Genome-Wide Estimates of Runs of Homozygosity, Heterozygosity, and Genetic Load in Two Chinese Indigenous Goat Breeds

Abstract

Runs of homozygosity (ROH) and heterozygosity (ROHet) are windows into population demographic history and adaptive evolution. Numerous studies have shown that deleterious mutations are enriched in the ROH of humans, pigs, cattle, and chickens. However, the relationship of deleterious variants to ROH and the pattern of ROHet in goats have been largely understudied. Here, 240 Guangfeng and Ganxi goats from Jiangxi Province, China, were genotyped using the Illumina GoatSNP50 BeadChip and genome-wide ROH, ROHet, and genetic load analyses were performed in the context of 32 global goat breeds. The classes with the highest percentage of ROH and ROHet were 0.5–2 Mb and 0.5–1 Mb, respectively. The results of inbreeding coefficients (based on SNP and ROH) and ROHet measurements showed that Guangfeng goats had higher genetic variability than most Chinese goats, while Ganxi goats had a high degree of inbreeding, even exceeding that of commercial goat breeds. Next, the predicted damaging homozygotes were more enriched in long ROHs, especially in Guangfeng goats. Therefore, we suggest that information on damaging alleles should also be incorporated into the design of breeding and conservation programs. A list of genes related to fecundity, growth, and environmental adaptation were identified in the ROH hotspots of two Jiangxi goats. A sense-related ROH hotspot (chromosome 12: 50.55–50.81 Mb) was shared across global goat breeds and may have undergone selection prior to goat domestication. Furthermore, an identical ROHet hotspot (chromosome 1: 132.21–132.54 Mb) containing two genes associated with embryonic development (STAG1 and PCCB) was detected in domestic goat breeds worldwide. Tajima’s D and BetaScan2 statistics indicated that this region may be caused by long-term balancing selection. These findings not only provide guidance for the design of conservation strategies for Jiangxi goat breeds but also enrich our understanding of the adaptive evolution of goats.

Genetic diversity and runs of homozygosity (ROH): A portrait of the quantitative academic publication dynamic and scientific metadata

“…It should also be noted that China, Italy, the United States stand out as key collaborating countries in the development and dissemination of genomic technologies, genetic studies, and bioinformatics related to polymorphisms, ROH, and inbreeding [4,[31][32][33][34]. Brazil in South America and Iran in Asia are recognized as emerging countries in this eld [35,36] (Tables 1 and 2).…”

Genome-wide detections for runs of homozygosity and selective signatures reveal novel candidate genes under domestication in chickens

“…F ROH is affected by the ratio of long homozygous segments to whole-genome length and is less impacted by the quality of experimental materials and DNA samples [ 51 ]. This increases the accuracy of inbreeding coefficient calculation based on ROH in humans [ 7 ], cattle [ 9 ], pigs [ 10 ], sheep and goats [ 11 , 52 ], etc. In this study, the inbreeding coefficients among the 13 populations indicated that F ROH generally presented a lower value than the other indices.…”

“…Furthermore, calculated runs of homozygosity (ROHs; long continuous homozygous stretches composed of two identical haplotypes in each individual) are more useful for elucidating inbreeding and detecting selection signatures in different populations [ 7 , 8 ]. This approach has been reported in cattle [ 9 ], pigs [ 10 ], goats [ 11 ], and chickens [ 12 ]. The inbreeding coefficient based on ROH (F ROH ) is more accurate and more closely represents real inbreeding at the population and individual levels, and a long ROH is more likely to be a result of recent inbreeding than a shorter ROH [ 13 ].…”

Transcriptomic profiling identifies differentially expressed genes and related pathways associated with wound healing and cuproptosis-related genes in Ganxi goats

“…DEGs were divided into up-DEGs and down-DEGs, and the correlation between DEGs and cuproptosis-related genes was analyzed using the website. 4 DE-CUGs were obtained for subsequent analysis.…”

“…Ganxi goats are an excellent local breed mainly raised in the western part of Jiangxi province, with the characteristics of small body size, strong adaptability, and a high reproductive rate. The existing studies mainly focus on transport stress ( 1 ), antioxidant capacity ( 2 ), intestinal immunity ( 3 ) and genome ( 4 ), but there is no study on wound healing in Ganxi goats. Therefore, in this study, transcriptomics was used for the first time to analyze the skin on 0d and 5d of wounds in Ganxi goats, and the physiological function of skin wound healing was discussed from the perspective of mRNA.…”