A genome-wide association study reveals novel elite allelic variations in seed oil content of Brassica napus
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A set of additive loci for seed oil content were identified using association mapping and one of the novel loci on the chromosome A5 was validated by linkage mapping.
Increasing seed oil content is one of the most important goals in the breeding of oilseed crops including Brassica napus, yet the genetic basis for variations in this important trait remains unclear. By genome-wide association study of seed oil content using 521 B. napus accessions genotyped with the Brassica 60K SNP array, we identified 50 loci significantly associated with seed oil content using three statistical models, the general linear model, the mixed linear model and the Anderson–Darling test. Together, the identified loci could explain approximately 80 % of the total phenotypic variance, and 29 of these loci have not been reported previously. Furthermore, a novel locus on the chromosome A5 that could increase 1.5–1.7 % of seed oil content was validated in an independent bi-parental linkage population. Haplotype analysis showed that the favorable alleles for seed oil content exhibit cumulative effects. Our results thus provide valuable information for understanding the genetic control of seed oil content in B. napus and may facilitate marker-based breeding for a higher seed oil content in this important oil crop.
KeywordsQuantitative Trait Locus Mixed Linear Model Double Haploid Double Haploid Line Favorable Allele
The work was financially supported by the funding from the Ministry of Science and Technology of China (2015CB150200, 2014DFA32210), Ministry of Agriculture of China (nycytx-00503 and 948 project (2011-G23)).
Compliance with ethical standards
Conflict of interest
The authors declare that they have no conflict of interest.
The authors declare that this study complies with the current laws of the country in which the experiments were performed.
- Drenkard E, Richter BG, Rozen S, Stutius LM, Angell NA, Mindrinos M, Cho RJ, Oefner PJ, Davis RW, Ausubel FM (2000) A simple procedure for the analysis of single nucleotide polymorphisms facilitates map-based cloning in Arabidopsis. Plant Physiol 124:1483–1492CrossRefPubMedPubMedCentralGoogle Scholar
- Gan L, Sun X, Jin L, Wang G, Xiu J, Wei Z, Fu T (2003) Establishment of math models of NIRS analysis for oil and protein contents in seed of Brassica napus. Sci Agric Sin 36:1609–1613Google Scholar
- Ihaka R, Gentleman R (1996) R: a language for data analysis and graphics. J Comput Graph Statist 5:299–314Google Scholar
- Lincoln SE, Daly MJ, Lander ES (1993) Constructing genetic linkage maps with MAPMAKER/EXP Version 3.0: a tutorial and reference manual. Whitehead Institute Technical Report. Whitehead Institute, CambridgeGoogle Scholar
- Qian W, Meng J, Li M, Frauen M, Sass O, Noack J, Jung C (2006) Introgression of genomic components from Chinese Brassica rapa contributes to widening the genetic diversity in rapeseed (B. napus L.), with emphasis on the evolution of Chinese rapeseed. Theor Appl Genet 113:49–54CrossRefPubMedGoogle Scholar
- USDA ERS (2014) Oil crops yearbook. http://www.ers.usda.gov/data-products/oil-crops-yearbook.aspx
- Van Ooijen J (2009) MapQTL® 6, Software for the mapping of quantitative trait in experiment populations of diploid species. Kyazma B V, WageningenGoogle Scholar
- Yang N, Lu Y, Yang X, Huang J, Zhou Y, Ali F, Wen W, Liu J, Li J, Yan J (2014) Genome wide association studies using a new nonparametric model reveal the genetic architecture of 17 agronomic traits in an enlarged maize association panel. PLoS Genet 10:e1004573CrossRefPubMedPubMedCentralGoogle Scholar