Assessment of genome complementarity in three beef-on-dairy crossbreds reveals sire-specific effects on production traits with comparable rates of genomic inbreeding reduction DOI Creative Commons
Dorothea Lindtke, Sylvain Lerch, I. Morel

и другие.

BMC Genomics, Год журнала: 2024, Номер 25(1)

Опубликована: Ноя. 20, 2024

Crossbreeding beef bulls with dairy cows can improve the economic value and fitness of calves not entering production owing to increased meat yield heterosis. However, outcrossing might reduce dosage alleles that confer local adaptation or result in a higher risk dystocia due calf size. Given clear phenotypic differences between breeds, varying phylogenetic distances genomic variations within attainable gains will strongly depend on selection sires for crossing. Thus, aim this study was assess genome complementarity Angus (AAN), Limousin (LIM), Simmental (SIM) Brown Swiss (BSW) by quantifying inbreeding reduction F1 crosses identifying genes potentially under BSW-specific be affected outcrossing. Low-pass sequencing data from 181 cows, 34 bulls, 301 their progeny, body weight carcass composition measurements 248 F1s were obtained. The high levels detected BSW substantially reduced crossbreds, only minor sire breeds. In 585 candidate identified, overrepresenting associated milk, carcass, traits. Only few differentiated at nonsynonymous variants including four tightly clustered (FAM184B, NCAPG, DCAF16, LCORL) nearly fixed alternate but mostly heterozygous homozygous reference AAN LIM bulls. allele these significantly correlated protein mass F1s. Some highly divergent breeds likely strong breed, trade-offs productions. As opposing effects still segregate cattle, marker-assisted mating pairs may used modulate desired phenotypes simultaneously decrease inbreeding.

Язык: Английский

Unraveling inbreeding patterns and selection signals in Alpine Grey cattle DOI Creative Commons
G. Gomez Proto, Enrico Mancin, Cristina Sartori

и другие.

animal, Год журнала: 2024, Номер 18(5), С. 101159 - 101159

Опубликована: Апрель 16, 2024

Inbreeding plays a crucial role in livestock breeding, influencing genetic diversity and phenotypic traits. Genomic data have helped address limitations posed by incomplete pedigrees, providing deeper insights into breed diversity. This study assesses inbreeding levels via pedigree genomic approaches analyzes old recent using runs of homozygosity (ROH), selection signals Alpine Grey cattle. Pedigree from 165 575 individuals, analyzed with INBUPGF90 software, computed coefficients. Genomic-based coefficients derived PLINK v1.9. or DetectRUNS R package analyses 1 180 individuals' genotypes. Common SNPs within ROH pinpointed regions, aggregating "ROH islands" indicative pressure. Overlaps USCS Genome Browser unveiled gene presence. Moderate correlations (0.20-0.54) existed between coefficients, most estimators having higher (>0.8) correlation values. averaged 0.04 <8 Mb segments, 0.03 >16 segments; >90% ROHs were Mb, indicating ancient prevalence. Recent proved less detrimental than cosmopolitan breeds. Two major islands on chromosomes 6 7 harbored genes linked to immune response, disease resistance (PYURF, HERC3), fertility (EIF4EBP3, SRA1). underscores the need for detailed understand characteristics historical changes local breeds like insights, especially ROH, facilitated overcoming limitations, illuminating Our findings reveal inbreeding's enduring impact potential selective sweeps, elucidating traits

Язык: Английский

Процитировано

3

Development and Application of a 40 K Liquid Capture Chip for Beef Cattle DOI Creative Commons
Qing Liu, Liangyu Shi,

Pu Zhang

и другие.

Animals, Год журнала: 2025, Номер 15(9), С. 1346 - 1346

Опубликована: Май 7, 2025

The availability of genome sequences and single-nucleotide polymorphism (SNP) chips allows us to investigate the various genomic characteristics species by exploring genetic diversity aid selection. SNP chip is a cost-effective genotyping platform essential for molecular breeding livestock. In this study, we developed liquid capture suitable five Hubei (China) indigenous beef cattle breeds based on whole-genome sequencing datasets. panel consisted 42,686 SNPs (~40 K). These were evenly distributed each bovine chromosome, with majority having minor allele frequencies >0.05 located within intergenic regions. performance evaluation was proceeded 200 individuals, revealing that has high call rate 99.48%. further used examine population structure 205 individuals demonstrated ability differentiate between foreign breeds. also determine runs homozygosity (ROH) local 195 individuals. We identified 2547 ROH several genes associated economically important traits in study population. Our findings demonstrate not only contributes understanding but provides valuable information future programs, thereby improving their production efficiency economic value.

Язык: Английский

Процитировано

0

Genetic legacy and adaptive signatures: investigating the history, diversity, and selection signatures in Rendena cattle resilient to eighteenth century rinderpest epidemics DOI Creative Commons
Elisa Somenzi,

Erika Partel,

Mario Barbato

и другие.

Genetics Selection Evolution, Год журнала: 2024, Номер 56(1)

Опубликована: Май 2, 2024

Abstract Background Rendena is a dual-purpose cattle breed, which primarily found in the Italian Alps and eastern areas of Po valley, recognized for its longevity, fertility, disease resistance adaptability to steep Alpine pastures. It categorized as 'vulnerable extinction' with only 6057 registered animals 2022, yet no comprehensive analyses molecular diversity have been performed date. The aim this study was analyse origin, genetic diversity, genomic signatures selection using data from samples collected 2000 2018, shed light on breed's evolution conservation needs. Results Genetic analysis revealed that breed shares components various valley breeds, marked proximity Original Braunvieh reflecting historical restocking efforts across region. shows related both milk meat production, environmental adaptation immune response, latter being possibly result multiple rinderpest epidemics swept eighteenth century. An population spanning 18 years showed an increase mean level inbreeding over time, confirmed by number runs homozygosity per individual, larger 2018 sample. Conclusions while sharing common origin Brown Swiss, has developed distinct traits enable it thrive environment make highly valued local farmers. Preserving these adaptive features essential, not maintaining enhancing ability traditional animal husbandry adapt changing environments, but also guaranteeing resilience sustainability livestock system livelihoods within valley.

Язык: Английский

Процитировано

2

Analyzing Runs of Homozygosity Reveals Patterns of Selection in German Brown Cattle DOI Open Access

Anna Wirth,

Jürgen Duda,

Reiner Emmerling

и другие.

Genes, Год журнала: 2024, Номер 15(8), С. 1051 - 1051

Опубликована: Авг. 9, 2024

An increasing trend in ancestral and classical inbreeding coefficients as well depression for longevity were found the German Brown population. In addition, proportion of US Swiss genes is steadily Browns. Therefore, aim present study was to analyze presence genomic localization runs homozygosity (ROH) order evaluate their associations with survival rates cows higher lactations. Genotype data sampled 2364 Browns from 258 herds. The final set included 49,693 autosomal SNPs. We identified on average 35.996 ± 7.498 ROH per individual a mean length 8.323 1.181 Mb. coefficient FROH 0.122 0.032 it decreased 0.074, 0.031 0.006, when homozygous segments > 8 Mb (FROH>8), >16 (FROH>16) >32 (FROH>32) considered. New showed highest correlation FROH>32, whereas had lowest correlations FROH>32. between 0.572. significantly lower FROH, FROH>4, FROH>8 FIS proportions <60% compared >80%. Cows surviving 2nd, 4th, 6th, 8th, 10th lactation up which due number shorter ROH. strongest island consensus shared by 50% animals BTA 6 at 85–88 located this region associated (NPFFR2 ADAMTS3), udder health morphology (SLC4A4, NPFFR2, GC RASSF6), milk production, protein percentage, coagulation properties milking speed (CSN3). On 2, detected only genes. Genes within are predominantly important dual-purpose cattle breeds including Original For reaching more than 9 lactations, an exclusive 7 assumed be longevity. analysis indicated that regions still also containing affecting may have been identified. breeding should prevent any further increase run program balanced weights robustness

Язык: Английский

Процитировано

2

Genome Wide Association Studies for milk production traits in two autochthonous Aosta cattle breeds DOI Creative Commons

Franco Bernini,

Enrico Mancin, Cristina Sartori

и другие.

animal, Год журнала: 2024, Номер 18(10), С. 101322 - 101322

Опубликована: Сен. 12, 2024

Язык: Английский

Процитировано

2

Assessing major genes allele frequencies and the genetic diversity of the native Aosta cattle female population DOI Creative Commons
Francesca Bernini, Chiara Punturiero,

Mario Vevey

и другие.

Italian Journal of Animal Science, Год журнала: 2023, Номер 22(1), С. 1008 - 1022

Опубликована: Сен. 27, 2023

The Aosta cattle breeds have a key role in the economy of Valley. In addition to meat and milk production these autochthonous are important for their cultural value, maintenance mountain environment. knowledge genetic makeup represents fundamental asset managing reproduction population order maintain existing diversity and, as possible input, apply genomic selection small population. A total 3195 cows were genotyped with GeneSeek Genomic Profiler® (GGP) Bovine 100K by Neogen framework DUALBREEDING-2 project. Black-Chestnut Chestnut-Herèn resulted be unique female had shorter ROH than bulls shared ROH_islands that harbour adaptative functional genes. Allele frequencies major genes highlight possibility both quality variants is free from known Mendelian inheritance diseases found cosmopolitan (e.g. BLAD, CVM, HCD).

Язык: Английский

Процитировано

3

MOCOS‐associated renal syndrome in a Brown Swiss cattle DOI Creative Commons
Joana G. P. Jacinto, Leonore Küchler, Laureen M. Peters

и другие.

Journal of Veterinary Internal Medicine, Год журнала: 2023, Номер 37(6), С. 2603 - 2609

Опубликована: Сен. 7, 2023

A recessive form of MOCOS-associated xanthinuria type II is described in Tyrolean grey cattle. similar case was identified a 5-month-old Brown Swiss calf with hoof overgrowth, rough coat, urine sediment, and pneumonia.To characterize the disease phenotype, to evaluate its genetic etiology, determine prevalence deleterious allele population.An affected calf, parents, 65 441 dairy cattle.The animal clinically examined necropsied. Microarray genotyping used genotypes assess frequency MOCOS control cohort.Ultrasonography revealed hyperechoic renal pyramids multifocal distal shadowing echogenic sediment urinary bladder. Necropsy suppurative bronchopneumonia urolithiasis. Histology numerous nephroliths chronic lymphohistiocytic interstitial infiltrates, fibrosis, tubular degeneration, glomerulonephritis sclerosis, bilateral hydronephrosis. Dysplastic changes were observed corium claw cornea. Genetic testing homozygous presence known frameshift variant case. Both parents heterozygous carriers genotyped cattle 1.4% (342/24337).The findings consistent diagnosis syndrome The low breed. However, mating should be avoided prevent further losses.

Язык: Английский

Процитировано

1

Genetic parameters, genomic prediction, and identification of regulatory regions located on chromosome 14 for weight traits in Nellore cattle DOI
Miller Teodoro, Amanda Marchi Maiorano, Gabriel Soares Campos

и другие.

Journal of Animal Breeding and Genetics, Год журнала: 2024, Номер unknown

Опубликована: Авг. 27, 2024

Abstract This study aimed to investigate functional variants in chromosome 14 (BTA14) and its impact genomic selection for birth weight (BW), weaning (WW), yearling (YW) Nellore cattle. Genetic parameter estimation the weighted single‐step best linear unbiased prediction (WssGBLUP) analyses were performed. Direct additive heritability estimates high WW YW, moderate BW. Trait‐associated distributed across multiple regions on BTA14 observed genome‐wide association studies (WssGWAS) results, implying a polygenic genetic architecture different ages. Several genes have been found with traits, including CUB And Sushi domains 3 ( CSMD3 ), thyroglobulin TG diacylglycerol O‐acyltransferase 1 DGAT1 ) genes. The variance explained per SNP was higher six classes of gene regulatory (5UTR, CpG islands, downstream, upstream, long non‐coding RNA, transcription factor binding sites (TFBS)), highlighting their importance traits A marginal increase accuracy when selected (SV) information considered WssGBLUP method, probably because small number SV available BTA14. identified genes, pathways, functions contribute better understanding physiological mechanisms regulating breed.

Язык: Английский

Процитировано

0

Assessment of genome complementarity in three beef-on-dairy crossbreds reveals sire-specific effects on production traits with comparable rates of genomic inbreeding reduction DOI Creative Commons
Dorothea Lindtke, Sylvain Lerch, I. Morel

и другие.

BMC Genomics, Год журнала: 2024, Номер 25(1)

Опубликована: Ноя. 20, 2024

Crossbreeding beef bulls with dairy cows can improve the economic value and fitness of calves not entering production owing to increased meat yield heterosis. However, outcrossing might reduce dosage alleles that confer local adaptation or result in a higher risk dystocia due calf size. Given clear phenotypic differences between breeds, varying phylogenetic distances genomic variations within attainable gains will strongly depend on selection sires for crossing. Thus, aim this study was assess genome complementarity Angus (AAN), Limousin (LIM), Simmental (SIM) Brown Swiss (BSW) by quantifying inbreeding reduction F1 crosses identifying genes potentially under BSW-specific be affected outcrossing. Low-pass sequencing data from 181 cows, 34 bulls, 301 their progeny, body weight carcass composition measurements 248 F1s were obtained. The high levels detected BSW substantially reduced crossbreds, only minor sire breeds. In 585 candidate identified, overrepresenting associated milk, carcass, traits. Only few differentiated at nonsynonymous variants including four tightly clustered (FAM184B, NCAPG, DCAF16, LCORL) nearly fixed alternate but mostly heterozygous homozygous reference AAN LIM bulls. allele these significantly correlated protein mass F1s. Some highly divergent breeds likely strong breed, trade-offs productions. As opposing effects still segregate cattle, marker-assisted mating pairs may used modulate desired phenotypes simultaneously decrease inbreeding.

Язык: Английский

Процитировано

0