Genomic Inbreeding and Runs of Homozygosity Analysis of Cashmere Goat

Abstract

Cashmere goats are valuable genetic resources which are famous worldwide for their high-quality fiber. Runs of homozygosity (ROHs) have been identified as an efficient tool to assess inbreeding level and identify related genes under selection. However, there is limited research on ROHs in cashmere goats. Therefore, we investigated the ROH pattern, assessed genomic inbreeding levels and examined the candidate genes associated with the cashmere trait using whole-genome resequencing data from 123 goats. Herein, the Inner Mongolia cashmere goat presented the lowest inbreeding coefficient of 0.0263. In total, we identified 57,224 ROHs. Seventy-four ROH islands containing 50 genes were detected. Certain identified genes were related to meat, fiber and milk production (FGF1, PTPRM, RERE, GRID2, RARA); fertility (BIRC6, ECE2, CDH23, PAK1); disease or cold resistance and adaptability (PDCD1LG2, SVIL, PRDM16, RFX4, SH3BP2); and body size and growth (TMEM63C, SYN3, SDC1, STRBP, SMG6). 135 consensus ROHs were identified, and we found candidate genes (FGF5, DVL3, NRAS, KIT) were associated with fiber length or color. These findings enhance our comprehension of inbreeding levels in cashmere goats and the genetic foundations of traits influenced by selective breeding. This research contributes significantly to the future breeding, reservation and use of cashmere goats and other goat breeds.

Keywords: cashmere goat; genetic diversity; inbreeding coefficient; runs of homozygosity; selection signatures.

Figure 1

Population genetics structures analyses and linkage disequilibrium. (A) Principle component analysis (PCA); each point represents a single individual. The colors in B and D represent the same groups as indication in the legend of A. (B) Phylogenetic tree constructed by the neighbor-joining (NJ) method. (C) Population structure plot of seven goat populations at K = 2–5, (D) LD decay map measured by r² over distance between SNPs in seven populations.

Figure 2

The distribution of ROHs identified in different populations across autosomes. (A) This graph is a bar chart showing the number of ROHs on different chromosomes. ROHs are divided into three length classes: small (0–0.3 Mb), medium (0.3–1.5 Mb) and large (>1.5 Mb). (B) Relationship between the number of runs of homozygosity (ROH) per individual and the total length of the genome covered by them. The x-axis shows the sum total length of ROHs (Mb), and the y-axis shows the total number of ROHs. Every circle represents a different individual within a population, with the groups labeled as ALG, HSC, IMC and so on. (C) Violin plots and boxplots of sum total length of ROHs (SROHs). The form of each violin reflects the distribution density of cohort, with wider sections of the violin plot indicating higher frequency of observation at that y -value. Inside each violin, there is a boxplot that shows the median, the interquartile range (the length of the box) and the outliers (the points outside the whiskers). (D) The descriptive statistics for the ROHs, categorized by ROH length class across different populations, are presented as mean counts of ROHs (Y-axis) by class of ROH length.

Figure 3

Manhattan plot of SNPs in ROHs for HSC (A) and BOE (B). The x-axis exhibits positions along each chromosome.

Figure 4

(A) A Gene Ontology (GO) functional enrichment analysis. (B) KEGG enrichment pathways of gene annotation in the consensus ROHs of IMC and HSC breeds.