Unravelling the complex trait of harvest index in rapeseed (Brassica napus L.) with association mapping

Abstract

BackgroundHarvest 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.ResultsIn 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.ConclusionsOur 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.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-015-1607-0) contains supplementary material, which is available to authorized users.

A combination of genome-wide association and transcriptome analysis reveals candidate genes controlling harvest index-related traits in Brassica napus

“…Correlation analyses showed that SY was significantly and positively related to HI (Supplementary Table S6), which is in line with the findings of several previous studies726. In another important crop, soybean, yield increase was also positively associated with HI27.…”

“…GWAS results showed that the most significant SNPs for HI in plants grown at CQ and YN, in 2014, were located on chromosomes C05 and A07, and explained 5.66% and 4.76% of the phenotypic variation, respectively. For BY, a previous GWAS only detected a single significant SNP, which explained 0.76% of phenotypic variation7, whereas the most significant SNP we identified on chromosome A03, in our GWAS results from 13CQ, explained 8.36% of phenotypic variation. Arguable, this identified higher contribution rate could well be related to the larger population size employed in our GWAS.…”

“…Recently, a GWAS of HI and HI-related traits of B. napus was carried out using a natural population of 155 B. napus cultivars7. The authors identified 9 significant SNPs associated with HI in the B. napus C subgenome, which explained 3.42% of the phenotypic variation7. Taken together, these findings illustrate the promise of GWAS for detecting QTLs that control important complex agronomic traits.…”

“…Several candidate genes associated with seed germination and vigor were also identified in a GWAS analysis6. Recently, a GWAS of HI and HI-related traits of B. napus was carried out using a natural population of 155 B. napus cultivars7. The authors identified 9 significant SNPs associated with HI in the B. napus C subgenome, which explained 3.42% of the phenotypic variation7.…”

Agronomic and Quality Assessment of Linseed Advanced Breeding Lines Varying in Seed Mucilage Content and Their Use for Food and Feed

“…In food production, optimizing grain yield, reducing production costs, and minimizing risks to the environment has became a primary objective under the current climate change scenario (Li et al, 2012). The negative and significant correlation between HI and PH has been reported in rice (Li et al, 2012), maize (Can and Yoshida 1999), and rapeseed (Brassica napus L.; Luo et al, 2015). The HI was superior for most of the ABLs as compared with the controls.…”