations.Netherlands:Wageningen University,2006.https://www.kyazma.nl/index.php/JoinMap/.
[27]Wang S C,Basten C J,Zeng Z B.Windows QTL Cartographer2.5.Raleigh,NC,USA:Department of Statistics,North Carolina State University,2012.http://statgen.ncsu.edu/qtlcart/WQTLCart.htm.
[28]Voorrips R E.MapChart:software for the graphical presentation of linkage maps and QTLs.J Hered,2002,93:77-78.
[29]Parkin I A P,Gulden S M,Sharpe A G,Lukens L,Trick M,Osborn T C,Lydiate D J.Segmental structure of the Brassica napus genome based on comparative analysis with Arabidopsis thaliana.Genetics.2005,171:765-781.
[30]Wang W X,Hu Q,Mei D S,Wang J,Cheng H T,Wang H,Fu L,Liu J.Identification of compact germplasm resources suitable for high density cultivation in Brassica napus L.Oil Crop Sci,2018,3:33-41.
[31]Li H T,Younas M,Wang X F,Li X M,Chen L,Zhao B,Chen X,Xu J S,Hou F,Hong B H,Liu G,Zhao H Y,Wu X L,Du H Z,Wu J S,Liu K D.Development of a core set of single-locus SSRmarkers for allotetraploid rapeseed(Brassica napus L.).Theor Appl Genet,2013,126:937-947.
[32]Shi J Q,Huang S M,Zhan J P,Yu J Y,Wang X F,Hua W,Liu S Y,Liu G H,Wang H Z.Genome-wide microsatellite characterization and marker development in the sequenced Brassica crop species.DNA Res,2014,21:53-68.
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