scholarly journals Local Ancestry to Identify Selection in Response to Trypanosome Infection in Baoulé x Zebu Crossbred Cattle in Burkina Faso

2021 ◽  
Vol 12 ◽  
Author(s):  
Bernadette Yougbaré ◽  
Dominique Ouédraogo ◽  
Arnaud S. R. Tapsoba ◽  
Albert Soudré ◽  
Bienvenue L. Zoma ◽  
...  
Keyword(s):  
Burkina Faso ◽  
Production Traits ◽  
Crossbred Cattle ◽  
Trypanosome Infection ◽  
Local Ancestry ◽  
Indigenous Breed ◽  
Genomic Marker ◽  
Direct Elisa ◽  
Ancestral Haplotypes ◽  
Genomic Regions

The genomes of crossbred (admixed) individuals are a mosaic of ancestral haplotypes formed by recombination in each generation. The proportion of these ancestral haplotypes in certain genomic regions can be responsible for either susceptibility or tolerance against pathogens, and for performances in production traits. Using a medium-density genomic marker panel from the Illumina Bovine SNP50 BeadChip, we estimated individual admixture proportions for Baoulé x Zebu crossbred cattle in Burkina Faso, which were tested for trypanosome infection by direct ELISA from blood samples. Furthermore, we calculated local ancestry deviation from average for each SNP across 29 autosomes to identify potential regions under selection in the trypanotolerant Baoulé cattle and their crossbreds. We identified significant deviation from the local average ancestry (above 5 and 10% genome-wide thresholds) on chromosomes 8 and 19 in the positive animals, while the negative ones showed higher deviation on chromosomes 6, 19, 21, and 22. Some candidate genes on chromosome 6 (PDGFRA) and chromosome 19 (CDC6) have been found associated to trypanotolerance in West African taurines. Screening for FST outliers in trypanosome positive/negative animals we detected seven variants putatively under selection. Finally, we identified a minimum set of highly ancestry informative markers for routine admixture testing. The results of this study contribute to a better understanding of the genetic basis of trypanotolerance in Baoulé cattle and their crossbreeds. Furthermore, we provide a small informative marker set to monitor admixture in this valuable indigenous breed. As such, our results are important for conserving the genetic uniqueness and trypanotolerance of Baoulé cattle, as well as for the improvement of Baoulé and Zebu crossbreds in specific community-based breeding programs.

scholarly journals Taurine and Indicine Haplotype Representation in Advanced Generation Individuals From Three American Breeds

2021 ◽  
Vol 12 ◽  
Author(s):  
Tamar E. Crum ◽  
Robert D. Schnabel ◽  
Jared E. Decker ◽  
Jeremy F. Taylor
Keyword(s):  
Bos Taurus ◽  
Association Studies ◽  
Selective Advantage ◽  
Production Traits ◽  
Local Ancestry ◽  
Generation Number ◽  
Genome Wide ◽  
Ancestry Estimation ◽  
Genomic Regions ◽  
Advanced Generation

Development of the American Breeds of beef cattle began in the 1920s as breeders and U. S. Experiment Station researchers began to create Bos taurus taurus × Bos taurus indicus hybrids using Brahman as the B. t. indicus source. By 1954, U.S. Breed Associations had been formed for Brangus (5/8 Angus × 3/8 Brahman), Beefmaster (½ Brahman × ¼ Shorthorn × ¼ Hereford), and Santa Gertrudis (5/8 Shorthorn × 3/8 Brahman). While these breeds were developed using mating designs expected to create base generation animals with the required genome contributions from progenitor breeds, each association has now registered advanced generation animals in which selection or drift may have caused the realized genome compositions to differ from initial expected proportions. The availability of high-density SNP genotypes for 9,161 Brangus, 3,762 Beefmaster, and 1,942 Santa Gertrudis animals allowed us to compare the realized genomic architectures of breed members to the base generation expectations. We used RFMix to estimate local ancestry and identify genomic regions in which the proportion of Brahman ancestry differed significantly from a priori expectations. For all three breeds, lower than expected levels of Brahman composition were found genome-wide, particularly in early-generation animals where we demonstrate that selection on beef production traits was likely responsible for the taurine enrichment. Using a proxy for generation number, we also contrasted the genomes of early- and advanced-generation animals and found that the indicine composition of the genome has increased with generation number likely due to selection on adaptive traits. Many of the most-highly differentiated genomic regions were breed specific, suggesting that differences in breeding objectives and selection intensities exist between the breeds. Global ancestry estimation is commonly performed in admixed animals to control for stratification in association studies. However, local ancestry estimation provides the opportunity to investigate the evolution of specific chromosomal segments and estimate haplotype effects on trait variation in admixed individuals. Investigating the genomic architecture of the American Breeds not only allows the estimation of indicine and taurine genome proportions genome-wide, but also the locations within the genome where either taurine or indicine alleles confer a selective advantage.

Genetic and Phenotypic Parameters of Milk Production Traits of Crossbred Cattle in a Selected Farm of Bangladesh

2004 ◽  
Vol 4 (4) ◽  
pp. 452-455 ◽  
Author(s):  
Ali Reza Ahmed . ◽  
Sarder Safiqul Islam . ◽  
Nargis Khanam . ◽  
Ayesha Ashraf .
Keyword(s):  
Milk Production ◽  
Production Traits ◽  
Crossbred Cattle ◽  
Milk Production Traits

scholarly journals Genomic Tools for the Conservation and Genetic Improvement of a Highly Fragmented Breed—The Ramo Grande Cattle from the Azores

Animals ◽  
2020 ◽  
Vol 10 (6) ◽  
pp. 1089
Author(s):  
Andreia J. Amaral ◽  
Ana L. Pavão ◽  
Luis T. Gama
Keyword(s):  
Population Size ◽  
Effective Population Size ◽  
Genome Wide Association Study ◽  
Cattle Breed ◽  
Production Traits ◽  
Effective Population ◽  
Age At First Calving ◽  
Large Effective Population Size ◽  
Genomic Inbreeding ◽  
Genomic Regions

Ramo Grande is a local cattle breed raised in the archipelago of Azores, with a small and dispersed census, where inbreeding control is of utmost importance. A single nucleotide polymorphism (SNP) Beadchip array was used to assess inbreeding, by analysis of genomic regions harboring contiguous homozygous genotypes named runs of homozygosity (ROH), and to estimate past effective population size by analysis of linkage disequilibrium (LD). Genetic markers associated with production traits were also investigated, exploiting the unique genetic and adaptation features of this breed. A total of 639 ROH with length >4 Mb were identified, with mean length of 14.96 Mb. The mean genomic inbreeding was 0.09, and long segments of ROH were common, indicating recent inbred matings. The LD pattern indicates a large effective population size, suggesting the inflow of exotic germplasm in the past. The genome-wide association study identified novel markers significantly affecting longevity, age at first calving and direct genetic effects on calf weight. These results provide the first evidence of the association of longevity with genes related with DNA recognition and repair, and the association of age at first calving with aquaporin proteins, which are known to have a crucial role in reproduction.

scholarly journals Assessment of variability of egg production traits based on analysis of SNP markers and search for traces of selection in the genome of Russian white chickens

2020 ◽  
Vol 18 (4) ◽  
pp. 423-432
Author(s):  
Olga V. Mitrofanova ◽  
Natalia V. Dementieva ◽  
Elena S. Fedorova ◽  
Marina V. Pozovnikova ◽  
Valentina I. Tyshchenko ◽  
...  
Keyword(s):  
Selection Pressure ◽  
Egg Production ◽  
Snp Markers ◽  
Chromosome 8 ◽  
Gwas Data ◽  
Production Traits ◽  
Egg Weight ◽  
Genome Region ◽  
Genomic Regions ◽  
The Relationship

Objective. To assess the variability of egg production traits for nine SNPs, to search for traces of selection in the genome of Russian white chickens based on ROH patterns. Methods. The material for the study was DNA isolated from the blood of Russian white chickens (n = 141). Nine SNPs associated with egg production at p 5.16 105 according to GWAS data were selected for analysis. The frequencies of alleles and genotypes, the relationship between genotypes and characteristics of egg production were calculated, and ROH patterns were identified. Results. Significant differences between genotypes were found in terms of age of laying the first egg (p 0.005) and egg weight (p 0.05). The genomic regions surrounding the target SNPs were analyzed according to the distribution of homozygous regions in them. Conclusions. The substitutions rs317565390 and rs16625488 located in the 4.810.2 Mb region on chromosome 8 showed polymorphism, despite the fact that homozygous loci in this region of the genome are found in 58% of animals. For most SNPs, the prevalence of the frequency of one of the alleles was observed. As a cluster of increased selection pressure, a chick genome region in the 4.810.2 Mb region on chromosome 8 was identified.

scholarly journals Runs of homozygosity analysis reveals consensus homozygous regions affecting production traits in Chinese Simmental beef cattle

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Guoyao Zhao ◽  
Yuqiang Liu ◽  
Qunhao Niu ◽  
Xu Zheng ◽  
Tianliu Zhang ◽  
...  
Keyword(s):  
Beef Cattle ◽  
Candidate Genes ◽  
Average Length ◽  
Snp Array ◽  
Reproductive Traits ◽  
Farm Animals ◽  
Production Traits ◽  
Runs Of Homozygosity ◽  
Exact Test ◽  
Genomic Regions

Abstract Background Genomic regions with a high frequency of runs of homozygosity (ROH) are related to important traits in farm animals. We carried out a comprehensive analysis of ROH and evaluated their association with production traits using the BovineHD (770 K) SNP array in Chinese Simmental beef cattle. Results We detected a total of 116,953 homozygous segments with 2.47Gb across the genome in the studied population. The average number of ROH per individual was 99.03 and the average length was 117.29 Mb. Notably, we detected 42 regions with a frequency of more than 0.2. We obtained 17 candidate genes related to body size, meat quality, and reproductive traits. Furthermore, using Fisher’s exact test, we found 101 regions were associated with production traits by comparing high groups with low groups in terms of production traits. Of those, we identified several significant regions for production traits (P < 0.05) by association analysis, within which candidate genes including ECT2, GABRA4, and GABRB1 have been previously reported for those traits in beef cattle. Conclusions Our study explored ROH patterns and their potential associations with production traits in beef cattle. These results may help to better understand the association between production traits and genome homozygosity and offer valuable insights into managing inbreeding by designing reasonable breeding programs in farm animals.

Polymorphism of beta (â) casein gene and their association with milk production traits in Sahiwal and HF crossbred cattle

2019 ◽  
Author(s):  
Akhilesh Pandey ◽  
M.S Thakur ◽  
Y. Pandey
Keyword(s):  
High Frequency ◽  
Restriction Site ◽  
Research Work ◽  
Production Traits ◽  
Veterinary Science ◽  
Crossbred Cattle ◽  
Milk Production Traits ◽  
Casein Gene ◽  
Restriction Sites ◽  
Endonuclease Enzyme

Present research work was carried out on 50 Sahiwal and 50 HF Crossbred cattle in the Department of Animal Genetics and Breeding of College of Veterinary Science and A H Jabalpur. During the research work the PCR amplified products of 121bp was digested by restriction endonuclease enzyme DdeI, which recognizes G^AATTC sites. The patterns evolved in the present study showed that the presence of one restriction site on one alleles and absence of restriction site on other alleles resulted in the appearance of three bands of 121, 86 and 35bp.This genotype was referred to as A1A2. When both strand had no restriction sites for the enzyme, only one band of 121bp was observed on the gel such genotype was designated as A2A2 type. The â- casein gene showed A2A2 and A1A2 genotypes were observed in Sahiwal and HF crossbred cattle. The genotypic frequencies of â-casein (CSN2)/ DdeI gene for A1A1, A1A2 and A2A2 are 0.00, 0.30, and 0.70 in Sahiwal and 0.00, 0.64 and 0.36 in HF crossbred cattle, respectively and the gene frequency A1 and A2 is 0.15 and 0.85 in Sahiwal and 0.32 and 0.68 in HF crossbred cattle. High frequency of A2 allele was observed in both the breeds of cattle under the study.

Identification of Genetic Variants in ABCG2 Gene Influencing Milk Production Traits in Dairy Cattle

2019 ◽  
Author(s):  
Arun Pratap Singh ◽  
A K Chakravarty ◽  
M A Mir ◽  
Ashwani Arya ◽  
Manvendra Singh
Keyword(s):  
Milk Yield ◽  
Rflp Analysis ◽  
Milk Composition ◽  
Breeding Value ◽  
Production Traits ◽  
Crossbred Cattle ◽  
Fat Percentage ◽  
Pcr Rflp ◽  
Karan Fries ◽  
Abcg2 Gene

This study was performed to investigate the polymorphisms in the ABCG2 (ATP-binding cassette sub-family G member 2) gene and to reveal the association of genotypes with breeding value (BV) for first lactation milk yield and milk composition traits of Karan Fries (HF crossbred) cattle. The traits were adjusted against the significant effect of non-genetic factors. PCR-RFLP analysis of ABCG2 (exon 14) gene revealed three genotypes. AA genotype in ABCG2 gene had significant effect on BV for average test day fat percentage. The identified potential genetic marker could be used for the development of Marker Assisted Selection (MAS) strategy for higher milk yield and milk composition traits in Karan Fries Cattle.

scholarly journals Mapping of Genomic Regions (Quantitative Trait Loci) Controlling Production and Quality in Industrial Cultures of the Edible Basidiomycete Pleurotus ostreatus

2003 ◽  
Vol 69 (6) ◽  
pp. 3617-3625 ◽  
Author(s):  
Luis M. Larraya ◽  
Mikel Alfonso ◽  
Antonio G. Pisabarro ◽  
Luc�a Ram�rez
Keyword(s):  
Quantitative Trait Loci ◽  
Quantitative Trait ◽  
Pleurotus Ostreatus ◽  
Production Traits ◽  
Trial And Error ◽  
Trait Loci ◽  
Industrial Strains ◽  
Culture Production ◽  
Culture Process ◽  
Genomic Regions

ABSTRACT Industrial production of the edible basidiomycete Pleurotus ostreatus (oyster mushroom) is based on a solid fermentation process in which a limited number of selected strains are used. Optimization of industrial mushroom production depends on improving the culture process and breeding new strains with higher yields and productivities. Traditionally, fungal breeding has been carried out by an empirical trial and error process. In this study, we used a different approach by mapping quantitative trait loci (QTLs) controlling culture production and quality within the framework of the genetic linkage map of P. ostreatus. Ten production traits and four quality traits were studied and mapped. The production QTLs identified explain nearly one-half of the production variation. More interestingly, a single QTL mapping to the highly polymorphic chromosome VII appears to be involved in control of all the productivity traits studied. Quality QTLs appear to be scattered across the genome and to have less effect on the variation of the corresponding traits. Moreover, some of the new hybrid strains constructed in the course of our experiments had production or quality values higher than those of the parents or other commercial strains. This approach opens the possibility of marker-assisted selection and breeding of new industrial strains of this fungus.

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