BackgroundHigh-density single-nucleotide polymorphism (SNP) genotyping arrays are a powerful tool for genome-wide association studies and can give valuable insight into patterns of population structure and linkage disequilibrium (LD). In this study we used the Brassica 60kSNP Illumina consortium genotyping array to assess the influence of selection and breeding for important agronomic traits on LD and haplotype structure in a diverse panel of 203 Chinese semi-winter rapeseed (Brassica napus) breeding lines.ResultsPopulation structure and principal coordinate analysis, using a subset of the SNPs, revealed diversification into three subpopulations and one mixed population, reflecting targeted introgressions from external gene pools during breeding. Pairwise LD analysis within the A- and C-subgenomes of allopolyploid B. napus revealed that mean LD, at a threshold of r2 = 0.1, decayed on average around ten times more rapidly in the A-subgenome (0.25-0.30 Mb) than in the C-subgenome (2.00-2.50 Mb). A total of 3,097 conserved haplotype blocks were detected over a total length of 182.49 Mb (15.17% of the genome). The mean size of haplotype blocks was considerably longer in the C-subgenome (102.85 Kb) than in the A-subgenome (33.51 Kb), and extremely large conserved haplotype blocks were found on a number of C-genome chromosomes. Comparative sequence analysis revealed conserved blocks containing homoloeogous quantitative trait loci (QTL) for seed erucic acid and glucosinolate content, two key seed quality traits under strong agronomic selection. Interestingly, C-subgenome QTL were associated with considerably greater conservation of LD than their corresponding A-subgenome homoeologues.ConclusionsThe data we present in this paper provide evidence for strong selection of large chromosome regions associated with important rapeseed seed quality traits conferred by C-subgenome QTL. This implies that an increase in genetic diversity and recombination within the C-genome is particularly important for breeding. The resolution of genome-wide association studies is also expected to vary greatly across different genome regions.Electronic supplementary materialThe online version of this article (doi:10.1186/1471-2164-15-1170) contains supplementary material, which is available to authorized users.

Stem rot caused by Sclerotinia sclerotiorum is one of the most devastating diseases of rapeseed (Brassica napus L.) which causes huge loss in rapeseed production. Genetic sources with high level of resistance has not been found in rapeseed. In this study, 68 accessions in six Brassica species, including 47 accessions of B. oleracea, were evaluated for leaf and stem resistance to S. sclerotiorum. Large variation of resistance was found in Brassica, with maximum differences of 5-and 57-folds in leaf and stem resistance respectively. B. oleracea, especially its wild types such as B. rupestris, B. incana, B. insularis, and B. villosa showed high level of resistance. Our data suggest that wild types of B. oleracea possess tremendous potential for improving S. sclerotiorum resistance of rapeseed.

Roots, the hidden half of crop plants, are essential for resource acquisition. However, knowledge about the genetic control of below-ground plant development in wheat, one of the most important small-grain crops in the world, is very limited. The molecular interactions connecting root and shoot development and growth, and thus modulating the plant's demand for water and nutrients along with its ability to access them, are largely unexplored. Here, we demonstrate that linkage drag in European bread wheat, driven by strong selection for a haplotype variant controlling heading date, has eliminated a specific combination of two flanking, highly conserved haplotype variants whose interaction confers increased root biomass. Reversing this inadvertent consequence of selection could recover root diversity that may prove essential for future food production in fluctuating environments. Highly conserved synteny to rice across this chromosome segment suggests that adaptive selection has shaped the diversity landscape of this locus across different, globally important cereal crops. By mining wheat gene expression data, we identified root-expressed genes within the region of interest that could help breeders to select positive variants adapted to specific target soil environments.

In order to meet future food, feed, fiber, and bioenergy demands, global yields of all major crops need to be increased significantly. At the same time, the increasing frequency of extreme weather events such as heat and drought necessitates improvements in the environmental resilience of modern crop cultivars. Achieving sustainably increase yields implies rapid improvement of quantitative traits with a very complex genetic architecture and strong environmental interaction. Latest advances in genome analysis technologies today provide molecular information at an ultrahigh resolution, revolutionizing crop genomic research, and paving the way for advanced quantitative genetic approaches. These include highly detailed assessment of population structure and genotypic diversity, facilitating the identification of selective sweeps and signatures of directional selection, dissection of genetic variants that underlie important agronomic traits, and genomic selection (GS) strategies that not only consider major-effect genes. Single-nucleotide polymorphism (SNP) markers today represent the genotyping system of choice for crop genetic studies because they occur abundantly in plant genomes and are easy to detect. SNPs are typically biallelic, however, hence their information content compared to multiallelic markers is low, limiting the resolution at which SNP–trait relationships can be delineated. An efficient way to overcome this limitation is to construct haplotypes based on linkage disequilibrium, one of the most important features influencing genetic analyses of crop genomes. Here, we give an overview of the latest advances in genomics-based haplotype analyses in crops, highlighting their importance in the context of polyploidy and genome evolution, linkage drag, and co-selection. We provide examples of how haplotype analyses can complement well-established quantitative genetics frameworks, such as quantitative trait analysis and GS, ultimately providing an effective tool to equip modern crops with environment-tailored characteristics.

Plants in temperate areas evolved vernalisation requirement to avoid pre-winter flowering. In Brassicaceae, a period of extended cold reduces the expression of the flowering inhibitor FLOWERING LOCUS C (FLC) and paves the way for the expression of downstream flowering regulators. As with all polyploid species of the Brassicaceae, the model allotetraploid Brassica napus (rapeseed, canola) is highly duplicated and carries 9 annotated copies of Bna.FLC. To investigate whether these multiple homeologs and paralogs have retained their original function in vernalisation or undergone subfunctionalisation, we compared the expression patterns of all 9 copies between vernalisation-dependent (biennial, winter type) and vernalisation-independent (annual, spring type) accessions, using RT-qPCR with copy-specific primers and RNAseq data from a diversity set. Our results show that only 3 copies – Bna.FLC.A03b, Bna.FLC.A10 and to some extent Bna.FLC.C02 – are differentially expressed between the two growth types, showing that expression of the other 6 copies does not correlate with growth type. One of those 6 copies, Bna.FLC.C03b, was not expressed at all, indicating a pseudogene, while three further copies, Bna.FLC.C03a and Bna.FLC.C09ab, did not respond to cold treatment. Sequence variation at the COOLAIR binding site of Bna.FLC.A10 was found to explain most of the variation in gene expression. However, we also found that Bna.FLC.A10 expression is not fully predictive of growth type.