Genome-Wide Runs of Homozygosity, Effective Population Size, and Detection of Positive Selection Signatures in Six Chinese Goat Breeds

Islam, Rabiul; Li, Yefang; Liu, Xuexue; Berihulay, Haile; Abied, Adam; Gebreselassie, Gebremedhin; Ma, Qing; Ma, Yue

doi:10.3390/genes10110938

Cited by 50 publications

(56 citation statements)

References 55 publications

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“…Long runs of homozygosity have been observed to be persistent in inbred individuals, suggestive of unusually low mutation rates, high linkage disequilibrium (LD), and low recombination rates at certain genomic regions [ 9 ]. ROH accumulation in certain genomic positions has been used to analyze the demographic history in humans [ 10 , 11 ] and livestock populations [ 12 , 13 ]. A study also used ROH to compare and characterize beef and dairy cattle breeds [ 14 ].…”

Section: Introductionmentioning

confidence: 99%

Runs of homozygosity analysis of South African sheep breeds from various production systems investigated using OvineSNP50k data

et al. 2021

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Background Population history, production system and within-breed selection pressure impacts the genome architecture resulting in reduced genetic diversity and increased frequency of runs of homozygosity islands. This study tested the hypothesis that production systems geared towards specific traits of importance or natural or artificial selection pressures influenced the occurrence and distribution of runs of homozygosity (ROH) in the South African sheep population. The Illumina OvineSNP50 BeadChip was used to genotype 400 sheep belonging to 13 breeds from South Africa representing mutton, pelt and mutton and wool dual-purpose breeds, including indigenous non-descript breeds that are reared by smallholder farmers. To get more insight into the autozygosity and distribution of ROH islands of South African breeds relative to global populations, 623 genotypes of sheep from worldwide populations were included in the analysis. Runs of homozygosity were computed at cut-offs of 1–6 Mb, 6–12 Mb, 12–24 Mb, 24–48 Mb and > 48 Mb, using the R package detectRUNS. The Golden Helix SVS program was used to investigate the ROH islands. Results A total of 121,399 ROH with mean number of ROH per animal per breed ranging from 800 (African White Dorper) to 15,097 (Australian Poll Dorset) were obtained. Analysis of the distribution of ROH according to their size showed that, for all breeds, the majority of the detected ROH were in the short (1–6 Mb) category (88.2%). Most animals had no ROH > 48 Mb. Of the South African breeds, the Nguni and the Blackhead Persian displayed high ROH based inbreeding (FROH) of 0.31 ± 0.05 and 0.31 ± 0.04, respectively. Highest incidence of common runs per SNP across breeds was observed on chromosome 10 with over 250 incidences of common ROHs. Mean proportion of SNPs per breed per ROH island ranged from 0.02 ± 0.15 (island ROH224 on chromosome 23) to 0.13 ± 0.29 (island ROH175 on chromosome 15). Seventeen (17) of the islands had SNPs observed in single populations (unique ROH islands). The MacArthur Merino (MCM) population had five unique ROH islands followed by Blackhead Persian and Nguni with three each whilst the South African Mutton Merino, SA Merino, White Vital Swakara, Karakul, Dorset Horn and Chinese Merino each had one unique ROH island. Genes within ROH islands were associated with predominantly metabolic and immune response traits and predomestic selection for traits such as presence or absence of horns. Conclusions Overall, the frequency and patterns of distribution of ROH observed in this study corresponds to the breed history and implied selection pressures exposed to the sheep populations under study.

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Section: Introductionmentioning

confidence: 99%

Runs of homozygosity analysis of South African sheep breeds from various production systems investigated using OvineSNP50k data

et al. 2021

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“…Long segments were abundant in the North West population. [25] recent study revealed a high mean ROH in the long length category (>30 Mb), and their study suggested that inbreeding is more recent and is indicative of demographic decline. This is possible considering the extensive management systems of goats in the region, where goats are on free-range or are herded with other ocks for some part of the year, although some researchers have argued that such extensive systems may lead to inbreeding [58,22].…”

Section: Discussionmentioning

confidence: 97%

Conservation Status and Historical Relatedness of South African Communal Indigenous Goat Populations Using Genome-Wide Snp Marker

Chokoe¹,

Hadebe

Muchadeyi

et al. 2020

Preprint

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Background: Indigenous goats forms the majority of populations in smallholder; low input, low output production systems and are considered an important genetic resource due to their adaptability to different production environments and support communal farming. Effective population size (Ne), inbreeding levels, and the runs of homozygosity (ROHs) are effective tools for exploring the genetic diversity and understanding the demographic history in efforts to support breeding strategies to use and conserve genetic resources. Results: Across populations, the current Ne of Gauteng was the lowest at 371 animals, while the historical Ne across populations suggests that the ancestor Ne has decreased by 53.86%, 44.58%, 42.16% and 41.16% in Free State (FS), North West (NW), Limpopo (LP) and Gauteng (GP), respectively, over the last 971 generations. Genomic inbreeding levels related to ancient kinship (FROH >5Mb) was highest in FS (0.08±0.09) and lowest for Eastern Cape (EC) (0.02±0.02). A total of 871 ROH island regions which include important environmental adaptation and hermo-tolerance genes such as IL10RB, IL23A, FGF9, IGF1, EGR1, MTOR and MAPK3 were identified (occurring in over 20% of the samples) in FS (n = 37), GP (n = 42), NW (n = 2) populations only. The mean length of ROH across populations was 7.76Mb and ranged from 1.61Mb KwaZulu-Natal (KZN) to 98.05Mb (GP and NW). Distribution of ROH according to their size showed that the majority (n = 1949) of the detected ROH were >5Mb in length than the other categories. Assuming two hypothetical ancestral populations, the population from KZN and LP are revealed, supporting PC 1. The genomes of KZN and LP shared an origin but have substantial admixture from the EC and NW populations.Conclusions: These findings indicated a greater negative impact of inbreeding in recent times which is important for planning conservation strategies. It was revealed that the occurrence of high Ne and autozygosity varied largely across breeds in communal indigenous goat populations at different recent and ancient events when a genome-wide SNP marker was used.

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“…The inbreeding coefficient based on ROH (F ROH ) was estimated as the proportion of genome in ROH over the overall length of the genome covered by the involved SNPs using detectRUNS packages in R software [ 19 ]. The following parameters were set to define the ROHs: (i) a minimum length of ROH was set to 1 Mb, (ii) the maximum distance between two consecutive SNPs was allowed to 1 Mb, (iii) one possible heterozygote and one missing genotype were allowed for each ROH, and (iv) to minimize the number of ROH that could occur by chance, the minimum number of SNPs that constituted an ROH was calculated by the formula proposed by Lencz, Lambert [ 20 ]:

where α is the false positive ROH in percentage (set to 0.05 in this study), n s is the number of SNPs per individual, n i is the number of individuals tested, and het is the proportion of heterozygosity across all SNPs.…”

Section: Methodsmentioning

confidence: 99%

“…The JGM goats presented the highest values and ACM displayed the lowest value for both H O (JGM = 0.401 ± 0.20, ACM = 0.367 ± 0. 19) and H E (JGM = 0.391 ± 0.20, ACM = 0.384 ± 0.20). The ACM exhibited the highest average values for both inbreeding coefficient estimators (F ROH = 0.086, F HOM = 0.074) whereas the ZWM showed the lowest F ROH (0.017).…”

Section: Genetic Diversity Within Breedsmentioning

confidence: 98%

Conservation Assessment of the State Goat Farms by Using SNP Genotyping Data

Islam

Liu²,

et al. 2020

Genes

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Conservation of genetic resources is of great concern globally to maintain genetic diversity for sustainable food security. Comprehensive identification of the breed composition, estimation of inbreeding and effective population size are essential for the effective management of farm animal genetic resources and to prevent the animals from genetic erosion. The Zhongwei male (ZWM), Arbas Cashmere male (ACM) and Jining Grey male (JGM) goats are conserved in three different state goat farms in China but their family information, level of inbreeding and effective population size are unknown. We investigated the genomic relationship, inbreeding coefficient and effective population size in these three breeds from three state goat farms using the Illumina goat SNP50 BeadChip. Genomic relationships and phylogenetic analysis revealed that the breeds are clearly separated and formed separate clusters based on their genetic relationship. We obtained a high proportion of informative SNPs, ranging from 91.8% in the Arbas Cashmere male to 96.2% in the Jining Grey male goat breeds with an average mean of 96.8%. Inbreeding, as measured by FROH, ranged from 1.79% in ZWM to 8.62% in ACM goat populations. High FROH values, elevated genomic coverage of very long ROH (>30 Mb) and severe decline in effective population size were recorded in ACM goat farm. The existence of a high correlation between FHOM and FROH indicates that FROH can be used as an alternative to inbreeding estimates in the absence of pedigree records. The Ne estimates 13 generations ago were 166, 69 and 79 for ZWM, ACM and JGM goat farm, respectively indicating that these goat breeds were strongly affected by selection pressure or genetic drift. This study provides insight into the genomic relationship, levels of inbreeding and effective population size in the studied goat populations conserved in the state goat farms which will be valuable in prioritizing populations for conservation and for developing suitable management practices for further genetic improvement of these Chinese male goats.

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Genome-Wide Runs of Homozygosity, Effective Population Size, and Detection of Positive Selection Signatures in Six Chinese Goat Breeds

Cited by 50 publications

References 55 publications

Runs of homozygosity analysis of South African sheep breeds from various production systems investigated using OvineSNP50k data

Runs of homozygosity analysis of South African sheep breeds from various production systems investigated using OvineSNP50k data

Conservation Status and Historical Relatedness of South African Communal Indigenous Goat Populations Using Genome-Wide Snp Marker

Conservation Assessment of the State Goat Farms by Using SNP Genotyping Data

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