| Literature DB >> 30073005 |
Hongli Dong1, Chuandong Tan1, Yuzhen Li1, Yan He1, Shuai Wei1, Yixin Cui1, Yangui Chen1, Dayong Wei2, Ying Fu3, Yajun He1, Huafang Wan1, Zhi Liu1, Qing Xiong4, Kun Lu1,5, Jiana Li1,5, Wei Qian1,5.
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.Entities:
Keywords: BnaA.ARF18.a; Brassica napus; genome-wide association study; seed weight; silique length
Year: 2018 PMID: 30073005 PMCID: PMC6058094 DOI: 10.3389/fpls.2018.00921
Source DB: PubMed Journal: Front Plant Sci ISSN: 1664-462X Impact factor: 5.753
Figure 5Development of two dCAPS markers in BnaA.ARF18a, BnaA.ARF18a-186 (Top) and BnaA.ARF18a-262 (Bottom). The primers and the restriction enzymes were displayed in the box. The blue letter represents the SNP among haplotypes, while the red letter represents the transversion in the restriction site.
Figure 1Distribution of seed weight and silique length in 4 years.
Phenotypic variation and analysis of variance (ANOVA) of seed weight and silique length in the association panel.
| Seed weight | Genotypes (G) | 153 | 420.842 | 2.7506 | 33.48 | < 0.0001 |
| Environments (E) | 3 | 55.86 | 18.620 | 226.66 | < 0.0001 | |
| G*E | 443 | 106.817 | 0.241 | 2.94 | < 0.0001 | |
| Repeatability | 2 | 0.393 | 0.197 | 2.39 | 0.092 | |
| Silique length | Genotypes (G) | 156 | 1185.069 | 7.597 | 42.09 | < 0.0001 |
| Environments (E) | 3 | 87.989 | 29.3298 | 162.5 | < 0.0001 | |
| G*E | 416 | 239.951 | 0.5768 | 3.2 | < 0.0001 | |
| Repeatability | 2 | 0.839 | 0.420 | 2.33 | 0.0984 |
Correlation of silique weight (SW) and silique length (SL).
| 2013 | 0.368 | 0.81 | 0.67 | 0.65 |
| 2014 | 0.69 | 0.444 | 0.67 | 0.58 |
| 2015 | 0.61 | 0.64 | 0.212 | 0.56 |
| 2016 | 0.75 | 0.76 | 0.70 | 0.305 |
Above diagonal line: correlation for SW between years; Diagonal line: correlation between SW and SL; Below diagonal line: correlation for SL between years
Significance level at p = 0.01,
Significance level at p = 0.001.
Figure 2Phylogenetic relationships among 157 inbred accessions. (A) Analysis of the population structure composed of 157 rapeseed lines with STRUCTURE. Each individual is represented by a vertical bar, partitioned into colored segments with the length of each segment representing the proportion of the individual's genome, and with the same colored segment representing the same genomic components. (B) Principle component analysis. The first two principal components are shown. The individuals with the same label have the same ecotype.
Figure 3Manhattan plots of the genome-wide association mapping for seed weight (up) and silique length (below). X-axis indicates the physical positions of single nucleotide polymorphism (SNP) along the 19 chromosomes; each environment is displayed by different colors, while y-axis is the value of -log10(P). The horizontal dashed line represents the significance threshold with -log10(P) = 6.02.
List of single nucleotide polymorphisms with significant association with seed weight (SW) and silique length (SL) using 4 years and BLUP field data among 157 rapeseed lines.
| 1 | 8207090 | 25.23 | A01 | 1 | BLUP | Shi et al., |
| 2 | 14308857 | 11.842 | A04 | 1 | 2015 | |
| 3 | 15814854-15980541 | 21.13–27.66 | A04 | 12 | 2013/BLUP | |
| 4 | 28116249-28180462 | 31.20–34.58 | A09 | 3 | BLUP | Basunanda et al., |
| 5 | 31325595 | 23.59 | A09 | 1 | 2013 | Basunanda et al., |
| 6 | 360417 | 16.87 | C02 | 1 | 2016 | Udall et al., |
| 7 | 31182079 | 28.82 | C06 | 1 | BLUP | Shi et al., |
| 1 | 11025788-17884044 | 18.26–25.95 | A02 | 2 | 2013/2015 | |
| 2 | 10984418-14247089 | 4.01–21.92 | A03 | 4 | 2013 | Zhang et al., |
| 3 | 15453957-16110806 | 12.34–34.21 | A04 | 27 | 2013/BLUP | |
| 4 | 8153268-8908552 | 14.85–30.97 | A07 | 53 | 2013/2016 | Zhang et al., |
| 5 | 16126618-16380176 | 23.97–30.17 | A07 | 4 | 2013/2016/BLUP | Yang et al., |
| 6 | 19760561-20567053 | 25.67–39.78 | A07 | 298 | 2013/2016/BLUP | |
| 7 | 10476202 | 32.23 | A08 | 1 | 2013 | Zhang et al., |
| 8 | 12872271-12949850 | 30.54–31.26 | A09 | 7 | 2014 | |
| 9 | 27782829-28612997 | 15.70–48.02 | A09 | 279 | 2013/2014/2015/2016/BLUP | Yang et al., |
| 10 | 3750581-3782227 | 27.73–39.13 | C01 | 16 | 2013/2016/BLUP | Chen et al., |
| 11 | 15053178 | 27.00–34.42 | C01 | 4 | 2013/2014/2016/BLUP | Li et al., |
| 12 | 30151703 | 24.95 | C01 | 1 | BLUP | |
| 13 | 21910179 | 14.55 | C03 | 1 | 2013 | Yang et al., |
| 14 | 46240742 | 30.88 | C04 | 1 | 2013 | |
| 15 | 106174-261914 | 23.42–23.85 | C06 | 2 | 2013 | Zhang et al., |
| 16 | 1214062-1825439 | 23.0823.58 | C06 | 2 | 2013 | |
| 17 | 6231767 | 22.59–28.12 | C06 | 2 | 2013/BLUP | |
| 18 | 30332388-31182079 | 31.28–43.56 | C06 | 5 | 2013/2016/BLUP | |
| 19 | 5380751-5960581 | 13.96–28.38 | C07 | 25 | 2013/2014/BLUP | |
| 20 | 7142765 | 17.31 | C07 | 1 | 2013 | |
| 21 | 29121920 | 6.46–6.76 | C07 | 2 | 2016/BLUP | |
| 22 | 31257717-31306490 | 35.48–38.13 | C08 | 5 | 2016/BLUP | |
Figure 4Association mapping and haplotypes of BnaA.ARF18a in natural population of rapeseed. (A) Plot describing marker-trait association for the trait SW (blue dot) and SL (orange dot) within the gene BnaA.ARF18.a. (B) Haploblock showing markers in linkage disequilibrium (LD) (>r2 = 0.6). (C) Exon-intron structure of BnaA.ARF18a and single nucleotide polymorphisms. Grey boxes and black lines indicated exon and intron, respectively. (D) Haplotype analysis for BnaA.ARF18.a. in three subgroups. S, W, and SW indicate the spring, winter, and semi-winter rapeseed subgroup, respectively.
Figure 6Association of SNPs with seed weight and silique length revealed with dCAPS. Screening accessions in the natural population using BnaA.ARF18a-186 (up) and BnaA.ARF18a-262 (below) (A); Haplotype analysis (B) and location of dCAPS in the interval of QTL for seed weight and silique length (C) in a DH population (Fu et al., 2015).