Assessment of Autozygosity Derived From Runs of Homozygosity in Jinhua Pigs Disclosed by Sequencing Data

Frontiers in Genetics, Journal Year: 2019, Volume and Issue: 10

Published: March 28, 2019

Jinhua pig, a well-known Chinese indigenous breed, has evolved as pig breed with excellent meat quality, greater disease resistance and higher prolificacy. The reduction in the number of pigs over past years raised concerns about inbreeding. Runs homozygosity (ROH) along genome been applied to quantify individual autozygosity improve understanding inbreeding depression identify genes associated traits interest. Here, we investigated occurrence distribution ROH using next-generation sequencing data characterize 202 well genomic regions high frequencies within individuals. average coefficient based on longer than 1Mb was 0.168 ± 0.052. In total, 18,690 were identified all individuals, among which shorter segments (1-5Mb) predominated. Individual autosome coverage ranged from 5.32% 29.14% population. On average, approximately 16.8% whole covered by segments, lowest SSC11 highest SSC17. A total 824 SNPs (less 1%) 11 islands (occurring 45% samples). Genes reproduction (HOXA3, HOXA7, HOXA10 HOXA11), quality (MYOD1, LPIN3 CTNNBL1), appetite (NUCB2) (MUC4, MUC13, MUC20, LMLN, ITGB5, HEG1, SLC12A8 MYLK) islands. Moreover, several quantitative trait loci (QTL) for ham weight fat thickness detected. suggested, at least partially, selection economic environmental adaptation, should be subject future investigation. These findings contribute effects artificial shaping functional variants genome.

Language: Английский

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Genetic Diversity and Signatures of Selection for Thermal Stress in Cattle and Other Two Bos Species Adapted to Divergent Climatic Conditions

Frontiers in Genetics, Journal Year: 2021, Volume and Issue: 12

Published: Feb. 3, 2021

Understanding the biological mechanisms of climatic adaptation is paramount importance for optimization breeding programs and conservation genetic resources. The aim this study was to investigate diversity unravel genomic regions potentially under selection heat and/or cold tolerance in thirty-two worldwide cattle breeds, with a focus on Chinese local breeds adapted divergent conditions, Datong yak ( Bos grunniens ; YAK), Bali javanicus ) based dense SNP data. In general, moderate levels were observed most populations. proportion polymorphic ranged from 0.197 (YAK) 0.992 (Mongolian cattle). Observed expected heterozygosity 0.023 0.366 (Sanhe cattle; SH), 0.021 0.358 (SH), respectively. overall average inbreeding (±SD) was: 0.118 ± 0.028, 0.228 0.059, 0.194 0.041, 0.004 versus number homozygous genotypes, excess homozygosity, correlation between uniting gametes, runs homozygosity (ROH), Signatures multiple scenarios methods F ST , HapFLK, ROH) revealed important candidate genes. genes identified are related various processes pathways such as heat-shock proteins, oxygen transport, anatomical traits, mitochondrial DNA maintenance, metabolic activity, feed intake, carcass conformation, fertility, reproduction. This highlights large involved thermal thus, polygenic nature resilience. A comprehensive description measures YAK carried out compared 24 avoid potential biases. Numerous positive detected using three signature identified. Enriched function analyses pinpointed pathways, molecular cellular components, which contribute better understanding underlying cattle. Based identified, has complex inheritance nature, considering stress response.

Language: Английский

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The value of genomic relationship matrices to estimate levels of inbreeding

Genetics Selection Evolution, Journal Year: 2021, Volume and Issue: 53(1)

Published: May 1, 2021

Abstract Background Genomic relationship matrices are used to obtain genomic inbreeding coefficients. However, there several methodologies compute these and is still an unresolved debate on which one provides the best estimate of inbreeding. In this study, we investigated measures obtained from five matrices, including Nejati-Javaremi allelic matrix ( F NEJ ), Li Horvitz based excess homozygosity L&H VanRaden (methods 1, VR 1 , 2, 2 ) Yang YAN matrices. We derived expectations for each coefficient, assuming a single locus model, explain patterns coefficients that were computed thousands nucleotide polymorphism genotypes in population Iberian pigs. Results Except evaluated do not match with original definitions coefficient Wright (correlation) or Malécot (probability). When interpreted as indicators variability (heterozygosity) was gained lost relative base population, both led sensible results but case . has increased base, can indicate it decreased. fact, expected increase. decreased, increased. Finally, three more than present be lost, also unreasonable. The observed pig very different, following expectations. As consequence, rate depression estimated differed only magnitude sign. Conclusions diagonal elements lead inconsistent terms gain loss genetic estimates, thus misleading interpretations. Although have proven efficient increasing accuracy predictions, they always provide useful measure

Language: Английский

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Genome-wide landscape of runs of homozygosity and differentiation across Egyptian goat breeds

BMC Genomics, Journal Year: 2023, Volume and Issue: 24(1)

Published: Sept. 26, 2023

Understanding the genomic features of livestock is essential for successful breeding programs and conservation. This information scarce local goat breeds in Egypt. In current study, regions with selection signatures were identified as well runs homozygosity (ROH), inbreeding coefficients (FROH) fixation index (FST) detected Egyptian Nubian, Damascus, Barki Boer breeds. A total 46,268 SNP markers 337 animals available analyses. On average, 145.44, 42.02, 87.90 126.95 ROHs per individual autosomal genome respective The mean accumulative ROH lengths ranged from 46.5 Mb Damascus to 360 Nubian. short segments (< 2 Mb) most frequent all breeds, while longest (> 16 exclusively found highest average FROH was observed Nubian (~ 0.12) followed by 0.11), lowest 0.05) breed 0.03). estimated FST 0.14 (Egyptian Boer), 0.077 Barki), 0.075 Damascus), 0.071 (Barki 0.064 (Damascus 0.015 each pair Interestingly, multiple SNPs that accounted high values on chromosome 6 harboring ALPK1 KCNIP4. Genomic overlapping both harbor genes related immunity (IL4R, PHF23, GABARAP, GPS2, CD68), reproduction (SPATA2L, TNFSF12, TMEM95, RNF17), embryonic development (TCF25 SOX15) adaptation (MC1R, KDR, KIT), suggesting potential genetic adaptations environmental conditions. Our results contribute understanding architecture different may provide valuable effective preservation

Language: Английский

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Comparing genomic signatures of domestication in two Atlantic salmon (Salmo salar L.) populations with different geographical origins

Evolutionary Applications, Journal Year: 2018, Volume and Issue: 12(1), P. 137 - 156

Published: Aug. 7, 2018

Abstract Selective breeding and genetic improvement have left detectable signatures on the genomes of domestic species. The elucidation such is fundamental for detecting genomic regions biological relevance to domestication improving management practices. In aquaculture, was carried out independently in different locations worldwide, which provides opportunities study parallel effects genome individuals that been selected similar traits. this study, we aimed detect potential two independent pairs wild/domesticated Atlantic salmon populations Canadian Scottish origins, respectively. Putative under divergent selection were investigated using a 200K SNP array by combining three statistical methods based either allele frequencies ( LFMM , Bayescan) or haplotype differentiation (Rsb). We identified 337 270 s potentially wild hatchery observed little overlap between results obtained from methods, highlighting need test complementary approaches broad range footprints selection. vast majority outliers detected population‐specific but found four candidate genes shared populations. propose these may play role process domestication. Overall, our suggest drift override effect artificial and/or point toward basis underlying expression traits domesticated strains. Finally, it likely predominantly target polygenic (e.g., growth) its impact might be more difficult with assuming selective sweeps.

Language: Английский

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Genome-wide association and genotype by environment interactions for growth traits in U.S. Gelbvieh cattle

BMC Genomics, Journal Year: 2019, Volume and Issue: 20(1)

Published: Dec. 1, 2019

Single nucleotide polymorphism (SNP) arrays have facilitated discovery of genetic markers associated with complex traits in domestic cattle; thereby enabling modern breeding and selection programs. Genome-wide association analyses (GWAA) for growth were conducted on 10,837 geographically diverse U.S. Gelbvieh cattle using a union set 856,527 imputed SNPs. Birth weight (BW), weaning (WW), yearling (YW) analyzed GEMMA EMMAX (via genotypes). Genotype-by-environment (GxE) interactions also investigated.GEMMA produced moderate marker-based heritability estimates that similar BW (0.36-0.37, SE = 0.02-0.06), WW (0.27-0.29, 0.01), YW (0.39-0.41, 0.01-0.02). GWAA 856K SNPs (GEMMA; EMMAX) revealed common positional candidate genes underlying pleiotropic QTL BTA6, BTA7, BTA14, BTA20. The estimated proportion phenotypic variance explained (PVE) by the lead SNP defining these (EMMAX) was larger most YW, smaller WW. Collectively, GWAAs highly concordant BW, WW, met nominal significance level (P ≤ 1e-05), prioritization genes; including previously stature, feed efficiency, (i.e., PLAG1, NCAPG, LCORL, ARRDC3, STC2). not consistent among at threshold 1e-05); although some shared apparent less stringent thresholds P 2e-05).Pleiotropic detected BTA20 beef cattle. Seven recently efficiency Angus, SimAngus, Hereford Marker-based detection segregating multiple breeds support implementation multiple-breed genomic selection.

Language: Английский

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Novel and known signals of selection for fat deposition in domestic sheep breeds from Africa and Eurasia

PLoS ONE, Journal Year: 2019, Volume and Issue: 14(6), P. e0209632 - e0209632

Published: June 14, 2019

Genomic regions subjected to selection frequently show signatures such as within-population reduced nucleotide diversity and outlier values of differentiation among differentially selected populations. In this study, we analyzed 50K SNP genotype data 373 animals belonging 23 sheep breeds different geographic origins using the Rsb (extended haplotype homozygosity) FST statistical approaches, identify loci associated with fat-tail phenotype. We also checked if these putative overlapped high-homozygosity (ROH). The analyses identified novel signals confirmed presence signature in genomic that harbor candidate genes known affect fat deposition. Several appeared ROH were within each breed, but only two islands signatures. results reported herein provide most complete genome-wide study for African Eurasian breeds; they contribute insights into genetic basis tail phenotype sheep, confirm great complexity mechanisms underlie quantitative traits, fat-tail.

Language: Английский

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Genome wide association study identifies novel candidate genes for growth and body conformation traits in goats

Scientific Reports, Journal Year: 2022, Volume and Issue: 12(1)

Published: June 14, 2022

Abstract Pakistan is third largest country in term of goat population with distinct characteristics breeds and estimated 78.2 million. Punjab province has 37% country’s total seven important documented namely Beetal, Daira Din Pannah, Nachi, Barbari, Teddi, Pahari Pothwari. There paucity literature on GWAS for economically traits i.e., body weight morphometric measurements. Therefore, we performed using 50 K SNP Chip growth age adjusted measurements order to identify genomic regions influencing these among breeds. Blood samples were collected from 879 unrelated animals along data including length, height, pubic bone heart girth chest length. Genomic DNA was extracted genotyped bead chip. Association genotypic the phenotypic Plink 1.9 software. Linear mixed model used association study. Genes annotated Capra hircus genome assembly ARS1. We have identified a number highly significant SNPs respective candidate genes associated conformation traits. The functional aspects suggested their potential role growth. Moreover, pleiotropic effects observed some results current study contributed better understanding goat.

Language: Английский

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Single-step genomic evaluation of milk production traits in Canadian Alpine and Saanen dairy goats

Journal of Dairy Science, Journal Year: 2022, Volume and Issue: 105(3), P. 2393 - 2407

Published: Jan. 5, 2022

Genomic evaluations are routine in most plant and livestock breeding programs but used infrequently dairy goat schemes. In this context, the purpose of study was to investigate use single-step genomic BLUP method for predicting values milk production traits (milk, protein, fat yields; protein percentages) Canadian Alpine Saanen goats. There were 6,409 12,236 records 3,434 5,008 each trait first later lactations, respectively, a total 1,707 genotyped animals (833 874 Saanen). Two validation approaches used, forward (i.e., born after 2013 with an average estimated value accuracy from full data set ≥0.50) cross-validation subsets all included successive replications). The approach resulted similar accuracies (0.55 0.66 versus 0.54 0.61) biases (-0.01 -0.07 -0.03 0.11) when averaged across traits. Additionally, both single multiple-breed analyses compared, observed However, there small gain models breed. A genomically enhanced (GEBV) relative pedigree-based (EBV) breed, not possibly due limitations design, heritability evaluated, size training populations. Trait-specific gains theoretical GEBV EBV ranged 17 31% 35 55% Saanen, using approach. predicted 12 16% more accurate than animals, no nongenotyped animals. largest found does without lactation (35-41%) bucks daughter (46-54%), consequently, implementation selection population would be expected increase young candidates. Overall, represents step toward

Language: Английский

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A comparison of marker-based estimators of inbreeding and inbreeding depression

Genetics Selection Evolution, Journal Year: 2022, Volume and Issue: 54(1)

Published: Dec. 27, 2022

The availability of genome-wide marker data allows estimation inbreeding coefficients (F, the probability identity-by-descent, IBD) and, in turn, rate depression (ΔID). We investigated, by computer simulations, accuracy most popular estimators based on molecular markers when computing F and ΔID populations under random mating, equalization parental contributions, artificially selected populations. assessed described Li Horvitz (FLH1 FLH2), VanRaden (FVR1 FVR2), Yang colleagues (FYA1 FYA2), homozygosity (FHOM), runs (FROH) estimates pedigree (FPED) comparison with obtained from IBD measures (FIBD).If allele frequencies a base population taken as reference for computation are known, all highly correlated FIBD provide accurate mean ΔID. If unknown current used estimations, largest correlation is generally FLH1 best estimator FYA2. FVR2 FLH2 have poorest performance scenarios. assumption that equal to 0.5 results very biased average coefficient but they give relatively good Estimates directly (FHOM) substantially overestimated Finally, show lower than rather An analysis pig supports main findings simulations.When marker-allele frequency-based high When unknown, FIBD, FYA2 provides FROH also precise performances.

Language: Английский

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