High density genetic maps built with SNP markers that are polymorphic in various genetic backgrounds are very useful for studying the genetics of agronomical traits as well as genome organization and evolution. Simultaneous dense SNP genotyping of segregating populations and variety collections was applied to oilseed rape (Brassica napus L.) to obtain a high density genetic map for this species and to study the linkage disequilibrium pattern. We developed an integrated genetic map for oilseed rape by high throughput SNP genotyping of four segregating doubled haploid populations. A very high level of collinearity was observed between the four individual maps and a large number of markers (>59%) was common to more than two maps. The precise integrated map comprises 5764 SNP and 1603 PCR markers. With a total genetic length of 2250 cM, the integrated map contains a density of 3.27 markers (2.56 SNP) per cM. Genotyping of these mapped SNP markers in oilseed rape collections allowed polymorphism level and linkage disequilibrium (LD) to be studied across the different collections (winter vs spring, different seed quality types) and along the linkage groups. Overall, polymorphism level was higher and LD decayed faster in spring than in “00” winter oilseed rape types but this was shown to vary greatly along the linkage groups. Our study provides a valuable resource for further genetic studies using linkage or association mapping, for marker assisted breeding and for Brassica napus sequence assembly and genome organization analyses.

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High-density SNP-based genetic map development and linkage disequilibrium assessment in Brassica napus L

Flowering time adaptation is a major breeding goal in the allopolyploid species Brassica napus. To investigate the genetic architecture of flowering time, a genome-wide association study (GWAS) of flowering time was conducted with a diversity panel comprising 523 B. napus cultivars and inbred lines grown in eight different environments. Genotyping was performed with a Brassica 60K Illumina Infinium SNP array. A total of 41 single-nucleotide polymorphisms (SNPs) distributed on 14 chromosomes were found to be associated with flowering time, and 12 SNPs located in the confidence intervals of quantitative trait loci (QTL) identified in previous researches based on linkage analyses. Twenty-five candidate genes were orthologous to Arabidopsis thaliana flowering genes. To further our understanding of the genetic factors influencing flowering time in different environments, GWAS was performed on two derived traits, environment sensitivity and temperature sensitivity. The most significant SNPs were found near Bn-scaff_16362_1-p380982, just 13 kb away from BnaC09g41990D, which is orthologous to A. thaliana CONSTANS (CO), an important gene in the photoperiod flowering pathway. These results provide new insights into the genetic control of flowering time in B. napus and indicate that GWAS is an effective method by which to reveal natural variations of complex traits in B. napus.

Genome-wide association study reveals the genetic architecture of flowering time in rapeseed (Brassica napus L.)

Rapeseed ( Brassica napus L.) is the largest oilseed crop in China and accounts for about 20% of world production. For the last 10 years, the production, planting area, and yield of rapeseed have been stable, with improvement of seed quality and especially seed oil content. China is among the leading countries in rapeseed genomic research internationally, having jointly with other countries accomplished the whole genome sequencing of rapeseed and its two parental species, Brassica oleracea and Brassica rapa . Progress on functional genomics including the identification of QTL governing important agronomic traits such as yield, seed oil content, fertility regulation, disease and insect resistance, abiotic stress, nutrition use efficiency, and pod shattering resistance has been achieved. As a consequence, molecular markers have been developed and used in breeding programs. During 2005–2014, 215 rapeseed varieties were registered nationally, including 210 winter- and 5 spring-type varieties. Mechanization across the whole process of rapeseed production was investigated and operating instructions for all relevant techniques were published. Modern techniques for rapeseed field management such as high-density planting, controlled-release fertilizer, and biocontrol of disease and pests combined with precision tools such as drones have been developed and are being adopted in China. With the application of advanced breeding and production technologies, in the near future, the oil yield and quality of rapeseed varieties will be greatly increased, and more varieties with desirable traits, especially early maturation, high yield, high resistance to biotic and abiotic stress, and suitability for mechanized harvesting will be developed. Application of modern technologies on the mechanized management of rapeseed will greatly increase grower profit.

Rapeseed research and production in China

Quantitative trait loci for seed yield and yield-related traits, and their responses to reduced phosphorus supply in Brassica napus

A genome-wide association study of plant height and primary branch number in rapeseed (Brassica napus)

To identify quantitative trait loci (QTL) controlling plant height (PH) and flowering time (FT), a high stalk/later bloom Brassica napus line '2091' was crossed with a dwarf/early bloom mutant '99CDAM'. A segregating population with 145 F 2:3 lines was constructed and grown in field for 2 years. Based on this population, a linkage map consisting of 199 amplified fragment length polymorphism and 42 simple sequence repeat loci was constructed. The LOD threshold of 3.0 was used for declaring the existence of putative QTL. In total, seven QTL related to PH were identified, accounting for 8.5-28.6% of phenotypic variation, respectively, of which two QTL were identified in both years. Six QTL for FT were detected, accounting for 8.1-30.4% of phenotypic variation individually, of which two QTL were identified in both years. The main QTL of PH and FT were both mapped on linkage group 13, with overlapped creditable regions. QTL ph17 and ft17 existed at the same location. These might be the genetic base for the significant correlation observed between PH and FT.

Y. D. Li

Papers

QTL analysis on plant height and flowering time in Brassica napus