Extent and structure of linkage disequilibrium in canola quality winter rapeseed (Brassica napus L.).
ABSTRACT: Linkage disequilibrium was investigated in canola quality winter rapeseed to analyze (1) the prospects for whole-genome association analyses and (2) the impact of the recent breeding history of rapeseed on linkage disequilibrium. A total of 845 mapped AFLP markers with allele frequencies >or=0.1 were used for the analysis of linkage disequilibrium in a population of 85 canola quality winter rapeseed genotypes. A low overall level of linkage disequilibrium was found with a mean r (2) of only 0.027 over all 356,590 possible marker pairs. At a significance threshold of P = 2.8 x 10(-7), which was derived by a Bonferroni correction from a global alpha-level of 0.1, only 0.78% of the marker pairs were in significant linkage disequilibrium. Among physically linked marker pairs, the level of linkage disequilibrium was about five times higher with more than 10% of marker pairs in significant linkage disequilibrium. Linkage disequilibrium decayed rapidly with distance between linked markers with high levels of linkage disequilibrium extending only for about 2 cM. Owing to the rapid decay of linkage disequilibrium with distance association analyses in canola quality rapeseed will have a significantly higher resolution than QTL analyses in segregating populations by interval mapping, but much larger number of markers will be necessary to cover the whole genome. A major impact of the recent breeding history of rapeseed on linkage disequilibrium could not be observed.
Project description:Development of oilseed rape (Brassica napus L.) breeding lines producing oil characterized by high oleic and low linolenic acid content is an important goal of rapeseed breeding programs worldwide. Such kind of oil is ideal for deep frying and can also be used as a raw material for biodiesel production. By performing chemical mutagenesis using ethyl methanesulfonate, we obtained mutant winter rapeseed breeding lines that can produce oil with a high content of oleic acid (C18:1, more than 75%) and a low content of linolenic acid (C18:3, less than 3%). However, the mutant lines revealed low agricultural value as they were characterized by low seed yield, low wintering, and high content of glucosinolates in seed meal. The aim of this work was to improve the mutant lines and develop high-oleic and low-linolenic recombinants exhibiting both good oil quality and high agronomic value. The plant materials used in this study included high-oleic and low-linolenic mutant breeding lines and high-yielding domestic canola-type breeding lines of good agricultural value with high oleic acid content and extremely low glucosinolates content. Field trials were conducted in four environments, in a randomized complete block design. Phenotyping was performed for wintering, yield of seed and oil, and seed quality traits. Genotype × environment interaction was investigated with respect to the content of C18:1 and C18:3 acids in seed oil. Genotyping was done for the selection of homozygous high oleic and low linolenic lines using allele-specific CAPS markers and SNaPshot assay, respectively. Finally, new high oleic and low linolenic winter rapeseed recombinant lines were obtained for use as a starting material for the development of new varieties that may be of high value on the oil crop market.
Project description:Rapeseed (Brassica napus L.) is an important oilseed crop. Despite a short period of domestication and breeding, rapeseed has formed three diverse ecotype groups, namely spring, winter, and semi-winter. However, the genetic changes among the three ecotype groups have remained largely unknown. To detect selective signals, a set of 327 accessions from a worldwide collection were genotyped using a Brassica array, producing 33 186 high-quality single nucleotide polymorphisms (SNPs). Linkage disequilibrium (LD) was unevenly distributed across the genome. A total of 705 (78.2%) weak LD regions were found in the A subgenome, whereas 445 (72.6%) strong LD regions were in the C subgenome. By calculating the nucleotide diversity and population differentiation indices, a total of 198 selective sweeps were identified across ecotype groups, spanning 5.91% (37.9 Mb) of the genome. Within these genome regions, a few known functional genes or loci were found to be in association with environmental adaptability and yield-related traits. In particular, all 12 SNPs detected in significant association with flowering time among accessions were in the selection regions between ecotype groups. These findings provide new insights into the structure of the B. napus genome and uncover the footprints of domestication and breeding.
Project description:Intense selection for specific seed qualities in winter oilseed rape breeding has had an inadvertent negative influence on seed germination performance. In a panel of 215 diverse winter oilseed rape varieties spanning over 50 years of breeding progress in winter-type rapeseed, we found that low seed erucic acid content and reduced seed glucosinolate content were significantly related with prolonged germination time. Genome-wide association mapping revealed that this relationship is caused by linkage drag between important loci for seed quality and germination traits. One QTL for mean germination time on chromosome A09 co-localized with significant but minor QTL for both seed erucic acid and seed glucosinolate content. This suggested either potential pleiotropy or close linkage of minor factors influencing all three traits. Therefore, a reduction in germination performance may be due to inadvertent co-selection of genetic variants associated with 00 seed quality that have a negative influence on germination. Our results suggest that marker-assisted selection of positive alleles for mean germination time within the modern quality pool can help breeders to maintain maximal germination capacity in new 00-quality oilseed rape cultivars.
Project description:Background:In plant breeding program to produce hybrid varieties, pair of male sterile and restorer fertility lines are required. Differentiation of lines possessing restorer fertility allele from the lines lacking it remove the need for the progeny test, and thus reducing the time and the cost in the hybrid production procedure. Canola breeding program in Iran has concentrated toward production of domestic hybrid varieties, however, it suffers from lack of molecular information in restore fertility status of lines, and therefore it needs time and tedious activities. Objectives:To design gene-based markers for distinguishing R-, A- lines and hybrids in sunflower breeding programs. Material and Methods:Aligning sequences of locus responsible for male sterility and that of male fertility resulted in finding differences in the loci, which used to define two set of suitable primer pairs. Genomic DNA from 25 R-lines (23 inbred lines and two commercial lines), 9 A-lines (7 inbred lines and two commercial lines), one B-line and two commercial hybrids were extracted and used in PCR as template. Results:Using one-primer pairs, a band of nearly 1500 bp was amplified in restorer lines but not in A-, B- lines. Another primer pair used to distinguish hybrids (heterozygout) from restorer lines. Results of the report is predicted to be used in canola breeding for hybrid production. Conclusions:Although the molecular bases for the male sterility and fertility restoration in rapeseed is not published, taking advantages of gene-based markers, make rapeseed breeding program more efficient regarding time and costs.
Project description:<h4>Background</h4>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.<h4>Results</h4>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.<h4>Conclusions</h4>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.
Project description:Life cycle timing is critical for yield and productivity of Brassica napus (rapeseed) cultivars grown in different environments. To facilitate breeding for earliness traits in rapeseed, SNP loci and underlying candidate genes associated with the timing of initial flowering, maturity and final flowering, as well as flowering period (FP) were investigated in two environments in a diversity panel comprising 300 B. napus inbred lines. Genome-wide association studies (GWAS) using 201,817 SNP markers previously developed from SLAF-seq (specific locus amplified fragment sequencing) revealed a total of 131 SNPs strongly linked (P?<?4.96E-07) to the investigated traits. Of these 131 SNPs, 40 fell into confidence intervals or were physically adjacent to previously published flowering time QTL or SNPs. Phenotypic effect analysis detected 35 elite allelic variants for early maturing, and 90 for long FP. Candidate genes present in the same linkage disequilibrium blocks (r2>0.6) or in 100 kb regions around significant trait-associated SNPs were screened, revealing 57 B. napus genes (33 SNPs) orthologous to 39 Arabidopsis thaliana flowering time genes. These results support the practical and scientific value of novel large-scale SNP data generation in uncovering the genetic control of agronomic traits in B. napus, and also provide a theoretical basis for molecular marker-assisted selection of earliness breeding in rapeseed.
Project description:Plant height is a key morphological trait of rapeseed. In this study, we measured plant height of a rapeseed population across six environments. This population contains 476 inbred lines representing the major Chinese rapeseed genepool and 44 lines from other countries. The 60K Brassica Infinium® SNP array was utilized to genotype the association panel. A genome-wide association study (GWAS) was performed via three methods, including a robust, novel, nonparametric Anderson-Darling (A-D) test. Consequently, 68 loci were identified as significantly associated with plant height (P < 5.22 × 10(-5)), and more than 70% of the loci (48) overlapped the confidence intervals of reported QTLs from nine mapping populations. Moreover, 24 GWAS loci were detected with selective sweep signals, which reflected the signatures of historical semi-dwarf breeding. In the linkage disequilibrium (LD) decay range up-and downstream of 65 loci (r (2) > 0.1), we found plausible candidates orthologous to the documented Arabidopsis genes involved in height regulation. One significant association found by GWAS colocalized with the established height locus BnRGA in rapeseed. Our results provide insights into the genetic basis of plant height in rapeseed and may facilitate marker-based breeding.
Project description:Orchardgrass (Dactylis glomerata L.), is a well-known perennial forage species; however, rust diseases have caused a noticeable reduction in the quality and production of orchardgrass. In this study, genetic diversity was assessed and the marker-trait associations for rust were examined using 18 EST-SSR and 21 SCoT markers in 75 orchardgrass accessions. A high level of genetic diversity was detected in orchardgrass with an average genetic diversity index of 0.369. For the EST-SSR and SCoT markers, 164 and 289 total bands were obtained, of which 148 (90.24%) and 272 (94.12%) were polymorphic, respectively. Results from an AMOVA analysis showed that more genetic variance existed within populations (87.57%) than among populations (12.43%). Using a parameter marker index, the efficiencies of the EST-SSR and SCoT markers were compared to show that SCoTs have higher marker efficiency (8.07) than EST-SSRs (4.82). The results of a UPGMA cluster analysis and a STRUCTURE analysis were both correlated with the geographic distribution of the orchardgrass accessions. Linkage disequilibrium analysis revealed an average r² of 0.1627 across all band pairs, indicating a high extent of linkage disequilibrium in the material. An association analysis between the rust trait and 410 bands from the EST-SSR and SCoT markers using TASSEL software revealed 20 band panels were associated with the rust trait in both 2011 and 2012. The 20 bands obtained from association analysis could be used in breeding programs for lineage selection to prevent great losses of orchardgrass caused by rust, and provide valuable information for further association mapping using this collection of orchardgrass.
Project description:Nested association mapping (NAM) populations have been widely applied to dissect the genetic basis of complex quantitative traits in a variety of crops. In this study, we developed a <i>Brassica napus</i> NAM (BN-NAM) population consisting of 15 recombination inbred line (RIL) families with 2,425 immortal genotypes. Fifteen high-density genetic linkage maps were constructed by genotyping by sequencing (GBS) based on all RIL families, with further integration into a joint linkage map (JLM) having 30,209 unique markers in common with multiple linkage maps. Furthermore, an ultra-density whole-genome variation map was constructed by projecting 4,444,309 high-quality variants onto the JLM. The NAM population captured a total of 88,542 recombination events (REs). The uneven distribution of recombination rate along chromosomes is positively correlated with the densities of genes and markers, but negatively correlated with the density of transposable elements and linkage disequilibrium (LD). Analyses of population structure and principal components revealed that the BN-NAM population could be divided into three groups with weak stratification. The LD decay distance across genome varied between 170 and 2,400 Kb, with LD decay more rapid in the A than in the C sub-genome. The pericentromeric regions contained large LD blocks, especially in the C sub-genome. This NAM population provides a valuable resource for dissecting the genetic basis of important traits in rapeseed, especially in semi-winter oilseed rape.
Project description:BACKGROUND: High-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. RESULTS: Population 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. CONCLUSIONS: The 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.