A combination of genome-wide association and transcriptome analysis reveals candidate genes controlling harvest index-related traits in Brassica napus.
Harvest index (HI), the ratio of seed mass to total biomass of the aboveground plant parts, is an important trait for harvestable yield of crops. Unfortunately, HI of Brassica napus is lower than that of other economically important crops. To identify candidate genes associated with high HI, a genome-wide association study of HI and four HI-related traits was conducted with 520 B. napus accessions cultivated in both Yunnan and Chongqing. We detected 294 single nucleotide polymorphisms significantly associated with the abovementioned traits, including 79 SNPs that affected two or more traits. Differentially expressed genes between extremely high- and low-HI accessions were identified in 8 tissues at two cultivated regions. Combination of linkage disequilibrium and transcriptome analyses revealed 33 functional candidate genes located within the confidence intervals of significant SNPs associated with more than one trait, such as SHOOT GRAVITROPISM 5 (Bna.SGR5), ATP-CITRATE LYASE A-3 (Bna.ACLA-3) and CAROTENOID CLEAVAGE DIOXYGENASE 1 (Bna.CCD1), their orthologs in the Arabidopsis thaliana have been shown to play key roles in photosynthesis, inflorescence, and silique development. Our results provide insight into the molecular mechanisms underlying establishment of high-HI B. napus and lay a foundation for characterization of candidate genes aimed at developing high-HI B. napus varieties.
College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing 400715, China.
Kun
K
Lu
College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing 400715, China.
Zhongchun
Z
Xiao
College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing 400715, China.
Hongju
H
Jian
College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing 400715, China.
Liu
L
Peng
College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing 400715, China.
Cunmin
C
Qu
Industrial Crops Institute, Yunnan Academy of Agricultural Sciences, Kunmimg 650205, China.
Minglian
M
Fu
Agricultural Technology Extension Stationin Lincang City, Lincang 677000, China.
Bin
B
He
Industrial Crops Institute, Yunnan Academy of Agricultural Sciences, Kunmimg 650205, China.
Linmei
L
Tie
College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing 400715, China.
Ying
Y
Liang
College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing 400715, China.
Xingfu
X
Xu
College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing 400715, China.
Jiana
J
Li
D001275:ATP Citrate (pro-S)-Lyase / Q000235:genetics / Q000378:metabolism; D029688:Brassica napus / Q000235:genetics* / Q000254:growth & development; D002874:Chromosome Mapping; D049308:Dioxygenases / Q000378:metabolism; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant; D017343:Genes, Plant; D055106:Genome-Wide Association Study; D005838:Genotype; D015810:Linkage Disequilibrium; D010788:Photosynthesis / Q000235:genetics; D010940:Plant Proteins / Q000235:genetics / Q000378:metabolism; D020641:Polymorphism, Single Nucleotide; D025341:Principal Component Analysis; D044767:Ubiquitin-Protein Ligases / Q000235:genetics / Q000378:metabolism
D010940:Plant Proteins; D049308:Dioxygenases; C431939:carotenoid cleavage dioxygenase 1; D044767:Ubiquitin-Protein Ligases; D001275:ATP Citrate (pro-S)-Lyase