Unravelling selection signatures in a single dog breed suggests recent selection for morphological and behavioral traits

The Dwarf Lagune and the Savannah Somba cattle in Benin are typical representatives of the endangered West African indigenous Shorthorn taurine. The Lagune was previously exported to African and European countries and bred as Dahomey cattle, whereas the Somba contributed to the formation of two indigenous hybrids known as Borgou and Pabli cattle. These breeds are affected by demographic, economic, and environmental pressures in local production systems. Considering current and historical genomic data, we applied a formal test of admixture, estimated admixture proportions, and computed genomic inbreeding coefficients to characterize the five breeds. Subsequently, we unraveled the most recent selection signatures using the cross-population extended haplotype homozygosity approach, based on the current and historical genotypes. Results from principal component analyses and high proportion of Lagune ancestry confirm the Lagune origin of the European Dahomey cattle. Moreover, the Dahomey cattle displayed neither indicine nor European taurine (EUT) background, but they shared on average 40% of autozygosity from common ancestors, dated approximately eight generations ago. The Lagune cattle presented inbreeding coefficients larger than 0.13; however, the Somba and the hybrids (Borgou and Pabli) were less inbred (≤0.08). We detected evidence of admixture in the Somba and Lagune cattle, but they exhibited a similar African taurine (AFT) ancestral proportion (≥96%) to historical populations, respectively. A moderate and stable AFT ancestral proportion (62%) was also inferred for less admixed hybrid cattle including the Pabli. In contrast, the current Borgou samples displayed a lower AFT ancestral proportion (47%) than historical samples (63%). Irrespective of the admixture proportions, the hybrid populations displayed more selection signatures related to economic traits (reproduction, growth, and milk) than the taurine. In contrast, the taurine, especially the Somba, presented several regions known to be associated with adaptive traits (immunity and feed efficiency). The identified subregion of bovine leukocyte antigen (BoLA) class IIb (including DSB and BOLA-DYA) in Somba cattle is interestingly uncommon in other African breeds, suggesting further investigations to understand its association with specific adaptation to endemic diseases in Benin. Overall, our study provides deeper insights into recent evolutionary processes in the Beninese indigenous cattle and their aptitude for conservation and genetic improvement.

Download Full-text

Whole genome detection of recent selection signatures in Sarabi cattle: a unique Iranian taurine breed

Genes & Genomics ◽

10.1007/s13258-019-00888-6 ◽

2019 ◽

Vol 42 (2) ◽

pp. 203-215

Author(s):

Hasan Moradian ◽

Ali Esmailizadeh Koshkoiyeh ◽

Mohammadreza Mohammadabadi ◽

Masood Asadi Fozi

Keyword(s):

Whole Genome ◽

Selection Signatures ◽

Taurine Breed ◽

Recent Selection

Download Full-text

The LCORL Locus Is under Selection in Large-Sized Pakistani Goat Breeds

Genes ◽

10.3390/genes11020168 ◽

2020 ◽

Vol 11 (2) ◽

pp. 168

Author(s):

Rashid Saif ◽

Jan Henkel ◽

Vidhya Jagannathan ◽

Cord Drögemüller ◽

Christine Flury ◽

...

Keyword(s):

Mammalian Species ◽

Causal Variant ◽

Whole Genome Sequencing Data ◽

Potential Candidate ◽

Sequencing Data ◽

Selection Signatures ◽

Selection Signature ◽

Replication Studies ◽

Independent Replication ◽

Selection For

Goat domestication and human selection for valued traits have formed diverse breeds with characteristic phenotypes. This process led to the fixation of causative genetic variants controlling breed-specific traits within regions of reduced genetic diversity—so-called “selection signatures”. We previously reported an analysis of selection signatures based on pooled whole-genome sequencing data of 20 goat breeds and bezoar goats. In the present study, we reanalyzed the data and focused on a subset of eight Pakistani goat breeds (Angora, Barbari, Beetal, Dera Din Panah, Kamori, Nachi, Pahari, Teddy). We identified 749 selection signatures based on reduced heterozygosity in these breeds. A search for signatures that are shared across large-sized goat breeds revealed that five medium-to-large-sized Pakistani goat breeds had a common selection signature on chromosome 6 in a region harboring the LCORL gene, which has been shown to modulate height or body size in several mammalian species. Fine-mapping of the region confirmed that all five goat breeds with the selection signature were nearly fixed for the same haplotype in a ~191 kb region spanning positions 37,747,447–37,938,449. From the pool sequencing data, we identified a frame-shifting single base insertion into an isoform-specific exon of LCORL as a potential candidate causal variant mediating the size-increasing effect. If this preliminary result can be confirmed in independent replication studies, genotyping of this variant might be used to improve breeding programs and the selection for stature in goats.

Download Full-text

SNP Marker Selection for Dog Breed Identification from Genotypes of High-density SNP Array and Machine Learning

Journal of Agriculture & Life Science ◽

10.14397/jals.2019.53.4.93 ◽

2019 ◽

Vol 53 (4) ◽

pp. 93-101

Author(s):

Hyung-Yong Kim ◽

◽

Bong-Hwan Choi ◽

Taeyun Oh ◽

Byeong-Chul Kang

Keyword(s):

Machine Learning ◽

Snp Array ◽

High Density ◽

Snp Marker ◽

Marker Selection ◽

Dog Breed ◽

Selection For

Download Full-text

On the Expenses and Selection as affecting the Pure Premium Method of Valuation

Journal of the Institute of Actuaries and Assurance Magazine ◽

10.1017/s2046167400045602 ◽

1878 ◽

Vol 21 (3) ◽

pp. 192-203 ◽

Cited By ~ 1

Author(s):

James Sorley

Keyword(s):

Practical Interest ◽

The Other ◽

Pure Premium ◽

New Business ◽

Selection For ◽

The One ◽

Selection Of ◽

Recent Selection

Although much has been written in recent years on the comparative merits of different methods of valuation, I am not aware that any attempt has yet been made to ascertain the ultimate bearing on the Pure Premium Method, of the facts that have been recently brought forward as to the pressure of the expenses and the effects of selection in an assurance company. Speaking generally, it will, I think, be found that proposals to diminish the pure premium reserve on account of the necessarily heavy expenses of new business, have been made without reference to the mortality profit that may be expected to arise from the recent selection of the lives, and vice versa. This being the case, it occurred to me that it might be of considerable practical interest to make an investigation in which effect would be given to the influence both of expenses and of selection, for it would enable us to estimate how far the one neutralized the other. In order to render the inquiry more clear, however, it will be well to begin by considering each separately.

Download Full-text

Stronger signal of recent selection for lactase persistence in Maasai than in Europeans

European Journal of Human Genetics ◽

10.1038/ejhg.2012.199 ◽

2012 ◽

Vol 21 (5) ◽

pp. 550-553 ◽

Cited By ~ 21

Author(s):

Carina M Schlebusch ◽

Per Sjödin ◽

Pontus Skoglund ◽

Mattias Jakobsson

Keyword(s):

Lactase Persistence ◽

Selection For ◽

Recent Selection

Download Full-text

Comparison of Genetic Merit for Weight and Meat Traits between the Polled and Horned Cattle in Multiple Beef Breeds

Animals ◽

10.3390/ani11030870 ◽

2021 ◽

Vol 11 (3) ◽

pp. 870

Author(s):

Imtiaz A. S. Randhawa ◽

Michael R. McGowan ◽

Laercio R. Porto-Neto ◽

Ben J. Hayes ◽

Russell E. Lyons

Keyword(s):

Birth Weight ◽

Live Weight ◽

Practical Solution ◽

Genetic Merit ◽

Production Parameters ◽

Genetic Potential ◽

Lower Productivity ◽

Selection For ◽

Estimated Breeding Values ◽

Recent Selection

Breeding for polled animals is deemed the most practical solution to eradicate horns naturally and circumvent management costs and risks on health and welfare. However, there has been a historical reluctance by some farmers to select polled animals due to perceived lower productivity of their calves. This study has compared estimated breeding values (EBVs) between horned and polled animals (N = 2,466,785) for 12 production and carcass traits to assess historical (before 2000) and recent (2000–2018) genetic implications of poll breeding. Older generations of the polled animals in most breeds had significantly lower (Bonferroni-corrected p = 0.05) genetic merits for live (birth to maturity) and carcass weights, milk, meat quality, and fat content traits. Substantial gains of genetic potential were achieved during 2000 to 2018 in each breed, such that polled animals have significantly improved for the majority of traits studied. Generally, polled cohorts showed advantageous EBVs for live and carcass weights irrespective of the lower birth weights in some breeds. While Polled Brahman showed inferior production parameters, the poll genetics’ effect size (d) and correlation (r) were very small on recent birth weight (d = −0.30, r = −0.08), 200 days (−0.19, −0.05), 400 days (−0.06, −0.02), 600 days (−0.05, −0.01), mature cow live weight (−0.08, −0.02), and carcass weight (−0.19, −0.05). In conclusion, although there is some evidence that historical selection for polled breeding animals may have reduced productivity, there is strong evidence that more recent selection for polled genotypes in the breeds studied has not resulted in any adverse effects on genetic merit.

Download Full-text

Canine Genetics and Genomics

Canine Genetics, Health and Medicine ◽

10.5772/intechopen.95781 ◽

2021 ◽

Author(s):

Edo D’Agaro ◽

Andrea Favaro ◽

Davide Rosa

Keyword(s):

Heart Disease ◽

Next Generation Sequencing ◽

Genomic Data ◽

Behavioral Traits ◽

Canine Genetics ◽

Genome Wide ◽

Tremendous Progress ◽

Dog Breed ◽

Next Generation Sequencing Ngs ◽

Generation Sequencing

In the past fifteen years, tremendous progress has been made in dog genomics. Several genetic aspects of cancer, heart disease, hip dysplasia, vision and hearing problems in dogs have been investigated and studied in detail. Genome-wide associative studies have made it possible to identify several genes associated with diseases, morphological and behavioral traits. The dog genome contains an extraordinary amount of genetic variability that distinguishes the different dog breeds. As a consequence of the selective programs, applied using stringent breed standards, each dog breed represents, today, a population isolated from the others. The availability of modern next generation sequencing (NGS) techniques and the identification of millions of single functional mutations (SNPs) has enabled us to obtain new and unknown detailed genomic data of the different breeds.

Download Full-text

Genome-Wide Association Studies Reveal Neurological Genes for Dog Herding, Predation, Temperament, and Trainability Traits

Frontiers in Veterinary Science ◽

10.3389/fvets.2021.693290 ◽

2021 ◽

Vol 8 ◽

Author(s):

Shuwen Shan ◽

Fangzheng Xu ◽

Bertram Brenig

Keyword(s):

Body Size ◽

Candidate Genes ◽

Genome Wide Association Study ◽

Association Studies ◽

Nervous System Development ◽

Genome Wide Association ◽

Genome Wide Association Studies ◽

Behavioral Traits ◽

Genome Wide ◽

Dog Breed

Genome-wide association study (GWAS) using dog breed standard values as phenotypic measurements is an efficient way to identify genes associated with morphological and behavioral traits. As a result of strong human purposeful selections, several specialized behavioral traits such as herding and hunting have been formed in different modern dog breeds. However, genetic analyses on this topic are rather limited due to the accurate phenotyping difficulty for these complex behavioral traits. Here, 268 dog whole-genome sequences from 130 modern breeds were used to investigate candidate genes underlying dog herding, predation, temperament, and trainability by GWAS. Behavioral phenotypes were obtained from the American Kennel Club based on dog breed standard descriptions or groups (conventional categorization of dog historical roles). The GWAS results of herding behavior (without body size as a covariate) revealed 44 significantly associated sites within five chromosomes. Significantly associated sites on CFA7, 9, 10, and 20 were located either in or near neuropathological or neuronal genes including THOC1, ASIC2, MSRB3, LLPH, RFX8, and CHL1. MSRB3 and CHL1 genes were reported to be associated with dog fear. Since herding is a restricted hunting behavior by removing killing instinct, 36 hounds and 55 herding dogs were used to analyze predation behavior. Three neuronal-related genes (JAK2, MEIS1, and LRRTM4) were revealed as candidates for predation behavior. The significantly associated variant of temperament GWAS was located within ACSS3 gene. The highest associated variant in trainability GWAS is located on CFA22, with no variants detected above the Bonferroni threshold. Since dog behaviors are correlated with body size, we next incorporate body mass as covariates into GWAS; and significant signals around THOC1, MSRB3, LLPH, RFX8, CHL1, LRRTM4, and ACSS3 genes were still detected for dog herding, predation, and temperament behaviors. In humans, these candidate genes are either involved in nervous system development or associated with mental disorders. In conclusion, our results imply that these neuronal or psychiatric genes might be involved in biological processes underlying dog herding, predation, and temperament behavioral traits.

Download Full-text

The Australian DRG classification:are we ready for structural changes?

Australian Health Review ◽

10.1071/ah010016 ◽

2001 ◽

Vol 24 (3) ◽

pp. 16

Author(s):

Don Hindle

Keyword(s):

Health Care ◽

Structural Changes ◽

Health Care Systems ◽

Empirical Studies ◽

The World ◽

Care Systems ◽

Selection For ◽

Recent Selection

The Australian DRG variant compares favourably with other variants in use around the world. This view is supported by a variety of empirical studies and by experiences of its adoption by several health care systems. An example is its recent selection for use in Germany (Hindle & Lenz, 2000).

Download Full-text