Identification of important genomic footprints using eight different selection signature statistics in domestic cattle breeds

Gene ◽  
2022 ◽  
pp. 146165
Author(s):  
Divya Rajawat ◽  
Manjit Panigrahi ◽  
Harshit Kumar ◽  
Sonali Sonejita Nayak ◽  
Subhashree Parida ◽  
...  
Keyword(s):  
Selection Signature ◽  
Cattle Breeds

scholarly journals Discovery of Genomic Characteristics and Selection Signatures in Southern Chinese Local Cattle

2020 ◽  
Vol 11 ◽  
Author(s):  
Yuqiang Liu ◽  
Lingyang Xu ◽  
Liu Yang ◽  
Guoyao Zhao ◽  
Junya Li ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Southern China ◽  
Local Environment ◽  
Candidate Snps ◽  
Signature Analysis ◽  
Significant Information ◽  
Selection Signature ◽  
Cattle Breeds ◽  
Southern Chinese ◽  
Candidate Regions

Chinese local cattle with a high level of genetic diversity mainly originate from two subspecies; the cattle in northern China are primarily Bos Taurus, and the cattle in southern China are primarily Bos indicus. Cattle from southern China are characterized by a specific phenotype and adapted to the local environment. This study explored the genetic diversity, degree of admixture, and selection signature in eight local cattle breeds in southern China. The lowest level of heterozygosity was found in Hainan and Nandan cattle from Hainan and Guangxi province, respectively, whereas the highest level of heterozygosity was detected in Zhaotong cattle from Yunnan province. A neighbor-joining phylogenetic tree analysis clearly separated Lufeng cattle from other breeds, whereas Leiqiong and Hainan cattle have some crossover. Based on linkage disequilibrium-filtered single nucleotide polymorphisms (SNPs), the admixture analysis revealed two clusters corresponding to the taurine and indicine cattle lineages, and the local cattle breeds from southern China showed a certain degree of admixture. When K = 4 and 9, we found a slight separation among Leiqiong, Lufeng, and Hainan cattle. Meanwhile, we performed a selection signature analysis in Hainan, Leiqiong, and Lufeng cattle distributed in the extreme south of China, using the integrated haplotype score (iHS), Rsb statistic, and BayeScan software. Using the iHS approach, we identified 251, 270, and 256 candidate regions in Lufeng, Leiqiong, and Hainan cattle, respectively. Moreover, we identified 184, 174, and 146 candidate regions in pairwise comparisons of Leiqiong vs. Lufeng, Leiqiong vs. Hainan, and Hainan vs. Lufeng cattle using the Rsb approach. In addition, we identified 76 loci with a total of 48 genes under selection, based on the FST approach. Several candidate genes under selection were found to be related to meat quality, immunity, and adaptation to the local environment in southern China. Our results provide significant information about the genetic differences among the cattle breeds from southern China and the possible cause of difference in breed-specific characteristics. Selection signature analysis identified a few candidate SNPs and genes related to certain important traits of these cattle. In general, our results provide valuable insights into the genetic basis of specific traits under selection in certain local cattle breeds.

REALIZATION OF PARENTAL INDICES OF COW PRODUCTIVITY IN DIFFERENT MILKING BREEDS AT BREEDING FARM "AGROFIRMA "PAKHMA"

2020 ◽  
Keyword(s):  
Milk Yield ◽  
Cattle Breed ◽  
Holstein Cattle ◽  
Milk Productivity ◽  
Cattle Breeds ◽  
Significant Difference ◽  
Production Indices ◽  
High Level ◽  
Beta Lactoglobulin ◽  
Percentage Protein

Combination of genotypes of main types’ genetic markers causes milk productivity in cattle. The article studies correlation between kappa casein genotypes (C3N3), beta-lactoglobulin (LGB), their complexes and milk production indices in cows bred under equal conditions at a breeding farm. The calculation of parental milk yield and fat indices between the three breeds showed a significant difference (P>0,999) of PCI of Ayrshire and Holstein cattle breed milk yield - 3395 kg, PCI of fat - 0,22%; between Holstein and Yaroslavl cattle breeds - 3200 kg, PCI offat - 0,16%. A significant difference of realization indices of protein between all three breeds was not stated. The highest realization ofparental milk yield index was stated - between Ayrshire and Yaroslavl cattle breeds- 113%, Holstein cattle breed - 88%. As for the fat and protein indices, all three cattle breeds showed a high realization of PCI from 98% to 109%. However, Holstein cattle breed showed the highest percentage: protein - 101%, fat - 109%. A significant difference of PCI realization of milk productivity in CSN3 and LGB genotypes was not stated. It was also stated that there is a tendency of high level parental indices realization when there is a higher number of B-allele variants in genotypes of cows.

Intrabreed and interbreed variation of the BOLA-DRB3.2 gene in the Kostroma and Yaroslavl indigenous Russian cattle breeds

2020 ◽  
Vol 72 (6-7) ◽  
pp. 355-366
Author(s):  
Irina V. Lazebnaya ◽  
Aleksey V. Perchun ◽  
Oleg E. Lazebny
Keyword(s):  
Cattle Breeds

scholarly journals The Water Footprint of Primary and Secondary Processing of Beef from Different Cattle Breeds: A Value Fraction Allocation Model

2021 ◽  
Vol 13 (12) ◽  
pp. 6914
Author(s):  
Frikkie Alberts Maré ◽  
Henry Jordaan
Keyword(s):  
Water Footprint ◽  
Negative Relationship ◽  
High Water ◽  
Allocation Model ◽  
Cattle Breeds ◽  
A Value ◽  
Average Production ◽  
High Water Intake ◽  
The Difference ◽  
By Products

The high water intake and wastewater discharge of slaughterhouses have been a concern for many years. One neglected factor in previous research is allocating the water footprint (WF) to beef production’s different products and by-products. The objective of this article was to estimate the WF of different cattle breeds at a slaughterhouse and cutting plant and allocate it according to the different cuts (products) and by-products of beef based on the value fraction of each. The results indicated a negative relationship between the carcass weight and the processing WF when the different breeds were compared. Regarding a specific cut of beef, a kilogram of rib eye from the heaviest breed had a processing WF of 614.57 L/kg, compared to the 919.91 L/kg for the rib eye of the lightest breed. A comparison of the different cuts indicated that high-value cuts had higher WFs than low-value cuts. The difference between a kilogram of rib eye and flank was 426.26 L/kg for the heaviest breed and 637.86 L/kg for the lightest breed. An option to reduce the processing WF of beef is to lessen the WF by slaughtering heavier animals. This will require no extra investment from the slaughterhouse. At the same time, the returns should increase as the average production inputs per kilogram of output (carcass) should reduce, as the slaughterhouse will process more kilograms.

scholarly journals Harmful mutation load in the mitochondrial genomes of cattle breeds

2021 ◽  
Vol 14 (1) ◽  
Author(s):  
Sankar Subramanian
Keyword(s):  
Population Size ◽  
Artificial Selection ◽  
Deleterious Mutation ◽  
Genetic Diseases ◽  
Mitochondrial Genomes ◽  
Deleterious Mutations ◽  
Founder Population ◽  
Mutation Load ◽  
Effective Population ◽  
Cattle Breeds

Abstract Objective Domestication of wild animals results in a reduction in the effective population size, and this could affect the deleterious mutation load of domesticated breeds. Furthermore, artificial selection will also contribute to the accumulation of deleterious mutations due to the increased rate of inbreeding among these animals. The process of domestication, founder population size, and artificial selection differ between cattle breeds, which could lead to a variation in their deleterious mutation loads. We investigated this using mitochondrial genome data from 364 animals belonging to 18 cattle breeds of the world. Results Our analysis revealed more than a fivefold difference in the deleterious mutation load among cattle breeds. We also observed a negative correlation between the breed age and the proportion of deleterious amino acid-changing polymorphisms. This suggests a proportionally higher deleterious SNPs in young breeds compared to older breeds. Our results highlight the magnitude of difference in the deleterious mutations present in the mitochondrial genomes of various breeds. The results of this study could be useful in predicting the rate of incidence of genetic diseases in different breeds.

scholarly journals On the origin and diversification of Podolian cattle breeds: testing scenarios of European colonization using genome-wide SNP data

2021 ◽  
Vol 53 (1) ◽  
Author(s):  
Gabriele Senczuk ◽  
Salvatore Mastrangelo ◽  
Paolo Ajmone-Marsan ◽  
Zsolt Becskei ◽  
Paolo Colangelo ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Diversity Indices ◽  
Melting Pot ◽  
Cattle Breeds ◽  
Snp Data ◽  
Early Migration ◽  
Genome Wide ◽  
European Colonization ◽  
Approximate Bayesian ◽  
European Cattle

Abstract Background During the Neolithic expansion, cattle accompanied humans and spread from their domestication centres to colonize the ancient world. In addition, European cattle occasionally intermingled with both indicine cattle and local aurochs resulting in an exclusive pattern of genetic diversity. Among the most ancient European cattle are breeds that belong to the so-called Podolian trunk, the history of which is still not well established. Here, we used genome-wide single nucleotide polymorphism (SNP) data on 806 individuals belonging to 36 breeds to reconstruct the origin and diversification of Podolian cattle and to provide a reliable scenario of the European colonization, through an approximate Bayesian computation random forest (ABC-RF) approach. Results Our results indicate that European Podolian cattle display higher values of genetic diversity indices than both African taurine and Asian indicine breeds. Clustering analyses show that Podolian breeds share close genomic relationships, which suggests a likely common genetic ancestry. Among the simulated and tested scenarios of the colonization of Europe from taurine cattle, the greatest support was obtained for the model assuming at least two waves of diffusion. Time estimates are in line with an early migration from the domestication centre of non-Podolian taurine breeds followed by a secondary migration of Podolian breeds. The best fitting model also suggests that the Italian Podolian breeds are the result of admixture between different genomic pools. Conclusions This comprehensive dataset that includes most of the autochthonous cattle breeds belonging to the so-called Podolian trunk allowed us not only to shed light onto the origin and diversification of this group of cattle, but also to gain new insights into the diffusion of European cattle. The most well-supported scenario of colonization points to two main waves of migrations: with one that occurred alongside with the Neolithic human expansion and gave rise to the non-Podolian taurine breeds, and a more recent one that favoured the diffusion of European Podolian. In this process, we highlight the importance of both the Mediterranean and Danube routes in promoting European cattle colonization. Moreover, we identified admixture as a driver of diversification in Italy, which could represent a melting pot for Podolian cattle.

scholarly journals Identifying Candidate Genes for Hypoxia Adaptation of Tibet Chicken Embryos by Selection Signature Analyses and RNA Sequencing

Genes ◽  
2020 ◽  
Vol 11 (7) ◽  
pp. 823
Author(s):  
Xiayi Liu ◽  
Xiaochen Wang ◽  
Jing Liu ◽  
Xiangyu Wang ◽  
Haigang Bao
Keyword(s):  
Candidate Genes ◽  
Rna Sequencing ◽  
Differentially Expressed Genes ◽  
Gallus Gallus ◽  
Differentially Expressed ◽  
Tibet Plateau ◽  
Embryonic Liver ◽  
Selection Signature ◽  
Chicken Embryos ◽  
Hypoxia Adaptation

The Tibet chicken (Gallus gallus) lives on the Qinghai–Tibet Plateau and adapts to the hypoxic environment very well. The objectives of this study was to obtain candidate genes associated with hypoxia adaptation in the Tibet chicken embryos. In the present study, we used the fixation index (Fst) and cross population extended haplotype homozygosity (XPEHH) statistical methods to detect signatures of positive selection of the Tibet chicken, and analyzed the RNA sequencing data from the embryonic liver and heart with HISAT, StringTie and Ballgown for differentially expressed genes between the Tibet chicken and White leghorn (Gallus gallus, a kind of lowland chicken) embryos hatched under hypoxia condition. Genes which were screened out by both selection signature analysis and RNA sequencing analysis could be regarded as candidate genes for hypoxia adaptation of chicken embryos. We screened out 1772 genes by XPEHH and 601 genes by Fst, and obtained 384 and 353 differentially expressed genes in embryonic liver and heart, respectively. Among these genes, 89 genes were considered as candidate genes for hypoxia adaptation in chicken embryos. ARNT, AHR, GSTK1 and FGFR1 could be considered the most important candidate genes. Our findings provide references to elucidate the molecular mechanism of hypoxia adaptation in Tibet chicken embryos.

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