Selection signatures of Fuzhong Buffalo based on whole-genome sequences
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RESEARCH ARTICLE
Open Access
Selection signatures of Fuzhong Buffalo based on whole-genome sequences Ting Sun1,2, Guang-yun Huang1, Zi-hao Wang1, Shao-hua Teng1, Yan-hong Cao1, Jun-li Sun1, Quratulain Hanif3,4, Ning-bo Chen2, Chu-zhao Lei2* and Yu-ying Liao1*
Abstract Background: Fuzhong buffalo, a native breed of Guangxi Zhuang Autonomous Region, is traditionally used as a draft animal to provide farm power in the rice cultivation. In addition, the Fuzhong buffalo also prepared for the bullfighting festival organized by the locals. The detection of the selective signatures in its genome can help in elucidating the selection mechanisms in its stamina and muscle development of a draft animal. Results: In this study, we analyzed 27 whole genomes of buffalo (including 15 Fuzhong buffalo genomes and 12 published buffalo genomes from Upper Yangtze region). The ZHp, ZFst, π-Ratio, and XP-EHH statistics were used to identify the candidate signatures of positive selection in Fuzhong buffalo. Our results detected a set of candidate genes involving in the pathways and GO terms associated with the response to exercise (e.g., ALDOA, STAT3, AKT2, EIF4E2, CACNA2D2, TCF4, CDH2), immunity (e.g., PTPN22, NKX2-3, PIK3R1, ITK, TMEM173), nervous system (e.g., PTPN21, ROBO1, HOMER1, MAGI2, SLC1A3, NRG3, SNAP47, CTNNA2, ADGRL3). In addition, we also identified several genes related to production and growth traits (e.g., PHLPP1, PRKN, MACF1, UCN3, RALGAPA1, PHKB, PKD1L). Our results depicted several pathways, GO terms, and candidate genes to be associated with response to exercise, immunity, nervous system, and growth traits. Conclusions: The selective sweep analysis of the Fuzhong buffalo demonstrated positive selection pressure on potential target genes involved in behavior, immunity, and growth traits, etc. Our findings provided a valuable resource for future research on buffalo breeding and an insight into the mechanisms of artificial selection. Keywords: Buffalo, Resequencing, Selection signatures
Background Buffalo has been an important livestock animal used as a source of food and draught power in tropical and subtropical regions. It can be divided into two types: river (2n = 50) and swamp buffalo (2n = 48) [1]. China is one of the countries with the largest population of swamp buffalo. A recent study showed that the swamp buffalo * Correspondence: [email protected]; [email protected] 2 College of Animal Science and Technology, Northwest A&F University, Yangling 712100, Shaanxi, China 1 Animal Husbandry Institute of Guangxi Zhuang Autonomous Region, Guangxi Key Laboratory of Livestock Genetic Improvement, Nanning 530001, China Full list of author information is available at the end of the article
can be divided into two divergent groups: Southeast Asian buffalo (including buffaloes from Southeast Asia and Southwest China) and South China buffalo (including the buffalo from Upper Yangtze and Middle-Lower Yangtze) [2]. In particular, the buffalo distributed in Upper Yangtze exhibited weak gene flow from the Southeast Asia
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