Skip to main content
SpringerLink
Log in

Molecular mapping and candidate gene identification of two major quantitative trait loci associated with silique length in oilseed rape (Brassica napus L.)

  • Published:
Molecular Breeding Aims and scope Submit manuscript

Abstract

Rapeseed is a significant global source of plant oil. Silique size, particularly silique length (SL), impacts rapeseed yield. SL is a typical quantitative trait controlled by multiple genes. In our previous study, we constructed a DH population of 178 families known as the 158A-SGDH population. In this study, through SL QTL mapping, we identified twenty-six QTL for SL across five replicates in two environments. A QTL meta-analysis revealed eight consensus QTL, including two major QTL: cqSL.A02-1 (11.32–16.44% of PVE for SL), and cqSL.C06-1 (10.90–11.95% of PVE for SL). Based on biparental resequencing data and microcollinearity analysis of target regions in Brassica napus and Arabidopsis, we identified 11 candidate genes at cqSL.A02-1 and 6 candidate genes at cqSL.C06-1, which are potentially associated with silique development. Furthermore, transcriptome analysis of silique valves from both parents on the 14th, 21st, and 28th days after pollination (DAP) combined with gene function annotation revealed three significantly differentially expressed genes at cqSL.A02-1, BnaA02G0058500ZS, BnaA02G0060100ZS, and BnaA02G0060900ZS. Only the gene BnaC06G0283800ZS showed significant differences in parental transcription at cqSL.C06-1. Two tightly linked insertion-deletion markers for the cqSL.A02-1 and cqSL.C06-1 loci were developed. Using these two QTL, we generated four combinations: A02SGDH284C06158A, A02SGDH284C06SGDH284, A02158AC06158A, and A02158AC06SGDH284. Subsequent analysis identified an ideal QTL combination, A02158AC06SGDH284, which exhibited the longest SL of this type, reaching 6.06 ± 0.10 cm, significantly surpassing the other three combinations. The results will provide the basis for the cloning of SL-related genes of rapeseed, along with the development of functional markers of target genes and the breeding of rapeseed varieties.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3
Fig. 4
Fig. 5
Fig. 6

Similar content being viewed by others

Data availability

The data presented in this study are available in the article and Supplementary Materials. The DH population linkage mapping information is available in Chen et al. (2022). The BioProject accession number of the sequencing data of 180 materials of 158A-SGDH population and their parents is PRJNA885910 (Chen et al. 2022).

References

  • Arcade A, Labourdette A, Falque M et al (2004) BioMercator: integrating genetic maps and QTL towards the discovery of candidate genes. Bioinformatics 20(14):2324–2326

    Article  CAS  PubMed  Google Scholar 

  • Barratt DH, Kölling K, Graf A et al (2011) Callose synthase GSL7 is necessary for normal phloem transport and inflorescence growth in Arabidopsis. Plant Physiol 155(1):328–341

    Article  CAS  PubMed  Google Scholar 

  • Brown DM, Zeef LA, Ellis J et al (2005) Identification of novel genes in Arabidopsis involved in secondary cell wall formation using expression profiling and reverse genetics. Plant Cell 17(8):2281–2295

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Burns MJ, Barnes SR, Bowman JG et al (2003) QTL analysis of an intervarietal set of substitution lines in Brassica napus: (i) Seed oil content and fatty acid composition. Heredity (edinb) 90(1):39–48

    Article  CAS  PubMed  Google Scholar 

  • Cai D, Xiao Y, Yang W et al (2014) Association mapping of six yield-related traits in rapeseed (Brassica napus L.). Theor Appl Genet 127(1):85–96

    Article  CAS  PubMed  Google Scholar 

  • Chalhoub B, Denoeud F, Liu SY et al (2014) Early allopolyploid evolution in the post-Neolithic Brassica napus oilseed genome. Science 345(6199):950–953

    Article  CAS  PubMed  Google Scholar 

  • Chay P, Thurling N (1989) Identification of genes controlling pod length in spring rapeseed, Brassica napus L. and their utilization for yield improvement. Plant Breed 103:54–62

    Article  Google Scholar 

  • Chen W, Zhang Y, Liu X et al (2007) Detection of QTL for six yield-related traits in oilseed rape (Brassica napus) using DH and immortalized F(2) populations. Theor Appl Genet 115(6):849–858

    Article  CAS  PubMed  Google Scholar 

  • Chen W, Salari H, Taylor MC et al (2018) NMT1 and NMT3 N-Methyltransferase Activity Is Critical to Lipid Homeostasis, Morphogenesis, and Reproduction. Plant Physiol 177(4):1605–1628

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Chen L, Lei WX, He WF et al (2022) Mapping of Two Major QTLs Controlling Flowering Time in Brassica napus Using a High-Density Genetic Map. Plants 11(19):2635

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Deng C, Liu HD, Yao Y et al (2019) QTL analysis of four yield-related traits for Brassica napus L. in multiple environments. Mol Breed 39(12):166

    Article  CAS  Google Scholar 

  • Diepenbrock W (2000) Yield analysis of winter oilseed rape (Brassica napus L.): a review. Field Crop Res 67:35–49

    Article  Google Scholar 

  • Doerge RW, Churchill GA (1996) Permutation tests for multiple loci affecting a quantitative character. Genetics 142(1):285–294

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Dong H, Tan C, Li Y et al (2018) Genome-Wide Association Study Reveals Both Overlapping and Independent Genetic Loci to Control Seed Weight and Silique Length in Brassica napus. Front Plant Sci 9:921

    Article  PubMed  PubMed Central  Google Scholar 

  • Doyle JJ, Doyle JL (1987) A rapid DNA isolation procedure for small quantities of fresh leaf tissue. Phytochem Bull 19:11–15

    Google Scholar 

  • Ensoz S, Angin D, Yorgun S et al (2000) Biooil production from an oilseed crop: fixed-bed pyrolysis of rapeseed (Brassica napus L). Energy Sources 22:891–899

    Article  Google Scholar 

  • Fu Y, Wei D, Dong H et al (2015) Comparative quantitative trait loci for silique length and seed weight in Brassica napus. Sci Rep 5(1):14407

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Griffith ME, Mayer U, Capron A et al (2007) The TORMOZ gene encodes a nucleolar protein required for regulated division planes and embryo development in Arabidopsis. Plant Cell 19(7):2246–2263

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Hussain Q, Zhan JP, Liang HB et al (2022) Key genes and mechanisms underlying natural variation of silique length in oilseed rape (Brassica napus L.) germplasm. Crop J 10:617–626

    Article  Google Scholar 

  • Izhaki A, Bowman JL (2007) KANADI and class III HD-Zip gene families regulate embryo patterning and modulate auxin flow during embryogenesis in Arabidopsis. Plant Cell 19(2):495–508

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Jamshed M, Sankaranarayanan S, Abhinandan K et al (2020) Stigma Receptivity Is Controlled by Functionally Redundant MAPK Pathway Components in Arabidopsis. Mol Plant 13(11):1582–1593

    Article  CAS  PubMed  Google Scholar 

  • Ke LP, Lei WX, Yang WG et al (2020) Genome-wide identification of cold responsive transcription factors in Brassica napus L. BMC Plant Biol 20(1):62

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Kim D, Langmead B, Salzberg SL (2015) HISAT: a fast spliced aligner with low memory requirements. Nat Methods 12(4):357–360

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Lebowitz RJ (1989) Image analysis measurements and repeatability estimates of siliqua morphological traits in Brassica campestris L. Euphytica 43:113–116

    Article  Google Scholar 

  • Lee YK, Kim GT, Kim IJ et al (2006) LONGIFOLIA1 and LONGIFOLIA2 two homologous genes regulate longitudinal cell elongation in Arabidopsis. Development 133(21):4305–4314

    Article  CAS  PubMed  Google Scholar 

  • Li H (2013) Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. Preprint at https://arxiv.org/abs/1303.3997

  • Li H, Handsaker B, Wysoker A et al (2009) The Sequence alignment/map (SAM) format and SAMtools. Bioinformatics 25(16):2078–2079

    Article  PubMed  PubMed Central  Google Scholar 

  • Li H, Zhang L, Wang J (2010) Analysis and answers to frequently asked questions in quantitative trait locus mapping. Acta Agron Sin 36(6):918–931

    Article  Google Scholar 

  • Li X, Ilarslan H, Brachova L et al (2011) Reverse-genetic analysis of the two biotin-containing subunit genes of the heteromeric acetyl-coenzyme A carboxylase in Arabidopsis indicates a unidirectional functional redundancy. Plant Physiol 155(1):293–314

    Article  CAS  PubMed  Google Scholar 

  • Li N, Shi J, Wang X et al (2014) A combined linkage and regional association mapping validation and fine mapping of two major pleiotropic QTLs for seed weight and silique length in rapeseed (Brassica napus L.). BMC Plant Biol 14(1):1–14

    Article  Google Scholar 

  • Liu J, Hua W, Hu ZY et al (2015) Natural variation in ARF18 gene simultaneously affects seed weight and silique length in polyploid rapeseed. Proc Natl Acad Sci USA 112(37):5123–5132

    Article  Google Scholar 

  • Liu D, Yu L, Wei L et al (2021) BnTIR: An online transcriptome platform for exploring RNA–seq libraries for oil crop Brassica napus. Plant Biotechnol J 19(10):1895–1897

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Maccaferri M, Mantovani P, Tuberosa R et al (2008) A major QTL for durable leaf rust resistance widely exploited in durum wheat breeding programs maps on the distal region of chromosome arm 7BL. Theor Appl Genet 117(8):1225–1240

    Article  CAS  PubMed  Google Scholar 

  • Merk HL, Yarnes SC, Van Deynze A et al (2012) Trait Diversity and Potential for Selection Indices Based on Variation Among Regionally Adapted Processing Tomato Germplasm. J Amer Soc Hortic Sci 137:27–437

    Google Scholar 

  • Nakajima K, Kawamura T, Hashimoto T et al (2006) Role of the SPIRAL1 gene family in anisotropic growth of Arabidopsis thaliana. Plant Cell Physiol 47(4):513–522

    Article  CAS  PubMed  Google Scholar 

  • Niu E, Fang S, Shang X et al (2018) Ectopic expression of GhCOBL9A, a cotton glycosyl-phosphatidyl inositol-anchored protein encoding gene promotes cell elongation thickening and increased plant biomass in transgenic Arabidopsis. Mol Genet Genomics 293(5):1191–1204

    Article  CAS  PubMed  Google Scholar 

  • Nozaki M, Sugiyama M, Duan J et al (2012) A missense mutation in the glucosamine-6-phosphate N-acetyltransferase-encoding gene causes temperature-dependent growth defects and ectopic lignin deposition in Arabidopsis. Plant Cell 24(8):3366–3379

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Ozer H, Oral E (1999) Relationships Between Yield and Yield Components on Currently Improved Spring Rapeseed Cultivars. Turk J Agric for 23:603–608

    Google Scholar 

  • Qi L, Mao L, Sun C et al (2014) Interpreting the genetic basis of silique traits in Brassica napus using a joint QTL network. Plant Breed 133(1):52–60

    Article  CAS  Google Scholar 

  • Roxrud I, Lid SE, Fletcher JC et al (2007) GASA4 one of the 14-member Arabidopsis GASA family of small polypeptides regulates flowering and seed development. Plant Cell Physiol 48(3):471–483

    Article  CAS  PubMed  Google Scholar 

  • Saze H, Kakutani T (2007) Heritable epigenetic mutation of a transposon-flanked Arabidopsis gene due to lack of the chromatin-remodeling factor DDM1. EMBO J 26(15):3641–3652

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Searing AM, Satyanarayan MB, Odonnell JP et al (2020) Two organelle RNA recognition motif proteins affect distinct sets of RNA editing sites in the Arabidopsis thaliana plastid. Plant direct 4(4):e00213

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Sebastian J, Ravi M, Andreuzza S et al (2009) The plant adherin AtSCC2 is required for embryogenesis and sister-chromatid cohesion during meiosis in Arabidopsis. Plant J 59(1):1–13

    Article  CAS  PubMed  Google Scholar 

  • Shen WH, Qin P, Yan MJ et al (2019) Fine mapping of a silique length- and seed weight- related gene in Brassica napus. Theor Appl Genet 132(11):2985–2996

    Article  CAS  PubMed  Google Scholar 

  • Shi J, Li R, Qiu D, Jiang C et al (2009) Unraveling the complex trait of crop yield with quantitative trait loci mapping in Brassica napus. Genetics 182(3):851–861

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Shi LL, Song JR, Guo CC et al (2019) A CACTA-like transposable element in the upstream region of BnaA9.CYP78A9 acts as an enhancer to increase silique length and seed weight in rapeseed. Plant J 98(3):524–539

    Article  CAS  PubMed  Google Scholar 

  • Song Y, Chen L, Zhang L et al (2010) Overexpression of OsWRKY72 gene interferes in the abscisic acid signal and auxin transport pathway of Arabidopsis. J Biosciences 35(3):459–471

    Article  CAS  Google Scholar 

  • Verna C, Sawchuk MG, Linh NM et al (2015) Control of vein network topology by auxin transport. BMC Biol 13:94

    Article  PubMed  PubMed Central  Google Scholar 

  • Wang K, Li M, Hakonarson H (2010) ANNOVAR: Functional annotation of genetic variants from nextgeneration sequencing data. Nucleic Acids Res 38:e164

    Article  PubMed  PubMed Central  Google Scholar 

  • Wang X, Wang H, Long Y et al (2013) Identification of QTLs associated with oil content in a high-oil Brassica napus cultivar and construction of a high-density consensus map for QTLs comparison in B. napus. PLoS One 8(12):e80569

    Article  PubMed  PubMed Central  Google Scholar 

  • Wang X, Chen L, Wang A et al (2016) Quantitative trait loci analysis and genome-wide comparison for silique related traits in Brassica napus. BMC Plant Biol 16(1):71

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Wang H, Zaman QU, Huang W et al (2019) QTL and Candidate Gene Identification for Silique Length Based on High-Dense Genetic Map in Brassica napus L. Front Plant Sci 10:1579

    Article  PubMed  PubMed Central  Google Scholar 

  • Wang J, Fan YL, Mao L et al (2021) Genome-wide association study and transcriptome analysis dissect the genetic control of silique length in Brassica napus L. Biotechnol Biofuels 14(1):214

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Wen J, Lease KA, Walker JC (2004) DVL, a novel class of small polypeptides: overexpression alters Arabidopsis development. Plant J 37(5):668–677

    Article  CAS  PubMed  Google Scholar 

  • Yang P, Shu C, Chen L et al (2012) Identification of a major QTL for silique length and seed weight in oilseed rape (Brassica napus L). Theor Appl Genet 125(2):285–296

    Article  PubMed  Google Scholar 

  • Yang Y, Shen Y, Li S et al (2017) High Density Linkage Map Construction and QTL Detection for Three Silique-Related Traits in Orychophragmus violaceus Derived Brassica napus Population. Front Plant Sci 8:1512

    Article  PubMed  PubMed Central  Google Scholar 

  • Yang Z, Liang C, Wei L et al (2022) BnVIR: Bridging the genotype-phenotype gap to accelerate mining of candidate variations underlying agronomic traits in Brassica napus. Mol Plant 15(10):779–782

    Article  CAS  PubMed  Google Scholar 

  • Zeng ZB (1994) Precision mapping of quantitative trait loci. Genetics 136:1457–1468

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Zhang L, Yang G, Liu P et al (2011) Genetic and correlation analysis of silique-traits in Brassica napus L by quantitative trait locus mapping. Theor Appl Genet 122(1):21–31

    Article  PubMed  Google Scholar 

  • Zhao WG, Zhang L, Chao HB et al (2019) Genome-wide identification of silique-related traits based on high-density genetic linkage map in Brassica napus. Mol Breed 39(6):86

    Article  Google Scholar 

  • Zhou XM, Dai LH, Wang PF et al (2021) Mining favorable alleles for five agronomic traits from the elite rapeseed cultivar zhongshuang 11 by QTL mapping and integration. Crop J 9(6):1449–1459

    Article  Google Scholar 

  • Zhou XM, Zhang HY, Wang PF et al (2022) BnaC7.ROT3, the causal gene of cqSL-C7, mediates silique length by affecting cell elongation in Brassica napus. J Exp Bot 73(1):154–167

    Article  CAS  PubMed  Google Scholar 

Download references

Acknowledgements

The authors thank Dr. Xiyuan Ni from Zhejiang Academy of Agricultural Sciences for providing seeds of Sollux.

Funding

This work was supported by the Natural Science Fund of Education Department of Anhui province (2023AH051876 and KJ2020A0064), the Talent Introduction Project of Anhui Science and Technology University (NXYJ201901), the research and development fund of Anhui Science and Technology University (FZ230121), the Collection, Evaluation and Conservation of Rape Germplasm Resources of Shanghai Agricultural Foundation (202001) and the Chinese College Student Innovation Fund Project (S202110879215).

Author information

Author notes

  1. Lei Chen and Wangfei He Contributed equally to this work.

Authors and Affiliations

  1. College of Agriculture, Anhui Science and Technology University, Fengyang, 233100, China

    Lei Chen, Wangfei He, Yulin Yu, Yifan Wang, Xueyang Zhai, Xinxiang Ling, Pan Lu & Xinxin Cheng

  2. Crop Institute, Anhui Academy of Agricultural Sciences, Hefei, 230031, China

    Weixia Lei & Zhixiong Fan

Authors
  1. Lei Chen
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Wangfei He
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Yulin Yu
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Yifan Wang
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Xueyang Zhai
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Xinxiang Ling
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Pan Lu
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. Xinxin Cheng
    View author publications

    You can also search for this author in PubMed Google Scholar

  9. Weixia Lei
    View author publications

    You can also search for this author in PubMed Google Scholar

  10. Zhixiong Fan
    View author publications

    You can also search for this author in PubMed Google Scholar

Contributions

LC and WL conceived and designed the study. LC conducted the experiment and wrote the manuscript. WL and ZF provided the experimental materials. WH, YY, YW, XZ, XL, and PL performed the silique length investigations. LC and WH analyzed the data, XC supervised the experiment and WL and LC reviewed and modified the manuscript. All authors have read and agreed to the published version of the manuscript.

Corresponding authors

Correspondence to Lei Chen or Weixia Lei.

Ethics declarations

Ethics approval and consent to participate

Not applicable.

Consent for publication

Not applicable.

Competing interests

The authors declare no competing interests.

Additional information

Publisher's Note

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Supplementary Information

Below is the link to the electronic supplementary material.

Supplementary file1 (DOCX 1363 KB)

Supplementary file2 (XLSX 88 KB)

Rights and permissions

Springer Nature or its licensor (e.g. a society or other partner) holds exclusive rights to this article under a publishing agreement with the author(s) or other rightsholder(s); author self-archiving of the accepted manuscript version of this article is solely governed by the terms of such publishing agreement and applicable law.

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Chen, L., He, W., Yu, Y. et al. Molecular mapping and candidate gene identification of two major quantitative trait loci associated with silique length in oilseed rape (Brassica napus L.). Mol Breeding 44, 26 (2024). https://doi.org/10.1007/s11032-024-01464-x

Download citation

  • Received:

  • Accepted:

  • Published:

  • DOI: https://doi.org/10.1007/s11032-024-01464-x

Keywords

Search

Navigation