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. 2024 Oct 23;14(21):3056.
doi: 10.3390/ani14213056.

Genomic Insights and Conservation Priorities for Kongshan Cattle: A Whole-Genome Resequencing Approach

Wenqiang Sun  1   2   3 , Hanjun Ren  1   2   3 , Mengze Li  1   2   3 , Liping Mei  1   2   3 , Bingfei Zhang  1   2   3 , Xianbo Jia  1   2   3 , Shiyi Chen  1   2   3 , Jie Wang  1   2   3 , Songjia Lai  1   2   3
Affiliations

Genomic Insights and Conservation Priorities for Kongshan Cattle: A Whole-Genome Resequencing Approach

Wenqiang Sun et al. Animals (Basel). .

Abstract

Kongshan Cattle, indigenous to Sichuan Province and recognized as China's 56th local cattle breed in 2024, exhibit unique adaptations including superior resistance to harsh conditions. Despite a declining population due to the influx of foreign breeds, there is a significant focus on preserving their genetic diversity through advanced genomic techniques. This study utilized whole-genome resequencing, a cost-effective and information-rich method, to perform a comprehensive genetic assessment of the Kongshan Cattle. High-quality resequencing data yielded an average of 17.5 billion clean bases per sample, with high proportions of Q20 and Q30 bases and a balanced GC content. SNP analysis revealed an average of 14 million SNPs per sample, with a notable transition-to-transversion ratio and a significant portion of heterozygosity. Further analysis of genomic and coding regions identified substantial insertions and deletions, particularly in coding sequences affecting gene functionality. A detailed examination of these genetic variations highlighted genes, including NEIL2 and PNKP, which are integral to stress resistance pathways, indicating potential adaptive advantages. This study not only underscores the genetic diversity of Kongshan Cattle but also contributes to broader efforts in germplasm conservation.

Keywords: Kongshan cattle; SNPs; functional annotation; small indel; whole-genome resequencing.

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Conflict of interest statement

The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as potential conflicts of interest.

Figures

Figure 1
Figure 1
Genome-wide and coding region InDel length distribution.
Figure 2
Figure 2
Gene ontology (GO) analysis of part of variant genes.
Figure 3
Figure 3
Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis of part of variant genes.
See this image and copyright information in PMC

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References

    1. He F., Wang W., Shi Y., Fang D., Aguo Y., Gan J., Deng X., Fu M., Yi J. Growth and Development Analysis of Kongshan Cattle. Agric. Biotechnol. 2022;11:62–65.
    1. Bayes M., Heath S., Gut I.G. Applications of second generation sequencing technologies in complex disorders. Curr. Top. Behav. Neurosci. 2012;12:321–343. - PubMed
    1. Martin J., Schackwitz W., Lipzen A. Genomic Sequence Variation Analysis by Resequencing. Methods Mol. Biol. 2018;1775:229–239. - PubMed
    1. Iqbal N., Liu X., Yang T., Huang Z., Hanif Q., Asif M., Khan Q.M., Mansoor S. Genomic variants identified from whole-genome resequencing of indicine cattle breeds from Pakistan. PLoS ONE. 2019;14:e0215065. doi: 10.1371/journal.pone.0215065. - DOI - PMC - PubMed
    1. Peripolli E., Reimer C., Ha N.T., Geibel J., Machado M.A., Panetto J., do Egito A.A., Baldi F., Simianer H., da Silva M. Genome-wide detection of signatures of selection in indicine and Brazilian locally adapted taurine cattle breeds using whole-genome re-sequencing data. BMC Genom. 2020;21:624. doi: 10.1186/s12864-020-07035-6. - DOI - PMC - PubMed

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