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Buffalo Genetics and Genomics
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Buffalo Genetics and Genomics

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

Deadline for manuscript submissions: 25 October 2025 | Viewed by 5016

Special Issue Editors

Prof. Dr. Qingyou Liu

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Guest Editor
State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning 530005, China
Interests: buffalo; ruminant; genomics; genetics; microbiome; metagenome
Dr. Laiba Shafique

E-Mail
Guest Editor Assistant
Guangxi Key Laboratory of Beibu Gulf Marine Biodiversity Conservation, Pinglu Canal and Beibu Gulf Coastal Ecosystem Observation and Research Station of Guangxi, Beibu Gulf University, Qinzhou 535011, China
Interests: genomics; evolution; structural chacterization; mutations; selection; genetics

Special Issue Information

Dear Colleagues,

The buffalo is a globally important domestic animal of immense value to humans. It is estimated that the global population of more than 200 million buffaloes is relied upon by more than 2 billion people—more than any other domesticated animal. Buffaloes are acclaimed for their unique, high-quality milk, which is characterized by its high fat and dry matter content. Buffalo milk is low in cholesterol but has more calories and fat than cow's milk and produces a high-value, thick, creamy cheese. Buffaloes exhibit a greater ability to degrade lignocellulose and reduce methane emissions compared to other cattle. The use of genetics and genomics in livestock breeding has significantly contributed to the development of the industry. It is crucial to understand the genetic capacity of the buffalo, the molecular mechanisms involved, and how its genome can be manipulated to improve the quality of livestock products. This information is of great importance to people worldwide. This Special Issue of Genetics on "Buffalo Genetics and Genomics" will focus on the applications of genetics and genomics technologies in buffalo, dairy, and beef cattle, and the new insights and approaches recently gained to provide scientific support for the healthy development of the buffalo industry. This Special Issue will provide an overview of recent developments in this area of research, including critical perspectives on current and upcoming challenges.

Prof. Dr. Qingyou Liu
Guest Editor

Dr. Laiba Shafique
Guest Editor Assistant

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Keywords

  • buffaloes
  • ruminant
  • genomics
  • genetics
  • evolution
  • structural characterization

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Published Papers (4 papers)

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Research

13 pages, 3178 KiB  
Article
Genome-Wide Association Study Identifies Potential Regulatory Loci and Pathways Related to Buffalo Reproductive Traits
by Wangchang Li, Qiyang Xie, Haiying Zheng, Anqin Duan, Liqing Huang, Chao Feng, Jianghua Shang and Chunyan Yang
Genes 2025, 16(4), 422; https://doi.org/10.3390/genes16040422 - 31 Mar 2025
Viewed by 282
Abstract
Background: The reproductive performance of water buffalo significantly impacts the economic aspects of production. Traditional breeding methods are constrained by low heritability and numerous influencing factors, making it difficult to effectively improve reproductive efficiency. Genome-wide association studies (GWAS) offer new possibilities for exploring [...] Read more.
Background: The reproductive performance of water buffalo significantly impacts the economic aspects of production. Traditional breeding methods are constrained by low heritability and numerous influencing factors, making it difficult to effectively improve reproductive efficiency. Genome-wide association studies (GWAS) offer new possibilities for exploring reproductive traits in water buffalo, opening up new avenues for efficient breeding. Methods: Using whole-genome resequencing, we identified quantitative trait loci (QTLs) associated with four suggestive reproductive traits: calving interval (CI), calf birth weight (CBW), dam birth weight (BW), and age at first calving (FCA). The study focused on identifying genetic variants that influence these reproductive traits. Results: Our research identified 52 suggestive regulatory loci associated with reproductive traits in water buffalo. Based on a 50 kb interval, we annotated these loci to 58 candidate genes. These loci involve genes such as AGBL4, GRM1, NCKAP5, and NRXN1, which are primarily enriched in pathways including the FOXO signaling pathway, calcium ion pathways, estrogen signaling pathway, and phospholipase D signaling pathway. These pathways directly or indirectly regulate the reproductive efficiency of water buffalo. Conclusions: This study has revealed suggestive regulatory genes (AGBL4, GRM1, NCKAP5, NRXN1) associated with reproductive traits in water buffalo. This not only enhances our understanding of the molecular mechanisms underlying complex traits but also points towards strategies for improving the reproductive capacity of water buffalo. These findings provide a solid foundation for future breeding programs aimed at enhancing water buffalo productivity. Full article
(This article belongs to the Special Issue Buffalo Genetics and Genomics)
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18 pages, 3208 KiB  
Article
GRM1 as a Candidate Gene for Buffalo Fertility: Insights from Genome-Wide Association Studies and Its Role in the FOXO Signaling Pathway
by Wangchang Li, Haiying Zheng, Duming Cao, Anqin Duan, Liqing Huang, Chao Feng and Chunyan Yang
Genes 2025, 16(2), 193; https://doi.org/10.3390/genes16020193 - 4 Feb 2025
Viewed by 801
Abstract
Background: Water buffaloes represent a crucial genetic resource for the global dairy industry, yet enhancements in their production performance remain relatively constrained. The advent of advanced sequencing technologies, coupled with genome-wide association studies (GWASs), has significantly boosted the potential for breeding superior-quality water [...] Read more.
Background: Water buffaloes represent a crucial genetic resource for the global dairy industry, yet enhancements in their production performance remain relatively constrained. The advent of advanced sequencing technologies, coupled with genome-wide association studies (GWASs), has significantly boosted the potential for breeding superior-quality water buffalo. Methods: An integrated genomic analysis was performed on sequencing data from 100 water buffaloes, utilizing the high-quality UOA_WB_1 genome assembly as a reference. This study particularly emphasized reproduction-related traits, with a focus on age at first calving (AFC). Results: Our analysis revealed two significant single-nucleotide polymorphisms (SNPs). Based on these genetic markers, the GRM1 gene was identified as a candidate gene. This gene shows substantial involvement in various reproduction-associated pathways, including the FOXO signaling pathway, calcium signaling pathway, and estrogen signaling pathway. Conclusions: The identification of GRM1 as a candidate gene provides a robust theoretical basis for molecular breeding strategies aimed at enhancing fertility in water buffaloes. These findings offer critical scientific support for optimizing breeding programs, thereby improving overall production efficiency. Full article
(This article belongs to the Special Issue Buffalo Genetics and Genomics)
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18 pages, 3031 KiB  
Article
In Silico Analysis: Molecular Characterization and Evolutionary Study of CLCN Gene Family in Buffalo
by Yiheng Fu, Muhammad Farhan Khan, Yingqi Wang, Shakeela Parveen, Mehwish Sultana, Qingyou Liu and Laiba Shafique
Genes 2024, 15(9), 1163; https://doi.org/10.3390/genes15091163 - 3 Sep 2024
Cited by 2 | Viewed by 1412
Abstract
Chloride channels (ClCs) have received global interest due to their significant role in the regulation of ion homeostasis, fluid transport, and electrical excitability of tissues and organs in different mammals and contributing to various functions, such as neuronal signaling, muscle contraction, and regulating [...] Read more.
Chloride channels (ClCs) have received global interest due to their significant role in the regulation of ion homeostasis, fluid transport, and electrical excitability of tissues and organs in different mammals and contributing to various functions, such as neuronal signaling, muscle contraction, and regulating the electrolytes’ balance in kidneys and other organs. In order to define the chloride voltage-gated channel (CLCN) gene family in buffalo, this study used in silico analyses to examine physicochemical properties, evolutionary patterns, and genome-wide identification. We identified eight CLCN genes in buffalo. The ProtParam tool analysis identified a number of important physicochemical properties of these proteins, including hydrophilicity, thermostability, in vitro instability, and basic nature. Based on their evolutionary relationships, a phylogenetic analysis divided the eight discovered genes into three subfamilies. Furthermore, a gene structure analysis, motif patterns, and conserved domains using TBtool demonstrated the significant conservation of this gene family among selected species over the course of evolution. A comparative amino acid analysis using ClustalW revealed similarities and differences between buffalo and cattle CLCN proteins. Three duplicated gene pairs were identified, all of which were segmental duplications except for CLCN4-CLCN5, which was a tandem duplication in buffalo. For each gene pair, the Ka/Ks test ratio findings showed that none of the ratios was more than one, indicating that these proteins were likely subject to positive selection. A synteny analysis confirmed a conserved pattern of genomic blocks between buffalo and cattle. Transcriptional control in cells relies on the binding of transcription factors to specific sites in the genome. The number of transcription factor binding sites (TFBSs) was higher in cattle compared to buffalo. Five main recombination breakpoints were identified at various places in the recombination analysis. The outcomes of our study provide new knowledge about the CLCN gene family in buffalo and open the door for further research on candidate genes in vertebrates through genome-wide studies. Full article
(This article belongs to the Special Issue Buffalo Genetics and Genomics)
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14 pages, 6815 KiB  
Article
Meta-Genomic Analysis of Different Bacteria and Their Genomes Found in Raw Buffalo Milk Obtained in Various Farms Using Different Milking Methods
by Ling Li, Wenhao Miao, Zhipeng Li, Li Huang, Enghuan Hau, Muhammad Farhan Khan, Qingyou Liu, Qingkun Zeng and Kuiqing Cui
Genes 2024, 15(8), 1081; https://doi.org/10.3390/genes15081081 - 15 Aug 2024
Cited by 3 | Viewed by 1702
Abstract
Milking methods have significant impacts on the microbiological composition, which could affect the quality of raw buffalo milk. Hence, the current study was conducted on the impact of milking methods on microorganisms in buffalo tank raw milk from 15 farms in Guangxi, China. [...] Read more.
Milking methods have significant impacts on the microbiological composition, which could affect the quality of raw buffalo milk. Hence, the current study was conducted on the impact of milking methods on microorganisms in buffalo tank raw milk from 15 farms in Guangxi, China. The farms were divided into two groups based on the milking method: mechanical milking (MM, n = 6) and hand milking (HM, n = 9). Somatic cell counts, bacterial cell counts and nutrients of the raw buffalo milk samples were analyzed. The comparison of raw buffalo milk samples was analyzed using metagenomic sequencing to detect any differences between the two groups. There was no significant difference in the basic nutritional compositions and somatic cell count of raw buffalo milk between the two milking methods. However, the HM samples had significantly higher bacterial counts and diversity compared to the MM samples. The results showed that Staphylococcus spp., Klebsiella spp., Streptococcus spp., and Pseudomonas spp. were the major microbes present in canned raw buffalo milk. However, the differences between the two milking methods were the relative abundance of core microorganisms and their potential mastitis-causing genera, including the content of antibiotic-resistance genes and virulence genes. Our study revealed that Staphylococcus spp. and Streptococcus spp. were significantly more abundant in the MM group, while Klebsiella spp. was more abundant in the HM group. Regardless of the milking method used, Pseudomonas spp. was identified as the primary genus contributing to antibiotic resistance and virulence genes in canned raw buffalo milk. These findings affirm that there are differences in the microbial and genomic levels in canned raw milk. To prove the functional roles of the discovered genes and how these genes affect milk quality, further research and experimental validation are necessary. Full article
(This article belongs to the Special Issue Buffalo Genetics and Genomics)
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