Genetic Diversity and Selection Signatures of Lvliang Black Goat Using Genome-Wide SNP Data

Abstract

Lvliang black goat (LBG) is an excellent local breed resource in China that is known for its black fur, excellent meat quality, and strong adaptability. Studying the genetic mechanism and germplasm characteristics of LBG can provide theoretical and practical basis for the protection of the genetic resources of this breed and help implement conservation and breeding. In this study, the genetic diversity of the LBG population was evaluated using whole-genome SNP data. It was found that the LBG population had a high genetic diversity and a low degree of inbreeding. According to the clustering results of male goats and the relationship between individuals, the LBG population was divided into 13 families. Then, through population structure analysis, it was found that LBG had a close genetic relationship with the Nanjiang goat and Qinggoda goat populations, and they may have the same ancestors. The LBG population has retained some ancient genetic characteristics and is a special population that integrates local genetic characteristics and foreign gene flow. Through four selection signal analyses, we detected multiple candidate genes related to economic traits (CFL2, SCD, NLRP14, etc.) and adaptability (C4BPA, FUT8, PRNP, etc.) in the LBG population. In addition, in a comparative analysis with three commercial breeds (Saanen goat, Boer goat and Angora goat) we also found multiple genes related to physical characteristics (ERG, NRG3, EDN3, etc.). Finally, we performed functional enrichment analysis on these genes and explored their genetic mechanisms. This study provides important data support for the protection and breeding of LBG and provides a new perspective for enriching the genetic diversity of goat populations.

Keywords: Lvliang black goat; family composition; genetic diversity; population structure; selection signal.

Figure 1

Workflow chart for this study.

Figure 2

Genetic diversity and family composition of LBG population. (A) MAF interval distribution of LBG population; (B) 48 LBGs’ identity by state matrix; (C) 48 LBGs’ genetic relationship matrix; (D) NJ tree and division of families of male goats in LBG population.

Figure 3

Geographical distribution and principal components of 12 goat populations. (A) Geographical regions of the country where the goat populations are located. (B) Principal component analysis of the goat populations. PC1 and PC2 on the left, PC1 and PC3 on the right. The 12 populations are represented by different colors, and the groups are represented by icons of different shapes. The circle represents Chinese (CHN) goats, the triangle represents commercial (COM) goats, and the rectangle represents wild (WILD) goats.

Figure 4

Population structure analysis of LBG and the remaining 11 goat breeds. (A) Ancestor component analysis of 12 goat populations. (B) NJ tree of 396 individuals in 12 goat populations. (C) Determination of the best migration model (m = 4 is the best migration model for 12 goat populations). (D) Migration model of 12 goat populations (m = 4).

Figure 5

Genome-wide candidate region detection in LBG populations. (A) Whole-genome distribution of iHS scores in DS-A. (B) Whole-genome distribution of CLR values in DS-A. (C,D) Whole-genome distribution of F_ST values in DS-B and DS-C. (E,F) Whole-genome distribution of XP-EHH scores in DS-B and DS-C. Ten alternating colors are used to distinguish adjacent chromosomes.

Figure 6

Gene annotation of the selected regions and functional enrichment analysis of the annotated genes. (A) Intersection of 6 candidate gene sets. (B) Functional enrichment results of candidate genes in DS-A. (C) Functional enrichment results of candidate genes in DS-B. (D) Functional enrichment results of candidate genes in DS-C.