Selection signatures of Fuzhong Buffalo based on whole-genome sequences.

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.

Mitogenome Diversity and Maternal Origins of Guangxi Buffalo Breeds.

Guangxi Province, in the southwest of China, is one of the putative migratory corridors or domestication centers for swamp buffalo. In this study, we investigated the evolutionary status of two Guangxi native buffalo breeds (Fuzhong buffalo, n = 15; Xilin buffalo, n = 25) based on the complete mitogenome sequencing. Our results revealed rich genetic diversity in the two buffalo breeds. We detected five haplogroups (SA1, SA2, SB1, SB2, SB3) in the two Guangxi buffalo breeds, and the haplogroup SB3 in the Fuzhong buffalo. Our results showed that the haplogroup SA1 was associated with the major domestication event that involved population expansion in Guangxi buffalo. In conclusion, our findings revealed a high level of maternal genetic diversity and the phylogenetic pattern of the two Guangxi buffalo breeds.

Mitogenome Diversity and Maternal Origins of Guangxi Cattle Breeds.

Guangxi Province is located in the southernmost region of China, adjacent to the hotspot that is considered to be the putative migratory corridor or domestication area for Chinese indicine cattle. Here, we investigated the evolutionary status of Guangxi native breeds, Longlin (n = 21), Nandan (n = 18), and Weizhou cattle (n = 17) using mitogenome sequencing. Our results show that Bos indicus sub-haplogroup I1a predominates in Guangxi cattle breeds. Population structure by multidimensional-scaling analysis significantly differentiates Weizhou from the other two breeds (Longlin and Nandan). Moreover, the mtDNA haplotype composition and FST values indicate that the formation of Longlin and Nandan breeds may have been affected by Indian indicine, whereas, Weizhou island might have preserved pure Chinese indicine cattle due to its geographical isolation. We speculate that following the initial entry of zebu into southern China, the subsequent introgression of Indian indicine may have influenced the matrilineal origin of local breeds in southwestern China.

Cloned Guangxi Bama minipig (Sus scrofa) and its offspring have normal reproductive performance.

Xenotransplantation is a rapidly expanding field of research, and cloned miniature pigs are considered to be good model animals for its development. Although many animal species have been cloned, the success rate is very low, especially in the pig. To optimize the protocols for somatic cell nuclear transfer in the Guangxi Bama minipig, the relationship between cell cycle synchronization and nuclear histone acetylation levels were investigated. The results showed that the cells were efficiently synchronized by either serum starvation or contact inhibition. The level of nuclear histone acetylation in G0/G1 donor cells had similar variation trends in serum starvation and contact inhibition groups. When the synchronized donor cells were introduced into the enucleated oocytes, 8.8% (serum starvation group) or 9.7% (contact inhibition group) of the reconstructed embryos developed to blastocysts. After embryo transfer, one healthy male Guangxi Bama minipig was obtained. To evaluate the fertility of the cloned pig and its offspring, a series of mating experiments were done. Ninety-eight F1 generation crossbred piglets were born, of which 93 piglets survived. Also, the F1 pigs gave birth to 22 F2 generation piglets, of which 14 piglets survived. In conclusion, a Guangxi Bama minipig was successfully cloned from cultured newborn male gonad fibroblast cells, and the cloned minipig and its offspring had normal fertility.