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.
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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
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
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
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
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
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
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
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
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
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
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
Diepenbrock W (2000) Yield analysis of winter oilseed rape (Brassica napus L.): a review. Field Crop Res 67:35–49
Doerge RW, Churchill GA (1996) Permutation tests for multiple loci affecting a quantitative character. Genetics 142(1):285–294
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
Doyle JJ, Doyle JL (1987) A rapid DNA isolation procedure for small quantities of fresh leaf tissue. Phytochem Bull 19:11–15
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
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
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
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
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
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
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
Kim D, Langmead B, Salzberg SL (2015) HISAT: a fast spliced aligner with low memory requirements. Nat Methods 12(4):357–360
Lebowitz RJ (1989) Image analysis measurements and repeatability estimates of siliqua morphological traits in Brassica campestris L. Euphytica 43:113–116
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
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
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
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
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
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
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
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
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
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
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
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
Ozer H, Oral E (1999) Relationships Between Yield and Yield Components on Currently Improved Spring Rapeseed Cultivars. Turk J Agric for 23:603–608
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
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
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
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
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
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
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
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
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
Verna C, Sawchuk MG, Linh NM et al (2015) Control of vein network topology by auxin transport. BMC Biol 13:94
Wang K, Li M, Hakonarson H (2010) ANNOVAR: Functional annotation of genetic variants from nextgeneration sequencing data. Nucleic Acids Res 38:e164
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
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
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
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
Wen J, Lease KA, Walker JC (2004) DVL, a novel class of small polypeptides: overexpression alters Arabidopsis development. Plant J 37(5):668–677
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
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
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
Zeng ZB (1994) Precision mapping of quantitative trait loci. Genetics 136:1457–1468
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
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
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
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
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).
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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.
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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
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DOI: https://doi.org/10.1007/s11032-024-01464-x