Genetic Variations in Southern High-protein Soybean Fudou 234 by Re-sequencing

ZHANG Yumei; XIAO Han; LAN Xinlong; XIA Chunying; LIN Guoqiang

doi:10.19303/j.issn.1008-0384.2024.06.004

Volume 39 Issue 6

Jun. 2024

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Article Navigation > Fujian Journal of Agricultural Sciences > 2024 > 39(6): 652-661

ZHANG Y M, XIAO H, LAN X L, et al. Genetic Variations in Southern High-protein Soybean Fudou 234 by Re-sequencing [J]. Fujian Journal of Agricultural Sciences，2024，39（6）：652−661 doi: 10.19303/j.issn.1008-0384.2024.06.004

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ZHANG Y M, XIAO H, LAN X L, et al. Genetic Variations in Southern High-protein Soybean Fudou 234 by Re-sequencing [J]. Fujian Journal of Agricultural Sciences，2024，39（6）：652−661 doi: 10.19303/j.issn.1008-0384.2024.06.004

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Genetic Variations in Southern High-protein Soybean Fudou 234 by Re-sequencing

doi: 10.19303/j.issn.1008-0384.2024.06.004

Crop Research Institute, Fujian Academy of Agricultural Sciences/Fujian Engineering Research Center for Characteristic Dry Crop Varieties Breeding/Fujian Key Laboratory of Vegetable Genetics and Breeding Fuzhou, Fuzhou, Fujian　350013, China

Received Date: 2024-05-17
Accepted Date: 2024-07-24
Rev Recd Date: 2024-06-11

Available Online: 2024-08-15

Publish Date: 2024-06-28

Abstract

Abstract

Objective Genetic variations in the southern high-protein soybeans were revealed by re-sequencing the whole genome. Method High-throughput sequencing was conducted on the whole genome of the southern high-protein soybean Fudou 234 to detect genetic variations. Result In the 64757037 clean reads, the sequencing depth was 17× with genome coverage of 98.08% (1×) and 96.25% (5×). There were 1478393 single nucleotide polymorphisms (SNPs) and 356739 small insertion-deletions (Small InDels) identified. Among them, 14323 non-synonymous SNP mutations and 4186Small InDel mutated genes were found in the coding sequence (CDS). Analysis by COG (Clusters of orthologous groups of proteins) revealed that signal transduction mechanisms, transcription, carbohydrate translocation and metabolism and KEGG(Kyoto encyclopedia of genes and genomes) analyses revealed that the pathways of carbon metabolism, starch and sucrose metabolism, amino acid biosynthesis, phytohormone signalling, and endoplasmic reticulum protein processing were associated with genetic variation in Fudou 234. In addition, by studying the candidate genes in two major segments of soybean kernel protein quantitative trait locus (QTL), 10 SNP and 7 Small InDel type variations were discovered in 65 genes. Conclusion The genetic variations in the southern high-protein soybeans deviated from the regular varieties were unveiled to provide new venue for breeding and developing molecular markers in studying soybeans.
- Fudou 234,
- whole genome re-sequencing,
- single nucleotide polymorphism,
- small InDel,
- variation

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References(40)

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