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Front Plant Sci. 2016 Jul 27;7:1102. doi: 10.3389/fpls.2016.01102. eCollection 2016.

Genome-Wide Association Study Provides Insight into the Genetic Control of Plant Height in Rapeseed (Brassica napus L.).

Author information

1
National Key Laboratory of Crop Genetic Improvement, National Sub-Center of Rapeseed Improvement in Wuhan, Huazhong Agricultural University Wuhan, China.
2
Southern Regional Collaborative Innovation Center for Grain and Oil Crops, College of Agronomy, Hunan Agricultural University Changsha, China.
3
Chongqing Rapeseed Engineering Technology Research Center, College of Agronomy and Biotechnology, Southwest University Chongqing, China.
4
Key Laboratory of Cotton and Rapeseed, Jiangsu Academy of Agricultural Science Nanjing, China.

Abstract

Plant height is a key morphological trait of rapeseed. In this study, we measured plant height of a rapeseed population across six environments. This population contains 476 inbred lines representing the major Chinese rapeseed genepool and 44 lines from other countries. The 60K Brassica Infinium® SNP array was utilized to genotype the association panel. A genome-wide association study (GWAS) was performed via three methods, including a robust, novel, nonparametric Anderson-Darling (A-D) test. Consequently, 68 loci were identified as significantly associated with plant height (P < 5.22 × 10(-5)), and more than 70% of the loci (48) overlapped the confidence intervals of reported QTLs from nine mapping populations. Moreover, 24 GWAS loci were detected with selective sweep signals, which reflected the signatures of historical semi-dwarf breeding. In the linkage disequilibrium (LD) decay range up-and downstream of 65 loci (r (2) > 0.1), we found plausible candidates orthologous to the documented Arabidopsis genes involved in height regulation. One significant association found by GWAS colocalized with the established height locus BnRGA in rapeseed. Our results provide insights into the genetic basis of plant height in rapeseed and may facilitate marker-based breeding.

KEYWORDS:

Brassica napus; association mapping; haplotype block; plant height; selective sweep

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