• Animal Bioscience
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• v.37 no.8
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• pp.1355-1366
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• 2024

Objective: The analysis of runs of homozygosity (ROH) has been applied to assess the level of inbreeding and identify selection signatures in various livestock species. The objectives of this study were to characterize the ROH pattern, estimate the rate of inbreeding, and identify signatures of selection in the red-brown Korean native chickens. Methods: The Illumina 60K single nucleotide polymorphism chip data of 651 chickens was used in the analysis. Runs of homozygosity were analysed using the PLINK v1.9 software. Inbreeding coefficients were estimated using the GCTA software and their correlations were examined. Genomic regions with high levels of ROH were explored to identify selection signatures. Results: A total of 32,176 ROH segments were detected in this study. The majority of the ROH segments were shorter than 4 Mb. The average ROH inbreeding coefficients (F_ROH) varied with the length of ROH segments. The means of inbreeding coefficients calculated from different methods were also variable. The correlations between different inbreeding coefficients were positive and highly variable (r = 0.18-1). Five ROH islands harbouring important quantitative trait loci were identified. Conclusion: This study assessed the level of inbreeding and patterns of homozygosity in Red-brown native Korean chickens. The results of this study suggest that the level of recent inbreeding is low which indicates substantial progress in the conservation of red-brown Korean native chickens. Additionally, Candidate genomic regions associated with important production traits were detected in homozygous regions.

• Animal Bioscience
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• v.37 no.10
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• pp.1683-1691
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• 2024

Objective: Yellow Korean native chicken (KNC-Y) is one of the five pure Korean indigenous chicken breeds that were restored through a government project in 1992. KNC-Y is recognized for its superior egg production performance compared to other KNC lines. In this study, we performed runs of homozygosity (ROH) analysis to discover selection signatures associated with egg production traits in the KNC-Y population. Methods: A total of 675 DNA samples from KNC-Y were genotyped to generate single nucleotide polymorphism (SNP) data using custom 60K Affymetrix SNP chips. ROH analysis was performed using PLINK software, with predefined parameters set for the analysis. The threshold of ROH island was defined as the top 1% frequency of SNPs withing the ROH among the population. Results: In the KNC-Y population, a total of 29,958 runs of homozygosity (ROH) fragments were identified. The average total length of ROH was 120.84 Mb, with each ROH fragment having an average length of 2.71 Mb. The calculated ROH-based inbreeding coefficient (F_ROH) was 0.13. Furthermore, we revealed the presence of ROH islands on chromosomes 1, 2, 4, 5, 7, 8, and 11. Within the identified regions, a total of 111 genes were annotated, and among them were genes related to economic traits, including PRMT3, ANO5, HDAC4, LSS, PLA2G4A, and PTGS2. Most of the overlapping quantitative trait locus regions with ROH islands were found to be associated with production traits. Conclusion: This study conducted a comprehensive analysis of ROH in the KNC-Y population. Notably, among the findings, the PTGS2 gene is believed to play a crucial role in influencing the laying performance of KNC-Y.

• Animal Bioscience
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• v.34 no.12
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• pp.1895-1902
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• 2021

Objective: Runs of homozygosity (ROH) are contiguous lengths of homozygous genotypes that can reveal inbreeding levels, selection pressure, and mating schemes. In this study, ROHs were evaluated in Wannan Black pigs to assess the inbreeding levels and the genome regions with high ROH frequency. Methods: In a previous study, we obtained 501.52 GB of raw data from resequencing (10×) of the genome and identified 21,316,754 single-nucleotide variants in 20 Wannan Black pig samples. We investigated the number, length, and frequency of ROH using resequencing data to characterize the homozygosity in Wannan Black pigs and identified genomic regions with high ROH frequencies. Results: In this work, 1,813 ROHs (837 ROHs in 100 to 500 kb, 449 ROHs in 500 to 1,000 kb, 527 ROHs in >1,000 kb) were identified in all samples, and the average genomic inbreeding coefficient (F_ROH) in Wannan Black pigs was 0.5234. Sixty-one regions on chromosomes 2, 3, 7, 8, 13, 15, and 16 harbored ROH islands. In total, 105 genes were identified in 42 ROH islands, among which some genes were related to production traits. Conclusion: This is the first study to identify ROH across the genome of Wannan Black pigs, the Chinese native breed of the Anhui province. Overall, Wannan Black pigs have high levels of inbreeding due to the influence of ancient and recent inbreeding due to the genome. These findings are a reliable resource for future studies and contribute to save and use the germplasm resources of Wannan Black pigs.

• Animal Bioscience
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• v.36 no.10
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• pp.1508-1516
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• 2023

Objective: To carry out a comprehensive production planning of the existing Rongchang pig population from both environmental and genetic aspects, and to establish a closed population with stable genetic diversity and strict pathogen control, it is necessary to fully understand the genetic background of the population. Methods: We genotyped 54 specific pathogen free (SPF) Rongchang pigs using the Zhongxin-1 Porcine Breeding Array PLUS, calculated their genetic diversity parameters and constructed their families. In addition, we also counted the runs of homozygosity (ROH) of each individual and calculated the value of inbreeding coefficient based on ROH for each individual. Results: Firstly, the results of genetic diversity analysis showed that the effective population size (N_e) of this population was 3.2, proportion of polymorphic markers (P_N) was 0.515, desired heterozygosity (H_e) and observed heterozygosity (H_o) were 0.315 and 0.335. H_o was higher than H_e, indicating that the heterozygosity of all the selected loci was high. Secondly, combining the results of genomic relatedness analysis and cluster analysis, it was found that the existing Rongchang pig population could be divided into four families. Finally, we also counted the ROH of each individual and calculated the inbreeding coefficient value accordingly, whose mean value was 0.09. Conclusion: Due to the limitation of population size and other factors, the genetic diversity of this Rongchang pig population is low. The results of this study can provide basic data to support the development of Rongchang pig breeding program, the establishment of SPF Rongchang pig closed herd and its experimental utilization.

• Animal Bioscience
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• v.35 no.12
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• pp.1839-1849
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• 2022

Objective: The study aims to uncover the genetic diversity and unique genetic structure of the Min pig conserved population, divide the nucleus conservation population, and construct the molecular pedigree. Methods: We used KPS Porcine Breeding Chip v1 50K for SNP detection of 94 samples (31♂, 63♀) in the Min pig conserved population from Lanxi breeding Farm. Results: The polymorphic marker ratio (PN), the observed heterozygosity (Ho), and the expected heterozygosity (He) were 0.663, 0.335, and 0.330, respectively. The pedigree-based inbreeding coefficients (F_PED) was significantly different from those estimated from runs of homozygosity (F_ROH) and single nucleotide polymorphism (F_SNP) based on genome. The Pearson correlation coefficient between F_ROH and F_SNP was significant (p<0.05). The effective population content (Ne) showed a continuously decreasing trend. The rate of decline was the slowest from 200 to 50 generations ago (r = 0.95), then accelerated slightly from 50 to 5 generations ago (1.40

• Journal of Animal Science and Technology
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• v.62 no.6
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• pp.777-789
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• 2020

Intense artificial selection has been imposed to Luzhong mutton sheep population in the past years. Improvements on growth and reproductive performance are two breeding goals in the present herd. Although some progresses were phenotypically observed possibly due to inbreeding induced by strong selection in terms of these traits, the genomic evaluation was poorly understood. Therefore, a high-density SNP array was used to characterize the pattern of runs of homozygosity (ROH), estimate inbreeding and inbreeding depressions on early growth performance and litter size based upon ROH, and scan positive selection signatures of recent population. Consequently, a low inbreeding level was observed which had negative effects on litter size, but not on early growth performance. And 160 genes were under selection, of which some were reported to be linked to several traits of sheep including body weight, litter size, carcass and meat quality, milk yield and composition, fiber quality and health, and the top genes were associated with growth (growth hormone [GH]- growth hormone receptor [GHR]- Insulin-like growth factor 1 [IGF1] axis) and litter size (bone morphogenic proteins [BMPs]-associated). The effectiveness of previous breeding measures was highlighted, but purging selection was proposed to alleviate the inbreeding depression on litter size, providing some genomic insights to breeding management of Luzhong mutton sheep.

• Animal Bioscience
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• v.34 no.7
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• pp.1105-1115
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• 2021

Objective: To conserve and utilize the genetic resources of a traditional Chinese indigenous pig breed, Liangshan pig, we assessed the genetic diversity, genetic structure, and genetic distance in this study. Methods: We used 50K single nucleotide polymorphism (SNP) chip for SNP detection of 139 individuals in the Liangshan Pig Conservation Farm. Results: The genetically closed conserved population consisted of five overlapping generations, and the total effective content of the population (Ne) was 15. The whole population was divided into five boar families and one non-boar family. Among them, the effective size of each generation subpopulation continuously decreased. However, the proportion of polymorphic markers (P_N) first decreased and then increased. The average genetic distance of these 139 Liangshan pigs was 0.2823±0.0259, and the average genetic distance of the 14 boars was 0.2723±0.0384. Thus, it can be deduced that the genetic distance changed from generation to generation. In the conserved population, 983 runs of homozygosity (ROH) were detected, and the majority of ROH (80%) were within 100 Mb. The inbreeding coefficient calculated based on ROH showed an average value of 0.026 for the whole population. In addition, the inbreeding coefficient of each generation subpopulation initially increased and then decreased. In the pedigree of the whole conserved population, the error rate of paternal information was more than 11.35% while the maternal information was more than 2.13%. Conclusion: This molecular study of the population genetic structure of Liangshan pig showed loss of genetic diversity during the closed cross-generation reproduction process. It is necessary to improve the mating plan or introduce new outside blood to ensure long-term preservation of Liangshan pig.

• Asian-Australasian Journal of Animal Sciences
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• v.31 no.11
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• pp.1691-1699
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• 2018

Objective: In Korea, there are three main cattle breeds, which are distinguished by coat color: Brown Hanwoo (BH), Brindle Hanwoo (BRH), and Jeju Black (JB). In this study, we sought to compare the genetic diversity and divergence among there Korean cattle breeds using a BovineHD chip genotyping array. Methods: Sample data were collected from 168 cattle in three populations of BH (48 cattle), BRH (96 cattle), and JB (24 cattle). The single-nucleotide polymorphism (SNP) genotyping was performed using the Illumina BovineHD SNP 777K Bead chip. Results: Heterozygosity, used as a measure of within-breed genetic diversity, was higher in BH (0.293) and BRH (0.296) than in JB (0.266). Linkage disequilibrium decay was more rapid in BH and BRH than in JB, reaching an average $r^2$ value of 0.2 before 26 kb in BH and BRH, whereas the corresponding value was reached before 32 kb in JB. Intra-population, interpopulation, and Fst analyses were used to identify candidate signatures of positive selection in the genome of a domestic Korean cattle population and 48, 11, and 11 loci were detected in the genomic region of the BRH breed, respectively. A Neighbor-Joining phylogenetic tree showed two main groups: a group comprising BH and BRH on one side and a group containing JB on the other. The runs of homozygosity analysis between Korean breeds indicated that the BRH and JB breeds have high inbreeding within breeds compared with BH. An analysis of differentiation based on a high-density SNP chip showed differences between Korean cattle breeds and the closeness of breeds corresponding to the geographic regions where they are evolving. Conclusion: Our results indicate that although the Korean cattle breeds have common features, they also show reliable breed diversity.