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The Lubei White (LUB) goat is an indigenous dual-purpose meat and skin breed kept mainly in the Shandong province of China. It is known for its remarkably high fecundity and resistance to disease (Li & Ran, 1997). Recently, the introduction of specialized commercial breeds such as Boer and Saanen goats has sharply decreased the population size of purebred LUB, so there is an urgent need to assess the present population structure and genetic diversity. Genomes of 14 male LUB individuals collected from farms in Wudi county of the Shandong province were sequenced with the Illumina Novaseq 6000 platform. A total of 432.265 G clean data with an average depth of 8.492× were obtained (Table S1). For comparison, a dataset for 169 individuals of 12 breeds was downloaded from the SRA database (Table S2). Single nucleotide polymorphisms were obtained by mapping on the goat reference genome (GCA_001704415.2, ARS1.2) as described by Liu et al. (2022). A total of 20 964 396 autosomal biallelic SNPs were used to analyze the genetic diversity. Nucleotide diversities (pi) were calculated using vcftools (Danecek et al., 2011) with the parameters ‘--window-pi 10000 --window-pi-step 5000’. Observed (HO), and expected (HE) heterozygosities and inbreeding coefficients (FHOM) were calculated with default settings using plink (v1.9, Purcell et al., 2007). The LUB had the highest pi (1.92 × 10−3) and HE (0.219) values and its HO values ranked fourth (Table S3), suggesting a high genetic diversity. A dataset of 2 830 636 SNPs obtained by linkage disequilibrium filtering with the parameter ‘--indep-pairwise 50 25 0.2’ was used for model-based clustering by the admixture software (Alexander et al., 2009) with an assumed number of ancestries K from 2 to 8. The patterns of k = 5 and 6 suggest that the LUB goat combines the ancestries of Boer and Chinese breeds (Figure 1). The principal component analysis (Figure S1; Yang et al., 2011) and neighbor joining tree (Figure S2; Tamura et al., 2021) confirm that most LUB individuals are intermediate between the Boer goat and Jining Grey goat. admixtools (Patterson et al., 2012) was used to perform f4 statistics to test potential gene introgression between Boer, Jining Grey and LUB goats, and the results (Table S4) show that there was gene flow between Boer and LUB. The mixed ancestry also explains the higher genetic diversity of LUB. In summary, the LUB goat has a high genetic diversity and a low level of inbreeding. However, the genomic background has been seriously affected by the introduction of the Boer goat. This work was supported by Agricultural Improved engineering Project of Shandong Province (2021LZGC010-05). The authors declare no conflict of interest. Sequence data have been deposited in GenBank (BioProject accession no. PRJNA940187). Figure S1. Table S1. Table S2. Table S3. Table S4. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.