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Selection signatures of litter size in Dazu black goats based on a whole genome sequencing mixed pools strategy

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Abstract

Litter size is considered to be the most important index for estimating domestic animal productivity. Due to its complexity, the molecular mechanism of litter size has not been elucidated, and it has restricted the use of marker-assisted selection to create high-yield populations in goats. A genome-wide selective sweep analysis was performed with 31 Dazu black goats to identify significant genomic regions and candidate genes related to litter size by a mixed pools strategy. A total of 96 candidate genes were identified, including NR6A1, STK3, IGF2BP2, AR, HMGA2, NPTX1, ANKRD17, DPYD, CLRB, PPP3CA, PLCB1, STK3 and HMGA2, using mixed pool analysis with ZHp and FST. We classified these candidate genes based on the functional classification and annotation of signaling pathways. According to the GO and KEGG analysis results, a total of 43 GO terms and 108 pathways were annotated from these genes. In particular, some novel candidate genes were enriched in reproduction-related pathways, such as the estrogen signaling pathway and oocyte meiosis. These findings provide insight into the influences of coding genes on the fecundity traits of goats.

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Fig. 1
Fig. 2

Data availability

Data analysis results for each stage are available from the corresponding author on reasonable request. The raw sequencing data generated has been uploaded to the NCBI (SRA: SRP152397).

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Acknowledgements

Fundamental Research Funds for the Central Universities (XDJK2018B014), and National Natural Science Foundation of China (No. 31172195), Characteristic Germplasm Resources Population Selection and Innovation on Mutton Sheeps and Goats (No. 2015BAD03B05) support for experimental animal costs. Chongqing Research Program of Basic Research and Frontier Technology (cstc2018jcyjAX0153) support for the costs of genomic sequencing. We are grateful to/thank Guangzhou Genedenovo Biotechnology Co., Ltd for assisting in sequencing and part of bioinformatics analysis.

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  1. Guang-Xin E and Yong-Ju Zhao have contributed equally to this work.

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  1. College of Animal Science and Technology, Southwest University, No. 2 Tiansheng Road, Chongqing, 400715, China

    Guang-Xin E, Yong-Ju Zhao & Yong-Fu Huang

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  1. Guang-Xin E
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GXE, and YFH conceived and designed the experiments. GXE, and YJZ performed the lab work, analyzed the data and wrote the paper.

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Correspondence to Yong-Fu Huang.

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E, GX., Zhao, YJ. & Huang, YF. Selection signatures of litter size in Dazu black goats based on a whole genome sequencing mixed pools strategy. Mol Biol Rep 46, 5517–5523 (2019). https://doi.org/10.1007/s11033-019-04904-6

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