Evaluating Genomic Selection in beef cattle: Insights from computer simulations using real SNP data DOI Creative Commons
Lino César Ramírez Ayala, Jordi Leno-Colorado, Laura M. Zingaretti

et al.

Investigaciones y Estudios - UNA, Journal Year: 2024, Volume and Issue: 15(2), P. 35 - 41

Published: Dec. 23, 2024

Genomic Selection (GS) is a method that employs genomic data to estimate breeding values and rank candidates for selection. Despite its numerous advantages, application in cattle programs remains the early stages many livestock systems developed tropical subtropical environments, such as those Paraguay. Computational simulations are powerful tools enhance our understanding of GS applications different scenarios invaluable an initial step before implementing this technique "real" genetic improvement programs. In study, real from single nucleotide polymorphisms (SNPs) Indicus Taurus breeds were employed simulate three crossing schemes: F1 crosses, grading up, rotational crosses. Phenotypes selected traits related shear force, growth, tolerance. The predictive accuracy 50k SNP chips, differing their selection methodologies, was compared: random selection, based on minimum allele frequency differences between breeds, with threshold 0.09 Taurus. findings indicate demonstrates optimal (0.38), while marker (0.18 0.17, respectively) does not benefit predictions significantly.

Language: Английский

Global and Local Ancestry and its Importance: A Review DOI

Rangasai Chandra Goli,

Kiyevi G Chishi,

Indrajit Ganguly

et al.

Current Genomics, Journal Year: 2024, Volume and Issue: 25(4), P. 237 - 260

Published: May 10, 2024

The fastest way to significantly change the composition of a population is through admixture, an evolutionary mechanism. In animal breeding history, genetic admixture has provided both short-term and long-term advantages by utilizing phenomenon complementarity heterosis in several traits diversity, respectively. traditional method analysis pedigree records now been replaced greatly genome-wide marker data that enables more precise estimations. Among these markers, SNPs have popular choice since they are cost-effective, not so laborious, automation genotyping easy. Certain markers can suggest possibility population's origin from sample DNA where source individual unknown or unwilling disclose their lineage, which called Ancestry-Informative Markers (AIMs). Revealing level at locus-specific termed as local ancestry be exploited identify signs recent selective response account for drift. Considering importance ancestry, this mini-review, concepts illustrated, encompassing basics, estimation/identification methods, tools/software used applications.

Language: Английский

Citations

8
Association Analysis Provides Insights into Plant Mitonuclear Interactions DOI Creative Commons
Qun Lian, Shuai Li, Shenglong Kan

et al.

Molecular Biology and Evolution, Journal Year: 2024, Volume and Issue: 41(2)

Published: Feb. 1, 2024

Abstract Cytonuclear interaction refers to the complex and ongoing process of coevolution between nuclear organelle genomes, which are responsible for cellular respiration, photosynthesis, lipid metabolism, etc. play a significant role in adaptation speciation. There have been large number studies detect signatures cytonuclear interactions. However, identification specific genetic polymorphisms that involved these interactions within species remains relatively rare. The recent surge whole genome sequencing has provided us an opportunity explore from population perspective. In this study, we analyzed total 3,439 genomes 7 identify signals by association (linkage disequilibrium) analysis variants both mitochondrial across flowering plants. We also investigated examples loci identified based on using subcellular localization assays, gene editing, transcriptome sequencing. Our study provides novel perspective investigation coevolution, thereby enriching our understanding plant fitness offspring sterility.

Language: Английский

Citations

7
Iron age genomic data from Althiburos – Tunisia renew the debate on the origins of African taurine cattle DOI Creative Commons
Catarina Ginja, Sílvia Guimarães, Rute R. da Fonseca

et al.

iScience, Journal Year: 2023, Volume and Issue: 26(7), P. 107196 - 107196

Published: June 25, 2023

The Maghreb is a key region for understanding the dynamics of cattle dispersal and admixture with local aurochs following their earliest domestication in Fertile Crescent more than 10,000 years ago. Here, we present data on autosomal genomes mitogenomes obtained four archaeological specimens Iron Age (∼2,800 cal BP-2,000 BP) domestic from Eastern Maghreb, i.e. Althiburos (El Kef, Tunisia). D-loop sequences were an additional eight this site. Maternal lineages assigned to elusive R ubiquitous African-T1 haplogroups found two ten specimens, respectively. Our results can be explained by post-domestication hybridization aurochs. However, cannot rule out independent North Africa considering shared ancestry pre-domestic Moroccan present-day African taurine cattle.

Language: Английский

Citations

15
Candidate signatures of positive selection for environmental adaptation in indigenous African cattle: A review DOI Creative Commons
Sumaya Kambal, Abdulfatai Tijjani, Sabah A. E. Ibrahim

et al.

Animal Genetics, Journal Year: 2023, Volume and Issue: 54(6), P. 689 - 708

Published: Sept. 11, 2023

Abstract Environmental adaptation traits of indigenous African cattle are increasingly being investigated to respond the need for sustainable livestock production in context unpredictable climatic changes. Several studies have highlighted genomic regions under positive selection probably associated with environmental challenges (e.g. heat stress, trypanosomiasis, tick and tick‐borne diseases). However, little attention has focused on pinpointing candidate causative variant(s) controlling traits. This review compiled information from 22 signatures breeds identify selection. We highlight some key genome genes relevance living extreme environments (high temperature, high altitude, infectious disease prevalence). They include involved biological pathways relating innate adaptive immunity BoLAs , SPAG11 IL1RL2 GFI1B ), stress HSPs SOD1 PRLH ) hypoxia responses BDNF INPP4A ). Notably, highest numbers found BTA3, BTA5 BTA7. overlap playing roles several functions pathways. These but not limited growth feed intake, cell stability, protein stability sweat gland development. may further guide targeted aiming assess importance mutations, within regulatory protein‐coding regions, understand mechanisms underlying cattle's unique adaption.

Language: Английский

Citations

13
The Genomic Legacy of Aurochs hybridization in ancient and modern Iberian Cattle DOI Open Access
Torsten Günther,

Jacob Chisausky,

María Ángeles Galindo-Pellicena

et al.

Published: Jan. 7, 2025

Cattle have been a valuable economic resource and cultural icon since prehistory. From the initial expansion of domestic cattle into Europe during Neolithic period, taurine ( Bos taurus ) their wild ancestor, aurochs B. primigenius ), had overlapping ranges, leading to ample opportunities for mating (whether intended by farmers or not). We performed bioarchaeological analysis 24 remains from Iberia dating Mesolithic Roman period. The archaeogenomic dataset allows us investigate extent domestic-wild hybridization over time, providing insight species’ behavior human hunting management practices aligning changes with genomic transitions in archaeological record. Our results show frequent Chalcolithic, likely reflecting mix herding relatively unmanaged herds, mostly male female involved hybridization. This is supported isotopic evidence consistent ecological niche sharing, only few possibly being managed. proportion ancestry constant about 4000 years ago, probably due herd selection against first generation hybrids, coinciding other transitions. level (∽20%) continues modern western European breeds including Spanish Lidia breed which bred its aggressiveness fighting ability, but does not display elevated levels ancestry. study takes glance at impact actions introgression establishment as one most important species today.

Language: Английский

Citations

0
The genomic legacy of aurochs hybridisation in ancient and modern Iberian cattle DOI Creative Commons
Torsten Günther,

Jacob Chisausky,

Ángeles M Galindo-Pellicena

et al.

eLife, Journal Year: 2025, Volume and Issue: 13

Published: March 19, 2025

Cattle ( Bos taurus ) play an important role in the life of humans Iberian Peninsula not just as a food source but also cultural events. When domestic cattle were first introduced to Iberia, wild aurochs primigenius still present, leaving ample opportunity for mating (whether intended by farmers or not). Using temporal bioarchaeological dataset covering eight millennia, we trace gene flow between two groups. Our results show frequent hybridisation during Neolithic and Chalcolithic, likely reflecting mix hunting herding relatively unmanaged herds, with mostly male female involved. This is supported isotopic evidence consistent ecological niche sharing, only few possibly being managed. The proportion ancestry remains constant from about 4000 years ago, probably due herd management selection against generation hybrids, coinciding other transitions. level (~20%) continues into modern Western European breeds including selected aggressiveness fighting ability. study illuminates genomic impact human actions introgression establishment one most species today.

Language: Английский

Citations

0
Rethinking River Buffalo Domestication Through the Lens of Population Genetics Tools: Mehsana Buffalo Is a Unique Population DOI

Rangasai Chandra Goli,

Kiyevi G Chishi,

Karan Mahar

et al.

OMICS A Journal of Integrative Biology, Journal Year: 2025, Volume and Issue: unknown

Published: April 15, 2025

Riverine buffalo domestication likely occurred around 6300 years ago in Northwestern India. Murrah and Surti are important breeds that originated this region the gene flow from these buffaloes to Mehsana has long been proposed. However, extent which ancestry diffused across not investigated thoroughly. Therefore, we global local of Indian using double digest restriction-site associated DNA sequencing data. Principal component analysis, admixture dating, three population tests revealed with statistical significance is a unique population. Hence, hypothesis crossbreed between supported by findings. noticed some individuals Mehsana, 6 out 15, were admixed having 41% Murrah-specific 11% Surti-specific ancestry. Local post-admixture selection signatures (PASS) PASS genome, is, on Bubalus bubalis autosomes (BBA), 1-23 linked BBA, 24 Murrah. Interestingly, upon functional enrichment signatures, several adaptation-related genes pathways ascertained Surti, while Murrah-derived regions featured involved fatty acid synthesis (Acyl-CoA Synthetase Short-Chain Family Member 2 (ACSS2)) milk production. Based infer introgression genome into happened recent times ancient generations. The finding an independent highlights importance recognizing distinct genetic lineages domesticated species. This implications for reevaluating origins uniqueness other livestock often assumed be hybrids. Practically, findings open up new avenues selective breeding preserve traits such as disease resistance, adaptability, production efficiency. Further studies larger samples called for.

Language: Английский

Citations

0
Recovery of mitogenomes from whole genome sequences to infer maternal diversity in 1883 modern taurine and indicine cattle DOI Creative Commons
Jigme Dorji, Christy J. Vander Jagt, Amanda J. Chamberlain

et al.

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

Published: April 4, 2022

Abstract Maternal diversity based on a sub-region of mitochondrial genome or variants were commonly used to understand past demographic events in livestock. Additionally, there is growing evidence direct association genetic with range phenotypes. Therefore, this study complete bovine mitogenomes from large sequence database explore the full spectrum maternal diversity. Mitogenome was evaluated among 1883 animals representing 156 globally important cattle breeds. Overall, diverse: presenting 11 major haplogroups, expanding 1309 unique haplotypes, nucleotide 0.011 and haplotype 0.999. A small proportion African taurine (3.5%) indicine (1.3%) haplogroups found European breeds composites. The haplogrouping largely consistent population structure derived alternate clustering methods (e.g. PCA hierarchical clustering). Further, we present confirming new subgroup (I1a, 64 animals) mainly consisting originating China characterised by two private mutations within I1 haplogroup. total variation attributed within-breed variance (96.9%). accuracy imputation missing genotypes high (99.8%) except for relatively rare heteroplasmic genotypes, suggesting potential trait studies breed.

Language: Английский

Citations

12
Genomic insights into the population history and adaptive traits of Latin American Criollo cattle DOI Creative Commons
James A. Ward, Said I. Ng’ang’a, Imtiaz A. S. Randhawa

et al.

Royal Society Open Science, Journal Year: 2024, Volume and Issue: 11(3)

Published: March 1, 2024

Criollo cattle, the descendants of animals brought by Iberian colonists to Americas, have been subject natural and human-mediated selection in novel tropical agroecological zones for centuries. Consequently, these breeds evolved distinct characteristics such as resistance diseases exceptional heat tolerance. In addition European taurine (

Language: Английский

Citations

2
Assessment of Genomic Diversity and Selective Pressures in Crossbred Dairy Cattle of Pakistan DOI
Fakhar un Nisa, Rubab Zahra Naqvi, Fazeela Arshad

et al.

Biochemical Genetics, Journal Year: 2024, Volume and Issue: 62(5), P. 4137 - 4156

Published: April 25, 2024

Language: Английский

Citations

2