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. 2023 Jan 6:13:1044017.
doi: 10.3389/fgene.2022.1044017. eCollection 2022.

Whole-genome resequencing reveals genetic diversity and selection characteristics of dairy goat

Jinke Xiong  1 , Jingjing Bao  1 , Wenping Hu  1 , Mingyu Shang  1 , Li Zhang  1
Affiliations

Whole-genome resequencing reveals genetic diversity and selection characteristics of dairy goat

Jinke Xiong et al. Front Genet. .

Abstract

The dairy goat is one of the earliest dairy livestock species, which plays an important role in the economic development, especially for developing countries. With the development of agricultural civilization, dairy goats have been widely distributed across the world. However, few studies have been conducted on the specific characteristics of dairy goat. In this study, we collected the whole-genome data of 89 goat individuals by sequencing 48 goats and employing 41 publicly available goats, including five dairy goat breeds (Saanen, Nubian, Alpine, Toggenburg, and Guanzhong dairy goat; n = 24, 15, 11, 6, 6), and three goat breeds (Guishan goat, Longlin goat, Yunshang Black goat; n = 6, 15, 6). Through compared the genomes of dairy goat and non-dairy goat to analyze genetic diversity and selection characteristics of dairy goat. The results show that the eight goats could be divided into three subgroups of European, African, and Chinese indigenous goat populations, and we also found that Australian Nubian, Toggenburg, and Australian Alpine had the highest linkage disequilibrium, the lowest level of nucleotide diversity, and a higher inbreeding coefficient, indicating that they were strongly artificially selected. In addition, we identified several candidate genes related to the specificity of dairy goat, particularly genes associated with milk production traits (GHR, DGAT2, ELF5, GLYCAM1, ACSBG2, ACSS2), reproduction traits (TSHR, TSHB, PTGS2, ESR2), immunity traits (JAK1, POU2F2, LRRC66). Our results provide not only insights into the evolutionary history and breed characteristics of dairy goat, but also valuable information for the implementation and improvement of dairy goat cross breeding program.

Keywords: dairy goat; genetic diversity; milk production traits; population structure; selective signal.

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Conflict of interest statement

The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.

Figures

FIGURE 1
FIGURE 1
Sample information and geographic distribution of the 89 goats included in this study. [Guishan goat (GS, n = 6), Yunshang black goat (YSB, n = 6), Toggenburg (TG, n = 6), and Chinese Nubian (CNB, n = 6) were collected from Yunnan Province, Guanzhong dairy goat (GZ, n = 6), Australian Saanen (ASN, n = 6), New Zealand Saanen (NSN, n = 6), Australian Alpine (AAP, n = 2) and New Zealand Alpine (NAP, n = 4) were collected from Shanxi Province. Australian Alpine* (AAP*, n = 5), Longlin goat (LL, n = 15), Australian Nubian (ANB, n = 5), Chinese Nubian* (CNB*, n = 4), Korean Saanen (KSN, n = 10), Australian Saanen* (ASN*, n = 2) were downloaded from NCBI].
FIGURE 2
FIGURE 2
(A) Neighbor-joining (NJ) tree of the 89 individuals based on the matrix of Hamming genetic distance, different colors represent different populations. (B) Plots of the first and the second principal components for the 89 individuals. (C) Plots of the first and the third principal components for the 89 individuals. (D) Ancestry proportions of each sample using k = 2–4.
FIGURE 3
FIGURE 3
(A) Genome-wide average linkage disequilibrium decay in each population. (B) The effective population size of each population in recent 1,000 generations ago.
FIGURE 4
FIGURE 4
(A) Identification of selective signals (F ST Manhattan plot). (B) Identification of selective signals (the θπ ratio Manhattan plot). (C) Distribution of log2 (θπ ratios) and F ST values calculated in 50-kb sliding windows between dairy goat and non-dairy goat. (D) Selective sweep on chromosome 13 (53.2–53.4 Mb) (gray area).
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