title: Linkage and regional association analysis reveal two new tightly-linked major-QTLs for pod number and seed number per pod in rapeseed (Brassica napus L.).
abstract: To facilitate the pseudochromosomes assembly and gene cloning in rapeseed, we developed a reference genetic population/map (named BnaZNF2) from two sequenced cultivars, Zhongshuang11 and No.73290, those exhibit significant differences in many traits, particularly yield components. The BnaZNF2 genetic map exhibited perfect collinearity with the physical map of B. napus, indicating its high quality. Comparative mapping revealed several genomic rearrangements between B. napus and B. rapa or B. oleracea. A total of eight and 16 QTLs were identified for pod number and seed number per pod, respectively, and of which three and five QTLs are identical to previously identified ones, whereas the other five and 11 are novel. Two new major QTL respectively for pod number and seed number per pod, qPN.A06-1 and qSN.A06-1 (R(2 )= 22.8% and 32.1%), were colocalised with opposite effects, and only qPN.A06-1 was confirmed and narrowed by regional association analysis to 180 kb including only 33 annotated genes. Conditional QTL analysis and subsequent NILs test indicated that tight linkage, rather than pleiotropy, was the genetic causation of their colocalisation. Our study demonstrates potential of this reference genetic population/map for precise QTL mapping and as a base for positional gene cloning in rapeseed.
authors.affiliation: Key Laboratory of Oil Crop Biology of the Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan 430062, China.
authors.forename: Jiaqin
authors.initials: J
authors.lastname: Shi
authors.affiliation: Key Laboratory of Oil Crop Biology of the Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan 430062, China.
authors.forename: Jiepeng
authors.initials: J
authors.lastname: Zhan
authors.affiliation: Key Laboratory of Oil Crop Biology of the Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan 430062, China.
authors.forename: Yuhua
authors.initials: Y
authors.lastname: Yang
authors.affiliation: Key Laboratory of Oil Crop Biology of the Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan 430062, China.
authors.forename: Jiang
authors.initials: J
authors.lastname: Ye
authors.affiliation: Key Laboratory of Oil Crop Biology of the Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan 430062, China.
authors.forename: Shunmou
authors.initials: S
authors.lastname: Huang
authors.affiliation: Key Laboratory of Information and Computing Science of Guizhou Province, Guizhou Normal University, Guiyang 550001, China.
authors.forename: Ruiyuan
authors.initials: R
authors.lastname: Li
authors.affiliation: Key Laboratory of Oil Crop Biology of the Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan 430062, China.
authors.forename: Xinfa
authors.initials: X
authors.lastname: Wang
authors.affiliation: Key Laboratory of Oil Crop Biology of the Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan 430062, China.
authors.forename: Guihua
authors.initials: G
authors.lastname: Liu
authors.affiliation: Key Laboratory of Oil Crop Biology of the Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan 430062, China.
authors.forename: Hanzhong
authors.initials: H
authors.lastname: Wang
mesh_terms: D029688:Brassica napus / Q000235:genetics* / Q000254:growth & development; D029741:Brassica rapa / Q000235:genetics* / Q000254:growth & development; D002874:Chromosome Mapping; D032461:Chromosomes, Plant / Q000235:genetics; D056726:Genetic Association Studies; D018745:Genome, Plant; D015810:Linkage Disequilibrium; D018895:Microsatellite Repeats; D058977:Molecular Sequence Annotation; D010641:Phenotype; D040641:Quantitative Trait Loci; D012639:Seeds / Q000235:genetics* / Q000254:growth & development; D017422:Sequence Analysis, DNA