Selection signatures of Fuzhong Buffalo based on whole-genome sequences

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.

Whole-Genome Resequencing of Xiangxi Cattle Identifies Genomic Diversity and Selection Signatures

“…Among them, 127 genes were overlapped which were considered to be candidate genes ( Supplementary Table S6 ). The annotations of candidate genes revealed the functions that may be associated with economic traits, including reproduction ( KHDRBS2 , GOLGA4 , BBX , BANF2 , INSL6 ) ( Cai et al, 2017 ; Guo et al, 2018 ; Ortega et al, 2016 ; Pini et al, 2020 ; Wang et al, 2016 ), growth ( RALGAPA1 , NCK1 , VGLL2, FGFR3 ) ( Aryal et al, 2015 ; Honda et al, 2017 ; Sun et al, 2020 ; Wen et al, 2016 ), meat quality ( PLIN4 ) ( Pena et al, 2019 ), and somatotype ( SYN3 ) ( An et al, 2019 ). We also obtained genes ( ELANE, AZU1 ) ( Cui et al, 2021 ; Zhang et al, 2021 ) related to immune response, which may result from long-term natural selection.…”

Assessing Genomic Diversity and Productivity Signatures in Dianzhong Cattle by Whole-Genome Scanning

“…The overlap of the top 1% windows in each method was considered as candidate signatures of selection. Genomic regions identified by at least two methods were considered to be candidate regions of positive selection (Sun et al, 2020). In addition, π and Fst were computed with 5 kb sliding window and 2 kb step by using VCFtools for each candidate gene.…”

Population structure, runs of homozygosity analysis and construction of single nucleotide polymorphism fingerprinting database of Longnan goat population

“…(2016) suggested that ARHGAP6 is indispensable in the growth and development of porcine. RALGAPA1 is linked to reproductive traits, hatching rate, and egg production in chickens (Sun et al., 2020). CCL19 is involved in the release of sequestered calcium ions into the cytosol.…”