Advances in Buffalo (Bubalus bubalis) Genetics and Genomics

A special issue of Animals (ISSN 2076-2615). This special issue belongs to the section "Animal Genetics and Genomics".

Deadline for manuscript submissions: 31 October 2024 | Viewed by 4362

Special Issue Editors

Department of Veterinary Medicine and Animal Production, University of Naples Federico II, Via Delpino 1, 80137 Naples, Italy
Interests: animal cytogenetics; animal genetics; congenital malformations; disorders of sex development; DNA methylation; animal breeding; animal genetic improvement
Special Issues, Collections and Topics in MDPI journals
Department of Veterinary Medicine and Animal Production, University of Naples Federico II, Via Delpino 1, 80137 Naples, Italy
Interests: autochthonous livestock breeds; promotion of typical foods; animal cytogenetics; genetic traceability of animal products; animal genetics; biomonitoring; congenital malformations
Special Issues, Collections and Topics in MDPI journals
Department of Veterinary Medicine and Animal Production, University of Naples Federico II, Via Delpino 1, 80137 Naples, Italy
Interests: animal cytogenetics; animal genetics; molecular basis of embryo development; congenital malformations; DNA extraction methods; disorders of sex development; biomonitoring
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

The world buffalo population is about 195 million, distributed across at least 129 different countries, mainly in tropical and subtropical areas. The buffalo species constitutes a primary resource for many small-scale farmers in developing countries.

Breeding programs are carried out in many countries, such as China, India, and Brazil. Italy represents the international point of reference for buffalo breeding as a result of innovations in management, dairy technologies, cheese manufacturing, feeding, and reproduction.

It has become essential to turn attention to new selection goals such as environmental sustainability, animal welfare, and further improving the quality of production. Therefore, genetics and genomics are strategic tools to increase and deepen our knowledge of buffalo biology.

Papers concerning genetic and genomic selection in buffalo, focusing on improving animal production with respect to environmental sustainability and animal welfare, are welcome for submission to this Special Issue.

Prof. Dr. Francesca Ciotola
Prof. Dr. Vincenzo Peretti
Dr. Sara Albarella
Guest Editors

Manuscript Submission Information

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Keywords

  • buffalo (Bubalus bubalis)
  • genomics
  • genetic improvement
  • production quality
  • reproduction
  • fertility
  • health
  • welfare
  • environmental sustainability
 

Published Papers (3 papers)

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Research

17 pages, 3350 KiB  
Article
A Single-Step Genome-Wide Association Study for Semen Traits of Egyptian Buffalo Bulls
by Ayman G. EL Nagar, Mohamed M. I. Salem, Amin M. S. Amin, Maher H. Khalil, Ayman F. Ashour, Mohammed M. Hegazy and Hamdy Abdel-Shafy
Animals 2023, 13(24), 3758; https://doi.org/10.3390/ani13243758 - 05 Dec 2023
Viewed by 1015
Abstract
The present study aimed to contribute to the limited research on buffalo (Bubalus bubalis) semen traits by incorporating genomic data. A total of 8465 ejaculates were collected. The genotyping procedure was conducted using the Axiom® Buffalo Genotyping 90 K array [...] Read more.
The present study aimed to contribute to the limited research on buffalo (Bubalus bubalis) semen traits by incorporating genomic data. A total of 8465 ejaculates were collected. The genotyping procedure was conducted using the Axiom® Buffalo Genotyping 90 K array designed by the Affymetrix Expert Design Program. After conducting a quality assessment, we utilized 67,282 SNPs genotyped in 192 animals. We identified several genomic loci explaining high genetic variance by employing single-step genomic evaluation. The aforementioned regions were located on buffalo chromosomes no. 3, 4, 6, 7, 14, 16, 20, 22, and the X-chromosome. The X-chromosome exhibited substantial influence, accounting for 4.18, 4.59, 5.16, 5.19, and 4.31% of the genomic variance for ejaculate volume, mass motility, livability, abnormality, and concentration, respectively. In the examined genomic regions, we identified five novel candidate genes linked to male fertility and spermatogenesis, four in the X-chromosome and one in chromosome no. 16. Additional extensive research with larger sample sizes and datasets is imperative to validate these findings and evaluate their applicability for genomic selection. Full article
(This article belongs to the Special Issue Advances in Buffalo (Bubalus bubalis) Genetics and Genomics)
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13 pages, 2814 KiB  
Article
A Novel Insight into the Identification of Potential SNP Markers for the Genomic Characterization of Buffalo Breeds in Pakistan
by Muhammad Anas, Muhammad Farooq, Muhammad Asif, Waqas Rafique Ali and Shahid Mansoor
Animals 2023, 13(15), 2543; https://doi.org/10.3390/ani13152543 - 07 Aug 2023
Cited by 1 | Viewed by 1279
Abstract
Domestic buffaloes (Bubalus bubalis), known as water buffaloes, play a key role as versatile multipurpose agricultural animals in the Asiatic region. Pakistan, with the second-largest buffalo population in the world, holds a rich domestication history of buffaloes. The overall trends in [...] Read more.
Domestic buffaloes (Bubalus bubalis), known as water buffaloes, play a key role as versatile multipurpose agricultural animals in the Asiatic region. Pakistan, with the second-largest buffalo population in the world, holds a rich domestication history of buffaloes. The overall trends in buffalo production demand the genomic characterization of Pakistani buffalo breeds. To this end, the resequencing data of Pakistani breeds, along with buffalo breeds from 13 other countries, were retrieved from our previous study. This dataset, which contained 34,671,886 single-nucleotide polymorphisms (SNPs), was analyzed through a pipeline that was developed to compare possible allele differences among breeds at each SNP position. In contrast, other available tools only check for positional SNP differences for breed-specific markers. In total, 1918, 1549, 404, and 341 breed-specific markers were identified to characterize the Nili, Nili–Ravi, Azakheli, and Kundi breeds of Pakistani buffalo, respectively. Sufficient evidence in the form of phenotypic data, principal component analysis, admixture analysis, and linkage analysis showed that the Nili breed has maintained its distinct breed status despite sharing a close evolutionary relationship with the Nili–Ravi breed of buffalo. In this era of genome science, the conservation of these breeds and the further validation of the given selection markers in larger populations is a pressing need. Full article
(This article belongs to the Special Issue Advances in Buffalo (Bubalus bubalis) Genetics and Genomics)
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18 pages, 2985 KiB  
Article
Genome-Wide Identification, Evolutionary and Mutational Analysis of the Buffalo Sox Gene Family
by Muhammad Abdullah, Muhammad Saif-ur Rehman, Muhammad Shah Nawaz-ul Rehman, Abdullah A. AlKahtane, Tahani Mohamed Al-Hazani, Faiz-ul Hassan and Saif ur Rehman
Animals 2023, 13(14), 2246; https://doi.org/10.3390/ani13142246 - 08 Jul 2023
Cited by 1 | Viewed by 1503
Abstract
The Sox gene family constitutes transcription factors with a conserved high mobility group box (HMG) that regulate a variety of developmental processes, including sex differentiation, neural, cartilage, and early embryonic development. In this study, we systematically analyzed and characterized the 20 Sox genes [...] Read more.
The Sox gene family constitutes transcription factors with a conserved high mobility group box (HMG) that regulate a variety of developmental processes, including sex differentiation, neural, cartilage, and early embryonic development. In this study, we systematically analyzed and characterized the 20 Sox genes from the whole buffalo genome, using comparative genomic and evolutionary analyses. All the buffalo Sox genes were divided into nine sub-groups, and each gene had a specific number of exons and introns, which contributed to different gene structures. Molecular phylogeny revealed more sequence similarity of buffalo Sox genes with those of cattle. Furthermore, evolutionary analysis revealed that the HMG domain remained conserved in the all members of the Sox gene family. Similarly, all the genes are under strong purifying selection pressure; seven segmental duplications occurred from 9.65 to 21.41 million years ago (MYA), and four potential recombination breakpoints were also predicted. Mutational analysis revealed twenty non-synonymous mutations with potential effects on physiological functions, including embryonic development and cell differentiation in the buffalo. The present study provides insights into the genetic architecture of the Sox gene family in buffalo, highlights the significance of mutations, and provides their potential utility for marker-assisted selection for targeted genetic improvement in buffalo. Full article
(This article belongs to the Special Issue Advances in Buffalo (Bubalus bubalis) Genetics and Genomics)
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