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Fine mapping of a silique length- and seed weight-related gene in Brassica napus

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Using microarray analysis combined with map-based cloning, a major locus positively regulating SL and SW was mapped to a 98.47 kb interval on A09 in rapeseed.

Abstract

In rapeseed, seed yield is closely associated with silique-related traits such as silique length (SL) and seed weight (SW). Previously identified quantitative trait loci (QTLs) revealed that SL and SW are complex traits and many QTLs overlap. However, the genetic characterization of the association between SL and SW is poorly understood. In the present study, a BC3F3 near isogenic line developed from a short silique plant and the long silique cultivar ‘ZS11’ was analyzed to identify the locus related to SL. Map-based cloning indicated that a major locus acting as a single Mendelian factor was mapped to a 98.47 kb region on chromosome A09. BLAST analysis and DNA sequencing showed SNP variations and a fragment replacement in the upstream region of the candidate gene BnaA09g55530D may alter gene expression and influence SL. The results showed that this SL locus may also positively affect SW as well as in the 186 rapeseed accessions identified by the associated markers. Therefore, selecting plants with appropriate SL and developing functional markers for the associated gene could play important roles in the molecular breeding of high-yield rapeseed varieties.

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Acknowledgements

We sincerely thank Professor Yongming Zhou and Professor Liang Guo for kindly providing the silique length and seed weight data of the 521 accessions. This work was financed by the funding from the National Key Research and Development Program of China (Grant Number 2016YFD0100305).

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Authors and Affiliations

  1. National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, National Sub-Center of Rapeseed Improvement in Wuhan, Huazhong Agricultural University, Wuhan, 430070, China

    Wenhao Shen, Pei Qin, Mengjiao Yan, Bao Li, Zengxiang Wu, Jing Wen, Bin Yi, Chaozhi Ma, Jinxiong Shen, Tingdong Fu & Jinxing Tu

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  1. Wenhao Shen
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  2. Pei Qin
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  3. Mengjiao Yan
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Correspondence to Jinxing Tu.

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122_2019_3400_MOESM1_ESM.tif

Phenotypic characterization of flowers and pollen between ‘ZS11’ (a, c, e) and ‘DH46’ (b, d, f). a, b, c, d Flower phenotypes of the two parents, bar, 0.5 cm. e and f Pollen viability by acetocarmine staining, bars, 100 μm (TIFF 4643 kb)

122_2019_3400_MOESM2_ESM.tif

Different silique phenotypes in BC3F2 generation. Siliques with no seed development defects (a and d) and have defects (b, c, e and f). Long siliques: a, b, and c; short siliques: d, e, and f. Bar, 2 cm (TIFF 2166 kb)

122_2019_3400_MOESM3_ESM.tif

Relative expression of BnaA09g55530D homoeologous genes in different silique development stages between L- and S-NIL plants. a BnaA04g00510D, b BnaC08g31760D, and c BnaCnng73170D. L1: 0–2 mm buds; L2–L4: 2–4, 4–6, and 6–8 mm pistils of buds. ***, significantly different at P < 0.001; **, significantly different at P < 0.01; *, significantly different at P < 0.05 (TIFF 25696 kb)

Molecular makers designed in this study (DOCX 13 kb)

Primer developed for co-segregation and relative expression analyses (DOCX 12 kb)

Descriptions of B. napus accessions and phenotype data used in this study (XLSX 19 kb)

Sequence alignments of the ~ 3.9 kb upstream sequences of BnaA09g55530D in ZS11 and DH46 (DOCX 14 kb)

Detailed sequence of~ 3.6 kb replaced fragment in ZS11 (DOCX 14 kb)

Detailed sequence of~ 12.4 kb replaced fragment in DH46 (DOCX 20 kb)

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Shen, W., Qin, P., Yan, M. et al. Fine mapping of a silique length- and seed weight-related gene in Brassica napus. Theor Appl Genet 132, 2985–2996 (2019). https://doi.org/10.1007/s00122-019-03400-6

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