A Combination of Genome-wide Association and Transcriptome Analysis Reveals Candidate Genes Controlling Harvest Index-related Traits in Brassica Napus

Overview

Journal Sci Rep

Specialty Science

Date 2016 Nov 5

PMID 27811979

Citations 26

Authors

Kun Lu

Zhongchun Xiao

Hongju Jian

Liu Peng

Cunmin Qu

Minglian Fu

Bin He

Linmei Tie

Ying Liang

Xingfu Xu

Jiana Li

Affiliations

Soon will be listed here.

Abstract

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.

Citing Articles

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