Dataset Information

Genome-Wide Association Study Reveals Both Overlapping and Independent Genetic Loci to Control Seed Weight and Silique Length in Brassica napus.

ABSTRACT: Seed weight (SW) is one of three determinants of seed yield, which positively correlates with silique length (SL) in Brassica napus (rapeseed). However, the genetic mechanism underlying the relationship between seed weight (SW) and silique length (SL) is largely unknown at present. A natural population comprising 157 inbred lines in rapeseed was genotyped by whole-genome re-sequencing and investigated for SW and SL over four years. The genome-wide association study identified 20 SNPs in significant association with SW on A01, A04, A09, C02, and C06 chromosomes and the phenotypic variation explained by a single locus ranged from 11.85% to 34.58% with an average of 25.43%. Meanwhile, 742 SNPs significantly associated with SL on A02, A03, A04, A07, A08, A09, C01, C03, C04, C06, C07, and C08 chromosomes were also detected and the phenotypic variation explained by a single locus ranged from 4.01 to 48.02% with an average of 33.33%, out of which, more than half of the loci had not been reported in the previous studies. There were 320 overlapping or linked SNPs for both SW and SL on A04, A09, and C06 chromosomes. It indicated that both overlapping and independent genetic loci controlled both SW and SL in B. napus. On the haplotype block on A09 chromosome, the allele variants of a known gene BnaA.ARF18.a controlling both SW and SL were identified in the natural population by developing derived cleaved amplified polymorphic sequence (dCAPS) markers. These findings are valuable for understanding the genetic mechanism of SW and SL and also for rapeseed molecular breeding programs.

SUBMITTER: Dong H

PROVIDER: S-EPMC6058094 | biostudies-literature | 2018

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

Genome-Wide Association Study Reveals Both Overlapping and Independent Genetic Loci to Control Seed Weight and Silique Length in <i>Brassica napus</i>.

Dong Hongli H Tan Chuandong C Li Yuzhen Y He Yan Y Wei Shuai S Cui Yixin Y Chen Yangui Y Wei Dayong D Fu Ying Y He Yajun Y Wan Huafang H Liu Zhi Z Xiong Qing Q Lu Kun K Li Jiana J Qian Wei W

Frontiers in plant science 20180718

Seed weight (SW) is one of three determinants of seed yield, which positively correlates with silique length (SL) in <i>Brassica napus</i> (rapeseed). However, the genetic mechanism underlying the relationship between seed weight (SW) and silique length (SL) is largely unknown at present. A natural population comprising 157 inbred lines in rapeseed was genotyped by whole-genome re-sequencing and investigated for SW and SL over four years. The genome-wide association study identified 20 SNPs in s ...[more]

PMID: 30073005

Similar Datasets

Project description:BACKGROUND: Seed weight (SW) and silique length (SL) are important determinants of the yield potential in rapeseed (Brassica napus L.). However, the genetic basis of both traits is poorly understood. The main objectives of this study were to dissect the genetic basis of SW and SL in rapeseed through the preliminary mapping of quantitative trait locus (QTL) by linkage analysis and fine mapping of the target major QTL by regional association analysis. RESULTS: Preliminary linkage mapping identified thirteen and nine consensus QTLs for SW and SL, respectively. These QTLs explained 0.7-67.1% and 2.1-54.4% of the phenotypic variance for SW and SL, respectively. Of these QTLs, three pairs of SW and SL QTLs were co-localized and integrated into three unique QTLs. In addition, the significance level and genetic effect of the three co-localized QTLs for both SW and SL showed great variation before and after the conditional analysis. Moreover, the allelic effects of the three QTLs for SW were highly consistent with those for SL. Two of the three co-localized QTLs, uq.A09-1 (mean R(2) = 20.1% and 19.0% for SW and SL, respectively) and uq.A09-3 (mean R(2) = 13.5% and 13.2% for SW and SL, respectively), were detected in all four environments and showed the opposite additive-effect direction. These QTLs were validated and fine mapped (their confidence intervals were narrowed down from 5.3 cM to 1 cM for uq.A09-1 and 13.2 cM to 2.5 cM for uq.A09-3) by regional association analysis with a panel of 576 inbred lines, which has a relatively rapid linkage disequilibrium decay (0.3 Mb) in the target QTL region. CONCLUSIONS: A few QTLs with major effects and several QTLs with moderate effects might contribute to the natural variation of SW and SL in rapeseed. The meta-, conditional and allelic effect analyses suggested that pleiotropy, rather than tight linkage, was the genetic basis of the three pairs of co-localized of SW and SL QTLs. Regional association analysis was an effective and highly efficient strategy for the direct fine mapping of target major QTL identified by preliminary linkage mapping.

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.

Project description:Seed number is a key character/trait tightly related to the plant fitness/evolution and crop domestication/improvement. The seed number per silique (SNPS) shows a huge variation from several to more than 30, however the underlying regulatory mechanisms are poorly known, which has hindered its improvement. To answer this question, several representative lines with extreme SNPS were previously subjected to systematic genetic and cytological analyses. The results showed that the natural variation of seed number per silique is mainly controlled by maternal and embryonic genotype, which are co-determined by ovule number per ovary, fertile ovule ratio, ovule fertilization rate, and fertilized ovule development rate. More importantly, we also mapped two repeatable quantitative trait loci (QTLs) for SNPS using the F2:3 population derived from Zhongshuang11 and No. 73290, of which the major QTL qSN.A6 has been fine-mapped. In the current study, the near-isogenic lines (NILs) of qSN.A7 were successfully developed by the successive backcross of F1 with Zhongshuang11. First, the effect of qSN.A7 was validated by evaluating the SNPS of two types of homozygous NILs from BC3F2 population, which showed a significant difference of 2.23 on average. Then, qSN.A7 was successfully fine-mapped from the original 4.237 to 1.389 Mb, using a BC4F2 segregating population of 2,551 individuals. To further clarify the regulatory mechanism of qSN.A7, the two types of homologous NILs were subjected to genetic and cytological analyses. The results showed that the difference in SNPS between the two homologous NILs was determined by the embryonic genotypic effect. Highly accordant with this, no significant difference was observed in ovule number per ovary, ovule fertility, fertilization rate, and pollen fertility between the two homologous NILs. Therefore, the regulatory mechanism of qSN.A7 is completely different from the cloned qSS.C9 and qSN.A6. These results will advance the understanding of SNPS and facilitate gene cloning and molecular breeding in Brassica napus.

Dataset Information

Genome-Wide Association Study Reveals Both Overlapping and Independent Genetic Loci to Control Seed Weight and Silique Length in Brassica napus.

Publications

Genome-Wide Association Study Reveals Both Overlapping and Independent Genetic Loci to Control Seed Weight and Silique Length in <i>Brassica napus</i>.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets