Signatures of selection and environmental adaptation across the goat genome post-domestication

Genetics Selection Evolution, Journal Year: 2018, Volume and Issue: 50(1)

Published: Nov. 14, 2018

Since goat was domesticated 10,000 years ago, many factors have contributed to the differentiation of breeds and these are classified mainly into two types: (i) adaptation different breeding systems and/or purposes (ii) environments. As a result, approximately 600 developed worldwide; they differ considerably from one another in terms phenotypic characteristics adapted wide range climatic conditions. In this work, we analyzed AdaptMap dataset, which is composed data more than 3000 animals collected worldwide genotyped with CaprineSNP50 BeadChip. These were partitioned groups based on geographical area, production uses, available records solid coat color environmental variables including sampling coordinates, investigate role natural artificial selection shaping genome breeds.Several signatures chromosomal regions detected across breeds, sub-geographical clusters, groups. contain genes that involved important biological processes, such as milk-, meat- or fiber-related production, color, glucose pathway, oxidative stress response, size, circadian clock differences. Our results confirm previous findings other species extreme environments human provide new could explain some differences between according their distribution environments.These analyses comprehensive first picture global domestication process highlight possible may worldwide.

Language: Английский

---

Genome-Wide Characterization of Selection Signatures and Runs of Homozygosity in Ugandan Goat Breeds

Frontiers in Genetics, Journal Year: 2018, Volume and Issue: 9

Published: Aug. 14, 2018

Both natural and artificial selection are among the main driving forces shaping genetic variation across genome of livestock species. Selection typically leaves signatures in genome, which often characterized by high differentiation breeds and/or a strong reduction diversity regions associated with traits under intense pressure. In this study, we evaluated genomic inbreeding coefficients, FROH, based on runs homozygosity (ROH), six Ugandan goat breeds: Boer (n = 13), indigenous Karamojong 15), Kigezi 29), Mubende Small East African Sebei 29). After genotyping quality control, 45,294 autosomal single nucleotide polymorphisms (SNPs) remained for further analyses. A total 394 6 breed-specific putative were identified all breeds, marker-specific fixation index (FST-values) haplotype (hapFLK), respectively. These enriched genes involved signaling pathways directly or indirectly environmental adaptation, such as immune response (e.g., IL10RB IL23A), growth fatty acid composition FGF9 IGF1), thermo-tolerance MTOR MAPK3). The study revealed little overlap between generally did not display typical classic expected due to complex nature traits. breed, candidate production traits, body size GJB2 GJA3) also identified. Furthermore, analysis ROH showed very low levels (with mean FROH per breed ranging from 0.8% 2.4%), compared higher (mean 13.8%). Short more frequent than long ROH, except Karamojong, providing insight developmental history these breeds. This provides insights into effects long-term relevant implementation breeding programs conservation resources, well their sustainable use management.

Language: Английский

---

Whole-genome sequencing reveals selection signatures associated with important traits in six goat breeds

Scientific Reports, Journal Year: 2018, Volume and Issue: 8(1)

Published: July 4, 2018

Abstract Comparative population genomics analysis is an effective approach to identify selection signatures in farm animals. In this study, we systematically investigated the six phenotypically diverse goat breeds using SNPs obtained from pooled whole-genome resequencing data. More than 95.5% of 446–642 million clean reads were mapped latest reference genome, which generated a sequencing depth ranging 22.30 31.75-fold for each breed. A total 5,802,307, 6,794,020, 7,562,312, 5,325,119, 8,764,136, and 9,488,057 putative detected Boer, Meigu, Jintang Black, Nanjiang Yellow, Tibetan, Tibetan cashmere goats, respectively. Based on genome-wide F ST expected heterozygosity scores along 100-kb sliding windows, 68, 89, 44, 19, 35 outlier windows deemed as breeds. After genome annotation, several genes within signals found be possibly associated with important traits such coat color ( IRF4 , EXOC2 RALY EIF2S2 KITLG ), high-altitude adaptation EPAS1 growth LDB2 reproduction KHDRBS2 ). summary, provide improved understanding genetic diversity genomic footprints under positive or adaptations local environments domestic genome.

Language: Английский

---

Selection signatures in livestock genome: A review of concepts, approaches and applications

Livestock Science, Journal Year: 2020, Volume and Issue: 241, P. 104257 - 104257

Published: Sept. 19, 2020

Language: Английский

---

Detecting signatures of positive selection in non-model species using genomic data

Zoological Journal of the Linnean Society, Journal Year: 2018, Volume and Issue: 184(2), P. 528 - 583

Published: Feb. 22, 2018

Understanding how natural selection shapes genetic variation in populations is of paramount importance evolutionary biology. Affordable high-throughput sequencing now allows the generation genome-wide data for non-model species, thereby stimulating research aimed at determining genomic basis adaptation to local environmental conditions. However, although these adaptive loci show characteristic signatures positive selection, several other processes can lead similar patterns, rendering search outlier a challenging task. Given that all methods rely on different explicit (data requirements) or implicit (underlying population models) assumptions, they have limitations often remain unknown non-population geneticists. Simply applying tests generated yield unreliable results include many false positives and negatives, therefore concealing true history. In this review, tailored biologists with standard background mathematics entering field genomics, we explain emerge describe principles state-of-the-art programs detect signatures. We highlight promises pitfalls approaches provide practical recommendations based simulation studies as well various case from animals.

Language: Английский

---

Genome-wide patterns of homozygosity provide clues about the population history and adaptation of goats

Genetics Selection Evolution, Journal Year: 2018, Volume and Issue: 50(1)

Published: Nov. 15, 2018

Patterns of homozygosity can be influenced by several factors, such as demography, recombination, and selection. Using the goat SNP50 BeadChip, we genotyped 3171 goats belonging to 117 populations with a worldwide distribution. Our objectives were characterize number length runs (ROH) detect ROH hotspots in order gain new insights into consequences neutral selection processes on genome-wide patterns goats. The proportion genome covered is, general, less than 15% an inverse relationship between frequency i.e. short (< 3 Mb) are most frequent ones. data also indicate that ~ 60% breeds display low FROH coefficients 0.10), while 30 10% show moderate (0.10 < 0.20) or high (> values. For from Asia, average is smaller their coverage lower Near East Central which consistent role Fertile Crescent primary centre domestication. We observed local small population sizes tend have larger fraction compared tens hundreds thousands individuals. Five regions three chromosomes 11, 12 18, contain overlap signatures (average 77 248 Mb; 0.15) similar different geographic areas. increased consequence size isolation well founder effects recent inbreeding. existence co-localize demonstrates has played important increasing specific genome. Finally, analysed this work levels homozygosity, favourable for genetic management viability.

Language: Английский

---

On the concepts and measures of diversity in the genomics era

Current Plant Biology, Journal Year: 2023, Volume and Issue: 33, P. 100278 - 100278

Published: Jan. 1, 2023

Diversity serves as the foundation for breeding and evolution. In science of genomics, investigation genetic variation has long been a prominent subject. Researchers now have access to previously unheard volumes data, thanks development new genomic technologies which allow them thoroughly examine complexity variation. As result, definitions measurements diversity created, taking into consideration things like how is distributed throughout populations, impact natural selection, connection between phenotypic diversity. One crucial idea "genetic ancestry" describes percentage person's composition that may be linked particular ancestral populations. Heterozygosity, measures degree within population, another indicator Recent developments in genomics resulted creation tools methodologies examining addition these conventional measurements. Generally, area research rapidly changing age, with theories being created on regular basis. The origins effects are expected continue revealed our knowledge deepens, substantial ramifications human health, evolutionary biology, variety other domains.

Language: Английский

---

Deciphering the molecular drivers for cashmere/pashmina fiber production in goats: a comprehensive review

Mammalian Genome, Journal Year: 2025, Volume and Issue: 36(1), P. 162 - 182

Published: Feb. 4, 2025

Language: Английский

---

Genetic effects of DSCAML1 identified in genome-wide association study revealing strong associations with litter size and semen quality in goat (Capra hircus)

Theriogenology, Journal Year: 2020, Volume and Issue: 146, P. 20 - 25

Published: Feb. 1, 2020

Language: Английский

---

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

Genes, Journal Year: 2019, Volume and Issue: 10(11), P. 938 - 938

Published: Nov. 17, 2019

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

Language: Английский

---