Abstract
Simple SummaryRuns of homozygosity (ROH) are commonly used to estimate inbreeding coefficients and identify selection signatures in livestock population. The present study determined ROH patterns, estimated the inbreeding levels, and identified the genome regions with high ROH frequency (ROH hotspots) in Chinese Merino. Our results showed that the genome of Chinese Merino harbored lower ROH abundance. Moreover, the inbreeding levels were relatively low. Thirteen ROH hotspots consisting of 190 genes were identified. The ROH hotspots overlapped the selective signatures might be associated with body size, horn traits, immune traits and environment adaption. These findings could contribute to an optimum breeding program by identifying the candidate genes related to economically traits in Chinese Merino.In this study, we estimated the number, length, and frequency of runs of homozygosity (ROH) in 635 Chinese Merino and identified genomic regions with high ROH frequency using the OvineSNP50 whole-genome genotyping array. A total of 6039 ROH exceeding 1 Mb were detected in 634 animals. The average number of ROH in each animal was 9.23 and the average length was 5.87 Mb. Most of the ROH were less than 10 Mb, accounting for 88.77% of the total number of detected ROH. In addition, Ovies aries chromosome (OAR) 21 and OAR3 exhibited the highest and lowest coverage of chromosomes by ROH, respectively. OAR1 displayed the highest number of ROH, while the lowest number of ROH was found on OAR24. An inbreeding coefficient of 0.023 was calculated from ROH greater than 1 Mb. Thirteen regions on chromosomes 1, 2, 3, 5, 6, 10, 11, and 16 were found to contain ROH hotspots. Within the genome regions of OAR6 and OAR11, NCAPG/LCORL, FGF11 and TP53 were identified as the candidate genes related to body size, while the genome region of OAR10 harbored RXFP2 gene responsible for the horn trait. These findings indicate the adaptive to directional trait selection in Chinese Merino.
Highlights
Runs of homozygosity (ROH) are defined as contiguous homozygous genotype segments that arise from the transmission of identical haplotypes from parents to their offspring [1]
A guilt-by-association study has revealed that TP53 is the most plausible functional candidate gene for body size in sheep [43]. These results suggest that the runs of homozygosity (ROH) hotspots detected on OAR6 (35.07–38.67 Mb) and
Our results demonstrated that the genome of Chinese Merino harbored a lower abundance of ROH, and the levels of ROH abundance were consistent with the effective population size
Summary
Runs of homozygosity (ROH) are defined as contiguous homozygous genotype segments that arise from the transmission of identical haplotypes from parents to their offspring [1]. The distribution, frequency, and length of ROH are commonly associated with several factors, such as selective breeding, Animals 2020, 10, 524; doi:10.3390/ani10030524 www.mdpi.com/journal/animals. Animals 2020, 10, 524 natural selection, recombination rate, and demographic history [2]. To avoid inbreeding depression, a highly sensitive and accurate estimation of inbreeding is of great importance [3]. The classical method for calculating the inbreeding coefficient is through the use of pedigree data. The pedigree-based inbreeding coefficient (FPED ) is largely dependent on the accuracy, completeness and depth of pedigree information, and pedigree errors are common in many livestock populations. FPED tends to ignore the history of selective breeding and underestimates the level of inbreeding, possibly due to the pedigree records [4]
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