1
|
Ahlawat S, Sharma U, Chhabra P, Arora R, Sharma R, Singh KV, Vijh RK. Maternal genetic diversity and phylogenetic analysis of Indian riverine and swamp buffaloes: insights from complete mitochondrial genomes. Mamm Genome 2024:10.1007/s00335-024-10048-1. [PMID: 38888811 DOI: 10.1007/s00335-024-10048-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2024] [Accepted: 06/13/2024] [Indexed: 06/20/2024]
Abstract
This study explored the genetic diversity and evolutionary history of riverine and swamp buffaloes in India, utilizing complete mitochondrial genome sequences. Through comprehensive sampling across varied agro-climatic zones, including 91 riverine buffaloes from 12 breeds and 6 non-descript populations, along with 16 swamp buffaloes of the Luit breed, this study employed next-generation sequencing techniques to map the mitogenomic landscape of these subspecies. Sequence alignments were performed with the buffalo mitochondrial reference genome to identify mitochondrial DNA (mtDNA) variations and distinct maternal haplogroups among Indian buffaloes. The results uncovered the existence of 212 variable sites in riverine buffaloes, yielding 67 haplotypes with high haplotype diversity (0.991), and in swamp buffaloes, 194 variable sites resulting in 12 haplotypes, displaying haplotype diversity of 0.950. Phylogenetic analyses elucidated the genetic relationships between Indian buffaloes and the recognized global haplogroups, categorizing Indian swamp buffaloes predominantly into the SA haplogroup. Intriguingly, the haplogroup SB2b was observed for the first time in swamp buffaloes. Conversely, riverine buffaloes conformed to established sub-haplogroups RB1, RB2, and RB3, underscoring the notion of Northwestern India as a pivotal domestication site for riverine buffaloes. The study supports the hypothesis of independent domestication events for riverine and swamp buffaloes, highlighting the critical role of genetic analysis in unraveling the complex evolutionary pathways of domestic animals. This investigation contributes to the global understanding of buffalo mitogenome diversity, offering insights into this important livestock species' domestication and dispersal patterns.
Collapse
Affiliation(s)
- Sonika Ahlawat
- ICAR-National Bureau of Animal Genetic Resources, Karnal, India.
| | - Upasna Sharma
- ICAR-National Bureau of Animal Genetic Resources, Karnal, India
| | - Pooja Chhabra
- ICAR-National Bureau of Animal Genetic Resources, Karnal, India
| | - Reena Arora
- ICAR-National Bureau of Animal Genetic Resources, Karnal, India
| | - Rekha Sharma
- ICAR-National Bureau of Animal Genetic Resources, Karnal, India
| | | | - R K Vijh
- ICAR-National Bureau of Animal Genetic Resources, Karnal, India
| |
Collapse
|
2
|
Xu Y, Feng T, Ding Z, Li L, Li Z, Cui K, Chen W, Pan H, Zhu P, Liu Q. Age-related compositional and functional changes in the adult and breastfed buffalo rumen microbiome. Front Microbiol 2024; 15:1342804. [PMID: 38881655 PMCID: PMC11177756 DOI: 10.3389/fmicb.2024.1342804] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Accepted: 05/07/2024] [Indexed: 06/18/2024] Open
Abstract
Introduction The buffalo is an important domestic animal globally, providing milk, meat, and labor to more than 2 billion people in 67 countries. The rumen microorganisms of buffaloes play an indispensable role in enabling the healthy functionality and digestive function of buffalo organisms. Currently, there is a lack of clarity regarding the differences in the composition and function of rumen microorganisms among buffaloes at different growth stages. Methods In this study, metagenomics sequencing technology was applied to examine the compositional and functional differences of rumen microorganisms in adult and breastfed buffaloes. Results The results revealed that the rumen of adult buffaloes had significantly higher levels of the following dominant genera: Prevotella, UBA1711, RF16, Saccharofermentans, F23-D06, UBA1777, RUG472, and Methanobrevibacter_A. Interestingly, the dominant genera specific to the rumen of adult buffaloes showed a significant positive correlation (correlation>0.5, p-value<0.05) with both lignocellulose degradation-related carbohydrate-active enzymes (CAZymes) and immune signaling pathways activated by antigenic stimulation. The rumen of breastfed buffaloes had significantly higher levels of the following dominant genera: UBA629, CAG- 791, Selenomonas_C, Treponema_D, Succinivibrio, and RC9. Simultaneously, the rumen-dominant genera specific to breastfed buffaloes were significantly positively correlated (correlation>0.5, p-value<0.05) with CAZymes associated with lactose degradation, amino acid synthesis pathways, and antibiotic-producing pathways. Discussion This indicates that rumen microorganisms in adult buffaloes are more engaged in lignocellulose degradation, whereas rumen microorganisms in breastfed buffaloes are more involved in lactose and amino acid degradation, as well as antibiotic production. In conclusion, these findings suggest a close relationship between differences in rumen microbes and the survival needs of buffaloes at different growth stages.
Collapse
Affiliation(s)
- Yixue Xu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, China
| | - Tong Feng
- Department of Bioinformatics and Systems Biology, Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-imaging, Center for Artificial Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Zixu Ding
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, China
| | - Ling Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, China
- Guangxi Key Laboratory of Buffalo Genetics, Nanning, China
| | - Zhipeng Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, China
| | - Kuiqing Cui
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, School of Life Science and Engineering, Foshan University, Foshan, China
| | - Weihua Chen
- Department of Bioinformatics and Systems Biology, Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-imaging, Center for Artificial Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Hongping Pan
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, China
| | - Peng Zhu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, China
- Guangxi Key Laboratory of Beibu Gulf Marine Biodiversity Conservation, Beibu Gulf Marine Ecological Environment Field Observation and Research Station of Guangxi, Beibu Gulf University, Qinzhou, China
| | - Qingyou Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, China
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, School of Life Science and Engineering, Foshan University, Foshan, China
| |
Collapse
|
3
|
Du X, Sun Y, Fu T, Gao T, Zhang T. Research Progress and Applications of Bovine Genome in the Tribe Bovini. Genes (Basel) 2024; 15:509. [PMID: 38674443 PMCID: PMC11050176 DOI: 10.3390/genes15040509] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2024] [Revised: 04/16/2024] [Accepted: 04/17/2024] [Indexed: 04/28/2024] Open
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 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.
Collapse
Affiliation(s)
- Xingjie Du
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China; (X.D.); (Y.S.); (T.F.); (T.G.)
- Henan International Joint Laboratory of Nutrition Regulation and Ecological Raising of Domestic Animal, College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China
| | - Yu Sun
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China; (X.D.); (Y.S.); (T.F.); (T.G.)
- Henan International Joint Laboratory of Nutrition Regulation and Ecological Raising of Domestic Animal, College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China
| | - Tong Fu
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China; (X.D.); (Y.S.); (T.F.); (T.G.)
- Henan International Joint Laboratory of Nutrition Regulation and Ecological Raising of Domestic Animal, College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China
| | - Tengyun Gao
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China; (X.D.); (Y.S.); (T.F.); (T.G.)
- Henan International Joint Laboratory of Nutrition Regulation and Ecological Raising of Domestic Animal, College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China
| | - Tianliu Zhang
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China; (X.D.); (Y.S.); (T.F.); (T.G.)
- Henan International Joint Laboratory of Nutrition Regulation and Ecological Raising of Domestic Animal, College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China
| |
Collapse
|
4
|
Zhang J, Sun J, Ou M, Ouyang Y, Shi D, Lu F. Testosterone Supplementation Promotes Estrogen Synthesis of Buffalo Cumulus Cells Surrounding In Vitro-Matured Oocytes. Cell Reprogram 2024; 26:79-84. [PMID: 38579133 DOI: 10.1089/cell.2023.0121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/07/2024] Open
Abstract
Cumulus cells (CCs) synthesize estrogens that are essential for follicular development. However, the effects of androgen on estrogen production in buffalo CCs remain unknown. In the present study, the impacts of testosterone on estrogen synthesis of buffalo CCs surrounding in vitro-matured oocytes were investigated. The results showed that testosterone supplementation improved both the expression levels of estrogen synthesis-related genes (CYP11A1, CYP19A1, and 17β-HSD) and the secretion levels of estradiol in buffalo CCs surrounding in vitro-matured oocytes. Furthermore, testosterone treatment enhanced the sensitivity of buffalo CCs surrounding in vitro-matured oocytes to follicle-stimulating hormone (FSH). This study indicated that testosterone supplementation promoted the estrogen synthesis of buffalo CCs surrounding in vitro-matured oocytes mainly through strengthening the responsiveness of CCs to FSH. The present study serves as a foundation of acquiring high-quality recipient oocytes for buffalo somatic cell nuclear transfer.
Collapse
Affiliation(s)
- Jun Zhang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Key Laboratory of Animal Breeding, Disease Control and Prevention, Guangxi University, Nanning, China
- Laboratory Animal Center, Guangxi Medical University, Nanning, China
| | - Junming Sun
- Laboratory Animal Center, Guangxi Medical University, Nanning, China
| | - Meizhen Ou
- Laboratory Animal Center, Guangxi Medical University, Nanning, China
| | - Yiqiang Ouyang
- Laboratory Animal Center, Guangxi Medical University, Nanning, China
| | - Deshun Shi
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Key Laboratory of Animal Breeding, Disease Control and Prevention, Guangxi University, Nanning, China
| | - Fenghua Lu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Key Laboratory of Animal Breeding, Disease Control and Prevention, Guangxi University, Nanning, China
| |
Collapse
|
5
|
Liu X, Zheng J, Ding J, Wu J, Zuo F, Zhang G. When Livestock Genomes Meet Third-Generation Sequencing Technology: From Opportunities to Applications. Genes (Basel) 2024; 15:245. [PMID: 38397234 PMCID: PMC10888458 DOI: 10.3390/genes15020245] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2023] [Revised: 01/30/2024] [Accepted: 02/10/2024] [Indexed: 02/25/2024] Open
Abstract
Third-generation sequencing technology has found widespread application in the genomic, transcriptomic, and epigenetic research of both human and livestock genetics. This technology offers significant advantages in the sequencing of complex genomic regions, the identification of intricate structural variations, and the production of high-quality genomes. Its attributes, including long sequencing reads, obviation of PCR amplification, and direct determination of DNA/RNA, contribute to its efficacy. This review presents a comprehensive overview of third-generation sequencing technologies, exemplified by single-molecule real-time sequencing (SMRT) and Oxford Nanopore Technology (ONT). Emphasizing the research advancements in livestock genomics, the review delves into genome assembly, structural variation detection, transcriptome sequencing, and epigenetic investigations enabled by third-generation sequencing. A comprehensive analysis is conducted on the application and potential challenges of third-generation sequencing technology for genome detection in livestock. Beyond providing valuable insights into genome structure analysis and the identification of rare genes in livestock, the review ventures into an exploration of the genetic mechanisms underpinning exemplary traits. This review not only contributes to our understanding of the genomic landscape in livestock but also provides fresh perspectives for the advancement of research in this domain.
Collapse
Affiliation(s)
- Xinyue Liu
- College of Animal Science and Technology, Southwest University, Rongchang, Chongqing 402460, China; (X.L.); (J.Z.); (J.D.); (J.W.); (F.Z.)
| | - Junyuan Zheng
- College of Animal Science and Technology, Southwest University, Rongchang, Chongqing 402460, China; (X.L.); (J.Z.); (J.D.); (J.W.); (F.Z.)
| | - Jialan Ding
- College of Animal Science and Technology, Southwest University, Rongchang, Chongqing 402460, China; (X.L.); (J.Z.); (J.D.); (J.W.); (F.Z.)
| | - Jiaxin Wu
- College of Animal Science and Technology, Southwest University, Rongchang, Chongqing 402460, China; (X.L.); (J.Z.); (J.D.); (J.W.); (F.Z.)
| | - Fuyuan Zuo
- College of Animal Science and Technology, Southwest University, Rongchang, Chongqing 402460, China; (X.L.); (J.Z.); (J.D.); (J.W.); (F.Z.)
- Beef Cattle Engineering and Technology Research Center of Chongqing, Southwest University, Rongchang, Chongqing 402460, China
| | - Gongwei Zhang
- College of Animal Science and Technology, Southwest University, Rongchang, Chongqing 402460, China; (X.L.); (J.Z.); (J.D.); (J.W.); (F.Z.)
- Beef Cattle Engineering and Technology Research Center of Chongqing, Southwest University, Rongchang, Chongqing 402460, China
| |
Collapse
|
6
|
Yang X, Li X, Bao Q, Wang Z, He S, Qu X, Tang Y, Song B, Huang J, Yi G. Uncovering Evolutionary Adaptations in Common Warthogs through Genomic Analyses. Genes (Basel) 2024; 15:166. [PMID: 38397156 PMCID: PMC10888464 DOI: 10.3390/genes15020166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Revised: 01/15/2024] [Accepted: 01/20/2024] [Indexed: 02/25/2024] Open
Abstract
In the Suidae family, warthogs show significant survival adaptability and trait specificity. This study offers a comparative genomic analysis between the warthog and other Suidae species, including the Luchuan pig, Duroc pig, and Red River hog. By integrating the four genomes with sequences from the other four species, we identified 8868 single-copy orthologous genes. Based on 8868 orthologous protein sequences, phylogenetic assessments highlighted divergence timelines and unique evolutionary branches within suid species. Warthogs exist on different evolutionary branches compared to DRCs and LCs, with a divergence time preceding that of DRC and LC. Contraction and expansion analyses of warthog gene families have been conducted to elucidate the mechanisms of their evolutionary adaptations. Using GO, KEGG, and MGI databases, warthogs showed a preference for expansion in sensory genes and contraction in metabolic genes, underscoring phenotypic diversity and adaptive evolution direction. Associating genes with the QTLdb-pigSS11 database revealed links between gene families and immunity traits. The overlap of olfactory genes in immune-related QTL regions highlighted their importance in evolutionary adaptations. This work highlights the unique evolutionary strategies and adaptive mechanisms of warthogs, guiding future research into the distinct adaptability and disease resistance in pigs, particularly focusing on traits such as resistance to African Swine Fever Virus.
Collapse
Affiliation(s)
- Xintong Yang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-Omics of MARA, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China; (X.Y.); (X.L.); (Q.B.); (Z.W.); (S.H.); (X.Q.); (Y.T.); (B.S.)
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning 530005, China;
| | - Xingzheng Li
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-Omics of MARA, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China; (X.Y.); (X.L.); (Q.B.); (Z.W.); (S.H.); (X.Q.); (Y.T.); (B.S.)
| | - Qi Bao
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-Omics of MARA, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China; (X.Y.); (X.L.); (Q.B.); (Z.W.); (S.H.); (X.Q.); (Y.T.); (B.S.)
| | - Zhen Wang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-Omics of MARA, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China; (X.Y.); (X.L.); (Q.B.); (Z.W.); (S.H.); (X.Q.); (Y.T.); (B.S.)
| | - Sang He
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-Omics of MARA, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China; (X.Y.); (X.L.); (Q.B.); (Z.W.); (S.H.); (X.Q.); (Y.T.); (B.S.)
| | - Xiaolu Qu
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-Omics of MARA, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China; (X.Y.); (X.L.); (Q.B.); (Z.W.); (S.H.); (X.Q.); (Y.T.); (B.S.)
| | - Yueting Tang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-Omics of MARA, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China; (X.Y.); (X.L.); (Q.B.); (Z.W.); (S.H.); (X.Q.); (Y.T.); (B.S.)
- School of Life Sciences, Henan University, Kaifeng 475004, China
| | - Bangmin Song
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-Omics of MARA, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China; (X.Y.); (X.L.); (Q.B.); (Z.W.); (S.H.); (X.Q.); (Y.T.); (B.S.)
- School of Life Sciences, Henan University, Kaifeng 475004, China
| | - Jieping Huang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning 530005, China;
| | - Guoqiang Yi
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-Omics of MARA, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China; (X.Y.); (X.L.); (Q.B.); (Z.W.); (S.H.); (X.Q.); (Y.T.); (B.S.)
- Kunpeng Institute of Modern Agriculture at Foshan, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Foshan 528226, China
- Bama Yao Autonomous County Rural Revitalization Research Institute, Bama 547500, China
| |
Collapse
|
7
|
Saravanan KA, Rajawat D, Kumar H, Nayak SS, Bhushan B, Dutt T, Panigrahi M. Signatures of selection in riverine buffalo populations revealed by genome-wide SNP data. Anim Biotechnol 2023; 34:3343-3354. [PMID: 36384399 DOI: 10.1080/10495398.2022.2145292] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The detection of selection signatures assists in understanding domestication, evolution, and the identification of genomic regions related to adaptation and production traits in buffaloes. The emergence of high-throughput technologies like Next Generation Sequencing and SNP genotyping had expanded our ability to detect these signatures of selection. In this study, we sought to identify signatures of selection in five buffalo populations (Brazilian Murrah, Bulgarian Murrah, Indian Murrah, Nili-Ravi, and Kundi) using Axiom Buffalo 90 K Genotyping Array data. Using seven different methodologies (Tajima's D, CLR, ROH, iHS, FST, FLK and hapFLK), we identified selection signatures in 374 genomic regions, spanning a total of 381 genes and 350 quantitative trait loci (QTLs). Among these, several candidate genes were associated with QTLs for milk production, reproduction, growth and carcass traits. The genes and QTLs reported in this study provide insight into selection signals shaping the genome of buffalo breeds. Our findings can aid in further genomic association studies, genomic prediction, and the implementation of breeding programmes in Indian buffaloes.
Collapse
Affiliation(s)
- K A Saravanan
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly, India
| | - Divya Rajawat
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly, India
| | - Harshit Kumar
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly, India
| | - Sonali Sonejita Nayak
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly, India
| | - Bharat Bhushan
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly, India
| | - Triveni Dutt
- Livestock Production and Management Section, Indian Veterinary Research Institute, Izatnagar, Bareilly, India
| | - Manjit Panigrahi
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly, India
| |
Collapse
|
8
|
Ghildiyal K, Nayak SS, Rajawat D, Sharma A, Chhotaray S, Bhushan B, Dutt T, Panigrahi M. Genomic insights into the conservation of wild and domestic animal diversity: A review. Gene 2023; 886:147719. [PMID: 37597708 DOI: 10.1016/j.gene.2023.147719] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 06/20/2023] [Accepted: 08/16/2023] [Indexed: 08/21/2023]
Abstract
Due to environmental change and anthropogenic activities, global biodiversity has suffered an unprecedented loss, and the world is now heading toward the sixth mass extinction event. This urges the need to step up our efforts to promote the sustainable use of animal genetic resources and plan effective strategies for their conservation. Although habitat preservation and restoration are the primary means of conserving biodiversity, genomic technologies offer a variety of novel tools for identifying biodiversity hotspots and thus, support conservation efforts. Conservation genomics is a broad area of science that encompasses the application of genomic data from thousands or tens of thousands of genome-wide markers to address important conservation biology concerns. Genomic approaches have revolutionized the way we understand and manage animal populations, providing tools to identify and preserve unique genetic variants and alleles responsible for adaptive genetic variation, reducing the deleterious consequences of inbreeding, and increasing the adaptive potential of threatened species. The advancement of genomic technologies, particularly comparative genomic approaches, and the increased accessibility of genomic resources in the form of genome-enabled taxa for non-model organisms, provides a distinct advantage in defining conservation units over traditional genetics approaches. The objective of this review is to provide an exhaustive overview of the concept of conservation genomics, discuss the rationale behind the transition from conservation genetics to genomic approaches, and emphasize the potential applications of genomic techniques for conservation purposes. We also highlight interesting case studies in both livestock and wildlife species where genomic techniques have been used to accomplish conservation goals. Finally, we address some challenges and future perspectives in this field.
Collapse
Affiliation(s)
- Kanika Ghildiyal
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
| | - Sonali Sonejita Nayak
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
| | - Divya Rajawat
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
| | - Anurodh Sharma
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
| | - Supriya Chhotaray
- Animal Genetics and Breeding Division, ICAR-National Dairy Research Institute, Karnal, Haryana, India
| | - Bharat Bhushan
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
| | - Triveni Dutt
- Livestock Production and Management Section, Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
| | - Manjit Panigrahi
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India.
| |
Collapse
|
9
|
Zhang J, Sun J, Xiao L, Ouyang Y, Shi D, Lu F. Testosterone supplementation improves estrogen synthesis of buffalo (Bubalus bubalis) granulosa cells. Reprod Domest Anim 2023; 58:1628-1635. [PMID: 37668268 DOI: 10.1111/rda.14467] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Revised: 07/26/2023] [Accepted: 08/18/2023] [Indexed: 09/06/2023]
Abstract
Granulosa cells (GCs) synthesize estrogens needed for follicular growth. However, the effects of androgen on estrogen production in buffalo GCs remain unclear. In this study, the impacts of testosterone on estrogen synthesis in buffalo GCs were examined. The results showed that testosterone that was added to cell medium at a concentration of 10-7 mol/L and applied to GCs for 48 or 72 h enhanced the estrogen synthesis of buffalo GCs. This study provides a theoretical basis for further exploration of ovarian endocrine mechanism for steroidogenesis.
Collapse
Affiliation(s)
- Jun Zhang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Key Laboratory of Animal Breeding, Disease Control and Prevention, Guangxi University, Nanning, China
- Laboratory Animal Center, Guangxi Medical University, Nanning, China
| | - Junming Sun
- Laboratory Animal Center, Guangxi Medical University, Nanning, China
| | - Linlin Xiao
- Laboratory Animal Center, Guangxi Medical University, Nanning, China
| | - Yiqiang Ouyang
- Laboratory Animal Center, Guangxi Medical University, Nanning, China
| | - Deshun Shi
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Key Laboratory of Animal Breeding, Disease Control and Prevention, Guangxi University, Nanning, China
| | - Fenghua Lu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Key Laboratory of Animal Breeding, Disease Control and Prevention, Guangxi University, Nanning, China
| |
Collapse
|
10
|
Zhang Y, Zhang J, Sun J, Ouyang Y, Shi D, Lu F. Hypoxia enhances steroidogenic competence of buffalo (Bubalus bubalis) granulosa cells. Theriogenology 2023; 210:214-220. [PMID: 37527623 DOI: 10.1016/j.theriogenology.2023.07.031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 07/18/2023] [Accepted: 07/21/2023] [Indexed: 08/03/2023]
Abstract
Granulosa cells (GCs) synthesize estrogens needed for follicular growth. However, the effects of hypoxia on steroidogenesis in buffalo GCs remain unclear. In this study, the impacts of hypoxic conditions (5% oxygen) on estrogen synthesis in buffalo GCs were examined. The results showed that hypoxia improved both the expression levels of estrogen synthesis-related genes (CYP11A1, CYP19A1, and 3β-HSD) and the secretion levels of estradiol in buffalo GCs. Hypoxic conditions promoted the sensitivity of buffalo GCs to FSH. Furthermore, inhibition of cAMP/PKA signaling pathway (H89, a cAMP/PKA signaling pathway inhibitor) reduced both the expression levels of estrogen synthesis-related genes (CYP11A1, CYP19A1, and 3β-HSD) and the secretion levels of estradiol in hypoxia-cultured buffalo GCs. Besides, inhibition of cAMP/PKA signaling pathway lowered the responsiveness of buffalo GCs to FSH under hypoxic conditions. The present study indicated that hypoxia enhanced the steroidogenic competence of buffalo GCs principal by affecting cAMP/PKA signaling pathway and subsequent sensitivity of GCs to FSH.
Collapse
Affiliation(s)
- Yu Zhang
- College of Animal Science and Technology, Guangxi Key Laboratory of Animal Breeding and Disease Control, Guangxi University, Nanning, 530005, China
| | - Jun Zhang
- Laboratory Animal Center, Guangxi Medical University, Nanning, 530021, China
| | - Junming Sun
- Laboratory Animal Center, Guangxi Medical University, Nanning, 530021, China
| | - Yiqiang Ouyang
- Laboratory Animal Center, Guangxi Medical University, Nanning, 530021, China
| | - Deshun Shi
- College of Animal Science and Technology, Guangxi Key Laboratory of Animal Breeding and Disease Control, Guangxi University, Nanning, 530005, China
| | - Fenghua Lu
- College of Animal Science and Technology, Guangxi Key Laboratory of Animal Breeding and Disease Control, Guangxi University, Nanning, 530005, China.
| |
Collapse
|
11
|
Anas M, Farooq M, Asif M, Ali WR, Mansoor S. A Novel Insight into the Identification of Potential SNP Markers for the Genomic Characterization of Buffalo Breeds in Pakistan. Animals (Basel) 2023; 13:2543. [PMID: 37570351 PMCID: PMC10416883 DOI: 10.3390/ani13152543] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Revised: 07/11/2023] [Accepted: 07/26/2023] [Indexed: 08/13/2023] Open
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 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.
Collapse
Affiliation(s)
- Muhammad Anas
- National Institute for Biotechnology and Genetic Engineering (NIBGE), Faisalabad 38000, Punjab, Pakistan
- Department of Animal Sciences and Center for Nutrition and Pregnancy, North Dakota State University, Fargo, ND 58105, USA
| | - Muhammad Farooq
- National Institute for Biotechnology and Genetic Engineering (NIBGE), Faisalabad 38000, Punjab, Pakistan
| | - Muhammad Asif
- National Institute for Biotechnology and Genetic Engineering (NIBGE), Faisalabad 38000, Punjab, Pakistan
| | - Waqas Rafique Ali
- National Institute for Biotechnology and Genetic Engineering (NIBGE), Faisalabad 38000, Punjab, Pakistan
| | - Shahid Mansoor
- National Institute for Biotechnology and Genetic Engineering (NIBGE), Faisalabad 38000, Punjab, Pakistan
| |
Collapse
|
12
|
Yang L, Han J, Deng T, Li F, Han X, Xia H, Quan F, Hua G, Yang L, Zhou Y. Comparative analyses of copy number variations between swamp buffaloes and river buffaloes. Anim Genet 2023; 54:199-206. [PMID: 36683294 DOI: 10.1111/age.13288] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Revised: 11/24/2022] [Accepted: 12/12/2022] [Indexed: 01/24/2023]
Abstract
As an important source of genomic variation, copy number variation (CNV) contributes to environmental adaptation in worldwide buffaloes. Despite this importance, CNV divergence between swamp buffaloes and river buffaloes has not been studied previously. Here, we report 21 152 CNV regions (CNVRs) in 141 buffaloes of 20 breeds detected through multiple CNV calling strategies. Only 248 CNVRs were shared between river buffalo and swamp buffalo, reflecting great variation of CNVRs between the two subspecies. Population structure analysis based on CNVs successfully separated the two buffalo subspecies. We further assessed CNV divergence by calculating FST for genome-wide CNVs. Totally, we identified 110 significantly divergent CNV segments and 44 putatively selected genes between river buffaloes and swamp buffaloes. In particular, LALBA, a key gene controlling milk production in cattle, presented a highly differentiated CNV in the promoter region, which makes it a strong functional candidate gene for differences between swamp buffaloes and river buffaloes in traits related to milk production. Our study provides useful information of CNVs in buffaloes, which may help explain the genetic differences between the two subspecies.
Collapse
Affiliation(s)
- Lv Yang
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan, China.,National Center for International Research on Animal Genetics, Breeding and Reproduction (NCIRAGBR), Frontiers Science Center for Animal Breeding and Sustainable Production, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Jiazheng Han
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan, China.,National Center for International Research on Animal Genetics, Breeding and Reproduction (NCIRAGBR), Frontiers Science Center for Animal Breeding and Sustainable Production, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Tingxian Deng
- Guangxi Provincial Key Laboratory of Buffalo Genetics, Breeding and Reproduction Technology, Buffalo Research Institute, Chinese Academy of Agricultural Sciences, Nanning, China
| | - Fan Li
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan, China.,National Center for International Research on Animal Genetics, Breeding and Reproduction (NCIRAGBR), Frontiers Science Center for Animal Breeding and Sustainable Production, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Xiaotao Han
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan, China.,National Center for International Research on Animal Genetics, Breeding and Reproduction (NCIRAGBR), Frontiers Science Center for Animal Breeding and Sustainable Production, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Han Xia
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan, China.,National Center for International Research on Animal Genetics, Breeding and Reproduction (NCIRAGBR), Frontiers Science Center for Animal Breeding and Sustainable Production, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Fanfan Quan
- Livestock and Poultry Breeding Center of Hubei Province, Wuhan, China
| | - Guohua Hua
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan, China.,National Center for International Research on Animal Genetics, Breeding and Reproduction (NCIRAGBR), Frontiers Science Center for Animal Breeding and Sustainable Production, Huazhong Agricultural University, Wuhan, Hubei, China.,Hubei Province's Engineering Research Center in Buffalo Breeding and Products, Wuhan, China
| | - Liguo Yang
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan, China.,National Center for International Research on Animal Genetics, Breeding and Reproduction (NCIRAGBR), Frontiers Science Center for Animal Breeding and Sustainable Production, Huazhong Agricultural University, Wuhan, Hubei, China.,Hubei Province's Engineering Research Center in Buffalo Breeding and Products, Wuhan, China
| | - Yang Zhou
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan, China.,National Center for International Research on Animal Genetics, Breeding and Reproduction (NCIRAGBR), Frontiers Science Center for Animal Breeding and Sustainable Production, Huazhong Agricultural University, Wuhan, Hubei, China.,Hubei Province's Engineering Research Center in Buffalo Breeding and Products, Wuhan, China
| |
Collapse
|
13
|
Parveen S, Zhu P, Shafique L, Lan H, Xu D, Ashraf S, Ashraf S, Sherazi M, Liu Q. Molecular Characterization and Phylogenetic Analysis of Casein Gene Family in Camelus ferus. Genes (Basel) 2023; 14:genes14020256. [PMID: 36833182 PMCID: PMC9957437 DOI: 10.3390/genes14020256] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 01/04/2023] [Accepted: 01/13/2023] [Indexed: 01/20/2023] Open
Abstract
Camel milk is known for its exceptional medical uses. It has been used since ancient times to treat infant diarrhea, hepatitis, insulin-dependent diabetes (IDDM), lactose intolerance, alcohol-induced liver damage, allergies, and autism. It has the power to treat several diseases, with cancer being the most significant. This study investigated the evolutionary relationship, physiochemical characteristics, and comparative genomic analysis of the casein gene family (CSN1S1, CSN2, CSN1S2, and CSN3) in Camelus ferus. Molecular phylogenetics showing the camelid species clustered casein nucleotide sequences into four groups: CSN1S1, CSN2, CSN1S2, and CSN3. The casein proteins from camels were evaluated and found to be unstable, thermostable, and hydrophilic. CSN1S2, CSN2, and CSN3 were acidic, but CSN1S1 was basic. CSN1S1 showed positive selection for one amino acid (Q), CSN1S2 and CSN2 for three (T, K, Q), and CSN3 showed no positive selection. We also compared high-milk-output species such as cattle (Bos Tarus) and low-milk-yield species such as sheep (Ovies Aries) with camels (Camel ferus) and discovered that YY1 sites are more frequent in sheep than in camels and very low in cattle. We concluded that the ratio of YY1 sites in these species may affect milk production.
Collapse
Affiliation(s)
- Shakeela Parveen
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, School of Life Science and Engineering, Foshan University, Foshan 528225, China
- Guangxi Key Laboratory of Beibu Gulf Marine Biodiversity Conservation, Beibu Gulf University, Guangxi 535011, China
- Department of Zoology, Government Sadiq College Women University, Bahawalpur 63100, Pakistan
| | - Peng Zhu
- Guangxi Key Laboratory of Beibu Gulf Marine Biodiversity Conservation, Beibu Gulf University, Guangxi 535011, China
| | - Laiba Shafique
- Guangxi Key Laboratory of Beibu Gulf Marine Biodiversity Conservation, Beibu Gulf University, Guangxi 535011, China
- Correspondence: (L.S.); (Q.L.)
| | - Hong Lan
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning 530005, China
| | - Dingyun Xu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning 530005, China
| | - Sana Ashraf
- Department of Zoology, Government Sadiq College Women University, Bahawalpur 63100, Pakistan
| | - Saba Ashraf
- Department of Zoology, Government Sadiq College Women University, Bahawalpur 63100, Pakistan
| | - Maryam Sherazi
- Department of Dairy Technology, University of Veterinary and Animal Sciences, Lahore 54000, Pakistan
| | - Qingyou Liu
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, School of Life Science and Engineering, Foshan University, Foshan 528225, China
- Correspondence: (L.S.); (Q.L.)
| |
Collapse
|
14
|
Wang X, Li Z, Feng T, Luo X, Xue L, Mao C, Cui K, Li H, Huang J, Huang K, Rehman SU, Shi D, Wu D, Ruan J, Liu Q. Chromosome-level genome and recombination map of the male buffalo. Gigascience 2022; 12:giad063. [PMID: 37589307 PMCID: PMC10433102 DOI: 10.1093/gigascience/giad063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 03/20/2023] [Accepted: 07/13/2023] [Indexed: 08/18/2023] Open
Abstract
BACKGROUND The swamp buffalo (Bubalus bubalis carabanesis) is an economically important livestock supplying milk, meat, leather, and draft power. Several female buffalo genomes have been available, but the lack of high-quality male genomes hinders studies on chromosome evolution, especially Y, as well as meiotic recombination. RESULTS Here, a chromosome-level genome with a contig N50 of 72.2 Mb and a fine-scale recombination map of male buffalo were reported. We found that transposable elements (TEs) and structural variants (SVs) may contribute to buffalo evolution by influencing adjacent gene expression. We further found that the pseudoautosomal region (PAR) of the Y chromosome is subject to stronger purification selection. The meiotic recombination map showed that there were 2 obvious recombination hotspots on chromosome 8, and the genes around them were mainly related to tooth development, which may have helped to enhance the adaption of buffalo to inferior feed. Among several genomic features, TE density has the strongest correlation with recombination rates. Moreover, the TE subfamily, SINE/tRNA, is likely to play a role in driving recombination into SVs. CONCLUSIONS The male genome and sperm sequencing will facilitate the understanding of the buffalo genomic evolution and functional research.
Collapse
Affiliation(s)
- Xiaobo Wang
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, School of Life Science and Engineering, Foshan University, Foshan 528225, China
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning 530005, China
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Zhipeng Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning 530005, China
| | - Tong Feng
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning 530005, China
| | - Xier Luo
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning 530005, China
| | - Lintao Xue
- Reproductive Medical and Genetic Center, The People's Hospital of Guangxi Zhuang Autonomous Region, Nanning, Guangxi 530021, China
| | - Chonghui Mao
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Kuiqing Cui
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, School of Life Science and Engineering, Foshan University, Foshan 528225, China
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning 530005, China
| | - Hui Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning 530005, China
| | - Jieping Huang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning 530005, China
| | - Kongwei Huang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning 530005, China
| | - Saif-ur Rehman
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning 530005, China
| | - Deshun Shi
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning 530005, China
| | - Dongdong Wu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
| | - Jue Ruan
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Qingyou Liu
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, School of Life Science and Engineering, Foshan University, Foshan 528225, China
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning 530005, China
| |
Collapse
|
15
|
De Novo Transcriptome Dataset Generation of the Swamp Buffalo Brain and Non-Brain Tissues. BIOMED RESEARCH INTERNATIONAL 2022; 2022:4472940. [PMID: 36408285 PMCID: PMC9668446 DOI: 10.1155/2022/4472940] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Accepted: 09/23/2022] [Indexed: 12/02/2022]
Abstract
The sequenced data availability opened new horizons related to buffalo genetic control of economic traits and genomic diversity. The visceral organs (brain, liver, etc.) significantly involved in energy metabolism, docility, or social interactions. We performed swamp buffalo transcriptomic profiling of 24 different tissues (brain and non-brain) to identify novel transcripts and analyzed the differentially expressed genes (DEGs) of brain vs. non-brain tissues with their functional annotation. We obtained 178.57 Gb clean transcriptomic data with GC contents 52.77%, reference genome alignment 95.36%, exonic coverage 88.49%. Totally, 26363 mRNAs transcripts including 5574 novel genes were obtained. Further, 7194 transcripts were detected as DEGs by comparing brain vs. non-brain tissues group, of which 3,999 were upregulated and 3,195 downregulated. These DEGs were functionally associated with cellular metabolic activities, signal transduction, cytoprotection, and structural and binding activities. The related functional pathways included cancer pathway, PI3k-Akt signaling, axon guidance, JAK-STAT signaling, basic cellular metabolism, thermogenesis, and oxidative phosphorylation. Our study provides an in-depth understanding of swamp buffalo transcriptomic data including DEGs potentially involved in basic cellular activities and development that helped to maintain their working capacity and social interaction with humans, and also, helpful to disclose the genetic architecture of different phenotypic traits and their gene expression regulation.
Collapse
|
16
|
Li X, He SG, Li WR, Luo LY, Yan Z, Mo DX, Wan X, Lv FH, Yang J, Xu YX, Deng J, Zhu QH, Xie XL, Xu SS, Liu CX, Peng XR, Han B, Li ZH, Chen L, Han JL, Ding XZ, Dingkao R, Chu YF, Wu JY, Wang LM, Zhou P, Liu MJ, Li MH. Genomic analyses of wild argali, domestic sheep, and their hybrids provide insights into chromosome evolution, phenotypic variation, and germplasm innovation. Genome Res 2022; 32:1669-1684. [PMID: 35948368 PMCID: PMC9528982 DOI: 10.1101/gr.276769.122] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Accepted: 07/29/2022] [Indexed: 11/24/2022]
Abstract
Understanding the genetic mechanisms of phenotypic variation in hybrids between domestic animals and their wild relatives may aid germplasm innovation. Here, we report the high-quality genome assemblies of a male Pamir argali (O ammon polii, 2n = 56), a female Tibetan sheep (O aries, 2n = 54), and a male hybrid of Pamir argali and domestic sheep, and the high-throughput sequencing of 425 ovine animals, including the hybrids of argali and domestic sheep. We detected genomic synteny between Chromosome 2 of sheep and two acrocentric chromosomes of argali. We revealed consistent satellite repeats around the chromosome breakpoints, which could have resulted in chromosome fusion. We observed many more hybrids with karyotype 2n = 54 than with 2n = 55, which could be explained by the selfish centromeres, the possible decreased rate of normal/balanced sperm, and the increased incidence of early pregnancy loss in the aneuploid ewes or rams. We identified genes and variants associated with important morphological and production traits (e.g., body weight, cannon circumference, hip height, and tail length) that show significant variations. We revealed a strong selective signature at the mutation (c.334C > A, p.G112W) in TBXT and confirmed its association with tail length among sheep populations of wide geographic and genetic origins. We produced an intercross population of 110 F2 offspring with varied number of vertebrae and validated the causal mutation by whole-genome association analysis. We verified its function using CRISPR-Cas9 genome editing. Our results provide insights into chromosomal speciation and phenotypic evolution and a foundation of genetic variants for the breeding of sheep and other animals.
Collapse
Affiliation(s)
- Xin Li
- College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences (UCAS), Beijing 100049, China
| | - San-Gang He
- MOA Key Laboratory of Ruminant Genetics, Breeding and Reproduction, Ministry of Agriculture (MOA); Key Laboratory of Animal Technology of Xinjiang, Xinjiang Academy of Animal Science, Urumqi, 830000, China
| | - Wen-Rong Li
- MOA Key Laboratory of Ruminant Genetics, Breeding and Reproduction, Ministry of Agriculture (MOA); Key Laboratory of Animal Technology of Xinjiang, Xinjiang Academy of Animal Science, Urumqi, 830000, China
| | - Ling-Yun Luo
- College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Ze Yan
- College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Dong-Xin Mo
- College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Xing Wan
- College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Feng-Hua Lv
- College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Ji Yang
- College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Ya-Xi Xu
- College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Juan Deng
- College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Qiang-Hui Zhu
- College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences (UCAS), Beijing 100049, China
| | - Xing-Long Xie
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences (UCAS), Beijing 100049, China
| | - Song-Song Xu
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences (UCAS), Beijing 100049, China
| | - Chen-Xi Liu
- MOA Key Laboratory of Ruminant Genetics, Breeding and Reproduction, Ministry of Agriculture (MOA); Key Laboratory of Animal Technology of Xinjiang, Xinjiang Academy of Animal Science, Urumqi, 830000, China
| | - Xin-Rong Peng
- MOA Key Laboratory of Ruminant Genetics, Breeding and Reproduction, Ministry of Agriculture (MOA); Key Laboratory of Animal Technology of Xinjiang, Xinjiang Academy of Animal Science, Urumqi, 830000, China
| | - Bin Han
- MOA Key Laboratory of Ruminant Genetics, Breeding and Reproduction, Ministry of Agriculture (MOA); Key Laboratory of Animal Technology of Xinjiang, Xinjiang Academy of Animal Science, Urumqi, 830000, China
| | - Zhong-Hui Li
- MOA Key Laboratory of Ruminant Genetics, Breeding and Reproduction, Ministry of Agriculture (MOA); Key Laboratory of Animal Technology of Xinjiang, Xinjiang Academy of Animal Science, Urumqi, 830000, China
| | - Lei Chen
- MOA Key Laboratory of Ruminant Genetics, Breeding and Reproduction, Ministry of Agriculture (MOA); Key Laboratory of Animal Technology of Xinjiang, Xinjiang Academy of Animal Science, Urumqi, 830000, China
| | - Jian-Lin Han
- CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100193, China
- Livestock Genetics Program, International Livestock Research Institute (ILRI), Nairobi, 00100, Kenya
| | - Xue-Zhi Ding
- MOA Key Laboratory of Veterinary Pharmaceutical Development of Ministry of Agriculture (MOA), Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, 730050, China
| | - Renqing Dingkao
- Institute of Animal Science and Veterinary Medicine, Gannan Tibetan Autonomous Prefecture, Hezuo, 747000, China
| | - Yue-Feng Chu
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, 730046, China
| | - Jin-Yan Wu
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, 730046, China
| | - Li-Min Wang
- Institute of Animal Husbandry and Veterinary Medicine, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi 832000, China
- State Key Laboratory of Sheep Genetic Improvement and Healthy Production, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi 832000, China
| | - Ping Zhou
- Institute of Animal Husbandry and Veterinary Medicine, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi 832000, China
- State Key Laboratory of Sheep Genetic Improvement and Healthy Production, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi 832000, China
| | - Ming-Jun Liu
- MOA Key Laboratory of Ruminant Genetics, Breeding and Reproduction, Ministry of Agriculture (MOA); Key Laboratory of Animal Technology of Xinjiang, Xinjiang Academy of Animal Science, Urumqi, 830000, China
| | - Meng-Hua Li
- College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| |
Collapse
|
17
|
Porrelli S, Gerbault-Seureau M, Rozzi R, Chikhi R, Curaudeau M, Ropiquet A, Hassanin A. Draft genome of the lowland anoa ( Bubalus depressicornis) and comparison with buffalo genome assemblies (Bovidae, Bubalina). G3 GENES|GENOMES|GENETICS 2022; 12:6701968. [PMID: 36111873 PMCID: PMC9635665 DOI: 10.1093/g3journal/jkac234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Accepted: 08/11/2022] [Indexed: 11/24/2022]
Abstract
Genomic data for wild species of the genus Bubalus (Asian buffaloes) are still lacking while several whole genomes are currently available for domestic water buffaloes. To address this, we sequenced the genome of a wild endangered dwarf buffalo, the lowland anoa (Bubalus depressicornis), produced a draft genome assembly and made comparison to published buffalo genomes. The lowland anoa genome assembly was 2.56 Gbp long and contained 103,135 contigs, the longest contig being 337.39 kbp long. N50 and L50 values were 38.73 and 19.83 kbp, respectively, mean coverage was 44× and GC content was 41.74%. Two strategies were adopted to evaluate genome completeness: (1) determination of genomic features with de novo and homology-based predictions using annotations of chromosome-level genome assembly of the river buffalo and (2) employment of benchmarking against universal single-copy orthologs (BUSCO). Homology-based predictions identified 94.51% complete and 3.65% partial genomic features. De novo gene predictions identified 32,393 genes, representing 97.14% of the reference’s annotated genes, whilst BUSCO search against the mammalian orthologs database identified 71.1% complete, 11.7% fragmented, and 17.2% missing orthologs, indicating a good level of completeness for downstream analyses. Repeat analyses indicated that the lowland anoa genome contains 42.12% of repetitive regions. The genome assembly of the lowland anoa is expected to contribute to comparative genome analyses among bovid species.
Collapse
Affiliation(s)
- Stefano Porrelli
- Department of Natural Sciences, Faculty of Science and Technology, Middlesex University , London NW4 4BT, UK
| | - Michèle Gerbault-Seureau
- Institut Systématique Evolution Biodiversité (ISYEB), Sorbonne Université, MNHN, CNRS, EPHE , UA, 75005 Paris, France
| | - Roberto Rozzi
- Museum für Naturkunde, Leibniz-Institut für Evolutions- und Biodiversitätsforschung , 10115 Berlin, Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, 04103 Leipzig , Germany
| | - Rayan Chikhi
- Institut Pasteur, Université Paris Cité, Sequence Bioinformatics , 75015 Paris, France
| | - Manon Curaudeau
- Institut Systématique Evolution Biodiversité (ISYEB), Sorbonne Université, MNHN, CNRS, EPHE , UA, 75005 Paris, France
| | - Anne Ropiquet
- Department of Natural Sciences, Faculty of Science and Technology, Middlesex University , London NW4 4BT, UK
| | - Alexandre Hassanin
- Institut Systématique Evolution Biodiversité (ISYEB), Sorbonne Université, MNHN, CNRS, EPHE , UA, 75005 Paris, France
| |
Collapse
|
18
|
Liu Y, Fu Y, Yang Y, Yi G, Lian J, Xie B, Yao Y, Chen M, Niu Y, Liu L, Wang L, Zhang Y, Fan X, Tang Y, Yuan P, Zhu M, Li Q, Zhang S, Chen Y, Wang B, He J, Lu D, Liachko I, Sullivan ST, Pang B, Chen Y, He X, Li K, Tang Z. Integration of multi-omics data reveals cis-regulatory variants that are associated with phenotypic differentiation of eastern from western pigs. GENETICS SELECTION EVOLUTION 2022; 54:62. [PMID: 36104777 PMCID: PMC9476355 DOI: 10.1186/s12711-022-00754-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Accepted: 09/02/2022] [Indexed: 11/10/2022]
Abstract
Abstract
Background
The genetic mechanisms that underlie phenotypic differentiation in breeding animals have important implications in evolutionary biology and agriculture. However, the contribution of cis-regulatory variants to pig phenotypes is poorly understood. Therefore, our aim was to elucidate the molecular mechanisms by which non-coding variants cause phenotypic differences in pigs by combining evolutionary biology analyses and functional genomics.
Results
We obtained a high-resolution phased chromosome-scale reference genome with a contig N50 of 18.03 Mb for the Luchuan pig breed (a representative eastern breed) and profiled potential selective sweeps in eastern and western pigs by resequencing the genomes of 234 pigs. Multi-tissue transcriptome and chromatin accessibility analyses of these regions suggest that tissue-specific selection pressure is mediated by promoters and distal cis-regulatory elements. Promoter variants that are associated with increased expression of the lysozyme (LYZ) gene in the small intestine might enhance the immunity of the gastrointestinal tract and roughage tolerance in pigs. In skeletal muscle, an enhancer-modulating single-nucleotide polymorphism that is associated with up-regulation of the expression of the troponin C1, slow skeletal and cardiac type (TNNC1) gene might increase the proportion of slow muscle fibers and affect meat quality.
Conclusions
Our work sheds light on the molecular mechanisms by which non-coding variants shape phenotypic differences in pigs and provides valuable resources and novel perspectives to dissect the role of gene regulatory evolution in animal domestication and breeding.
Collapse
|
19
|
Genomic analysis of arginine vasopressin gene in riverine buffalo reveals its potential association with silent estrus behavior. Mol Biol Rep 2022; 49:9315-9324. [PMID: 35902449 DOI: 10.1007/s11033-022-07776-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Accepted: 07/06/2022] [Indexed: 10/16/2022]
Abstract
BACKGROUND Poor estrus expression behavior causes suboptimal reproductive efficiency through poor conception rate. Various signaling pathways are involved in estrus expression but arginine vasopressin (AVP) gene with oxytocin predominantly regulates estrus behavior. This study aimed to perform genomic characterization and evolutionary dynamics of AVP gene through association testing of the novel polymorphic loci and comparative genomic analysis to explore the potential effect of AVP gene on estrus behavior of Nili-Ravi buffaloes. METHODS AND RESULTS 198 Nili-Ravi buffaloes were screened for the quest of novel polymorphism in the AVP gene. In exon-1, five polymorphic sites were detected including deletion of two (c.47delA and c.57delA) nucleotides that caused drastic variation in subsequent amino acid sequence due to frame shift including functional short peptide of nine residues. The 3-D structure revealed a loss of transmembrane loop between 16 and 31 residues in Nili-Ravi buffalo AVP protein sequence, suggesting that missing loop apparently reduced the gene functionality in Nili-Ravi buffalo by inhibiting cellular reactions and muting the animal estrus cyclicity. Three polymorphisms detected in AVP gene were significantly associated with silent estrus (P < 0.05). The comparative genomic analysis revealed that AVP gene is present on chromosome 14 having one conserved motif (Neurohypophysial) in buffalo. CONCLUSIONS This study suggested the potential use of polymorphic sites as promising genetic markers for selection of buffaloes with pronounced estrus expression.
Collapse
|
20
|
Rehman MSU, Mushtaq M, Hassan FU, Zia-ur Rehman, Mushahid M, Shokrollahi B. Comparative Genomic Characterization of Insulin-Like Growth Factor Binding Proteins in Cattle and Buffalo. BIOMED RESEARCH INTERNATIONAL 2022; 2022:5893825. [PMID: 35924270 PMCID: PMC9343199 DOI: 10.1155/2022/5893825] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 06/30/2022] [Accepted: 07/06/2022] [Indexed: 11/30/2022]
Abstract
The somatotropic axis consists of genes associated with economic traits like muscle growth and carcass traits in livestock. Insulin-like growth factor binding proteins (IGFBPs) are the major proteins that play a vital role in the somatotropic axis. The present study performed a genome-wide characterization of IGFBP genes in cattle. Genomic sequences of the IGFBP gene family for different mammals (cattle, buffalo, goat, and sheep) were recovered from the NCBI database. Sequence analyses were performed to investigate cattle's genomic variations in the IGFBP gene family. Phylogenetic analysis, gene structure, motif patterns, and conserved domain analysis (CDA) of the IGFBP family revealed the evolutionarily conserved nature of the IGFBP genes in cattle and other studied species. Physicochemical properties of IGFBP proteins in cattle revealed that most of these proteins are unstable, hydrophilic, thermostable, and acidic. Comparative amino acid analysis revealed variations in all protein sequences with single indels in IGFBP3 and IGFBP6. Mutation analysis revealed only one nonsynonymous mutation D212 > E in the IGFBP6 protein of cattle. A total of 245 nuclear hormone receptor (NHRs) sites were detected, including 139 direct repeats (DR), 65 everted repeats (ER), and 41 inverted repeats (IR). Out of 133 transcription factors (TFs), 10 TFs (AHR, AHRARNT, AP4, CMYB, E47, EGR2, GATA, SP1, and SRF) had differential distribution (P value < 0.05) of putative transcriptional binding sites (TFBS) in cattle compared to buffalo. Synteny analysis revealed the conserved nature of genes between cattle and buffalo. Two gene pairs (IGFBP1/IGFBP3 and IGFBP2/IGFBP5) showed tandem duplication events in cattle and buffalo. This study highlights the functional importance of genomic variation in IGFBP genes and necessitates further investigations better to understand the role and mechanisms of IGFBPs in bovines.
Collapse
Affiliation(s)
- Muhammad Saif-ur Rehman
- Institute of Animal and Dairy Sciences, University of Agriculture, Faisalabad 38040, Pakistan
| | - Muqeet Mushtaq
- Institute of Animal and Dairy Sciences, University of Agriculture, Faisalabad 38040, Pakistan
| | - Faiz-ul Hassan
- Institute of Animal and Dairy Sciences, University of Agriculture, Faisalabad 38040, Pakistan
| | - Zia-ur Rehman
- University of Agriculture, Faisalabad–Subcampus Toba Tek Singh, Pakistan
| | - Muhammad Mushahid
- Institute of Animal and Dairy Sciences, University of Agriculture, Faisalabad 38040, Pakistan
| | - Borhan Shokrollahi
- Department of Animal Science, Sanandaj Branch, Islamic Azad University, Sanandaj, Iran
| |
Collapse
|
21
|
Zhang X, Chen N, Chen H, Lei C, Sun T. Comparative analyses of copy number variations between swamp and river buffalo. Gene X 2022; 830:146509. [PMID: 35460806 DOI: 10.1016/j.gene.2022.146509] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Revised: 04/08/2022] [Accepted: 04/14/2022] [Indexed: 11/30/2022] Open
Abstract
Domestic buffalo is an important livestock in the tropical and sub-tropical region, including two types: swamp and river buffalo. The swamp buffalo is mainly used as draft animal, while the river buffalo is raised for milk production. In this study, based on the new high-quality buffalo reference genome UOA_WB_1, we firstly investigated the copy number variants in buffalo using whole-genome Illumina sequencing. A total of 3,734 CNV regions (CNVRs) were detected in 106 buffalo population with a total length of 23,429,066 bp, corresponding to ∼ 0.88% of the water buffalo genome (UOA_WB_1). Our results revealed a clear population differentiation in CNV between swamp and river buffalo. In addition, a total of 667 highly differentiated CNVRs (covering 886 genes) were detected between river and swamp buffalo population. We detected a set of CNVR-overlapping genes associated with exercise, immunity, nerve, and milk trait which exhibited different copy numbers between swamp and river buffalo population. This study provides valuable genome variation resources for buffalo and would contribute to understanding the genetic differences between swamp and river buffalo.
Collapse
Affiliation(s)
- Xianfu Zhang
- Key Laboratory of Applied Technology on Green-Eco-Healthy Animal Husbandry of Zhejiang Province, Zhejiang Provincial Engineering Laboratory for Animal Health Inspection and Internet Technology, College of Animal Science and Technology, College of Veterinary Medicine, Zhejiang A & F University, Hangzhou, Zhejiang 311300, China.
| | - Ningbo Chen
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Hong Chen
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Chuzhao Lei
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Ting Sun
- College of Life Sciences, Shaanxi Normal University, Xi'an 710062, China.
| |
Collapse
|
22
|
Marcos S, Parejo M, Estonba A, Alberdi A. Recovering High-Quality Host Genomes from Gut Metagenomic Data through Genotype Imputation. ADVANCED GENETICS (HOBOKEN, N.J.) 2022; 3:2100065. [PMID: 36620197 PMCID: PMC9744478 DOI: 10.1002/ggn2.202100065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/27/2021] [Revised: 03/05/2022] [Indexed: 01/11/2023]
Abstract
Metagenomic datasets of host-associated microbial communities often contain host DNA that is usually discarded because the amount of data is too low for accurate host genetic analyses. However, genotype imputation can be employed to reconstruct host genotypes if a reference panel is available. Here, the performance of a two-step strategy is tested to impute genotypes from four types of reference panels built using different strategies to low-depth host genome data (≈2× coverage) recovered from intestinal samples of two chicken genetic lines. First, imputation accuracy is evaluated in 12 samples for which both low- and high-depth sequencing data are available, obtaining high imputation accuracies for all tested panels (>0.90). Second, the impact of reference panel choice in population genetics statistics on 100 chickens is assessed, all four panels yielding comparable results. In light of the observations, the feasibility and application of the applied imputation strategy are discussed for different species with regard to the host DNA proportion, genomic diversity, and availability of a reference panel. This method enables leveraging insofar discarded host DNA to get insights into the genetic structure of host populations, and in doing so, facilitates the implementation of hologenomic approaches that jointly analyze host and microbial genomic data.
Collapse
Affiliation(s)
- Sofia Marcos
- Applied Genomics and BioinformaticsUniversity of the Basque Country (UPV/EHU)LeioaBilbao48940Spain
| | - Melanie Parejo
- Applied Genomics and BioinformaticsUniversity of the Basque Country (UPV/EHU)LeioaBilbao48940Spain
| | - Andone Estonba
- Applied Genomics and BioinformaticsUniversity of the Basque Country (UPV/EHU)LeioaBilbao48940Spain
| | - Antton Alberdi
- Center for Evolutionary HologenomicsGLOBE InstituteUniversity of CopenhagenCopenhagen1353Denmark
| |
Collapse
|
23
|
Liu H, Jiang F, Wang S, Wang H, Wang A, Zhao H, Xu D, Yang B, Fan W. Chromosome-level genome of the globe skimmer dragonfly (Pantala flavescens). Gigascience 2022; 11:6563153. [PMID: 35373834 PMCID: PMC8978299 DOI: 10.1093/gigascience/giac009] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Revised: 11/24/2021] [Accepted: 01/19/2022] [Indexed: 11/29/2022] Open
Abstract
Background The globe skimmer dragonfly (Pantala flavescens) is a notable Odonata insect distributed in nature fields and farmlands worldwide, and it is commonly recognized as a natural enemy because it preys on agricultural pests and health pests. As one of the sister groups of winged insects, odonatan species are key to understanding the evolution of insect wings. Findings We present a high-quality reference genome of P. flavescens, which is the first chromosome-level genome in the Palaeoptera (Odonata and Ephemeroptera). The assembled genome size was 662 Mb, with a contig N50 of 16.2 Mb. Via Hi-C scaffolding, 648 Mb (97.9%) of contig sequences were clustered, ordered, and assembled into 12 large scaffolds, each corresponding to a natural chromosome. The X chromosome was identified by sequence coverage depth. The repetitive sequences and gene density of the X chromosome are similar to those of autosomal sequences, but the X chromosome shows a much lower degree of heterozygosity. Our analysis shows that the effective population size experienced 3 declining events, which may have been caused by climate change and environmental pollution. Conclusions The genome of P. flavescens provides more information on the biology and evolution of insects and will help for the use of this species in pest control.
Collapse
Affiliation(s)
- Hangwei Liu
- Guangdong Laboratory for Lingnan Modern Agriculture (Shenzhen Branch), Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong 518120, China
| | - Fan Jiang
- Guangdong Laboratory for Lingnan Modern Agriculture (Shenzhen Branch), Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong 518120, China
| | - Sen Wang
- Guangdong Laboratory for Lingnan Modern Agriculture (Shenzhen Branch), Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong 518120, China
| | - Hengchao Wang
- Guangdong Laboratory for Lingnan Modern Agriculture (Shenzhen Branch), Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong 518120, China
| | - Anqi Wang
- Guangdong Laboratory for Lingnan Modern Agriculture (Shenzhen Branch), Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong 518120, China
| | - Hanbo Zhao
- Guangdong Laboratory for Lingnan Modern Agriculture (Shenzhen Branch), Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong 518120, China
| | - Dong Xu
- Guangdong Laboratory for Lingnan Modern Agriculture (Shenzhen Branch), Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong 518120, China
| | - Boyuan Yang
- Guangdong Laboratory for Lingnan Modern Agriculture (Shenzhen Branch), Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong 518120, China
| | - Wei Fan
- Guangdong Laboratory for Lingnan Modern Agriculture (Shenzhen Branch), Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong 518120, China
| |
Collapse
|
24
|
Hu RS, Zhang FK, Ma QN, Ehsan M, Zhao Q, Zhu XQ. Transcriptomic landscape of hepatic lymph nodes, peripheral blood lymphocytes and spleen of swamp buffaloes infected with the tropical liver fluke Fasciola gigantica. PLoS Negl Trop Dis 2022; 16:e0010286. [PMID: 35320269 PMCID: PMC8942208 DOI: 10.1371/journal.pntd.0010286] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Accepted: 02/28/2022] [Indexed: 11/22/2022] Open
Abstract
The tropical liver fluke Fasciola gigantica is a parasitic helminth that has been frequently reported to infect mammals, typically involving water buffaloes. In this study, we characterized the tissue transcriptional landscape of buffaloes following infection by F. gigantica. RNAs were isolated from hepatic lymph nodes (hLNs), peripheral blood lymphocytes (pBLs), and spleen at 3-, 42- and 70-days post-infection (dpi), and all samples were subjected to RNA sequencing analyses. At 3 dpi, 2603, 460, and 162 differentially expressed transcripts (DETs) were detected in hLNs, pBLs, and spleen, respectively. At 42 dpi, 322, 937, and 196 DETs were detected in hLNs, pBLs, and spleen, respectively. At 70 dpi, 376, 334, and 165 DETs were detected in hLNs, pBLs, and spleen, respectively. Functional enrichment analysis identified upregulated immune-related pathways in the infected tissues involved in innate and adaptive immune responses, especially in hLNs at 42 and 70 dpi, and pBLs at 3 and 42 dpi. The upregulated transcripts in spleen were not enriched in any immune-related pathway. Co-expression network analysis further identified transcriptional changes associated with immune response to F. gigantica infection. Receiver operating characteristic (ROC) curve analysis showed that 107 genes in hLNs, 32 genes in pBLs, and 36 genes in spleen correlated with F. gigantica load. These findings provide new insight into molecular mechanisms and signaling pathways associated with F. gigantica infection in buffaloes. Fasciola gigantica is a socioeconomically important tropical liver fluke of mammals, causing fascioliasis–a neglected tropical disease. In the present study, RNA sequencing and bioinformatic approach were employed to explore the global transcriptional changes of hepatic lymph nodes (hLNs), peripheral blood lymphocytes (pBLs), and spleen of water buffaloes during F. gigantica infection at 3-, 42-, and 70-days post-infection (dpi). The results revealed significant transcriptional upregulation of genes associated with innate and adaptive immune responses in infected hLNs (42 and 70 dpi) and pBLs (3 and 42 dpi). However, downregulation of transcripts involved in immune response was detected in pBLs at 70 dpi. The downregulated transcripts were enriched in metabolic pathways, such as drug metabolism-cytochrome P450 in infected hLNs at 3 dpi. These findings provide new insight into the pathogenesis of F. gigantica in its natural mammalian host.
Collapse
Affiliation(s)
- Rui-Si Hu
- College of Life Science, Changchun Sci-Tech University, Shuangyang, Jilin Province, People’s Republic of China
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu Province, People’s Republic of China
| | - Fu-Kai Zhang
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu Province, People’s Republic of China
| | - Qiao-Ni Ma
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu Province, People’s Republic of China
| | - Muhammad Ehsan
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu Province, People’s Republic of China
- Department of Parasitology, Faculty of Veterinary and Animal Sciences, The Islamia University of Bahawalpur, Bahawalpur, Punjab Province, Pakistan
| | - Quan Zhao
- College of Life Science, Changchun Sci-Tech University, Shuangyang, Jilin Province, People’s Republic of China
- * E-mail: (QZ); (X-QZ)
| | - Xing-Quan Zhu
- College of Veterinary Medicine, Shanxi Agricultural University, Taigu, Shanxi Province, People’s Republic of China
- Key Laboratory of Veterinary Public Health of Yunnan Province, College of Veterinary Medicine, Yunnan Agricultural University, Kunming, Yunnan Province, People’s Republic of China
- * E-mail: (QZ); (X-QZ)
| |
Collapse
|
25
|
Abstract
Buffalo is an important livestock species. Here, we present a comprehensive metagenomic survey of the microbial communities along the buffalo digestive tract. We analysed 695 samples covering eight different sites in three compartments (four-chambered stomach, intestine, and rectum). We mapped ~85% of the raw sequence reads to 4,960 strain-level metagenome-assembled genomes (MAGs) and 3,255 species-level MAGs, 90% of which appear to correspond to new species. In addition, we annotated over 5.8 million nonredundant proteins from the MAGs. In comparison with the rumen microbiome of cattle, the buffalo microbiota seems to present greater potential for fibre degradation and less potential for methane production. Our catalogue of microbial genomes and the encoded proteins provides insights into microbial functions and interactions at distinct sites along the buffalo digestive tract.
Collapse
|
26
|
Zhang J, Yang X, Chen M, Yan X, Gao L, Xu Y, Lu J, Li Z, Lu C, Deng Y, Li H, Shi D, Lu F. Hypoxia promotes steroidogenic competence of buffalo (Bubalus bubalis) theca cells. Theriogenology 2021; 180:113-120. [PMID: 34971972 DOI: 10.1016/j.theriogenology.2021.12.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Revised: 11/29/2021] [Accepted: 12/15/2021] [Indexed: 10/19/2022]
Abstract
Theca cells (TCs) play an important role in follicular development and atresia. TCs synthesize androgens that act as substrate for granulosa cells aromatization to estrogens needed for follicular growth. However, the effects of hypoxia on steroidogenesis in buffalo TCs remain unclear. In the present study, the impacts of hypoxic conditions (5% oxygen) on androgen synthesis in buffalo TCs were examined. The results showed that hypoxia improved both the expression levels of androgen synthesis-related genes (CYP11A1, CYP17A1, and 3β-HSD) and the secretion levels of testosterone in buffalo TCs. Hypoxic conditions promoted the sensitivity of buffalo TCs to LH. Furthermore, inhibition of PI3K/AKT signaling pathway reduced both the expression levels of androgen synthesis-related genes (CYP11A1, CYP17A1, and 3β-HSD) and the secretion levels of testosterone in hypoxia-cultured buffalo TCs. Besides, inhibition of PI3K/AKT signaling pathway lowered the sensitivity of buffalo TCs to LH under hypoxic conditions. This study indicated that hypoxia enhanced the steroidogenic competence of buffalo TCs main through activating PI3K/AKT signaling pathway and subsequently facilitating the responsiveness of TCs to LH. This study provides a basis for further exploration of ovarian endocrine mechanism for steroidogenesis.
Collapse
Affiliation(s)
- Jun Zhang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi University, Nanning, Guangxi, 530004, China
| | - Xiaofen Yang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi University, Nanning, Guangxi, 530004, China
| | - Mengjia Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi University, Nanning, Guangxi, 530004, China
| | - Xi Yan
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi University, Nanning, Guangxi, 530004, China
| | - Lv Gao
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi University, Nanning, Guangxi, 530004, China
| | - Ye Xu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi University, Nanning, Guangxi, 530004, China
| | - Jiaka Lu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi University, Nanning, Guangxi, 530004, China
| | - Zhengda Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi University, Nanning, Guangxi, 530004, China
| | - Canqiang Lu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi University, Nanning, Guangxi, 530004, China
| | - Yanfei Deng
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi University, Nanning, Guangxi, 530004, China
| | - Hui Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi University, Nanning, Guangxi, 530004, China
| | - Deshun Shi
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi University, Nanning, Guangxi, 530004, China
| | - Fenghua Lu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi University, Nanning, Guangxi, 530004, China.
| |
Collapse
|
27
|
Luo X, Cui K, Wang Z, Li Z, Wu Z, Huang W, Zhu XQ, Ruan J, Zhang W, Liu Q. High-quality reference genome of Fasciola gigantica: Insights into the genomic signatures of transposon-mediated evolution and specific parasitic adaption in tropical regions. PLoS Negl Trop Dis 2021; 15:e0009750. [PMID: 34610021 PMCID: PMC8519440 DOI: 10.1371/journal.pntd.0009750] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 10/15/2021] [Accepted: 08/23/2021] [Indexed: 12/31/2022] Open
Abstract
Fasciola gigantica and Fasciola hepatica are causative pathogens of fascioliasis, with the widest latitudinal, longitudinal, and altitudinal distribution; however, among parasites, they have the largest sequenced genomes, hindering genomic research. In the present study, we used various sequencing and assembly technologies to generate a new high-quality Fasciola gigantica reference genome. We improved the integration of gene structure prediction, and identified two independent transposable element expansion events contributing to (1) the speciation between Fasciola and Fasciolopsis during the Cretaceous-Paleogene boundary mass extinction, and (2) the habitat switch to the liver during the Paleocene-Eocene Thermal Maximum, accompanied by gene length increment. Long interspersed element (LINE) duplication contributed to the second transposon-mediated alteration, showing an obvious trend of insertion into gene regions, regardless of strong purifying effect. Gene ontology analysis of genes with long LINE insertions identified membrane-associated and vesicle secretion process proteins, further implicating the functional alteration of the gene network. We identified 852 predicted excretory/secretory proteins and 3300 protein-protein interactions between Fasciola gigantica and its host. Among them, copper/zinc superoxide dismutase genes, with specific gene copy number variations, might play a central role in the phase I detoxification process. Analysis of 559 single-copy orthologs suggested that Fasciola gigantica and Fasciola hepatica diverged at 11.8 Ma near the Middle and Late Miocene Epoch boundary. We identified 98 rapidly evolving gene families, including actin and aquaporin, which might explain the large body size and the parasitic adaptive character resulting in these liver flukes becoming epidemic in tropical and subtropical regions.
Collapse
Affiliation(s)
- Xier Luo
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi University, Nanning, China
| | - Kuiqing Cui
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi University, Nanning, China
| | - Zhiqiang Wang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi University, Nanning, China
| | - Zhipeng Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi University, Nanning, China
| | - Zhengjiao Wu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi University, Nanning, China
| | - Weiyi Huang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi University, Nanning, China
| | - Xing-Quan Zhu
- College of Veterinary Medicine, Shanxi Agricultural University, Taigu, China
| | - Jue Ruan
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi University, Nanning, China
| | - Weiyu Zhang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi University, Nanning, China
| | - Qingyou Liu
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi University, Nanning, China
| |
Collapse
|
28
|
Raza SHA, Hassanin AA, Dhshan AI, Abdelnour SA, Khan R, Mei C, Zan L. In silico genomic and proteomic analyses of three heat shock proteins (HSP70, HSP90-α, and HSP90-β) in even-toed ungulates. ELECTRON J BIOTECHN 2021. [DOI: 10.1016/j.ejbt.2021.07.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
|
29
|
Ren Y, MacPhillamy C, To TH, Smith TPL, Williams JL, Low WY. Adaptive selection signatures in river buffalo with emphasis on immune and major histocompatibility complex genes. Genomics 2021; 113:3599-3609. [PMID: 34455036 DOI: 10.1016/j.ygeno.2021.08.021] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 08/11/2021] [Accepted: 08/23/2021] [Indexed: 11/27/2022]
Abstract
River buffalo is an agriculturally important species with many traits, such as disease tolerance, which promote its use worldwide. Highly contiguous genome assemblies of the river buffalo, goat, pig, human and two cattle subspecies were aligned to study gene gains and losses and signs of positive selection. The gene families that have changed significantly in river buffalo since divergence from cattle play important roles in protein degradation, the olfactory receptor system, detoxification and the immune system. We used the branch site model in PAML to analyse single-copy orthologs to identify positively selected genes that may be involved in skin differentiation, mammary development and bone formation in the river buffalo branch. The high contiguity of the genomes enabled evaluation of differences among species in the major histocompatibility complex. We identified a Babesia-like L1 LINE insertion in the DRB1-like gene in the river buffalo and discuss the implication of this finding.
Collapse
Affiliation(s)
- Yan Ren
- The Davies Research Centre, School of Animal and Veterinary Sciences, University of Adelaide, Roseworthy, SA 5371, Australia
| | - Callum MacPhillamy
- The Davies Research Centre, School of Animal and Veterinary Sciences, University of Adelaide, Roseworthy, SA 5371, Australia
| | - Thu-Hien To
- Norwegian University of Life Sciences: NMBU, Universitetstunet 3, 1430 Ås, Norway
| | | | - John L Williams
- The Davies Research Centre, School of Animal and Veterinary Sciences, University of Adelaide, Roseworthy, SA 5371, Australia; Dipartimento di Scienze Animali, della Nutrizione e degli Alimenti, Università Cattolica del Sacro Cuore, Piacenza, Italy
| | - Wai Yee Low
- The Davies Research Centre, School of Animal and Veterinary Sciences, University of Adelaide, Roseworthy, SA 5371, Australia.
| |
Collapse
|
30
|
Zhang S, Liu W, Liu X, Du X, Zhang K, Zhang Y, Song Y, Zi Y, Qiu Q, Lenstra JA, Liu J. Structural Variants Selected during Yak Domestication Inferred from Long-Read Whole-Genome Sequencing. Mol Biol Evol 2021; 38:3676-3680. [PMID: 33944937 PMCID: PMC8382902 DOI: 10.1093/molbev/msab134] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Structural variants (SVs) represent an important genetic resource for both natural and artificial selection. Here we present a chromosome-scale reference genome for domestic yak (Bos grunniens) that has longer contigs and scaffolds (N50 44.72 and 114.39 Mb, respectively) than reported for any other ruminant genome. We further obtained long-read resequencing data for 6 wild and 23 domestic yaks and constructed a genetic SV map of 372,220 SVs that covers the geographic range of the yaks. The majority of the SVs contains repetitive sequences and several are in or near genes. By comparing SVs in domestic and wild yaks, we identified genes that are predominantly related to the nervous system, behavior, immunity, and reproduction and may have been targeted by artificial selection during yak domestication. These findings provide new insights in the domestication of animals living at high altitude and highlight the importance of SVs in animal domestication.
Collapse
Affiliation(s)
- Shangzhe Zhang
- State Key Laboratory of Grassland and Agro-ecosystem, Institute of Innovation Ecology and School of Life Science, Lanzhou University, Lanzhou, China
| | - Wenyu Liu
- State Key Laboratory of Grassland and Agro-ecosystem, Institute of Innovation Ecology and School of Life Science, Lanzhou University, Lanzhou, China
| | - Xinfeng Liu
- State Key Laboratory of Grassland and Agro-ecosystem, Institute of Innovation Ecology and School of Life Science, Lanzhou University, Lanzhou, China
| | - Xin Du
- State Key Laboratory of Grassland and Agro-ecosystem, Institute of Innovation Ecology and School of Life Science, Lanzhou University, Lanzhou, China
| | - Ke Zhang
- State Key Laboratory of Grassland and Agro-ecosystem, Institute of Innovation Ecology and School of Life Science, Lanzhou University, Lanzhou, China
| | - Yang Zhang
- The Supercomputing Center, Lanzhou University, Lanzhou, China
| | - Yongwu Song
- Animal Disease Prevention and Control Center of Gangcha County, Haibei Tibetan Autonomous Prefecture, China
| | - Yunnan Zi
- Animal Husbandry Workstation of Xiahe County, Gannan Tibetan Autonomous Prefecture, China
| | - Qiang Qiu
- State Key Laboratory of Grassland and Agro-ecosystem, Institute of Innovation Ecology and School of Life Science, Lanzhou University, Lanzhou, China
| | - Johannes A Lenstra
- Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Jianquan Liu
- State Key Laboratory of Grassland and Agro-ecosystem, Institute of Innovation Ecology and School of Life Science, Lanzhou University, Lanzhou, China
| |
Collapse
|
31
|
Hao M, Jiang J, Zhang Y, Wang S, Fu G, Zou F, Xie Y, Zhao S, Li W. Transcriptional profiling of buffalo mammary gland with different milk fat contents. Gene 2021; 802:145864. [PMID: 34352300 DOI: 10.1016/j.gene.2021.145864] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2021] [Revised: 06/08/2021] [Accepted: 07/30/2021] [Indexed: 10/20/2022]
Abstract
Milk fat is the most important energy substance in milk and contributes to its quality and health benefits. Water buffalo milk is well known for its high milk quality with higher fat contents compared with cattle milk. Dehong buffalo is a unique local swamp breed in Yunnan Province with higher milk fat and excellent milk quality which provides a good model for the investigation of the molecular mechanisms of milk fat deposition. In this study, we used RNA-seq to obtain mammary tissue transcriptomics of buffalo with different milk fat phenotypes including high(H), medium (M)and low (L) fat content groups. Comparative analyses of buffalo among three groups yielded differentially expressed genes (DEGs). Analyzing the number of different genes among H_VS_L, H_VS_M, and M_VS_L showed the same expression pattern between H_VS_M. The increasing expression levels of genes including CSN1S1, BTN1A1, LALBA, ALDH1L2, SCD and MUC15, and down-regulated expression levels of genes containing CCL2, CRABP2, ADTRP, CLU and C4A in H_VS_L and M_VS_L were found. GO and KEGG enriched pathways revealed these DEGs involved in milk protein and fat as well as immune response. The findings would enhance the understanding of the interplay between the milk composition and immune response, which suggests that the immune capacity should be considered when we tried to improve the milk quality.
Collapse
Affiliation(s)
- Meilin Hao
- College of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China; College of Biology and Agriculture (College of Food Science and Technology), Zunyi Normal College, Zunyi 563006, China
| | - Juncai Jiang
- College of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China; Chongqing Institute of Medicinal Plant Cultivation, Chongqing 408435, China
| | - Yongyun Zhang
- Teaching Demonstration Center of the Basic Experiments of Agricultural Majors, Yunnan Agricultural University, Kunming 650201, China
| | - Shaoqing Wang
- College of Veterinary Medicine, Yunnan Agricultural University, Kunming, 650201, China
| | - Guowen Fu
- College of Veterinary Medicine, Yunnan Agricultural University, Kunming, 650201, China
| | - Fengcai Zou
- College of Veterinary Medicine, Yunnan Agricultural University, Kunming, 650201, China
| | - Yuxiao Xie
- College of Biology and Agriculture (College of Food Science and Technology), Zunyi Normal College, Zunyi 563006, China
| | - Sumei Zhao
- College of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China.
| | - Weizhen Li
- College of Veterinary Medicine, Yunnan Agricultural University, Kunming, 650201, China.
| |
Collapse
|
32
|
Zhang J, Wang H, Lu J, Yu Q, Fu P, Li Z, Feng Y, Wang Y, Deng Y, Shi D, Lu F. Granulosa cells affect in vitro maturation and subsequent parthenogenetic development of buffalo (Bubalus bubalis) oocytes. Reprod Domest Anim 2021; 57:141-148. [PMID: 34057767 DOI: 10.1111/rda.13974] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Accepted: 05/27/2021] [Indexed: 12/17/2022]
Abstract
Granulosa cells (GCs) play a crucial role in follicular development and atresia. Previous studies have showed that GCs in the form of monolayer influenced in vitro maturation (IVM) of oocytes. However, the effects of GCs in the form of conditioned medium and monolayer on IVM and development competence of buffalo oocytes remain unclear. In the present study, we examined the impacts of GC-conditioned medium (GCCM) and monolayer GC on maturation efficiency and embryo development of buffalo oocytes after parthenogenetic activation (PA). Our results showed that GCCM that was collected on day 2 and added to IVM medium at a 20% proportional level (2 days and 20%) exerted significant negative effects on IVM rate (41.6% vs. 44.5%), but significantly enhanced embryo development (oocyte cleavage, 81.3% vs. 69.3%; blastocyst formation, 36.3% vs. 29.3%) of buffalo oocytes after PA compared with the control group. Furthermore, monolayer GC significantly reduced both maturation efficiency (40.2% vs. 44.5%) and embryo development (oocyte cleavage, 60.6% vs. 69.3%; blastocyst formation, 20.6% vs. 29.3%) of buffalo oocytes after PA compared to the control group. Our study indicated that GCs in the form of GCCM (2 days and 20%) and monolayer GC had different effects on IVM and subsequent parthenogenetic development of buffalo oocytes.
Collapse
Affiliation(s)
- Jun Zhang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi University, Nanning, China
| | - Haoxin Wang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi University, Nanning, China
| | - Jiaka Lu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi University, Nanning, China
| | - Qing Yu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi University, Nanning, China
| | - Penghui Fu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi University, Nanning, China
| | - Zhengda Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi University, Nanning, China
| | - Yun Feng
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi University, Nanning, China
| | - Yanxin Wang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi University, Nanning, China
| | - Yanfei Deng
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi University, Nanning, China
| | - Deshun Shi
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi University, Nanning, China
| | - Fenghua Lu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi University, Nanning, China
| |
Collapse
|
33
|
Wrangham RW. Targeted conspiratorial killing, human self-domestication and the evolution of groupishness. EVOLUTIONARY HUMAN SCIENCES 2021; 3:e26. [PMID: 37588548 PMCID: PMC10427284 DOI: 10.1017/ehs.2021.20] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Groupishness is a set of tendencies to respond to group members with prosociality and cooperation in ways that transcend apparent self-interest. Its evolution is puzzling because it gives the impression of breaking the ordinary rules of natural selection. Boehm's solution is that moral elements of groupishness originated and evolved as a result of group members becoming efficient executioners of antisocial individuals, and he noted that self-domestication would have proceeded from the same dynamic. Self-domestication is indicated first at ~300,000 years ago and has probably gathered pace ever since, suggesting selection for self-domestication and groupishness for at least 12,000 generations. Here I propose that a specifically human style of violence, targeted conspiratorial killing, contributed importantly to both self-domestication and to promoting groupishness. Targeted conspiratorial killing is unknown in chimpanzees or any other vertebrate, and is significant because it permits coalitions to kill antisocial individuals cheaply. The hypothesis that major elements of groupishness are due to targeted conspiratorial killing helps explain why they are much more elaborated in humans than in other species.
Collapse
Affiliation(s)
- Richard W. Wrangham
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA
| |
Collapse
|
34
|
Zhang J, Qin X, Deng Y, Lu J, Li Z, Feng Y, Yan X, Chen M, Gao L, Xu Y, Shi D, Lu F. Transforming Growth Factor-β1 Enhances Mesenchymal Characteristics of Buffalo ( Bubalus bubalis) Bone Marrow-Derived Mesenchymal Stem Cells. Cell Reprogram 2021; 23:127-138. [PMID: 33861638 DOI: 10.1089/cell.2020.0093] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Bone marrow-derived mesenchymal stem cells (BMSCs) from livestock are valuable resources for animal reproduction and veterinary therapeutics. Previous studies have shown that BMSCs were prone to malignant transformation of mesenchymal-to-epithelial transition in vitro, which can cause many barriers to further application of BMSCs. The transforming growth factor β (TGF-β) signaling pathway has been widely studied as the most important signaling pathway involved in regulating mesenchymal features of BMSCs. However, the effects of the TGF-β signaling pathway on mesenchymal characteristics of buffalo BMSCs (bBMSCs) remain unclear. In the present study, the impacts of the growth factor, TGF-β1, on cell proliferation, apoptosis, migration, and karyotype of bBMSCs were tested. Besides, the effects of TGF-β1 on pluripotency, mesenchymal markers, and epithelial-to-mesenchymal transition (EMT)-related gene expression of bBMSCs were also examined. Results showed that the suitable concentration and time of TGF-β1 treatment (2 ng/mL and 24 hours) promoted cell proliferation and significantly reduced cell apoptosis (p < 0.05) in bBMSCs. The cell migration capacity and normal karyotype rate of bBMSCs were significantly (p < 0.05) improved under TGF-β1 treatment. The expression levels of pluripotency-related genes (Sox2 and Nanog) and mesenchymal markers (N-cadherin and Fn1) were significantly (p < 0.05) up-regulated under TGF-β1 treatment. Furthermore, TGF-β1 activated the EMT process, thereby contributing to significantly enhancing the expression levels of EMT-related genes (Snail and Slug) (p < 0.05), which in turn improved maintenance of the mesenchymal nature in bBMSCs. Finally, bBMSCs underwent self-transformation more easily and efficiently and exhibited more characteristics of mesenchymal stem cells under TGF-β1 treatment. This study provides theoretical guidance for elucidating the detailed mechanism of the TGF-β signaling pathway in mesenchymal feature maintenance of bBMSCs and is of significance to establish a stable culture system of bBMSCs.
Collapse
Affiliation(s)
- Jun Zhang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, China
| | - Xiling Qin
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, China
| | - Yanfei Deng
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, China
| | - Jiaka Lu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, China
| | - Zhengda Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, China
| | - Yun Feng
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, China
| | - Xi Yan
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, China
| | - Mengjia Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, China
| | - Lv Gao
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, China
| | - Ye Xu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, China
| | - Deshun Shi
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, China
| | - Fenghua Lu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, China
| |
Collapse
|
35
|
Curaudeau M, Rozzi R, Hassanin A. The genome of the lowland anoa (Bubalus depressicornis) illuminates the origin of river and swamp buffalo. Mol Phylogenet Evol 2021; 161:107170. [PMID: 33798669 DOI: 10.1016/j.ympev.2021.107170] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Revised: 03/12/2021] [Accepted: 03/25/2021] [Indexed: 10/21/2022]
Abstract
Two types of domestic water buffalo are currently recognized: the river buffalo from the Indian subcontinent and Mediterranean countries and the swamp buffalo from China and Southeast Asia. To test the hypothesis of two separate species of water buffalo, we sequenced the genome of the lowland anoa, Bubalus depressicornis, which is a dwarf wild buffalo endemic to Sulawesi, and two genomes of swamp buffalo, and made comparisons with 12 additional genomes. Three genomic data sets were constructed to infer phylogenetic relationships: the mitochondrial genome (15,468 bp; maternal transmission), two concatenated Y-chromosomal genes, AMELY and DDX3Y (20,036 bp; paternal transmission), and a selection of 30 nuclear genes representing all cattle chromosomes (364,887 bp; biparental transmission). The comparisons between our 30 nuclear gene sequences obtained by read mapping and those directly extracted from Bos taurus and Bubalus bubalis genome assemblies show that the mapping approach revealed higher levels of heterozygosity at both nucleotide sites and indels (insertions and deletions) (0.09-0.15%), as well as several sequence errors (0.07%). Our phylogenetic and molecular dating analyses provide strong evidence that the lowland anoa, river buffalo, and swamp buffalo are three distinct taxa which separated rapidly from each other during the Pleistocene epoch. We therefore conclude that two species of domestic water buffalo should be distinguished: Bubalus bubalis for the river buffalo and Bubalus kerabau for the swamp buffalo. The new classification can have deep implications for understanding the evolution and selection of domesticated forms and for the conservation and management of wild buffalo populations in South and Southeast Asia.
Collapse
Affiliation(s)
- Manon Curaudeau
- Institut Systématique Evolution Biodiversité (ISYEB), Sorbonne Université, MNHN, CNRS, EPHE, UA, 57 rue Cuvier, CP 51, 75005 Paris, France
| | - Roberto Rozzi
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Synthesis Centre for Biodiversity Sciences (sDiv), Puschstr. 4, D-04103 Leipzig, Germany; Museum für Naturkunde, Leibniz-Institut für Evolutions- und Biodiversitätsforschung, 10115 Berlin, Germany
| | - Alexandre Hassanin
- Institut Systématique Evolution Biodiversité (ISYEB), Sorbonne Université, MNHN, CNRS, EPHE, UA, 57 rue Cuvier, CP 51, 75005 Paris, France.
| |
Collapse
|
36
|
Rehman SU, Feng T, Wu S, Luo X, Lei A, Luobu B, Hassan FU, Liu Q. Comparative Genomics, Evolutionary and Gene Regulatory Regions Analysis of Casein Gene Family in Bubalus bubalis. Front Genet 2021; 12:662609. [PMID: 33833782 PMCID: PMC8021914 DOI: 10.3389/fgene.2021.662609] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Accepted: 03/01/2021] [Indexed: 12/27/2022] Open
Abstract
Buffalo is a luxurious genetic resource with multiple utilities (as a dairy, draft, and meat animal) and economic significance in the tropical and subtropical regions of the globe. The excellent potential to survive and perform on marginal resources makes buffalo an important source for nutritious products, particularly milk and meat. This study was aimed to investigate the evolutionary relationship, physiochemical properties, and comparative genomic analysis of the casein gene family (CSN1S1, CSN2, CSN1S2, and CSN3) in river and swamp buffalo. Phylogenetic, gene structure, motif, and conserved domain analysis revealed the evolutionarily conserved nature of the casein genes in buffalo and other closely related species. Results indicated that casein proteins were unstable, hydrophilic, and thermostable, although αs1-CN, β-CN, and κ-CN exhibited acidic properties except for αs2-CN, which behaved slightly basic. Comparative analysis of amino acid sequences revealed greater variation in the river buffalo breeds than the swamp buffalo indicating the possible role of these variations in the regulation of milk traits in buffalo. Furthermore, we identified lower transcription activators STATs and higher repressor site YY1 distribution in swamp buffalo, revealing its association with lower expression of casein genes that might subsequently affect milk production. The role of the main motifs in controlling the expression of casein genes necessitates the need for functional studies to evaluate the effect of these elements on the regulation of casein gene function in buffalo.
Collapse
Affiliation(s)
- Saif ur Rehman
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, China
| | - Tong Feng
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, China
| | - Siwen Wu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, China
| | - Xier Luo
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, China
| | - An Lei
- National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics, Breeding and Reproduction of the Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Basang Luobu
- Shannan Animal Husbandry and Veterinary Terminus, Xizang, China
| | - Faiz-ul Hassan
- Faculty of Animal Husbandry, Institute of Animal and Dairy Sciences, University of Agriculture, Faisalabad, Pakistan
| | - Qingyou Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, China
| |
Collapse
|
37
|
Rehman SU, Hassan FU, Luo X, Li Z, Liu Q. Whole-Genome Sequencing and Characterization of Buffalo Genetic Resources: Recent Advances and Future Challenges. Animals (Basel) 2021; 11:904. [PMID: 33809937 PMCID: PMC8004149 DOI: 10.3390/ani11030904] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Revised: 03/16/2021] [Accepted: 03/18/2021] [Indexed: 12/17/2022] Open
Abstract
The buffalo was domesticated around 3000-6000 years ago and has substantial economic significance as a meat, dairy, and draught animal. The buffalo has remained underutilized in terms of the development of a well-annotated and assembled reference genome de novo. It is mandatory to explore the genetic architecture of a species to understand the biology that helps to manage its genetic variability, which is ultimately used for selective breeding and genomic selection. Morphological and molecular data have revealed that the swamp buffalo population has strong geographical genomic diversity with low gene flow but strong phenotypic consistency, while the river buffalo population has higher phenotypic diversity with a weak phylogeographic structure. The availability of recent high-quality reference genome and genotyping marker panels has invigorated many genome-based studies on evolutionary history, genetic diversity, functional elements, and performance traits. The increasing molecular knowledge syndicate with selective breeding should pave the way for genetic improvement in the climatic resilience, disease resistance, and production performance of water buffalo populations globally.
Collapse
Affiliation(s)
- Saif ur Rehman
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning 530005, China; (S.u.R.); (X.L.); (Z.L.)
| | - Faiz-ul Hassan
- Institute of Animal and Dairy Sciences, Faculty of Animal Husbandry, University of Agriculture, Faisalabad 38040, Pakistan;
| | - Xier Luo
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning 530005, China; (S.u.R.); (X.L.); (Z.L.)
| | - Zhipeng Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning 530005, China; (S.u.R.); (X.L.); (Z.L.)
| | - Qingyou Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning 530005, China; (S.u.R.); (X.L.); (Z.L.)
| |
Collapse
|
38
|
Pineda PS, Flores EB, Herrera JRV, Low WY. Opportunities and Challenges for Improving the Productivity of Swamp Buffaloes in Southeastern Asia. Front Genet 2021; 12:629861. [PMID: 33828581 PMCID: PMC8021093 DOI: 10.3389/fgene.2021.629861] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Accepted: 02/26/2021] [Indexed: 11/18/2022] Open
Abstract
The swamp buffalo is a domesticated animal commonly found in Southeast Asia. It is a highly valued agricultural animal for smallholders, but the production of this species has unfortunately declined in recent decades due to rising farm mechanization. While swamp buffalo still plays a role in farmland cultivation, this species' purposes has shifted from draft power to meat, milk, and hide production. The current status of swamp buffaloes in Southeast Asia is still understudied compared to its counterparts such as the riverine buffaloes and cattle. This review discusses the background of swamp buffalo, with an emphasis on recent work on this species in Southeast Asia, and associated genetics and genomics work such as cytogenetic studies, phylogeny, domestication and migration, genetic sequences and resources. Recent challenges to realize the potential of this species in the agriculture industry are also discussed. Limited genetic resource for swamp buffalo has called for more genomics work to be done on this species including decoding its genome. As the economy progresses and farm mechanization increases, research and development for swamp buffaloes are focused on enhancing its productivity through understanding the genetics of agriculturally important traits. The use of genomic markers is a powerful tool to efficiently utilize the potential of this animal for food security and animal conservation. Understanding its genetics and retaining and maximizing its adaptability to harsher environments are a strategic move for food security in poorer nations in Southeast Asia in the face of climate change.
Collapse
Affiliation(s)
- Paulene S. Pineda
- Philippine Carabao Center National Headquarters and Genepool, Science City of Muñoz, Philippines
| | - Ester B. Flores
- Philippine Carabao Center National Headquarters and Genepool, Science City of Muñoz, Philippines
| | | | - Wai Yee Low
- The Davies Research Centre, School of Animal and Veterinary Sciences, University of Adelaide, Adelaide, SA, Australia
| |
Collapse
|
39
|
Liang D, Zhao P, Si J, Fang L, Pairo-Castineira E, Hu X, Xu Q, Hou Y, Gong Y, Liang Z, Tian B, Mao H, Yindee M, Faruque MO, Kongvongxay S, Khamphoumee S, Liu GE, Wu DD, Barker JSF, Han J, Zhang Y. Genomic Analysis Revealed a Convergent Evolution of LINE-1 in Coat Color: A Case Study in Water Buffaloes (Bubalus bubalis). Mol Biol Evol 2021; 38:1122-1136. [PMID: 33212507 PMCID: PMC7947781 DOI: 10.1093/molbev/msaa279] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Visible pigmentation phenotypes can be used to explore the regulation of gene expression and the evolution of coat color patterns in animals. Here, we performed whole-genome and RNA sequencing and applied genome-wide association study, comparative population genomics and biological experiments to show that the 2,809-bp-long LINE-1 insertion in the ASIP (agouti signaling protein) gene is the causative mutation for the white coat phenotype in swamp buffalo (Bubalus bubalis). This LINE-1 insertion (3' truncated and containing only 5' UTR) functions as a strong proximal promoter that leads to a 10-fold increase in the transcription of ASIP in white buffalo skin. The 165 bp of 5' UTR transcribed from the LINE-1 is spliced into the first coding exon of ASIP, resulting in a chimeric transcript. The increased expression of ASIP prevents melanocyte maturation, leading to the absence of pigment in white buffalo skin and hairs. Phylogenetic analyses indicate that the white buffalo-specific ASIP allele originated from a recent genetic transposition event in swamp buffalo. Interestingly, as a similar LINE-1 insertion has been identified in the cattle ASIP gene, we discuss the convergent mechanism of coat color evolution in the Bovini tribe.
Collapse
Affiliation(s)
- Dong Liang
- National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics and Breeding and Reproduction of MOAR, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Pengju Zhao
- National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics and Breeding and Reproduction of MOAR, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Jingfang Si
- National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics and Breeding and Reproduction of MOAR, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Lingzhao Fang
- Medical Research Council Human Genetics Unit at the Medical Research Council Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom
| | - Erola Pairo-Castineira
- Medical Research Council Human Genetics Unit at the Medical Research Council Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom
| | - Xiaoxiang Hu
- State Key Laboratory of AgroBiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Qing Xu
- College of Life Sciences and Bioengineering, Beijing Jiaotong University, Beijing, China
| | - Yali Hou
- Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
| | - Yu Gong
- Guizhou Domestic Animal Genetic Resources Management Station, Guiyang, China
| | - Zhengwen Liang
- Agriculture and Rural Affairs Bureau of Fenggang County, Zunyi, China
| | - Bing Tian
- Animal Disease Prevention and Control Station of Zunyi City, Zunyi, China
| | - Huaming Mao
- College of Animal Science and Technology, Yunnan Agricultural University, Kunming, China
| | - Marnoch Yindee
- Akkhararatchakumari Veterinary College (AVC), Walailak University, Nakorn Si Thammarat, Thailand
| | - Md Omar Faruque
- Department of Animal Breeding and Genetics, Bangladesh Agricultural University, Mymensingh, Bangladesh
| | - Siton Kongvongxay
- Livestock Research Center, National Agriculture and Forestry Research Institute, Ministry of Agriculture and Forestry, Vientiane, Lao PDR
| | - Souksamlane Khamphoumee
- Livestock Research Center, National Agriculture and Forestry Research Institute, Ministry of Agriculture and Forestry, Vientiane, Lao PDR
| | - George E Liu
- Animal Genomics and Improvement Laboratory, Henry A. Wallace Beltsville Agricultural Research Center, Agricultural Research Service, USDA, Beltsville, MD
| | - Dong-Dong Wu
- Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - James Stuart F Barker
- School of Environmental and Rural Science, University of New England, Armidale, NSW, Australia
| | - Jianlin Han
- International Livestock Research Institute (ILRI), Nairobi, Kenya
- CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
| | - Yi Zhang
- National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics and Breeding and Reproduction of MOAR, College of Animal Science and Technology, China Agricultural University, Beijing, China
| |
Collapse
|
40
|
Cosenza G, Gallo D, Auzino B, Gaspa G, Pauciullo A. Complete CSN1S2 Characterization, Novel Allele Identification and Association With Milk Fatty Acid Composition in River Buffalo. Front Genet 2021; 11:622494. [PMID: 33613624 PMCID: PMC7890360 DOI: 10.3389/fgene.2020.622494] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Accepted: 12/24/2020] [Indexed: 11/22/2022] Open
Abstract
The αs2-casein is one of the phosphoproteins secreted in all ruminants' milk, and it is the most hydrophilic of all caseins. However, this important gene (CSN1S2) has not been characterized in detail in buffaloes with only two alleles detected (reported as alleles A and B), and no association studies with milk traits have been carried out unlike what has been achieved for other species of ruminants. In this study, we sequenced the whole gene of two Mediterranean river buffalo homozygotes for the presence/absence of the nucleotide C (g.7539G>C) realized at the donor splice site of exon 7 and, therefore, responsible for the skipping of the same exon at mRNA level (allele B). A high genetic variability was found all over the two sequenced CSN1S2 alleles. In particular, 74 polymorphic sites were found in introns, six in the promoter, and three SNPs in the coding region (g.11072C>T, g.12803A>T, and g.14067A>G) with two of them responsible for amino acid replacements. Considering this genetic diversity, those found in the database and the SNP at the donor splice site of exon 7, it is possible to deduce at least eight different alleles (CSN1S2 A, B, B1, B2, C, D, E, and F) responsible for seven different possible translations of the buffalo αs2-casein. Haplotype data analysis suggests an evolutionary pathway of buffalo CSN1S2 gene consistent with our proposal that the published allele CSN1S2 A is the ancestral αs2-CN form, and the B2 probably arises from interallelic recombination (single crossing) between the alleles D and B (or B1). The allele CSN1S2 C is of new identification, while CSN1S2 B, B1, and B2 are deleted alleles because all are characterized by the mutation g.7539G>C. Two SNPs (g.7539G>C and g.14067A>G) were genotyped in 747 Italian buffaloes, and major alleles had a relative frequency of 0.83 and 0.51, respectively. An association study between these SNPs and milk traits including fatty acid composition was carried out. The SNP g.14067A>G showed a significant association (P < 0.05) on the content of palmitic acid in buffalo milk, thus suggesting its use in marker-assisted selection programs aiming for the improvement of buffalo milk fatty acid composition.
Collapse
Affiliation(s)
- Gianfranco Cosenza
- Department of Agriculture, University of Napoli Federico II, Portici, Italy
| | - Daniela Gallo
- Department of Agriculture, University of Napoli Federico II, Portici, Italy
| | - Barbara Auzino
- Department of Agriculture, University of Napoli Federico II, Portici, Italy
| | - Giustino Gaspa
- Department of Agricultural, Forest and Food Sciences, University of Torino, Grugliasco, Italy
| | - Alfredo Pauciullo
- Department of Agricultural, Forest and Food Sciences, University of Torino, Grugliasco, Italy
| |
Collapse
|
41
|
Rehman SU, Nadeem A, Javed M, Hassan FU, Luo X, Khalid RB, Liu Q. Genomic Identification, Evolution and Sequence Analysis of the Heat-Shock Protein Gene Family in Buffalo. Genes (Basel) 2020; 11:E1388. [PMID: 33238553 PMCID: PMC7700627 DOI: 10.3390/genes11111388] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Revised: 11/15/2020] [Accepted: 11/18/2020] [Indexed: 02/06/2023] Open
Abstract
Heat-shock proteins (HSP) are conserved chaperones crucial for protein degradation, maturation, and refolding. These adenosine triphosphate dependent chaperones were classified based on their molecular mass that ranges between 10-100 kDA, including; HSP10, HSP40, HSP70, HSP90, HSPB1, HSPD, and HSPH1 family. HSPs are essential for cellular responses and imperative for protein homeostasis and survival under stress conditions. This study performed a computational analysis of the HSP protein family to better understand these proteins at the molecular level. Physiochemical properties, multiple sequence alignment, and phylogenetic analysis were performed for 64 HSP genes in the Bubalus bubalis genome. Four genes were identified as belonging to the HSP90 family, 10 to HSP70, 39 to HSP40, 8 to HSPB, one for each HSPD, HSPH1, and HSP10, respectively. The aliphatic index was higher for HSP90 and HSP70 as compared to the HSP40 family, indicating their greater thermostability. Grand Average of hydropathicity Index values indicated the hydrophilic nature of HSP90, HSP70, and HSP40. Multiple sequence alignment indicated the presence of highly conserved consensus sequences that are plausibly significant for the preservation of structural integrity of proteins. In addition, this study has expanded our current knowledge concerning the genetic diversity and phylogenetic relatedness of HSPs of buffalo with other mammalian species. The phylogenetic tree revealed that buffalo is more closely related to Capra hircus and distantly associated with Danio rerio. Our findings provide an understanding of HSPs in buffalo at the molecular level for the first time. This study highlights functionally important HSPs and indicates the need for further investigations to better understand the role and mechanism of HSPs.
Collapse
Affiliation(s)
- Saif ur Rehman
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning 530005, China; (S.u.R.); (X.L.)
| | - Asif Nadeem
- Department of Biotechnology, Virtual University of Pakistan, Lahore-54000, Pakistan;
| | - Maryam Javed
- Institute of Biochemistry and Biotechnology, University of Veterinary and Animal Sciences, Lahore-54000, Pakistan; (M.J.); (R.B.K.)
| | - Faiz-ul Hassan
- Institute of Animal and Dairy Sciences, Faculty of Animal Husbandry, University of Agriculture, Faisalabad-38040, Pakistan;
| | - Xier Luo
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning 530005, China; (S.u.R.); (X.L.)
| | - Ruqayya Bint Khalid
- Institute of Biochemistry and Biotechnology, University of Veterinary and Animal Sciences, Lahore-54000, Pakistan; (M.J.); (R.B.K.)
| | - Qingyou Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning 530005, China; (S.u.R.); (X.L.)
| |
Collapse
|
42
|
Zhang K, Lenstra JA, Zhang S, Liu W, Liu J. Evolution and domestication of the Bovini species. Anim Genet 2020; 51:637-657. [PMID: 32716565 DOI: 10.1111/age.12974] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/03/2020] [Indexed: 12/17/2022]
Abstract
Domestication of the Bovini species (taurine cattle, zebu, yak, river buffalo and swamp buffalo) since the early Holocene (ca. 10 000 BCE) has contributed significantly to the development of human civilization. In this study, we review recent literature on the origin and phylogeny, domestication and dispersal of the three major Bos species - taurine cattle, zebu and yak - and their genetic interactions. The global dispersion of taurine and zebu cattle was accompanied by population bottlenecks, which resulted in a marked phylogeographic differentiation of the mitochondrial and Y-chromosomal DNA. The high diversity of European breeds has been shaped through isolation-by-distance, different production objectives, breed formation and the expansion of popular breeds. The overlapping and broad ranges of taurine and zebu cattle led to hybridization with each other and with other bovine species. For instance, Chinese gayal carries zebu mitochondrial DNA; several Indonesian zebu descend from zebu bull × banteng cow crossings; Tibetan cattle and yak have exchanged gene variants; and about 5% of the American bison contain taurine mtDNA. Analysis at the genomic level indicates that introgression may have played a role in environmental adaptation.
Collapse
Affiliation(s)
- K Zhang
- State Key Laboratory of Grassland Agro-ecosystem, Institute of Innovation Ecology and College of Life Sciences, Lanzhou University, Lanzhou, 730000, China
| | - J A Lenstra
- Faculty of Veterinary Medicine, Utrecht University, Utrecht Yalelaan 104, Utrecht, 3584 CM, The Netherlands
| | - S Zhang
- State Key Laboratory of Grassland Agro-ecosystem, Institute of Innovation Ecology and College of Life Sciences, Lanzhou University, Lanzhou, 730000, China
| | - W Liu
- State Key Laboratory of Grassland Agro-ecosystem, Institute of Innovation Ecology and College of Life Sciences, Lanzhou University, Lanzhou, 730000, China
| | - J Liu
- State Key Laboratory of Grassland Agro-ecosystem, Institute of Innovation Ecology and College of Life Sciences, Lanzhou University, Lanzhou, 730000, China
- Key Laboratory for Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China
| |
Collapse
|