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Evaluation of Linkage Disequilibrium Pattern and Association Study on Seed Oil Content in Brassica napus Using ddRAD Sequencing.

ABSTRACT: High-density genetic markers are the prerequisite for understanding linkage disequilibrium (LD) and genome-wide association studies (GWASs) of complex traits in crops. To evaluate the LD pattern in oilseed rape, we sequenced a previous association panel containing 189 B. napus inbred lines using double-digested restriction-site associated DNA (ddRAD) and genotyped 19,327 RAD tags. A total of 15,921 RAD tags were assigned to a published genetic linkage map and the majority (71.1%) of these tags was uniquely mapped to the draft reference genome "Darmor-bzh." The distance of LD decay was 1,214 kb across the genome at the background level (r2 = 0.26), with the distances of LD decay being 405 kb and 2,111 kb in the A and C subgenomes, respectively. A total of 361 haplotype blocks with length > 100 kb were identified in the entire genome. The association panel could be classified into two groups, P1 and P2, which are essentially consistent with the geographical origins of varieties. A large number of group-specific haplotypes were identified, reflecting that varieties in the P1 and P2 groups experienced distinct selection in breeding programs to adapt their different growth habitats. GWAS repeatedly detected two loci significantly associated with oil content of seeds based on the developed SNPs, suggesting that the high-density SNPs were useful for understanding the genetic determinants of complex traits in GWAS.

SUBMITTER: Wu Z

PROVIDER: S-EPMC4701484 | biostudies-literature | 2016

REPOSITORIES: biostudies-literature

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Project description:BackgroundAlthough the seed oil content in canola is a crucial quality determining trait, the regulatory mechanisms of its formation are not fully discovered. This study compared the silique and seed physiological characteristics including fresh and dry weight, seed oil content, chlorophyll content, and carbohydrate content in a high oil content line (HOCL) and a low oil content line (LOCL) of canola derived from a recombinant inbred line in 2010, 2011, and 2012. The aim of the investigation is to uncover the physiological regulation of silique and seed developmental events on seed oil content in canola.ResultsOn average, 83% and 86% of silique matter while 69% and 63% of seed matter was produced before 30 days after anthesis (DAA) in HOCL and LOCL, respectively, over three years. Furthermore, HOCL exhibited significantly higher fresh and dry matter at most developmental stages of siliques and seeds. From 20 DAA, lipids were deposited in the seed of HOCL significantly faster than that of LOCL, which was validated by transmission electron microscopy, showing that HOCL accumulates considerable more oil bodies in the seed cells. Markedly higher silique chlorophyll content was observed in HOCL consistently over the three consecutive years, implying a higher potential of photosynthetic capacity in siliques of HOCL. As a consequence, HOCL exhibited significantly higher content of fructose, glucose, sucrose, and starch mainly at 20 to 45 DAA, a key stage of seed lipid deposition. Moreover, seed sugar content was usually higher than silique indicating the importance of sugar transportation from siliques to seeds as substrate for lipid biosynthesis. The much lower silique cellulose content in HOCL was beneficial for lipid synthesis rather than consuming excessive carbohydrate for cell wall.ConclusionsSuperior physiological characteristics of siliques in HOCL showed advantage to produce more photosynthetic assimilates, which were highly correlated to seed oil contents.

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Evaluation of Linkage Disequilibrium Pattern and Association Study on Seed Oil Content in Brassica napus Using ddRAD Sequencing.

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