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.

[Genetic diversity of common wild rice (Oryza rufipogon Griff) by using SSR markers and phenotypic traits in Guangxi Province].

In this paper, allelic variation and genetic diversity among geographies and growth habit types were studied by using 223 accessions of common wild rice primary core collection in Guangxi Province, with 34 SSR primers locating on 12 chromosomes of rice and 19 phenotypic traits. In the results, 24.91 alleles were detected per locus on average with a range from 7 to 48. Compared to the cultivated rice, the wild rice showed more allelic variations. The ratio of heterozygote of SSR locus was 32.01% on average, and it's range was 1.35% 81.31%. The frequency of heterozygote of SSR locus in Oryza rufipogon Griff was much higher than in Oryza sativa L. The geographical distribution of genetic diversity measured by SSR markers was not completely accordant with that by phenotypic traits. At DNA level, more wild rice individuals and higher genetic diversity were included within the area covering north latitude 22 degrees - 23 degrees and 23 degrees - 24 degrees (comprising Longan, Fusui, Yongning, Xiangzhou, Laibin, Xuanwu, Yulin and Guigang county), which formed the center of genetic diversity. But the center of genetic diversity at the phenotypic level located within north latitude 21 degrees - 22 degrees and 22 degrees - 23 degrees. Among the four growth habit types, the genetic diversity from high to low was found respectively in prostrate type, sloping type, slighting type, and erect type at both DNA and phenotypic levels.