Change in genetic size of small-closed populations: lessons from a domestic mammal population

Ghafouri‐Kesbi, Farhad

doi:10.1590/s1415-47572010000400011

Cited by 6 publications

(3 citation statements)

References 26 publications

(30 reference statements)

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“…Among all groups in this study, the observed heterozygosity, expected heterozygosity, and pi of CRS were 0.387, 0.375, 0.000043, respectively, which were at the relatively high level of genomic diversity among the 16 cattle populations in this study. One reason may be that CRS was crossed with local breeds, which is consistent with previous research [54]. On the other hand, the bovine SNP chips were optimized for use in taurine, which has a little bias and is not suitable for studying the genetic diversity and origin of domestic cattle in other regions [55].…”

Section: Discussionsupporting

confidence: 65%

Assessing Genomic Diversity and Signatures of Selection in Chinese Red Steppe Cattle Using High-Density SNP Array

Jiang

Lai

et al. 2023

Animals

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Chinese Red Steppe Cattle (CRS), a composite cattle breed, is well known for its milk production, high slaughter rate, carcass traits, and meat quality. Nowadays, it is widely bred in Jilin and Hebei Province and the Inner Mongolia Autonomous region. However, the population structure and the genetic basis of prominent characteristics of CRS are still unknown. In this study, we systematically describe their population structure, genetic diversity, and selection signature based on genotyping data from 61 CRS individuals with GGP Bovine 100 K chip. The results showed that CRS cattle had low inbreeding levels and had formed a unique genetic structure feature. Using two complementary methods (including comprehensive haplotype score and complex likelihood ratio), we identified 1291 and 1285 potentially selected genes, respectively. There were 141 genes annotated in common 106 overlapping genomic regions covered 5.62 Mb, including PLAG1, PRKG2, DGAT1, PARP10, TONSL, ADCK5, and BMP3, most of which were enriched in pathways related to muscle growth and differentiation, milk production, and lipid metabolism. This study will contribute to understanding the genetic mechanism behind artificial selection and give an extensive reference for subsequent breeding.

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Section: Discussionsupporting

confidence: 65%

Assessing Genomic Diversity and Signatures of Selection in Chinese Red Steppe Cattle Using High-Density SNP Array

Jiang

Lai

et al. 2023

Animals

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“…The value of f ge represents the cumulative loss of genetic diversity since the base population and directly relates to N e [18,19]. Ratios of the above mentioned parameters of gene origin have been used to interpret the loss in genetic diversity by several authors [23,24,30], but definition and interpretation of the parameter ratios have been diverse and non-quantifiable (in absolute sense).…”

Section: Resultsmentioning

confidence: 99%

Cross-Breeding Is Inevitable to Conserve the Highly Inbred Population of Puffin Hunter: The Norwegian Lundehund

Kettunen¹,

Daverdin

Helfjord

et al. 2017

PLoS ONE

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The Norwegian Lundehund is a highly endangered native dog breed. Low fertility and high frequency predisposition to intestinal disorder imply inbreeding depression. We assessed the genetic diversity of the Lundehund population from pedigree data and evaluated the potential of optimal contribution selection and cross-breeding in the long-term management of the Lundehund population. The current Norwegian Lundehund population is highly inbred and has lost 38.8% of the genetic diversity in the base population. Effective population size estimates varied between 13 and 82 depending on the method used. Optimal contribution selection alone facilitates no improvement in the current situation in the Lundehund due to the extremely high relatedness of the whole population. Addition of (replacement with) 10 breeding candidates of foreign breed to 30 Lundehund breeders reduced the parental additive genetic relationship by 40–42% (48–53%). Immediate actions are needed to increase the genetic diversity in the current Lundehund population. The only option to secure the conservation of this rare breed is to introduce individuals from foreign breeds as breeding candidates.

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“…Our results showed that hybridization of the Taurine and Indicine breeds conferred a higher genetic diversity of the Simbra breed in comparison with the purebred breeds (Ghafouri-Kesbi, 2010;Zhang et al, 2015). This was obvious from the negative inbreeding coefficient (f ) estimate that indicated an excess of heterozygosity even beyond what is expected under Hardy-Weinberg equilibrium in the Simbra population (Maiorano et al, 2018).…”

Section: Discussionmentioning

confidence: 70%

Breed Ancestry, Divergence, Admixture, and Selection Patterns of the Simbra Crossbreed

et al. 2021

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In this study, we evaluated an admixed South African Simbra crossbred population, as well as the Brahman (Indicine) and Simmental (Taurine) ancestor populations to understand their genetic architecture and detect genomic regions showing signatures of selection. Animals were genotyped using the Illumina BovineLD v2 BeadChip (7K). Genomic structure analysis confirmed that the South African Simbra cattle have an admixed genome, composed of 5/8 Taurine and 3/8 Indicine, ensuring that the Simbra genome maintains favorable traits from both breeds. Genomic regions that have been targeted by selection were detected using the linkage disequilibrium-based methods iHS and Rsb. These analyses identified 10 candidate regions that are potentially under strong positive selection, containing genes implicated in cattle health and production (e.g., TRIM63, KCNA10, NCAM1, SMIM5, MIER3, and SLC24A4). These adaptive alleles likely contribute to the biological and cellular functions determining phenotype in the Simbra hybrid cattle breed. Our data suggested that these alleles were introgressed from the breed's original indicine and taurine ancestors. The Simbra breed thus possesses derived parental alleles that combine the superior traits of the founder Brahman and Simmental breeds. These regions and genes might represent good targets for ad-hoc physiological studies, selection of breeding material and eventually even gene editing, for improved traits in modern cattle breeds. This study represents an important step toward developing and improving strategies for selection and population breeding to ultimately contribute meaningfully to the beef production industry.

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Change in genetic size of small-closed populations: lessons from a domestic mammal population

Cited by 6 publications

References 26 publications

Assessing Genomic Diversity and Signatures of Selection in Chinese Red Steppe Cattle Using High-Density SNP Array

Assessing Genomic Diversity and Signatures of Selection in Chinese Red Steppe Cattle Using High-Density SNP Array

Cross-Breeding Is Inevitable to Conserve the Highly Inbred Population of Puffin Hunter: The Norwegian Lundehund

Breed Ancestry, Divergence, Admixture, and Selection Patterns of the Simbra Crossbreed

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