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Construction of a high-density genetic linkage map and identification of gene controlling resistance to cucumber mosaic virus in Luffa cylindrica (L.) Roem. based on specific length amplified fragment sequencing

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Abstract

Luffa cylindrica L. is a cash crop which has important health, medicinal and industrial value, but no high saturation genetic map has been constructed owing to a lack of efficient markers. Furthermore, no genes were reportedly responsible for CMV resistance in Luffa spp. Specific length amplified fragment sequencing (SLAF-seq) is a valuable tool for large-scale discovery of markers and genetic mapping. The present study reported the construction of a high-density genetic map and the mapping of CMV resistant genes by using an F2 population of 130 individuals and their two inbred line parents. A total of 271.01 Mb pair-end reads were generated. 100,077 high-quality SLAFs were detected, and 7404 of them were polymorphic. Finally, 3701 of the polymorphic markers were selected for genetic map construction, and 13 linkage groups were generated. The map spanned 1518.56 cM with an average distance of 0.41 cM between adjacent markers. Based on the newly constructed high-density map, one gene located on chromosome 1 (100.072–100.457 cM) was identified to regulate CMV resistance in L. cylindrica. A gag-polypeptide of LTR copia-type retrotransposon was predicted as the candidate gene responsible for CMV resistance in L. cylindrica. The high-density genetic map and the CMV resistant gene mapped and predicted in this study will be useful in future research.

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All data generated or analysed during this study are included herein.

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Acknowledgements

This study was funded by the National Natural Science Foundation of China (Grant No. 31501778). We thank Dr. Jeroen A. Berg for valuable suggestions during the preparation of the manuscript. We also acknowledge the reviewers for their constructive comments to improve the manuscript. We would give thanks to Biomarker Technologies Co., Ltd., Beijing for technical support in bioinformatics. Also we would like to thank Biomics (Beijing) Biotech Co. Ltd for providing technical support for the RNA-seq data. The datasets generated and analyzed during the current study are available from the corresponding author on reasonable request.

Funding

This study was funded by the National Natural Science Foundation of China (Grant No. 31501778).

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Authors and Affiliations

  1. Institute of Vegetable Crops, Jiangsu Academy of Agricultural Sciences/Laboratory for Horticultural Crop Genetic Improvement, Zhongling Street 50, Nanjing, 210014, Jiangsu Province, China

    Lina Lou, Xiaojun Su, Xiaohong Liu & Zhe Liu

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  1. Lina Lou
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  2. Xiaojun Su
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Contributions

LL designed, performed, analyses and drafted the experiments. With valuable suggestions by SX as well as technical assistance by LZ and LX. All authors read and approved the manuscript.

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Correspondence to Lina Lou.

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Supplementary file1 (JPG 279 kb)

Number of SLAF markers in each of eight segregation patterns.

Supplementary file2 (JPG 140 kb)

Distribution of all mapped SNP markers on all individuals. The X-axes indicate individual F2 plants. The Y-axes indicate the distribution of all mapped markers.

Supplementary file3 (PDF 1796 kb)

Haplotype map of the genetic map. Green represents ʻP1-21ʼ, blue represent ʻP2-16ʼ, gray represents missing data, and red indicates heterozygosity. The two columns represent the genotype of an individual. Rows correspond to genetic markers.

Supplementary file4 (PDF 419 kb)

Heat map of the genetic map. Each cell represents the recombination rate of two markers. Yellow indicates a lower recombination rate and purple indicates a higher one.

Supplementary file5 (DOCX 13 kb)

Supplementary file6 (XLSX 10210 kb)

Supplementary file7 (XLSX 467 kb)

Supplementary file8 (XLSX 94 kb)

Supplementary file9 (DOCX 13 kb)

Supplementary file10 (XLSX 11 kb)

Supplementary file11 (DOCX 14 kb)

Supplementary file12 (DOCX 13 kb)

Supplementary file13 (XLSX 17 kb)

Supplementary file14 (XLSX 32 kb)

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Lou, L., Su, X., Liu, X. et al. Construction of a high-density genetic linkage map and identification of gene controlling resistance to cucumber mosaic virus in Luffa cylindrica (L.) Roem. based on specific length amplified fragment sequencing. Mol Biol Rep 47, 5831–5841 (2020). https://doi.org/10.1007/s11033-020-05652-8

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