title: Unravelling the complex trait of harvest index in rapeseed (Brassica napus L.) with association mapping.
abstract: BACKGROUND
  Harvest index (HI), the ratio of grain yield to total biomass, is considered as a measure of biological success in partitioning assimilated photosynthate to the harvestable product. While crop production can be dramatically improved by increasing HI, the underlying molecular genetic mechanism of HI in rapeseed remains to be shown.
  
  
  RESULTS
  In this study, we examined the genetic architecture of HI using 35,791 high-throughput single nucleotide polymorphisms (SNPs) genotyped by the Illumina BrassicaSNP60 Bead Chip in an association panel with 155 accessions. Five traits including plant height (PH), branch number (BN), biomass yield per plant (BY), harvest index (HI) and seed yield per plant (SY), were phenotyped in four environments. HI was found to be strongly positively correlated with SY, but negatively or not strongly correlated with PH. Model comparisons revealed that the A-D test (ADGWAS model) could perfectly balance false positives and statistical power for HI and associated traits. A total of nine SNPs on the C genome were identified to be significantly associated with HI, and five of them were identified to be simultaneously associated with HI and SY. These nine SNPs explained 3.42% of the phenotypic variance in HI.
  
  
  CONCLUSIONS
  Our results showed that HI is a complex polygenic phenomenon that is strongly influenced by both environmental and genotype factors. The implications of these results are that HI can be increased by decreasing PH or reducing inefficient transport from pods to seeds in rapeseed. The results from this association mapping study can contribute to a better understanding of natural variations of HI, and facilitate marker-based breeding for HI.
authors.affiliation: National Key Laboratory of Crop Genetic Improvement, National Center of Rapeseed Improvement in Wuhan, Huazhong Agricultural University, Wuhan, 430070, P.R. China. tjaulx@126.com.
authors.forename: Xiang
authors.initials: X
authors.lastname: Luo
authors.affiliation: National Key Laboratory of Crop Genetic Improvement, National Center of Rapeseed Improvement in Wuhan, Huazhong Agricultural University, Wuhan, 430070, P.R. China. yuanbeauty@mail.hzau.edu.cn.
authors.forename: Chaozhi
authors.initials: C
authors.lastname: Ma
authors.affiliation: National Key Laboratory of Crop Genetic Improvement, National Center of Rapeseed Improvement in Wuhan, Huazhong Agricultural University, Wuhan, 430070, P.R. China. hzauyaoyue@163.com.
authors.forename: Yao
authors.initials: Y
authors.lastname: Yue
authors.affiliation: National Key Laboratory of Crop Genetic Improvement, National Center of Rapeseed Improvement in Wuhan, Huazhong Agricultural University, Wuhan, 430070, P.R. China. hukaining@gmail.com.
authors.forename: Kaining
authors.initials: K
authors.lastname: Hu
authors.affiliation: National Key Laboratory of Crop Genetic Improvement, National Center of Rapeseed Improvement in Wuhan, Huazhong Agricultural University, Wuhan, 430070, P.R. China. liyaya_135@163.com.
authors.forename: Yaya
authors.initials: Y
authors.lastname: Li
authors.affiliation: National Key Laboratory of Crop Genetic Improvement, National Center of Rapeseed Improvement in Wuhan, Huazhong Agricultural University, Wuhan, 430070, P.R. China. hzaudzq@163.com.
authors.forename: Zhiqiang
authors.initials: Z
authors.lastname: Duan
authors.affiliation: National Key Laboratory of Crop Genetic Improvement, National Center of Rapeseed Improvement in Wuhan, Huazhong Agricultural University, Wuhan, 430070, P.R. China. tjaulx@163.com.
authors.forename: Ming
authors.initials: M
authors.lastname: Wu
authors.affiliation: National Key Laboratory of Crop Genetic Improvement, National Center of Rapeseed Improvement in Wuhan, Huazhong Agricultural University, Wuhan, 430070, P.R. China. tujx@mail.hzau.edu.cn.
authors.forename: Jinxing
authors.initials: J
authors.lastname: Tu
authors.affiliation: National Key Laboratory of Crop Genetic Improvement, National Center of Rapeseed Improvement in Wuhan, Huazhong Agricultural University, Wuhan, 430070, P.R. China. jxshen@mail.hzau.edu.cn.
authors.forename: Jinxiong
authors.initials: J
authors.lastname: Shen
authors.affiliation: National Key Laboratory of Crop Genetic Improvement, National Center of Rapeseed Improvement in Wuhan, Huazhong Agricultural University, Wuhan, 430070, P.R. China. yibin@mail.hzau.edu.cn.
authors.forename: Bin
authors.initials: B
authors.lastname: Yi
authors.affiliation: National Key Laboratory of Crop Genetic Improvement, National Center of Rapeseed Improvement in Wuhan, Huazhong Agricultural University, Wuhan, 430070, P.R. China. futing@mail.hzau.edu.cn.
authors.forename: Tingdong
authors.initials: T
authors.lastname: Fu
mesh_terms: D018533:Biomass; D029688:Brassica napus / Q000235:genetics* / Q000254:growth & development*; D002874:Chromosome Mapping; D010641:Phenotype; D000069600:Plant Breeding; D020641:Polymorphism, Single Nucleotide