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Analysis of Anasplatyrhynchos genome resequencing data reveals genetic signatures of artificial selection

文献类型： 外文期刊

作者： Xu, Tieshan 1 ; Gu, Lihong 3 ; Yu, Haopeng 4 ; Jiang, Xuefei 5 ; Zhang, Yunsheng 1 ; Zhang, Xiaohui 6 ; Rong, Guang 2 ; Z 1 ;

作者机构： 1.Chinese Acad Trop Agr Sci, Trop Crop Genet Resource Res Inst, Danzhou, Peoples R China

2.Chinese Acad Agr Sci, Inst Anim Sci, Beijing, Peoples R China

3.Hainan Acad Agr Sci, Inst Anim Sci & Vet, Haikou, Hainan, Peoples R China

4.Sichuan Univ, West China Sch Med, West China Hosp, West China Biomed Big Data Ctr, Chengdu, Sichuan, Peoples R China

5.Hainan Univ, Inst Trop Agr & Forestry, Haikou, Hainan, Peoples R China

6.Henan Univ Sci & Technol, Coll Anim Sci, Luoyang, Peoples R China

7.Univ Illinois, Dept Radiol, Chicago, IL USA

期刊名称：PLOS ONE （ 影响因子：3.24； 五年影响因子：3.788 ）

ISSN： 1932-6203

年卷期： 2019 年 14 卷 2 期

页码：

收录情况： SCI

摘要： Three artificially selected duck populations (AS), higher lean meat ratios (LTPD), higher fat ratios (FTPD) and higher quality meat (CMD), have been developed in China, providing excellent populations for investigation of artificial selection effects. However, the genetic signatures of artificial selection are unclear. In this study, we sequenced the genome sequences of these three artificially selected populations and their ancestral population (mallard, M). We then compared the genome sequences between AS and M and between LTPD and FTPD using integrated strategies such as anchoring scaffolds to pseudo-chromosomes, mutation detection, selective screening, GO analysis, qRT-PCR, and protein multiple sequences alignment to uncover genetic signatures of selection. We anchored duck scaffolds to pseudo-chromosomes and obtained 28 pseudo-chromosomes, accounting for 84% of duck genome in length. Totally 78 and 99 genes were found to be under selection between AS and M and between LTPD and FTPD. Genes under selection between AS and M mainly involved in pigmentation and heart rates, while genes under selection between LTPD and FTPD involved in muscle development and fat deposition. A heart rate regulator (HCN1), the strongest selected gene between AS and M, harbored a GC deletion in AS and displayed higher mRNA expression level in M than in AS. IGF2R, a regulator of skeletal muscle mass, was found to be under selection between FTPD and LTPD. We also found two nonsynonymous substitutions in IGF2R, which might lead to higher IGF2R mRNA expression level in FTPD than LTPD, indicating the two nonsynonymous substitutions might play a key role for the regulation of duck skeletal muscle mass. Taken together, these results of this study provide valuable insight for the genetic basis of duck artificial selection.

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