Abstract
BackgroundFuzhong 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.ResultsIn 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.ConclusionsThe 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.
Highlights
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
Genome resequencing of Fuzhong buffalo A total of 15 FZ buffaloes were selected for genome resequencing, while 12 Upper Yangtze (UY) buffaloes genomic DNA sequences were obtained from previously published data [2] (Additional file 1: Table S1)
707 overlapping genes were identified as the candidate genes for UY buffalo, while 58 candidate genes were shared between FZ and UY buffalo
Summary
A native breed of Guangxi Zhuang Autonomous Region, is traditionally used as a draft animal to provide farm power in the rice cultivation. Buffalo has been an important livestock animal used as a source of food and draught power in tropical and subtropical regions. Another study detected genes associated with the body size, immunity and coat color by analyzing the ROH of the Azeri and Khuzestani buffalo breeds using the same dataset [7]. A recent study described the genetic history and population structure of swamp and river buffalo by analyzing 121 whole genomes from 25 breeds with different geographical origins [2], intercepting the candidate genes associated with nervous system and muscle development in swamp buffalo, while genes related to heat-stress and immunity were detected in the river buffalo [2]
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