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Research on Genetics and Genomics of Cattle
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Research on Genetics and Genomics of Cattle

A special issue of Genes (ISSN 2073-4425). This special issue belongs to the section "Animal Genetics and Genomics".

Deadline for manuscript submissions: 20 May 2024 | Viewed by 6418

Special Issue Editor

Dr. Hanfang Cai

E-Mail Website
Guest Editor
Henan Innovative Engineering Research Center of Poultry Germplasm Resource, College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, China
Interests: biotechnology; animal breeding

Special Issue Information

Dear Colleagues,

Cattle are the most widespread species of large ruminants. They have incredibly high economic value and provide us with meat (such as Japanese beef, Angus, and Simmental), milk (Holstein and Jersey), leather, and other useful products. With the development of biotechnology, molecular biology, genetics, and bioinformatics, multi-omics approaches are commonly used to reveal the mechanisms underlying bovine milk performance, reproductive traits, beef quality, growth traits, disease resistance, and other important traits from the DNA level (such as polymorphisms and chromosome modification), RNA level (ncRNA, alternative splicing, and RNA modification), and protein level (protein phosphorylation and acetylation). However, much of their detailed regulatory mechanism is unknown. Genes is now inviting submissions for a Special Issue on the topic of “Genetics and Genomics of Cattle”. Research articles, reviews, short communications, brief reports, and other forms of original articles on this topic are all welcome. Your contribution will open new avenues to discover the theoretical and practical aspects of cattle phenotype traits and provide valuable information for cattle breeding projects.

Dr. Hanfang Cai
Guest Editor

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Genes is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2600 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • cattle
  • regulatory mechanisms
  • epigenetics
  • transcriptome
  • proteome
  • sequencing
  • gene
  • polymorphisms

Published Papers (7 papers)

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Research

Jump to: Review, Other

13 pages, 1799 KiB  
Article
Molecular Mechanisms Associated with the Development of the Metritis Complex in Dairy Cattle
by Leanna Sanchez, Fernando Campos-Chillon, Mehdi Sargolzaei, Daniel G. Peterson, Kim A. Sprayberry, Garry McArthur, Paul Anderson, Bruce Golden, Siroj Pokharel and Mohammed K. Abo-Ismail
Genes 2024, 15(4), 439; https://doi.org/10.3390/genes15040439 - 30 Mar 2024
Viewed by 519
Abstract
The metritis complex (MC), a group of post-partum uterine diseases, is associated with increased treatment costs and reduced milk yield and fertility. The goal of this study was to identify genetic variants, genes, or genomic regions that modulate MC disease. A genome-wide association [...] Read more.
The metritis complex (MC), a group of post-partum uterine diseases, is associated with increased treatment costs and reduced milk yield and fertility. The goal of this study was to identify genetic variants, genes, or genomic regions that modulate MC disease. A genome-wide association study was performed using a single-locus mixed linear model of 1967 genotypes (624,460 SNPs) and metritis complex records. Then, in-silico functional analyses were performed to detect biological mechanisms and pathways associated with the development of MC. The ATP8A2, COX16, AMN, and TRAF3 genes, located on chromosomes 12, 10, and 21, were associated with MC at p ≤ 0.0001. These genes are involved in the regulation of cholesterol metabolism in the stromal tissue of the uterus, which can be directly associated with the mode of transmission for pathogens causing the metritis complex. The modulation of cholesterol abundance alters the efficiency of virulence factors and may affect the susceptibility of the host to infection. The SIPA1L1, DEPDC5, and RNF122 genes were also significantly associated with MC at p ≤ 0.0001 and are involved in the PI3k-Akt pathway, responsible for activating the autophagic processes. Thus, the dysregulation of these genes allows for unhindered bacterial invasion, replication, and survival within the endometrium. Full article
(This article belongs to the Special Issue Research on Genetics and Genomics of Cattle)
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12 pages, 1916 KiB  
Article
Genetic Background of Blood β-Hydroxybutyrate Acid Concentrations in Early-Lactating Holstein Dairy Cows Based on Genome-Wide Association Analyses
by Yueqiang Wang, Zhenyu Wang, Wenhui Liu, Shuoqi Xie, Xiaoli Ren, Lei Yan, Dong Liang, Tengyun Gao, Tong Fu, Zhen Zhang and Hetian Huang
Genes 2024, 15(4), 412; https://doi.org/10.3390/genes15040412 - 26 Mar 2024
Viewed by 516
Abstract
Ketosis is a common metabolic disorder in the early lactation of dairy cows. It is typically diagnosed by measuring the concentration of β-hydroxybutyrate (BHB) in the blood. This study aimed to estimate the genetic parameters of blood BHB and conducted a genome-wide association [...] Read more.
Ketosis is a common metabolic disorder in the early lactation of dairy cows. It is typically diagnosed by measuring the concentration of β-hydroxybutyrate (BHB) in the blood. This study aimed to estimate the genetic parameters of blood BHB and conducted a genome-wide association study (GWAS) based on the estimated breeding value. Phenotypic data were collected from December 2019 to August 2023, comprising blood BHB concentrations in 45,617 Holstein cows during the three weeks post-calving across seven dairy farms. Genotypic data were obtained using the Neogen Geneseek Genomic Profiler (GGP) Bovine 100 K SNP Chip and GGP Bovine SNP50 v3 (Illumina Inc., San Diego, CA, USA) for genotyping. The estimated heritability and repeatability values for blood BHB levels were 0.167 and 0.175, respectively. The GWAS result detected a total of ten genome-wide significant associations with blood BHB. Significant SNPs were distributed in Bos taurus autosomes (BTA) 2, 6, 9, 11, 13, and 23, with 48 annotated candidate genes. These potential genes included those associated with insulin regulation, such as INSIG2, and those linked to fatty acid metabolism, such as HADHB, HADHA, and PANK2. Enrichment analysis of the candidate genes for blood BHB revealed the molecular functions and biological processes involved in fatty acid and lipid metabolism in dairy cattle. The identification of novel genomic regions in this study contributes to the characterization of key genes and pathways that elucidate susceptibility to ketosis in dairy cattle. Full article
(This article belongs to the Special Issue Research on Genetics and Genomics of Cattle)
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11 pages, 2173 KiB  
Article
Population Structure and Selection Signal Analysis of Nanyang Cattle Based on Whole-Genome Sequencing Data
by Yan Zhang, Zhitong Wei, Man Zhang, Shiwei Wang, Tengyun Gao, Hetian Huang, Tianliu Zhang, Hanfang Cai, Xian Liu, Tong Fu and Dong Liang
Genes 2024, 15(3), 351; https://doi.org/10.3390/genes15030351 - 11 Mar 2024
Viewed by 781
Abstract
With a rich breeding history, Nanyang cattle (NY cattle) have undergone extensive natural and artificial selection, resulting in distinctive traits such as high fertility, excellent meat quality, and disease resistance. This makes them an ideal model for studying the mechanisms of environmental adaptability. [...] Read more.
With a rich breeding history, Nanyang cattle (NY cattle) have undergone extensive natural and artificial selection, resulting in distinctive traits such as high fertility, excellent meat quality, and disease resistance. This makes them an ideal model for studying the mechanisms of environmental adaptability. To assess the population structure and genetic diversity of NY cattle, we performed whole-genome resequencing on 30 individuals. These data were then compared with published whole-genome resequencing data from 432 cattle globally. The results indicate that the genetic structure of NY cattle is significantly different from European commercial breeds and is more similar to North–Central Chinese breeds. Furthermore, among all breeds, NY cattle exhibit the highest genetic diversity and the lowest population inbreeding levels. A genome-wide selection signal analysis of NY cattle and European commercial breeds using Fst, θπ-ratio, and θπ methods revealed significant selection signals in genes associated with reproductive performance and immunity. Our functional annotation analysis suggests that these genes may be responsible for reproduction (MAP2K2, PGR, and GSE1), immune response (NCOA2, HSF1, and PAX5), and olfaction (TAS1R3). We provide a comprehensive overview of sequence variations in the NY cattle genome, revealing insights into the population structure and genetic diversity of NY cattle. Additionally, we identify candidate genes associated with important economic traits, offering valuable references for future conservation and breeding efforts of NY cattle. Full article
(This article belongs to the Special Issue Research on Genetics and Genomics of Cattle)
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14 pages, 823 KiB  
Article
Genetic Parameters for Limousine Interbeef Genetic Evaluation of Calving Traits
by Zdeňka Veselá, Michaela Brzáková, Alexandra Novotná and Luboš Vostrý
Genes 2024, 15(2), 216; https://doi.org/10.3390/genes15020216 - 07 Feb 2024
Viewed by 628
Abstract
The aim of this study was to estimate across-country genetic correlations for calving traits (birth weight, calving ease) in the Limousine breed. Correlations were estimated for eight populations (Czech Republic, joint population of Denmark, Finland, and Sweden, France, Great Britain, Ireland, Slovenia, Switzerland, [...] Read more.
The aim of this study was to estimate across-country genetic correlations for calving traits (birth weight, calving ease) in the Limousine breed. Correlations were estimated for eight populations (Czech Republic, joint population of Denmark, Finland, and Sweden, France, Great Britain, Ireland, Slovenia, Switzerland, and Estonia). An animal model on raw performance accounting for across-country interactions (AMACI) was used. (Co)variance components were estimated for pairwise combinations of countries. Fixed and random effects were defined by each country according to its national genetic evaluation system. The average across-country genetic correlation for the direct genetic effect was 0.85 for birth weight (0.69–0.96) and 0.75 for calving ease (0.62–0.94). The average correlation for the maternal genetic effect was 0.57 for birth weight and 0.61 for calving ease. After the estimation of genetic parameters, the weighted bending procedure was used to compute the full Interbeef genetic correlation matrix. After bending, direct genetic correlations ranged from 0.62 to 0.84 (with an average of 0.73) for birth weight and from 0.58 to 0.82 (with an average of 0.68) for calving ease. Full article
(This article belongs to the Special Issue Research on Genetics and Genomics of Cattle)
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Review

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13 pages, 509 KiB  
Review
Research Progress and Applications of Bovine Genome in the Tribe Bovini
by Xingjie Du, Yu Sun, Tong Fu, Tengyun Gao and Tianliu Zhang
Genes 2024, 15(4), 509; https://doi.org/10.3390/genes15040509 - 18 Apr 2024
Viewed by 104
Abstract
Various bovine species have been domesticated and bred for thousands of years, and they provide adequate animal-derived products, including meat, milk, and leather, to meet human requirements. Despite the review studies on economic traits in cattle, the genetic basis of traits has only [...] Read more.
Various bovine species have been domesticated and bred for thousands of years, and they provide adequate animal-derived products, including meat, milk, and leather, to meet human requirements. Despite the review studies on economic traits in cattle, the genetic basis of traits has only been partially explained by phenotype and pedigree breeding methods, due to the complexity of genomic regulation during animal development and growth. With the advent of next-generation sequencing technology, genomics projects, such as the 1000 Bull Genomes Project, Functional Annotation of Animal Genomes project, and Bovine Pangenome Consortium, have advanced bovine genomic research. These large-scale genomics projects gave us a comprehensive concept, technology, and public resources. In this review, we summarize the genomics research progress of the main bovine species during the past decade, including cattle (Bos taurus), yak (Bos grunniens), water buffalo (Bubalus bubalis), zebu (Bos indicus), and gayal (Bos frontalis). We mainly discuss the development of genome sequencing and functional annotation, focusing on how genomic analysis reveals genetic variation and its impact on phenotypes in several bovine species. Full article
(This article belongs to the Special Issue Research on Genetics and Genomics of Cattle)
11 pages, 9846 KiB  
Review
Progress in Research on Key Factors Regulating Lactation Initiation in the Mammary Glands of Dairy Cows
by Haoyue Guo, Jianyuan Li, Yuhao Wang, Xiang Cao, Xiaoyang Lv, Zhangping Yang and Zhi Chen
Genes 2023, 14(6), 1163; https://doi.org/10.3390/genes14061163 - 26 May 2023
Cited by 1 | Viewed by 2459
Abstract
Lactation initiation refers to a functional change in the mammary organ from a non-lactating state to a lactating state, and a series of cytological changes in the mammary epithelium from a non-secreting state to a secreting state. Like the development of the mammary [...] Read more.
Lactation initiation refers to a functional change in the mammary organ from a non-lactating state to a lactating state, and a series of cytological changes in the mammary epithelium from a non-secreting state to a secreting state. Like the development of the mammary gland, it is regulated by many factors (including hormones, cytokines, signaling molecules, and proteases). In most non-pregnant animals, a certain degree of lactation also occurs after exposure to specific stimuli, promoting the development of their mammary glands. These specific stimuli can be divided into two categories: before and after parturition. The former inhibits lactation and decreases activity, and the latter promotes lactation and increases activity. Here we present a review of recent progress in research on the key factors of lactation initiation to provide a powerful rationale for the study of the lactation initiation process and mammary gland development. Full article
(This article belongs to the Special Issue Research on Genetics and Genomics of Cattle)
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Other

Jump to: Research, Review

8 pages, 573 KiB  
Brief Report
Evaluation of GSTP1, GSTA4 and AChE Gene Methylation in Bovine Lymphocytes Cultured In Vitro with Miconazole Alone and in Combination with Mospilan 20SP
by Jana Halušková, Beáta Holečková, Viera Schwarzbacherová, Martina Galdíková, Silvia Sedláková and Jaroslav Bučan
Genes 2023, 14(9), 1791; https://doi.org/10.3390/genes14091791 - 12 Sep 2023
Viewed by 805
Abstract
5-methylcytosine (5mC) is one of the most important epigenetic modifications. Its increased occurrence in regulatory sequences of genes, such as promoters and enhancers, is associated with the inhibition of their expression. Methylation patterns are not stable but are sensitive to factors such as [...] Read more.
5-methylcytosine (5mC) is one of the most important epigenetic modifications. Its increased occurrence in regulatory sequences of genes, such as promoters and enhancers, is associated with the inhibition of their expression. Methylation patterns are not stable but are sensitive to factors such as the environment, diet, and age. In the present study, we investigated the effects of fungicide miconazole, both alone and in combination with the insecticide Mospilan 20SP, on the methylation status of bovine GSTP1, GSTA4, and AChE genes in bovine lymphocytes cultured in vitro. The methylation-specific PCR technique was used for the objectives of this study. We found that miconazole alone at concentrations of 1.25, 2.5, 5, 10, 25, and 50 µg/mL after 24 h exposure probably did not induce changes in methylation for all three genes analysed. The same results were found for the combination of pesticides at 24 h exposure and the following concentrations for each of them: 0.625, 1.25, 2.5, 5, and 12.5 µg/mL. Thus, we can conclude that the fungicide miconazole alone, as well as in combination with the insecticide Mospilan 20SP, was unlikely to cause changes to the methylation of bovine GSTP1, GSTA4, and AChE genes. Full article
(This article belongs to the Special Issue Research on Genetics and Genomics of Cattle)
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Planned Papers

The below list represents only planned manuscripts. Some of these manuscripts have not been received by the Editorial Office yet. Papers submitted to MDPI journals are subject to peer-review.

1. Title: KBeagle: An Adaptive Strategy and Tool for Improving Imputation Accuracy and Computing Time

Abstract: Deep sequencing is now the primary way to uncover genetic variation and genomic. However, the complexity of entire genomes means that large segments remain missing even after sequencing. This issue has led to the development of computing intensive and efficient imputation software. In particular, the imputation software Beagle has been widely preferred for its low memory consumption and fast running speed. Here, we combined K-Means clustering algorithm with Beagle to improve the program’s imputation matching rate and shorten its computing time. We named this strategy as “KBeagle” (code freely available on Github: https://github.com/QinJieqq/KBeagle). The datasets used in the genomic selection test with imputed, unimputed, and real genotype show similar prediction accuracy under five-fold cross validation. However, estimated heritability using the KBeagle-imputed genotype dataset was closer to the estimations using the dataset containing real genotype. We envisage a major application of KBeagle will be focus on livestock sequencing studies under strong genetic structure. In conclusion, wimputation matching rate and computing time.

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