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

: Detection of selection footprints provides insight into the evolution process and the underlying mechanisms controlling the phenotypic diversity of traits that have been exposed to selection. Selection focused on certain characters, mapping certain genomic regions often shows a loss of genetic diversity with an increased level of homozygosity. Therefore, the runs of homozygosity (ROHs), homozygosity by descent (HBD), and effective population size (Ne) are effective tools for exploring the genetic diversity, understanding the demographic history, foretelling the signature of directional selection, and improving the breeding strategies to use and conserve genetic resources. We characterized the ROH, HBD, Ne, and signature of selection of six Chinese goat populations using single nucleotide polymorphism (SNP) 50K Illumina beadchips. Our results show an inverse relationship between the length and frequency of ROH. A long ROH length, higher level of inbreeding, long HBD segment, and smaller Ne in Guangfeng (GF) goats suggested intensive selection pressure and recent inbreeding in this breed. We identified six reproduction-related genes within the genomic regions with a high ROH frequency, of which two genes overlapped with a putative selection signature. The estimated pair-wise genetic differentiation (FST) among the populations is 9.60% and the inter- and intra-population molecular variations are 9.68% and 89.6%, respectively, indicating low to moderate genetic differentiation. Our selection signatures analysis revealed 54 loci harboring 86 putative candidate genes, with a strong signature of selection. Further analysis showed that several candidate genes, including MARF1, SYCP2, TMEM200C, SF1, ADCY1, and BMP5, are involved in goat fecundity. We identified 11 candidate genes by using cross-population extended haplotype homozygosity (XP-EHH) estimates, of which MARF1 and SF1 are under strong positive selection, as they are differentiated in high and low reproduction groups according to the three approaches used. Gene ontology enrichment analysis revealed that different biological pathways could be involved in the variation of fecundity in female goats. This study provides a new insight into the ROHs patterns for maintenance of within breed diversity and suggests a role of positive selection for genetic variation influencing fecundity in Chinese goat.

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Genomic Uniqueness of Local Sheep Breeds From Morocco

Frontiers in Genetics ◽

10.3389/fgene.2021.723599 ◽

2021 ◽

Vol 12 ◽

Author(s):

Abdessamad Ouhrouch ◽

Simon Boitard ◽

Frédéric Boyer ◽

Bertrand Servin ◽

Anne Da Silva ◽

...

Keyword(s):

Genetic Diversity ◽

Demographic History ◽

Large Set ◽

Whole Genome ◽

Selection Signatures ◽

Effective Population ◽

High Genetic Diversity ◽

Sheep Breeds ◽

Genome Data ◽

Genomic Regions

Sheep farming is a major source of meat in Morocco and plays a key role in the country’s agriculture. This study aims at characterizing the whole-genome diversity and demographic history of the main Moroccan sheep breeds, as well as to identify selection signatures within and between breeds. Whole genome data from 87 individuals representing the five predominant local breeds were used to estimate their level of neutral genetic diversity and to infer the variation of their effective population size over time. In addition, we used two methods to detect selection signatures: either for detecting selective sweeps within each breed separately or by detecting differentially selected regions by contrasting different breeds. We identified hundreds of genomic regions putatively under selection, which related to several biological terms involved in local adaptation or the expression of zootechnical performances such as Growth, UV protection, Cell maturation or Feeding behavior. The results of this study revealed selection signatures in genes that have an important role in traits of interest and increased our understanding of how genetic diversity is distributed in these local breeds. Thus, Moroccan local sheep breeds exhibit both a high genetic diversity and a large set of adaptive variations, and therefore, represent a valuable genetic resource for the conservation of sheep in the context of climate change.

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Genomics Confirm an Alarming Status of the Genetic Diversity of Belgian Red and Belgian White Red Cattle

Animals ◽

10.3390/ani11123574 ◽

2021 ◽

Vol 11 (12) ◽

pp. 3574

Author(s):

Roel Meyermans ◽

Wim Gorssen ◽

Nadine Buys ◽

Steven Janssens

Keyword(s):

Genetic Diversity ◽

Population Size ◽

Effective Population Size ◽

Size Estimation ◽

Runs Of Homozygosity ◽

Effective Population ◽

Genetic Management ◽

Cattle Breeds ◽

Signature Of Selection ◽

Genomic Inbreeding

Genetic diversity is increasingly important for researchers and society. Small and local populations deserve more attention especially, as they may harbor important characteristics. Moreover, small populations are at greater risk and their genetic management is often more challenging. Likewise, European red cattle populations are threatened, as they are outcompeted by more specialized cattle breeds. In this study, we investigate the genetic diversity of two local Belgian red cattle breeds: Belgian Red and Belgian White Red cattle. A total of 270 animals were genotyped via medium density SNP arrays. Genetic diversity was assessed using runs of homozygosity screening, effective population size estimation and Fst analyses. Genomic inbreeding coefficients based on runs of homozygosity were estimated at 7.0% for Belgian Red and 6.1% for Belgian White Red cattle, and both populations had a low effective population size (68 and 86, respectively). PCA, Fst and admixture analyses revealed the relationship to 52 other international breeds, where they were closest related to some Belgian, French, Scandinavian and Dutch breeds. Moreover, Fst analyses revealed for Belgian Red cattle a signature of selection on BTA6, adjacent to the KIT gene. This study gains important knowledge on the genetic diversity of these two small local red cattle breeds, and will aid in their (genetic) management.

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Genetic Diversity and Natural Selection of Plasmodium vivax Duffy Binding Protein-II From China-Myanmar Border of Yunnan Province, China

Frontiers in Microbiology ◽

10.3389/fmicb.2021.758061 ◽

2021 ◽

Vol 12 ◽

Author(s):

Tian-Qi Shi ◽

Hai-Mo Shen ◽

Shen-Bo Chen ◽

Kokouvi Kassegne ◽

Yan-Bing Cui ◽

...

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Natural Selection ◽

Genetic Differentiation ◽

Positive Selection ◽

Plasmodium Vivax ◽

Yunnan Province ◽

Duffy Binding Protein ◽

Synonymous Mutations ◽

Selection Of

Malaria incidence has declined dramatically over the past decade and China was certified malaria-free in 2021. However, the presence of malaria in border areas and the importation of cases of malaria parasites are major challenges for the consolidation of the achievements made by China. Plasmodium vivax Duffy binding protein (PvDBP) performs a significant role in erythrocyte invasion, and is considered a promising P. vivax vaccine. However, the highly polymorphic region of PvDBP (PvDBP-II) impedes the development of blood-stage vaccine against P. vivax. In this study, we investigated the genetic diversity and natural selection of PvDBP-II among 124 P. vivax isolates collected from the China-Myanmar border (CMB) in Yunnan Province, China, during 2009–2011. To compare genetic diversity, natural selection, and population structure with CMB isolates, 85 pvdbp-II sequences of eastern Myanmar isolates were obtained from GenBank. In addition, global sequences of pvdbp-II were retrieved from GenBank to establish genetic differentiation relationships and networks with the CMB isolates. In total, 22 single nucleotide polymorphisms reflected in 20 non-synonymous and two synonymous mutations were identified. The overall nucleotide diversity of PvDBP-II from the 124 CMB isolates was 0.0059 with 21 haplotypes identified (Hd = 0.91). The high ratio of non-synonymous to synonymous mutations suggests that PvDBP-II had evolved under positive selection. Population structure analysis of the CMB and eastern Myanmar isolates were optimally grouped into five sub-populations (K = 5). Polymorphisms of PvDBP-II display that CMB isolates were genetically diverse. Mutation, recombination, and positive selection promote polymorphism of PvDBP-II of P. vivax population. Although low-level genetic differentiation in eastern Myanmar was identified along with the more effective malaria control measures, the complexity of population structure in malaria parasites has maintained. In conclusion, findings from this study advance knowledge of the understanding of the dynamic of P. vivax population, which will contribute to guiding the rational design of a PvDBP-II based vaccine.

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Sardinians Genetic Background Explained by Runs of Homozygosity and Genomic Regions under Positive Selection

PLoS ONE ◽

10.1371/journal.pone.0091237 ◽

2014 ◽

Vol 9 (3) ◽

pp. e91237 ◽

Cited By ~ 27

Author(s):

Cornelia Di Gaetano ◽

Giovanni Fiorito ◽

Maria Francesca Ortu ◽

Fabio Rosa ◽

Simonetta Guarrera ◽

...

Keyword(s):

Positive Selection ◽

Genetic Background ◽

Runs Of Homozygosity ◽

Genomic Regions

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Runs of homozygosity for autozygosity estimation and genomic analysis in production animals

Pesquisa Agropecuária Brasileira ◽

10.1590/s0100-204x2018000900001 ◽

2018 ◽

Vol 53 (9) ◽

pp. 975-984 ◽

Cited By ~ 1

Author(s):

Arnaldo Basso Rebelato ◽

Alexandre Rodrigues Caetano

Keyword(s):

Evolutionary History ◽

Genomic Analysis ◽

Runs Of Homozygosity ◽

Demographic Information ◽

Genomic Information ◽

Selection Signatures ◽

Effective Population ◽

High Frequencies ◽

Production Animals ◽

Genealogical Information

Abstract: Runs of homozygosity (ROHs) are long stretches of homozygous genomic segments, identifiable by molecular markers, which can provide genomic information for accurate estimates to characterize populations, determine evolutionary history and demographic information, estimate levels of consanguinity, and identify selection signatures in production animals. This review paper aims to perform a survey of the works on the efficiency of ROHs for these purposes. Factors such as genetic drift, natural or artificial selection, founder effect, and effective population size directly influence the size and distribution of ROHs along the genome. Individually, genome estimates of consanguinity based on ROHs can be obtained using the FROH index, which is generally considered more accurate than indexes based on other types of genomic or genealogical information. High frequencies of specific ROHs in a population can be used to identify selection signatures. The results of recent studies with ROHs in domestic animals have shown the efficiency of their use to characterize herds in a reliable and accessible way, using genomic information.

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Genetic Diversity of Indigenous Pigs from South China Area Revealed by SNP Array

Animals ◽

10.3390/ani9060361 ◽

2019 ◽

Vol 9 (6) ◽

pp. 361 ◽

Cited By ~ 3

Author(s):

Shuqi Diao ◽

Shuwen Huang ◽

Zhiting Xu ◽

Shaopan Ye ◽

Xiaolong Yuan ◽

...

Keyword(s):

Genetic Diversity ◽

Population Size ◽

Effective Population Size ◽

Conservation Status ◽

Snp Array ◽

Size Analysis ◽

Selection Signatures ◽

Effective Population ◽

Low Genetic Diversity ◽

Indigenous Pigs

To investigate the genetic diversity, population structure, extent of linkage disequilibrium (LD), effective population size (Ne), and selection signatures in indigenous pigs from Guangdong and Guangxi in China, 226 pigs belonging to ten diverse populations were genotyped using single nucleotide polymorphism (SNP) chips. The genetic divergence between Chinese and Western pigs was determined based on the SNP chip data. Low genetic diversity of Dahuabai (DHB), Luchuan (LC), Lantang (LT), and Meihua (MH) pigs, and introgression of Western pigs into Longlin (LL), MH, and Yuedonghei (YDH) pigs were detected. Analysis of the extent of LD showed that indigenous pigs had low LD when pairwise SNP distance was short and high LD when pairwise SNP distance was long. Effective population size analysis showed a rapid decrease for Chinese indigenous pigs, and some pig populations had a relatively small Ne. This result indicated the loss of genetic diversity in indigenous pigs, and introgression from Western commercial pigs. Selection signatures detected in this study overlapped with meat quality traits, such as drip loss, intramuscular fat content, meat color b*, and average backfat thickness. Our study deepened understanding of the conservation status and domestication of Chinese indigenous pigs.

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Identifying genomic regions and candidate genes selected during the breeding of rice in Vietnam

10.1101/2021.08.04.455072 ◽

2021 ◽

Author(s):

Janet Higgins ◽

Bruno Santos ◽

Tran Dang Khanh ◽

Khuat Huu Trung ◽

Tran Duy Duong ◽

...

Keyword(s):

Candidate Genes ◽

Continuous Improvement ◽

Rice Genome ◽

Selection Signatures ◽

Genome Scanning ◽

Selective Pressures ◽

Rice Landraces ◽

Rich Diversity ◽

Genomic Regions ◽

New Generation

Background and aims: Vietnam harnesses a rich diversity of rice landraces adapted to a broad range of conditions, which constitute a largely untapped source of genetic diversity for the continuous improvement of rice cultivars. We previously identified a strong population structure in Vietnamese rice, which is captured in five Indica and four Japonica subpopulations, including an outlying Indica-5 group. Here, we leveraged on that strong differentiation, and the 672 rice genomes generated, to identify genes within genomic regions putatively selected during domestication and breeding of rice in Vietnam. Methodology: We identified significant distorted patterns in allele frequency (XP-CLR method) and population differentiation scores (FST), resulting from differential selective pressures between native subpopulations, and compared them with QTLs previously identified by GWAS in the same panel. We particularly focused on the outlying Indica-5 subpopulation because of its likely novelty and differential evolution. Results: We identified selection signatures in each of the Vietnamese subpopulations and carried out a comprehensive annotation of the 52 regions selected in Indica-5, which represented 8.1% of the rice genome. We annotated the 4,576 genes in these regions, verified the overlap with QTLs identified in the same diversity panel and the comparison with a FST analysis between subpopulations, to select sixty-five candidate genes as promising breeding targets, several of which harboured alleles with non-synonymous substitutions. Conclusions: Our results highlight genomic differences between traditional Vietnamese landraces, which are likely the product of adaption to multiple environmental conditions and regional culinary preferences in a very diverse country. We also verified the applicability of this genome scanning approach to identify potential regions harbouring novel loci and alleles to breed a new generation of sustainable and resilient rice.

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Selection signatures in two oldest Russian native cattle breeds revealed using high-density single nucleotide polymorphism analysis

PLoS ONE ◽

10.1371/journal.pone.0242200 ◽

2020 ◽

Vol 15 (11) ◽

pp. e0242200

Author(s):

Natalia Anatolievna Zinovieva ◽

Arsen Vladimirovich Dotsev ◽

Alexander Alexandrovich Sermyagin ◽

Tatiana Evgenievna Deniskova ◽

Alexandra Sergeevna Abdelmanova ◽

...

Keyword(s):

Single Nucleotide Polymorphism ◽

Candidate Genes ◽

High Density ◽

Fixation Index ◽

Nucleotide Polymorphism ◽

Selection Signatures ◽

Single Nucleotide ◽

Cattle Breeds ◽

Native Cattle ◽

Genomic Regions

Native cattle breeds can carry specific signatures of selection reflecting their adaptation to the local environmental conditions and response to the breeding strategy used. In this study, we comprehensively analysed high-density single nucleotide polymorphism (SNP) genotypes to characterise the population structure and detect the selection signatures in Russian native Yaroslavl and Kholmogor dairy cattle breeds, which have been little influenced by introgression with transboundary breeds. Fifty-six samples of pedigree-recorded purebred animals, originating from different breeding farms and representing different sire lines, of the two studied breeds were genotyped using a genome-wide bovine genotyping array (Bovine HD BeadChip). Three statistical analyses—calculation of fixation index (FST) for each SNP for the comparison of the pairs of breeds, hapFLK analysis, and estimation of the runs of homozygosity (ROH) islands shared in more than 50% of animals—were combined for detecting the selection signatures in the genome of the studied cattle breeds. We confirmed nine and six known regions under putative selection in the genomes of Yaroslavl and Kholmogor cattle, respectively; the flanking positions of most of these regions were elucidated. Only two of the selected regions (localised on BTA 14 at 24.4–25.1 Mbp and on BTA 16 at 42.5–43.5 Mb) overlapped in Yaroslavl, Kholmogor and Holstein breeds. In addition, we detected three novel selection sweeps in the genome of Yaroslavl (BTA 4 at 4.74–5.36 Mbp, BTA 15 at 17.80–18.77 Mbp, and BTA 17 at 45.59–45.61 Mbp) and Kholmogor breeds (BTA 12 at 82.40–81.69 Mbp, BTA 15 at 16.04–16.62 Mbp, and BTA 18 at 0.19–1.46 Mbp) by using at least two of the above-mentioned methods. We expanded the list of candidate genes associated with the selected genomic regions and performed their functional annotation. We discussed the possible involvement of the identified candidate genes in artificial selection in connection with the origin and development of the breeds. Our findings on the Yaroslavl and Kholmogor breeds obtained using high-density SNP genotyping and three different statistical methods allowed the detection of novel putative genomic regions and candidate genes that might be under selection. These results might be useful for the sustainable development and conservation of these two oldest Russian native cattle breeds.

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Genomic measures of inbreeding coefficients and genome-wide scan for runs of homozygosity islands in Iranian river buffalo, Bubalus bubalis

10.21203/rs.2.17561/v3 ◽

2020 ◽

Author(s):

Seyed Mohammad Ghoreishifar ◽

Hossein Moradi-Shahrbabak ◽

Mohammad Hossein Fallahi ◽

Ali Jalil Sarghale ◽

Mohammad Moradi-Shahrbabak ◽

...

Keyword(s):

Muscle Development ◽

Bone Development ◽

Genomic Relationship Matrix ◽

Relationship Matrix ◽

River Buffalo ◽

Runs Of Homozygosity ◽

Effective Population ◽

A Genome ◽

Genomic Inbreeding ◽

Genomic Regions

Abstract Background: Consecutive homozygous fragments of a genome inherited by offspring from a common ancestor are known as runs of homozygosity (ROH). ROH can be used to calculate genomic inbreeding and to identify genomic regions that are potentially under historical selection pressure. The dataset of our study consisted of 254 Azeri (AZ) and 115 Khuzestani (KHZ) river buffalo genotyped for ~65000 SNPs for the following two purposes: 1) to estimate and compare inbreeding calculated using ROH (FROH), excess of homozygosity (FHOM), correlation between uniting gametes (FUNI), and diagonal elements of the genomic relationship matrix (FGRM); 2) to identify frequently occurring ROH (i.e. ROH islands) for our selection signature and gene enrichment studies. Results: In this study, 9102 ROH were identified, with an average number of 21.2±13.1 and 33.2±15.9 segments per animal in AZ and KHZ breeds, respectively. On average in AZ, 4.35% (108.8±120.3 Mb), and in KHZ, 5.96% (149.1±107.7 Mb) of the genome was autozygous. The estimated inbreeding values based on FHOM, FUNI and FGRM were higher in AZ than they were in KHZ, which was in contrast to the FROH estimates. We identified 11 ROH islands (four in AZ and seven in KHZ). In the KHZ breed, the genes located in ROH islands were enriched for multiple Gene Ontology (GO) terms (P≤0.05). The genes located in ROH islands were associated with diverse biological functions and traits such as body size and muscle development (BMP2), immune response (CYP27B1), milk production and components (MARS, ADRA1A, and KCTD16), coat colour and pigmentation (PMEL and MYO1A), reproductive traits (INHBC, INHBE, STAT6 and PCNA), and bone development (SUOX). Conclusion: The calculated FROH was in line with expected higher inbreeding in KHZ than in AZ because of the smaller effective population size of KHZ. Thus, we find that FROH can be used as a robust estimate of genomic inbreeding. Further, the majority of ROH peaks were overlapped with or in close proximity to the previously reported genomic regions with signatures of selection. This tells us that it is likely that the genes in the ROH islands have been subject to artificial or natural selection.

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Runs of homozygosity analysis reveals consensus homozygous regions affecting production traits in Chinese Simmental beef cattle

BMC Genomics ◽

10.1186/s12864-021-07992-6 ◽

2021 ◽

Vol 22 (1) ◽

Author(s):

Guoyao Zhao ◽

Yuqiang Liu ◽

Qunhao Niu ◽

Xu Zheng ◽

Tianliu Zhang ◽

...

Keyword(s):

Beef Cattle ◽

Candidate Genes ◽

Average Length ◽

Snp Array ◽

Reproductive Traits ◽

Farm Animals ◽

Production Traits ◽

Runs Of Homozygosity ◽

Exact Test ◽

Genomic Regions

Abstract Background Genomic regions with a high frequency of runs of homozygosity (ROH) are related to important traits in farm animals. We carried out a comprehensive analysis of ROH and evaluated their association with production traits using the BovineHD (770 K) SNP array in Chinese Simmental beef cattle. Results We detected a total of 116,953 homozygous segments with 2.47Gb across the genome in the studied population. The average number of ROH per individual was 99.03 and the average length was 117.29 Mb. Notably, we detected 42 regions with a frequency of more than 0.2. We obtained 17 candidate genes related to body size, meat quality, and reproductive traits. Furthermore, using Fisher’s exact test, we found 101 regions were associated with production traits by comparing high groups with low groups in terms of production traits. Of those, we identified several significant regions for production traits (P < 0.05) by association analysis, within which candidate genes including ECT2, GABRA4, and GABRB1 have been previously reported for those traits in beef cattle. Conclusions Our study explored ROH patterns and their potential associations with production traits in beef cattle. These results may help to better understand the association between production traits and genome homozygosity and offer valuable insights into managing inbreeding by designing reasonable breeding programs in farm animals.

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