Genome-Wide Assessment of Runs of Homozygosity in Chinese Wagyu Beef Cattle

Zhao, Guangshan; Zhang, Tianliu; Liu, Yuqiang; Wang, Zezhao; Liu, Xu; Zhu, Bo; Gao, Xue; Zhang, Lupei; Gao, Huijiang; Liu, George E.; Li, Junya; Xu, Lingyang

doi:10.3390/ani10081425

Cited by 23 publications

(18 citation statements)

References 72 publications

(99 reference statements)

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“…Scanning the auto-zygosity may present inbred as well as non-bred populations due to several population phenomena, e.g. inbreeding, consanguineous matings, population bottleneck, genetic drift and natural and human-mediated selection [ 7 , 8 ]. Revealing the homozygosity of cattle genome, using high-density SNPs, has been an effective way to identify non-auto-zygosity identical by state (IBS) segments from auto-zygotic (IBD) [ 9 ].…”

Section: Introductionmentioning

confidence: 99%

Genome-Wide Analysis Revealed Homozygosity and Demographic History of Five Chinese Sheep Breeds Adapted to Different Environments

Abied

Liu

Sahlu

et al. 2020

Genes

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Homozygosity of long sequence genotypes are a result of parents transmitting identical haplotypes, which can be used to estimate their auto-zygosity. Therefore, we used high-density SNP Chip data to characterize the auto-zygosity of each breed according to the occurrence and distribution of runs of homozygosity (ROH). Subsequently, we identified the genomic regions with high runs of homozygosity frequencies within individuals of each breed. We selected 96 sheep samples from five local Chinese sheep breeds belonging to different geographical locations. We identified 3046 ROHs within the study breed individuals, among which the longer segments (>1–5 Mb) were dominant. On average, ROH segments covered about 12% of the genomes; the coverage rate of OAR20 was the lowest and that of OAR2 was the highest. The distribution analysis of runs of homozygosity showed that the detected ROH mainly distributed between >26 and 28 Mb. The Hetian and Hu sheep showed the lowest ROH distribution. The estimation of homozygosity level reflects the history of modern and ancient inbreeding, which may affect the genomes of Chinese indigenous sheep breeds and indicate that some animals have experienced recent self-pollination events (Yabuyi, Karakul and Wadi). In these sheep breeds, the genomic regions were assumed to be under selection signatures frequently in line with long ROH. These regions included candidate genes associated with disease resistance traits (5S_rRNA), the innate and adaptive immune response (HERC2 and CYFIP1), digestion and metabolism (CENPJ), growth (SPP1), body size and developments (GJB2 and GJA3). This study highlighted new insights into the ROH patterns and provides a basis for future breeding and conservation strategies of Chinese sheep breeds.

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Section: Introductionmentioning

confidence: 99%

Genome-Wide Analysis Revealed Homozygosity and Demographic History of Five Chinese Sheep Breeds Adapted to Different Environments

Abied

Liu

Sahlu

et al. 2020

Genes

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“…Thyroglobulin (TG) gene is located on the quantitative trait loci affecting IMF content and encodes key factors in the metabolic pathway 19 . Another research for body height, two significant Runs of homozygosity(ROHs) were found at BTA23 and BTA7, but fat coverage at BTA28 20 . The possible reason is that the population combinations are completely different and different genetic background generate different regulatory mechanism.…”

Section: Discussionmentioning

confidence: 93%

Investigation of genetic markers for intramuscular fat in the hybrid Wagyu cattle with bulked segregant analysis

Zhu

Han

Kang

et al. 2021

Sci Rep

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Abstractulked Segregant Analysis (BSA) is a rapid strategy for identifying genetic markers in specific regions of the phenotypical population and it has been widely used for QTLs mapping in smaller mixed F2 and F3 populations. We applied a modified BSA method to assessed genome-wide homozygous and heterozygous linkage patterns in the Chinese Wagyu Beef Cattle F2/F3 mixed population. Two overlapped regions from F2 and F3 populations on autosomes were found with high-density heterozygote alleles between high and low intramuscular fat groups. Regions from 24.8 M ~ 29.6 M of chromosome 23 were identified as most significantly correlated to the intramuscular fat in our samples. We also identified other 4 potential loci on chromosomes 5, 9, 15, and 21 correlated with Intramuscular fat. This study provided a novel low-cost method for QTLs mapping and identify molecular markers of phenotypical changes in a small mixed population.

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“…ROH were identified for each animal using PLINK v1.07 software [ 26 ]. The following criteria were chosen for ROH estimation [ 27 – 29 ]: i) the minimum length of the filter input regions was set to 1 Mb; ii) one heterozygous and five missing calls were allowed per window to account for genotyping error; iii) the minimum number of SNPs was set to 100; and iv) the minimum quality of bases in the filter input regions was set to 10.…”

Section: Methodsmentioning

confidence: 99%

Genome-wide scan for runs of homozygosity identifies candidate genes in Wannan Black pigs

et al. 2021

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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 g of raw data from resequencing (10×) of the genome and identified 21,316,754 single-nucleotide variants (SNVs) 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 100-500 kb, 449 ROHs in 500-1,000 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 on the genome. These findings are a reliable resource for future studies A c c e p t e d A r t i c l e 4 and contribute to save and use the germplasm resources of Wannan Black pigs.

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Genome-Wide Assessment of Runs of Homozygosity in Chinese Wagyu Beef Cattle

Cited by 23 publications

References 72 publications

Genome-Wide Analysis Revealed Homozygosity and Demographic History of Five Chinese Sheep Breeds Adapted to Different Environments

Genome-Wide Analysis Revealed Homozygosity and Demographic History of Five Chinese Sheep Breeds Adapted to Different Environments

Investigation of genetic markers for intramuscular fat in the hybrid Wagyu cattle with bulked segregant analysis

Genome-wide scan for runs of homozygosity identifies candidate genes in Wannan Black pigs

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