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6. Transcriptome-Wide Association Study Reveals Potentially Candidate Genes Responsible for Milk Production Traits in Buffalo.

Author

Wei, Kelong, Lu, Ying, Ma, Xiaoya, Duan, Anqian, Lu, Xingrong, Abdel-Shafy, Hamdy, and Deng, Tingxian

Subjects
MILK yield, GENOME-wide association studies, SINGLE nucleotide polymorphisms, GENES, RNA sequencing, NUCLEOTIDE sequencing
Abstract

Identifying key causal genes is critical for unraveling the genetic basis of complex economic traits, yet it remains a formidable challenge. The advent of large-scale sequencing data and computational algorithms, such as transcriptome-wide association studies (TWASs), offers a promising avenue for identifying potential causal genes. In this study, we harnessed the power of TWAS to identify genes potentially responsible for milk production traits, including daily milk yield (MY), fat percentage (FP), and protein percentage (PP), within a cohort of 100 buffaloes. Our approach began by generating the genotype and expression profiles for these 100 buffaloes through whole-genome resequencing and RNA sequencing, respectively. Through comprehensive genome-wide association studies (GWAS), we pinpointed a total of seven and four single nucleotide polymorphisms (SNPs) significantly associated with MY and FP traits, respectively. By using TWAS, we identified 55, 71, and 101 genes as significant signals for MY, FP, and PP traits, respectively. To delve deeper, we conducted protein–protein interaction (PPI) analysis, revealing the categorization of these genes into distinct PPI networks. Interestingly, several TWAS-identified genes within the PPI network played a vital role in milk performance. These findings open new avenues for identifying potentially causal genes underlying important traits, thereby offering invaluable insights for genomics and breeding in buffalo populations. [ABSTRACT FROM AUTHOR]

Published
2024
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8. Evolutionary analysis of buffalo sterol regulatory element-binding factor (SREBF) family genes and their affection on milk traits.

Author

Ye, Tingzhu, Yuan, Jing, Raza, Sayed Haidar Abbas, Deng, Tingxian, Yang, Lv, Ahmad, Muhammad Jamil, Hosseini, Seyed Mahdi, Zhang, Xinxin, Alamoudi, Muna O, AlGabbani, Qwait, Alghamdi, Youssef S, Chen, Chao, Liang, Aixin, Schreurs, Nicola M., and Yang, Liguo

Subjects
GENE families, GENETIC regulation, SINGLE nucleotide polymorphisms, PROTEIN binding, MILK yield, FAMILY farms, CHROMOSOMES
Abstract

The sterol regulatory element-binding factor (SREBF) genes are a vital group of proteins binding to the sterol regulatory element 1 (SRE-1) regulating the synthesis of fatty acid. Two potential candidate genes (SREBF1 and SREBF2) have been identified as affecting milk traits. This study aims to identify the SREBF family of genes and find candidate markers or SREBF genes influencing lactation production in buffalo. A genome-wide study was performed and identified seven SREBF genes randomly distributed on 7 chromosomes and 24 protein isoforms in buffalos. The SREBF family of genes were also characterized in cattle, goat, sheep and horse, and using these all-protein sequences, a phylogenetic tree was built. The SREBF family genes were homologous between each other in the five livestock. Eight single nucleotide polymorphisms (SNPs) within or near the SREBF genes in the buffalo genome were identified and at least one milk production trait was associated with three of the SNP. The expression of SREBF genes at different lactation stages in buffalo and cattle from published data were compared and the SREBF genes retained a high expression throughout lactation with the trend being the same for buffalo and cattle. These results provide valuable information for clarifying the evolutionary relationship of the SREBF family genes and determining the role of SREBF genes in the regulation of milk production in buffalo. [ABSTRACT FROM AUTHOR]

Published
2023
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9. Comparative Genomic Analysis of the Thiolase Family and Functional Characterization of the Acetyl-Coenzyme A Acyltransferase-1 Gene for Milk Biosynthesis and Production of Buffalo and Cattle

Author

Deng, Tingxian, primary, Wu, Jiyun, additional, Abdel-Shafy, Hamdy, additional, Wang, Xiaojie, additional, Lv, Haimiao, additional, Shaukat, Aftab, additional, Zhou, Xiang, additional, Zhou, Yang, additional, Sun, Hui, additional, Wei, Pengfei, additional, Sun, Nan, additional, Huang, Qianzhi, additional, Xu, Linghua, additional, Liu, Miaoyu, additional, Lin, Yuxin, additional, Yang, Liguo, additional, and Hua, Guohua, additional

Published
2023
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12. Whole-genome SNP markers reveal runs of homozygosity in indigenous cattle breeds of Pakistan.

Author

Saif-ur-Rehman, Muhammad, Hassan, Faiz-ul, Reecy, James, and Deng, Tingxian

Subjects
CATTLE breeds, CATTLE breeding, SINGLE nucleotide polymorphisms, CATTLE genetics, DAIRY cattle, HOMOZYGOSITY, MILK yield, INBREEDING
Abstract

The runs of homozygosity (ROH) were identified in 14 Pakistani cattle breeds (n = 105) by genotyping with the Illumina 50 K SNP BeadChip. These breeds were categorized into Dairy, Dual, and Draft breeds based on their utility and production performance. We identified a total of 10,936 ROHs which mainly consisted of a high number of shorter segments (1–4 Mb). Dairy group exhibited the highest level of inbreeding (FROH: 0.078 ± 0.028) while the lowest (FROH: 0.002 ± 0.008) was observed in Dual group. In 48 genomic regions identified with a high frequency of ROH, 207 genes were detected in the three breed groups. A substantially higher number of ROH islands detected in dairy breeds indicated the impact of the positive selection pressure over the years. Important candidate genes and QTL were detected in the ROH islands associated with economic traits like milk production, reproduction, meat, carcass, and health traits in dairy cattle. [ABSTRACT FROM AUTHOR]

Published
2023
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16. Evolutionary analysis of buffalo sterol regulatory element-binding factor (SREBF) family genes and their affection on milk traits

Author

Ye, Tingzhu, primary, Yuan, Jing, additional, Raza, Sayed Haidar Abbas, additional, Deng, Tingxian, additional, Yang, Lv, additional, Ahmad, Muhammad Jamil, additional, Hosseini, Seyed Mahdi, additional, Zhang, Xinxin, additional, Alamoudi, Muna O, additional, AlGabbani, Qwait, additional, Alghamdi, Youssef S, additional, Chen, Chao, additional, Liang, Aixin, additional, Schreurs, Nicola M., additional, and Yang, Liguo, additional

Published
2022
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17. The whole genome sequencing and de novo assembly of swamp buffalo

Author

Deng, Tingxian

Subjects
Agricultural, Monoisolate, Assembly, Genome sequencing
Abstract

Water buffalo (Bubalus bubalis) is an important farm animal that holds great promise and potential for animal production. The animal is generally divided in two types (river and swamp buffalo), which differ in morphology, behaviour and number of chromosomes. Swamp buffalo (Bubalus bubalis carabanesis, 2n=48) is mainly kept in Northeast India, China and Southeast Asia, which is widely used for the draught power.

Published
2022
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23. Global transcriptome analysis of different stages of preimplantation embryo development in river buffalo

Author

Liang Shasha, Duan Anqin, Yun-Qi Huang, Zhihui Xiu, Junhui Chen, Ma Xiaoya, Chi Zhang, Pang Chunying, Lu Xingrong, Liang Xianwei, Ming-Zhou Bai, and Deng Tingxian

Subjects
Bioinformatics, Cellular differentiation, lcsh:Medicine, RNA-Seq, Preimplantation embryo, Biology, Cell fate determination, General Biochemistry, Genetics and Molecular Biology, Transcriptome, 03 medical and health sciences, 0302 clinical medicine, medicine, Blastocyst, Agricultural Science, Gene, Molecular Biology, 030304 developmental biology, Genetics, 0303 health sciences, General Neuroscience, lcsh:R, Embryogenesis, General Medicine, Embryonic stem cell, medicine.anatomical_structure, 030220 oncology & carcinogenesis, River buffalo, Transcription factor, RNA-seq, General Agricultural and Biological Sciences, Zoology, Cell lineages, Developmental Biology
Abstract

Background Water buffalo (Bubalus bubalis) are divided into river buffalo and swamp buffalo subspecies and are essential livestock for agriculture and the local economy. Studies on buffalo reproduction have primarily focused on optimal fertility and embryonic mortality. There is currently limited knowledge on buffalo embryonic development, especially during the preimplantation period. Assembly of the river buffalo genome offers a reference for omics studies and facilitates transcriptomic analysis of preimplantation embryo development (PED). Methods We revealed transcriptomic profile of four stages (2-cell, 8-cell, Morula and Blastocyst) of PED via RNA-seq (Illumina HiSeq4000). Each stage comprised three biological replicates. The data were analyzed according to the basic RNA-seq analysis process. Ingenuity analysis of cell lineage control, especially transcription factor (TF) regulatory networks, was also performed. Results A total of 21,519 expressed genes and 67,298 transcripts were predicted from approximately 81.94 Gb of raw data. Analysis of transcriptome-wide expression, gene coexpression networks, and differentially expressed genes (DEGs) allowed for the characterization of gene-specific expression levels and relationships for each stage. The expression patterns of TFs, such as POU5F1, TEAD4, CDX4 and GATAs, were elucidated across diverse time series; most TF expression levels were increased during the blastocyst stage, during which time cell differentiation is initiated. All of these TFs were involved in the composition of the regulatory networks that precisely specify cell fate. These findings offer a deeper understanding of PED at the transcriptional level in the river buffalo.

Published
2019

24. Effect of season and breed on physiological and blood parameters in buffaloes

Author

Li Jun, Li Zipeng, Liu Shenhe, Zhou Zichao, Zia Ur Rehman, Yang Li-guo, and Deng Tingxian

Subjects
Thermotolerance, 0301 basic medicine, Body surface temperature, Buffaloes, Hydrocortisone, Respiratory rate, animal diseases, Biology, Crossbreed, Body Temperature, 03 medical and health sciences, Animal science, Species Specificity, parasitic diseases, Animals, HSP70 Heat-Shock Proteins, HSP90 Heat-Shock Proteins, Cortisol level, Heat index, Temperature, 0402 animal and dairy science, food and beverages, Humidity, 04 agricultural and veterinary sciences, General Medicine, 040201 dairy & animal science, Breed, Hsp70, 030104 developmental biology, Hybridization, Genetic, Animal Science and Zoology, Seasons, Blood parameters, Food Science
Abstract

In this Research Communication we describe the effect of temperature and humidity index (THI) on various physiological traits, the plasma heat shock protein 70 (HSP70), heat shock protein 90 (HSP90) and cortisol levels and other blood parameters in crossbred buffalo (Nili-Ravi × Murrah) and Mediterranean buffalo to compare their tolerance to heat stress. As expected, crossbred buffalo had a significantly higher rectal temperature (RT), body surface temperature (BT), respiratory rate (RR), HSP70 and HSP90 levels in summer compared to spring and winter. RT and BT were also significantly higher in spring compared to winter. A significant correlation existed between THI and RT (r = 0·81) and RR (r = 0·84). Importantly, in summer the crossbred buffalo had a significantly lower RT, BT and RR and higher HSP70, HSP90 and cortisol levels than the Mediterranean buffalo. In conclusion, higher THI was associated with significant increase in RT, RR, BT, HSP70, HSP90 and cortisol levels, and the crossbred buffalo were more heat tolerant than Mediterranean buffalo.

Published
2018

29. Genome-wide analysis reveals genetic diversity, linkage disequilibrium, and selection for milk traits in Chinese buffalo breeds

Author

Deng Tingxian, Liang Shasha, Lu Xingrong, Ma Xiaoya, Duan Anqin, and Liang Xianwei

Subjects
geography, education.field_of_study, Linkage disequilibrium, Genetic diversity, geography.geographical_feature_category, animal diseases, Population, food and beverages, Population genetics, Zoology, Biology, Quantitative trait locus, Swamp, Genetic analysis, Breed, parasitic diseases, education
Abstract

Water buffalo holds the tremendous potential of milk and meat that widespread throughout central and southern China. However, characterization of the population genetics of Chinese buffalo is poorly understood. Using Axiom® buffalo genotyping array, we performed the genetic diversity, linkage disequilibrium (LD) pattern and signature of selection in the 176 Chinese buffaloes from thirteen breeds. A total of 35,547 SNPs passed quality control and were used for further analyses. Population genetic analysis revealed a clear separation between the swamp and river types. Ten Chinese indigenous breeds clustered into the swamp group, Murrah and Nili-Ravi breeds were the river group, and the crossbred breed was closer to the river group. Genetic diversity analysis showed that the swamp group had a lower average expected heterozygosities compared to the river group. LD decay distance was much shorter in the swamp group compared with the river group with value of approximately 50 Kb. Analysis of runs of homozygosity indicated that extensive remote and recent inbreeding activity was respectively found within swamp and river groups. Moreover, a total of 12 genomic regions under selection were detected between river and swamp groups. Further, 12 QTL regions were found associated with buffalo milk production traits. Some candidate genes within these QTLs were predicted to be involved in the cell structure and function, suggesting that these genes might play vital roles in the buffalo milk performance. Our data contribute to our understanding of the characterization of population genetics in Chinese buffaloes, which in turn may be utilized in buffalo breeding programs.Author SummaryIdentifying the causal genes or markers associated with important economic traits in livestock is critical to increasing the production level on the species. However, current understanding of the genetic basis for milk production traits in buffalo is limited. Here, we confirmed the divergent evolution, distinct population structure, and LD extent among Chinese buffalo breeds. We also identified 12 QTL regions associated with milk production traits in buffaloes using the selective sweeps and haplotype analysis. Further, a total of 7 genes involved in the cell structure and function were predicted within the identified QTLs. These findings suggested that these genes can serve as the candidate genes associated with buffalo milk production, which hold a vital role in the milk trait improvement of dairy buffalo industry.

Published
2019

30. Molecular characterisation of the buffalo SCAP gene and its association with milk production traits in water buffaloes

Author

Lu Xingrong, Duan Anqin, Xianwei Liang, Liang Shasha, Ma Xiaoya, Pang Chunying, and Deng Tingxian

Subjects
0301 basic medicine, Genetic Markers, Candidate gene, China, Buffaloes, Genotype, Sequence analysis, Mammary gland, Quantitative Trait Loci, Gene Expression, Single-nucleotide polymorphism, Biology, Breeding, Polymorphism, Single Nucleotide, 03 medical and health sciences, Lactation, medicine, Animals, Gene, Genetics, Intracellular Signaling Peptides and Proteins, Membrane Proteins, General Medicine, Sequence Analysis, DNA, Open reading frame, 030104 developmental biology, medicine.anatomical_structure, Genetic marker, Animal Science and Zoology, Female, Food Science
Abstract

The study reported in this Research Communication was conducted to investigate the molecular characterisation of buffaloSCAPgene, expression analysis, and the association between single nucleotide polymorphisms and milk production traits in 384 buffaloes. Sequence analysis revealed theSCAPgene had an open reading frame of 3837 bp encoding 1279 amino acids. A ubiquitous expression profile ofSCAPgene was detected in various tissues with extreme predominance in the mammary gland during early lactation. Moreover, eleven SNPs in buffaloSCAPgene were identified, six of them (g.1717600A>G, g.1757922C>T, g.1758953G>A, g.1759142C>T, g.1760740G>A, and g.1766036T>C) were found to be significantly associated with 305-day milk yield. Thus, buffaloSCAPcould sever as a candidate gene affecting milk production traits in buffalo and the identified SNPs might potentially be genetic markers.

Published
2018

33. Draft genome of the river water buffalo

Author

Mintoo, Abdul Awal, primary, Zhang, Hailin, additional, Chen, Chunhai, additional, Moniruzzaman, Mohammad, additional, Deng, Tingxian, additional, Anam, Mahbub, additional, Emdadul Huque, Quazi Mohammad, additional, Guang, Xuanmin, additional, Wang, Ping, additional, Zhong, Zhen, additional, Han, Pengfei, additional, Khatun, Asma, additional, Awal, Tabith M., additional, Gao, Qiang, additional, and Liang, Xianwei, additional

Published
2019
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34. Integrative Analysis of Transcriptome and GWAS Data to Identify the Hub Genes Associated With Milk Yield Trait in Buffalo

Author

Deng, Tingxian, primary, Liang, Aixin, additional, Liang, Shasha, additional, Ma, Xiaoya, additional, Lu, Xingrong, additional, Duan, Anqin, additional, Pang, Chunying, additional, Hua, Guohua, additional, Liu, Shenhe, additional, Campanile, Giuseppe, additional, Salzano, Angela, additional, Gasparrini, Bianca, additional, Neglia, Gianluca, additional, Liang, Xianwei, additional, and Yang, Liguo, additional

Published
2019
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35. Genome-Wide SNP Data Revealed the Extent of Linkage Disequilibrium, Persistence of Phase and Effective Population Size in Purebred and Crossbred Buffalo Populations

Author

Deng, Tingxian, primary, Liang, Aixin, additional, Liu, Jiajia, additional, Hua, Guohua, additional, Ye, Tingzhu, additional, Liu, Shenhe, additional, Campanile, Giuseppe, additional, Plastow, Graham, additional, Zhang, Chunyan, additional, Wang, Zhiquan, additional, Salzano, Angela, additional, Gasparrini, Bianca, additional, Cassandro, Martino, additional, Riaz, Hasan, additional, Liang, Xianwei, additional, and Yang, Liguo, additional

Published
2019
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36. Integrated Analysis of Quantitative Proteome and Transcriptional Profiles Reveals the Dynamic Function of Maternally Expressed Proteins After Parthenogenetic Activation of Buffalo Oocyte

Author

Chen, Fumei, primary, Fu, Qiang, additional, Pu, Liping, additional, Zhang, Pengfei, additional, Huang, Yulin, additional, Hou, Zhen, additional, Xu, Zhuangzhuang, additional, Chen, Dongrong, additional, Huang, Fengling, additional, Deng, Tingxian, additional, Liang, Xianwei, additional, Lu, Yangqing, additional, and Zhang, Ming, additional

Published
2018
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38. Comparative Analysis of V-Akt Murine Thymoma Viral Oncogene Homolog 3 (AKT3) Gene between Cow and Buffalo Reveals Substantial Differences for Mastitis

Author

Ullah, Farman, primary, Bhattarai, Dinesh, additional, Cheng, Zhangrui, additional, Liang, Xianwei, additional, Deng, Tingxian, additional, Rehman, Zia Ur, additional, Talpur, Hira Sajjad, additional, Worku, Tesfaye, additional, Brohi, Rahim Dad, additional, Safdar, Muhammad, additional, Ahmad, Muhammad Jamil, additional, Salim, Mohammad, additional, Khan, Momen, additional, Ahmad, Hafiz Ishfaq, additional, and Zhang, Shujun, additional

Published
2018
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41. Molecular characterisation of the buffalo SCAP gene and its association with milk production traits in water buffaloes.

Author

Deng, Tingxian, Ma, Xiaoya, Pang, Chunying, Liang, Shasha, Lu, Xingrong, Duan, Anqin, and Liang, Xianwei

Subjects
MOLECULAR cloning, MILK yield, WATER buffalo, SINGLE nucleotide polymorphisms, GENE expression profiling, MAMMARY glands
Abstract

The study reported in this Research Communication was conducted to investigate the molecular characterisation of buffalo SCAP gene, expression analysis, and the association between single nucleotide polymorphisms and milk production traits in 384 buffaloes. Sequence analysis revealed the SCAP gene had an open reading frame of 3837 bp encoding 1279 amino acids. A ubiquitous expression profile of SCAP gene was detected in various tissues with extreme predominance in the mammary gland during early lactation. Moreover, eleven SNPs in buffalo SCAP gene were identified, six of them (g.1717600A>G, g.1757922C>T, g.1758953G>A, g.1759142C>T, g.1760740G>A, and g.1766036T>C) were found to be significantly associated with 305-day milk yield. Thus, buffalo SCAP could sever as a candidate gene affecting milk production traits in buffalo and the identified SNPs might potentially be genetic markers. [ABSTRACT FROM AUTHOR]

Published
2018
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44. Metagenomic and metabolomic analyses reveal the role of gut microbiome-associated metabolites in diarrhea calves.

Author

Shi Z, Wang Y, Yan X, Ma X, Duan A, Hassan F-u, Wang W, and Deng T

Subjects
Animals, Cattle, Diarrhea veterinary, Feces, Metagenome, Metabolomics, Gastrointestinal Microbiome genetics
Abstract

Importance: Calf diarrhea is of great concern to the global dairy industry as it results in significant economic losses due to lower conception rates, reduced milk production, and early culling. Although there is evidence of an association between altered gut microbiota and diarrhea, remarkably little is known about the microbial and metabolic mechanisms underlying the link between gut microbiota dysbiosis and the occurrence of calf diarrhea. Here, we used fecal metagenomic and metabolomic analyses to demonstrate that gut microbiota-driven metabolic disorders of purine or arachidonic acid were associated with calf diarrhea. These altered gut microbiotas play vital roles in diarrhea pathogenesis and indicate that gut microbiota-targeted therapies could be useful for both prevention and treatment of diarrhea., Competing Interests: The authors declare no conflict of interest.

Published
2023
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