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油菜株高QTL定位、整合和候选基因鉴定
引用本文:张江江,詹杰鹏,刘清云,师家勤,王新发,刘贵华,王汉中.油菜株高QTL定位、整合和候选基因鉴定[J].中国农业科学,2017,50(17):3247-3258.
作者姓名:张江江  詹杰鹏  刘清云  师家勤  王新发  刘贵华  王汉中
基金项目:国家油菜产业技术体系(CARS-13)、中国农业科学院科技创新工程(CAAS-ASTIP-2013-OCRI)、国家公益性科研院所基本科研业务费(1610172017001)、湖北农业科技创新中心
摘    要:【目的】通过对油菜株高进行多环境QTL定位并与已报道的油菜株高QTL和植物株高基因分别进行整合和比对分析,揭示油菜株高的遗传结构和候选基因并为其分子改良提供依据。【方法】以油菜优良品种中双11(测序)和No.73290(重测序)衍生的含184个单株的Bna ZNF2群体为试验材料。首先,对Bna ZNF2群体进行基因型分析,利用Joinmap 4.0软件构建了一张含803个分子标记的高密度遗传图谱。其次,对F2:3和F2:4家系进行连续两年(2010—2011)两点(武汉和西宁)田间试验和表型鉴定。然后,利用Bna ZNF2群体的基因型数据和F2:3以及F2:4家系的株高表型数据,采用Win QTLCart 2.5软件的复合区间作图法进行QTL检测。最后,利用元分析的方法采用Bio Mercator软件对不同环境中检测到的株高QTL进行整合。【结果】对两年两点环境下分别检测到的株高QTL进行整合总共得到5个株高QTL的位点:q PH.A2-1、q PH.A2-2、q PH.C2-1、q PH.C3-1和q PH.C3-2,分布于A2、C2和C3染色体上,解释2.6%—55.6%的表型方差。其中,q PH.A2-1和q PH.A2-2只在武汉检测到,而q PH.C2-1、q PH.C3-1和q PH.C3-2只在西宁检测到。位于C2连锁群的主效QTL-q PH.C2-1只在西宁被重复检测到,而且LOD值、加性效应和贡献率(分别为23.4、-16.0和55.6%)均高于前人报道,是目前发现的效应最大的一个油菜株高QTL。基于油菜基因组物理图谱对本研究和已报道的油菜株高QTL和植物株高基因分别进行整合和比对分析,获得了一个由183个QTL和287个候选基因组成的相对完整的油菜株高遗传结构图。其中,有18个株高QTL簇能在不同研究中被共同检测到,分布在A1、A2、A3、A6、A7、A9、C6和C7染色体上。另外,本研究定位到的5个油菜株高QTL的物理位置和已报道的油菜株高QTL均不重叠,因而是新的株高QTL位点。其中,q PH.A2-2、q PH.C3-1和q PH.C3-2物理区间内总共找到了15个株高同源基因,而11个在2个亲本中存在序列变异,被选作候选基因进行进一步研究。【结论】QTL定位和整合获得5个油菜株高QTL,均为首次报道而且都只在武汉或西宁被检测到。其中位于C2连锁群的主效QTL效应值超过以往报道,表现出极强的QTL与环境的互作。通过与已报道的油菜株高QTL和植物株高基因分别进行整合和比对分析,较为全面地揭示了油菜株高的遗传结构和候选基因,生物信息学分析还鉴定到11个位于本研究定位到的3个株高QTL区间内的候选基因。

关 键 词:甘蓝型油菜  株高  遗传结构  QTL  候选基因  QTL与环境的互作
收稿时间:2017-01-20

QTL Mapping and Integration as well as Candidate Genes Identification for Plant Height in Rapeseed (Brassica napus L.)
ZHANG JiangJiang,ZHAN JiePeng,LIU QingYun,SHI JiaQin,WANG XinFa,LIU GuiHua,WANG HanZhong.QTL Mapping and Integration as well as Candidate Genes Identification for Plant Height in Rapeseed (Brassica napus L.)[J].Scientia Agricultura Sinica,2017,50(17):3247-3258.
Authors:ZHANG JiangJiang  ZHAN JiePeng  LIU QingYun  SHI JiaQin  WANG XinFa  LIU GuiHua  WANG HanZhong
Affiliation:1.Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062;2.Oil Crops Extension Station of the Agricultural Bureau of Xishui County, Huanggang 438200, Hubei
Abstract:【Objective】In order to reveal the genetic architecture and candidate genes for plant height in rapeseed, QTLs were mapped in multiple environments and were integrated withpreviously reported plant height QTLs and then aligned with the plant height genes, which will provide a basis for the molecular improvement of plant height in rapeseed. 【Method】 The BnaZNF2 population of 184 individuals derived from the elite rapeseed cultivar Zhongshuang11 (de novo sequencing) and No.73290 (re-sequencing) was used as the experimental material. First, the BnaZNF2 population was subjected to genotype analysis and a high-density linkage map of 803 molecular markers was constructed using Joinmap 4.0. Second, the F2:3 and F2:4 family of BnaZNF2 population were planted and phenotyped at two locations (Wuhan and Xining) for successive two years (2010 and 2011). Then QTL mapping was conducted by the composite interval mapping method incorporated into WinQTLCart 2.5 software, using the genotype of BnaZNF2 population and the plant height phenotype of its F2:3 and F2:4 family. 【Result】 After integration of QTLs detected in two locations over two years, a total of 5 consensus QTLs (qPH.A2-1, qPH.A2-2, qPH.C2-1, qPH.C3-1, qPH.C3-2) were obtained, which were distributed on A2, C2 and C3 chromosomes and, explained 2.6%-55.6% of the phenotypic variance. A major QTL on the C2 chromosome, qPH.C2-1, was only detected repeatedly in Xining and its LOD value, additive effect and R2 (23.4, -16.0 and 55.6%, respectively) were largest among all of the reported plant height QTLs. Based on the physical map of rapeseed, all of the currently and previously reported plant height QTLs in rapeseed were integrated and then aligned with the plant height genes, which revealed a relatively completed genetic architecture map consisting of 183 QTLs in rapeseed and 287 candidate genes in rapeseed. Of these, a total of 18 QTL cluster were commonly detected in different studies, which were distributed on A1, A2, A3, A6, A7, A9, C6 and C7 chromosomes. In addition, the physical positions of the five QTL detected in the current study were all not overlapped with those of the previously detected plant height QTL, which should be novel. A total of 15 homologues of plant height genes were found within the physical intervals of qPH.A2-2, qPH.C3-1 and qPH.C3-2, of which 11 homologues showed sequence variations between the two parents, which were chosen as the candidates for further study. 【Conclusion】 QTL mapping and integration identified five QTL for plant height in rapeseed, which were all novel. The effect of the major QTL on the C2 chromosome was larger than those of the previously reported plant height QTL, which also showed the strong interaction with the environment. The integration of the reported plant height QTLs and the alignment with the plant height genes systematically revealed the genetic architecture and candidate genes for plant height in rapeseed. By bioinformatics analysis, a total of 11 candidates were identified within the physical intervals of three plant height QTLs detected in the current study.
Keywords:Brassica napus L    plant height  genetic architecture  QTL  candidate genes  QTL by environment interaction
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