Genetic diversity and selection signatures in Hainan black goats revealed by whole-genome sequencing data

An, Z.X.; Shi, L.G.; Hou, G.Y.; Zhou, H.L; Xun, W.J.

doi:10.1016/j.animal.2024.101147

animal

2024

DOI: 10.1016/j.animal.2024.101147

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Genetic diversity and selection signatures in Hainan black goats revealed by whole-genome sequencing data

Z.X. An,

L.G. Shi,

G.Y. Hou

et al.

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2024

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Cited by 4 publications

References 82 publications

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Nano-Selenium Reduces Concentrations of Fecal Minerals by Altering Bacteria Composition in Feedlot Goats

Liu,

Mao,

Peng

et al. 2024

Agriculture

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This study examined the effect of dietary supplementation of nano-selenium (nano-Se) on the average daily gain (ADG), fecal bacteria community, and concentrations of fecal minerals and volatile fatty acids in feedlot Hainan black goats. Eighteen goats (18.6 ± 0.69 kg) were divided randomly into three groups, with each group receiving a different level of supplementary nano-Se (n = six goats per treatment) as follows: (1) 0.0 mg (CON); (2) 0.2 mg; and (3) 0.4 mg nano-Se/kg dry matter intake (DMI). The final body weight (p = 0.012) and ADG increased linearly (p < 0.01), whereas the ratio of DMI to ADG decreased linearly (p < 0.01) with increasing dietary nano-Se levels. Fecal concentrations of Se increased linearly (p < 0.001), whereas Cu (p < 0.01), Zn (p = 0.020), and Fe (p = 0.010) decreased linearly with increasing dietary nano-Se levels. The relative abundances of Treponema (p = 0.046), norank_f__norank_o__Clostridia_UCG-014 (p < 0.01), norank_ f_norank_o__RF39 (p < 0.01), Eubacterium_siraeum_group (p < 0.001), and Family_XIII_AD3011_group (p = 0.040) increased linearly, and unclassified_f__Lachnospiraceae (p < 0.001), Rikenellaceae_RC9_gut_group (p < 0.01), Eubacterium_ruminantium_group (p = 0.021), and Prevotella (p < 0.001) decreased linearly with increasing dietary nano-Se levels. It was concluded that supplementary nano-Se could improve ADG and reduce the DMI to ADG ratio and fecal heavy metals by altering the bacterial community in feedlot goats. We recommend a dietary supplementation of approximately 0.4 mg nano-Se/kg DM for feedlot Hainan black goats, but further research is warranted to determine the precise dose and the possible contamination risks of Se.

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Nano-Selenium Reduces Concentrations of Fecal Minerals by Altering Bacteria Composition in Feedlot Goats

Liu,

Mao,

Peng

et al. 2024

Agriculture

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Genetic Diversity and Selection Signal Analysis of Hu Sheep Based on SNP50K BeadChip

Ma,

Song,

et al. 2024

Animals

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This research is designed to examine the genetic diversity and kinship among Hu sheep, as well as to discover genes associated with crucial economic traits. A selection of 50 unrelated adult male Hu sheep underwent genotyping with the SNP50K BeadChip. Seven indicators of genetic diversity were assessed based on high-quality SNP data: effective population size (Ne), polymorphic information content (PIC), polymorphic marker ratio (PN), expected heterozygosity (He), observed heterozygosity (Ho), effective number of alleles, and minor allele frequency (MAF). Plink software was employed to compute the IBS genetic distance matrix and detect runs of homozygosity (ROHs), while the G matrix and principal component analysis were performed using GCTA software. Selective sweep analysis was carried out using ROH, Pi, and Tajima’s D methodologies. This study identified a total of 64,734 SNPs, of which 56,522 SNPs remained for downstream analysis after quality control. The population displayed relatively high genetic diversity. The 50 Hu sheep were ultimately grouped into 12 distinct families, with families 6, 8, and 10 having the highest numbers of individuals, each consisting of 6 sheep. Furthermore, a total of 294 ROHs were detected, with the majority having lengths between 1 and 5 Mb, and the inbreeding coefficient FROH was 0.01. In addition, 41, 440, and 994 candidate genes were identified by ROH, Pi, and Tajima’s D methods, respectively, with 3 genes overlapping (BMPR1B, KCNIP4, and FAM13A). These results offer valuable insights for future Hu sheep breeding, genetic assessment, and population management.

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Comparative Whole-Genome Analysis of Production Traits and Genetic Structure in Baiyu and Chuanzhong Black Goats

Luo,

Min,

Sun

et al. 2024

Animals

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Natural selection and artificial breeding are crucial methods for developing new animal groups. The Baiyu black goats and Chuanzhong black goats are indigenous goat breeds from distinct ecological regions in Sichuan Province, with dramatically different growth and reproductivity. To systematically elucidate the differences in production performance and genetic characteristics between the Baiyu black goats and Chuanzhong black goats, we measured their growth and reproductive traits and comprehensively analyzed their genetic diversity, population structure, and selection signatures, utilizing whole-genome resequencing data from 30 Baiyu black goats and 41 Chuanzhong black goats, along with published genomic data from 59 individuals representing three additional goat breeds, including Chengdu grey goats, Tibetan cashmere goats, and Jianchang black goats. The comparative analysis of production performance revealed that the weight and body size of Chuanzhong black goats were significantly higher than those of Baiyu black goats (p < 0.01). At the same time, the average kidding rate and kid-weaning survival rate of Chuanzhong black goats were also notably superior to those of Baiyu black goats (p < 0.01). Moreover, the Baiyu black goat exhibited a more abundant genetic diversity and distinct genetic differences compared to the Chuanzhong black goat, according to an analysis grounded on genomic variation. The Baiyu black goats are more closely related to Tibetan cashmere goats, whereas Chuanzhong black goats share a closer genetic relationship with Chengdu grey goats. Additionally, we employed the π, Fst, and XP-EHH methodologies to identify genes related to immunity (TRIM10, TRIM15, TRIM26, and TRIM5), neurodevelopment (FOXD4L1, PCDHB14, PCDHB4, PCDHB5, PCDHB6, and PCDHB7), reproduction (BTNL2 and GABBR1), body size (NCAPG, IBSP, and MKNK1), and meat quality traits (SUCLG2 and PGM5). These results provide a theoretical basis for further resource conservation and breeding improvement of the Baiyu black goat and Chuanzhong black goat.

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Genetic diversity and selection signatures in Hainan black goats revealed by whole-genome sequencing data

Cited by 4 publications

References 82 publications

Nano-Selenium Reduces Concentrations of Fecal Minerals by Altering Bacteria Composition in Feedlot Goats

Nano-Selenium Reduces Concentrations of Fecal Minerals by Altering Bacteria Composition in Feedlot Goats

Genetic Diversity and Selection Signal Analysis of Hu Sheep Based on SNP50K BeadChip

Comparative Whole-Genome Analysis of Production Traits and Genetic Structure in Baiyu and Chuanzhong Black Goats

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