Genomic Inbreeding and Runs of Homozygosity Analysis of Cashmere Goat

Animals, Год журнала: 2024, Номер 14(8), С. 1246 - 1246

Опубликована: Апрель 22, 2024

Cashmere goats are valuable genetic resources which famous worldwide for their high-quality fiber. Runs of homozygosity (ROHs) have been identified as an efficient tool to assess inbreeding level and identify related genes under selection. However, there is limited research on ROHs in cashmere goats. Therefore, we investigated the ROH pattern, assessed genomic levels examined candidate associated with trait using whole-genome resequencing data from 123 Herein, Inner Mongolia goat presented lowest coefficient 0.0263. In total, 57,224 ROHs. Seventy-four islands containing 50 were detected. Certain meat, fiber milk production (FGF1, PTPRM, RERE, GRID2, RARA); fertility (BIRC6, ECE2, CDH23, PAK1); disease or cold resistance adaptability (PDCD1LG2, SVIL, PRDM16, RFX4, SH3BP2); body size growth (TMEM63C, SYN3, SDC1, STRBP, SMG6). 135 consensus identified, found (FGF5, DVL3, NRAS, KIT) length color. These findings enhance our comprehension foundations traits influenced by selective breeding. This contributes significantly future breeding, reservation use other breeds.

Язык: Английский

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Genomics and transcriptomics identify quantitative trait loci affecting growth-related traits in silver pomfret (Pampus argenteus)

Comparative Biochemistry and Physiology Part D Genomics and Proteomics, Год журнала: 2025, Номер 54, С. 101414 - 101414

Опубликована: Янв. 13, 2025

Язык: Английский

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大规模全基因组SNP分析揭示了鸡品种的全球祖先、种群发展和种群历史的复杂(和多样)的遗传图谱

Journal of Zhejiang University SCIENCE B, Год журнала: 2024, Номер 25(4), С. 324 - 340

Опубликована: Апрель 1, 2024

Язык: Английский

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Assessing genetic diversity and defining signatures of positive selection on the genome of dromedary camels from the southeast of the Arabian Peninsula

Frontiers in Veterinary Science, Год журнала: 2023, Номер 10

Опубликована: Ноя. 30, 2023

Dromedary camels (Camelus dromedarius) are members of the Camelini tribe within Camelidae family. They distributed throughout North Africa, Arabian Peninsula and Southeast Asia. This domestic species is characterized by its superior adaptability to harsh desert environment. In this study, whole autosomal data 29 dromedary samples from in Oman; 10 Muscat, 14 Al-Batinah, 5 Al-Sharqiya, were investigated assess their genetic relationship define candidate signatures positive selection. A minimal distinction that separates Muscat dromedaries other two populations was observed, with a degree admixture between them. Using de-correlated composite multiple signals (DCMS) approach, total 47 regions autosomes these defined These harbor 154 genes mainly associated functional categories related immune response, lipid metabolism energy expenditure, optical auditory functions, long-term memory. Different genomic variants called on respective warrant further investigation find possible association different favorable phenotypes dromedaries. The output study paves way for research efforts aimed at defining markers use breeding programs, goal conserving diversity enhancing productivity.

Язык: Английский

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Dissecting Selective Signatures and Candidate Genes in Grandparent Lines Subject to High Selection Pressure for Broiler Production and in a Local Russian Chicken Breed of Ushanka

Genes, Год журнала: 2024, Номер 15(4), С. 524 - 524

Опубликована: Апрель 22, 2024

Breeding improvements and quantitative trait genetics are essential to the advancement of broiler production. The impact artificial selection on genomic architecture genetic markers sought remains a key area research. Here, we used whole-genome resequencing data analyze architecture, diversity, selective sweeps in Cornish White (CRW) Plymouth Rock (PRW) transboundary breeds selected for meat production and, comparatively, an aboriginal Russian breed Ushanka (USH). Reads were aligned reference genome bGalGal1.mat.broiler.GRCg7b filtered remove PCR duplicates low-quality reads using BWA-MEM2 bcftools software; 12,563,892 SNPs produced subsequent analyses. Compared CRW PRW, USH had lower diversity higher distinctiveness. Selective sweep regions corresponding candidate genes examined based ZFST, hapFLK, ROH assessment procedures. Twenty-seven prioritized chicken functional projection from human homologs suggest their importance signals studied breeds. These have relationship with such categories as body weight, muscles, fat metabolism deposition, reproduction, etc., mainly QTLs regions. This information is pivotal further executing enhance phenotypic traits.

Язык: Английский

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Whole genome resequencing reveals the adaptability of native chickens to drought, tropical and frigid environments in Xinjiang

Poultry Science, Год журнала: 2024, Номер 103(9), С. 103947 - 103947

Опубликована: Июнь 19, 2024

Chickens exhibit extensive genetic diversity and are distributed worldwide. Different chicken breeds have evolved to thrive in diverse environmental conditions. However, research on the mechanisms underlying adaptation extreme environments, such as tropical, frigid drought-prone regions, remains limited. In this study, we conducted whole-genome sequencing of 240 individuals from six native Xinjiang, China, well 4 publicly available inhabiting regions with varying annual precipitations, temperatures, altitudes. Our analysis revealed several variants among examined breeds. Furthermore, investigated population structure residing drought temperature environments by comparing them. Notably, exhibited different structures. Moreover, identified candidate genes associated adaptability environment, CORO2A, CTNNA3, AGMO, GRID2, BBOX1, COL3A1, INSR, SOX5, MAP2 PLPPR1. Additionally, pathways lysosome, cysteine methionine metabolism, glycosaminoglycan degradation, Wnt signaling may be play crucial roles regulating environments. Overall, these findings contribute our understanding governing also offer insights for enhancing resilience climatic

Язык: Английский

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Investigation of selection signatures of dairy goats using whole-genome sequencing data

BMC Genomics, Год журнала: 2025, Номер 26(1)

Опубликована: Март 12, 2025

Dairy goats, a livestock species with long history of milk production, are essential for the economic advancement nations, particularly in regions experiencing growth. In this study, we gathered whole-genome resequencing data 58 including 34 dairy goats and 24 wild (Bezoar), to explore selection signatures linked production traits using ROH (Runs homozygosity), CLR (composite likelihood ratio), Fst (Fixation index), XP-EHH (Ex-tended haplotype homozygosity across populations) XP-CLR(Cross-population composite ratio test) methods. Analysis five tests revealed total 210 genes, genes consistently identified at least two approaches. These associated fat, protein, fat yield. Gene enrichment analysis highlighted important GO KEGG pathways related such as "acyl-CoA metabolic process", "glycerolipid biosynthetic "cellular response fatty ac-id", "hormone "Galactose metabolism". Additionally, repro-duction, immune response, environmental adaptation were goats. The findings from our study offer profound understanding into critical features practical guidance improvement development crossbreeding initiatives different goat breeds.

Язык: Английский

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Analysis of Identical Runs of Homozygosity in the Genome of Egg-Laying and Ornamental Chicken Breeds

Russian Journal of Genetics, Год журнала: 2025, Номер 61(4), С. 405 - 416

Опубликована: Апрель 1, 2025

Язык: Английский

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Changes in Expression of Key Genes in Ceca of Chicken Broilers as Affected by Glyphosate, Antibiotics and a Coccidiostat

Animals, Год журнала: 2024, Номер 14(23), С. 3544 - 3544

Опубликована: Дек. 8, 2024

Studies have shown the presence of residual amounts herbicide glyphosate in poultry feed, which leads to its bioaccumulation body. Recently, it has been established that exposure low levels over a long period may serious negative effects on health. Moreover, combined several toxicants can potentially lead additive and/or synergistic effects. The purpose this study was analyze changes meat productivity and expression dynamics key genes (

Язык: Английский

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Whole Genome Screening Procures a Holistic Hold of the Russian Chicken Gene Pool Heritage and Demographic History

Biology, Год журнала: 2023, Номер 12(7), С. 979 - 979

Опубликована: Июль 10, 2023

A study for genomic variation that may reflect putative selective signaling and be associated with economically important traits is instrumental obtaining information about demographic selection history in domestic animal species populations. rich variety of the Russian chicken gene pool breeds warrants a further detailed study. Specifically, their features can derive implications from genome architecture footprints subsequent breeding practical efficient exploitation. In present work, whole genotyping 19 (20 populations up to 71 samples each) was performed using Chicken 50 K BeadChip DNA chip. The studied breed sample included six native chickens developed 17th-19th centuries, as well eight breeds, including White (RW), created 20th century on basis improving local foreign selection. Five specialized chickens, Leghorn (WL), were used along other representing pool. characteristics genetic diversity phylogenetic relationships represented comparison breeds. It established demonstrate own structure distinguishes them each other. For example, we previously made an assumption what could cause differences between two RW populations, RW1 RW2. From data obtained here, it verified WL additionally crossed RW2, unlike RW1. Thus, inherently, purer population this improved breed. significant contribution global shown. general, based results multilateral survey concluded variability robustly known, postulated newly discovered patterns evolution chickens. herein presented will aid work

Язык: Английский

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