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SNPRBb: economically important trait specific SNP resources of buffalo (Bubalus bubalis)

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Abstract

Throughout Asian countries including India, water buffalo (Bubalus bubalis) plays a crucial role in socio-economic status of the farmers by providing nutritional security. The concept of genomic selection through genetic markers has been widely used in various livestock species and this is extended to buffalo species as well. Molecular markers have been extensively used in animal breeding for improvements of desirable animal traits. Single Nucleotide Polymorphism (SNP), one of the important molecular markers is widely used in animal breeding program. In this study, SNPs related to four important traits of buffalo i.e., milk volume, age at first calving, post-partum cyclicity and feed conversion efficiency have been identified based on genome sequence data generated using ddRAD (double digest Restriction-site Associated DNA) sequencing technology. These identified SNPs have been compiled as database accessible through Web and can be used in molecular breeding program of buffalo species. This database facilitates easy search of SNPs, Polymorphic Loci and Haplotypes along with their important features like minor and major allele frequencies, observed and expected heterozygosity, observed and expected homozygosity and nucleotide diversity. This database will help to accelerate the molecular breeding program for developing trait specific breeds of buffalo to meet the need of food and nutritional security of the world including India.

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Data availability

Database URL:http://snprbb.icar.gov.in/

References

  • Amaral MEJ, Grant JR, Riggs PK, Stafuzza NB, Rodrigues Filho EA, Goldammer T, Weikard R, Brunner RM, Kochan KJ, Greco AJ (2008) A first generation whole genome RH map of the river buffalo with comparison to domestic cattle. BMC Genomics 9:631

    Article  Google Scholar 

  • Barker J (1994) A global protocol for determining genetic distances among domestic livestock breeds. In: Proceedings of the 5th World congress on genetics applied to livestock production, Guelph, Ontario, Canada, pp 501–508

  • Bibi F, Vrba ES (2010) Unraveling bovin phylogeny: accomplishments and challenges. BMC Biology 8:50

    Article  Google Scholar 

  • Bolger AM, Lohse M, Usadel B (2014) Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30:2114–2120

    Article  CAS  Google Scholar 

  • Borghese A, Mazzi M (2005) Buffalo population and strategies in the world. Buffalo Product Res 67:1–39

    Google Scholar 

  • Borquis R, Baldi F, de Camargo G, Cardoso D, Santos D, Lugo N, Sargolzaei M, Schenkel F, Albuquerque L, Tonhati H (2014) Water buffalo genome characterization by the Illumina BovineHD BeadChip. Genet Mol Res 13(2):4202–4215

    Article  CAS  Google Scholar 

  • Bowman JS, Emerson SL, Darnovsky M (1996) The practical SQL handbook: using structured query language, 3rd edn. Addison-Wesley

  • Catchen J, Hohenlohe PA, Bassham S, Amores A, Cresko WA (2013) Stacks: an analysis tool set for population genomics. Mol Ecol 22:3124–3140

    Article  Google Scholar 

  • Davey JW, Hohenlohe PA, Etter PD, Boone JQ, Catchen JM, Blaxter ML (2011) Genome-wide genetic marker discovery and genotyping using next-generation sequencing. Nat Rev Genet 12:499

    Article  CAS  Google Scholar 

  • Department of Animal Husbandry and Dairying, Annual Report (2018–19)

  • Duarte D, Newbold CJ, Detmann E, Silva F, Freitas PHF, Veroneze R, Duarte M (2019) Genome-wide association studies pathway-based meta-analysis for residual feed intake in beef cattle. Animal Genet 50(2):150–153

    Article  CAS  Google Scholar 

  • Dutt G, Yadav M (1988) A Genetic-Study of Milk-Yield in Nili Buffalos. Indian Veter J 65:512–515

    Google Scholar 

  • Faostat (2014) Food and Agriculture Organization of the United Nations. http://www.fao.org/faostat/en/

  • Gogoi P, Johar K, Singh A (1985) Genetic analysis of milk yield in Murrah buffaloes Indian. Veter J 62:970–975

    Google Scholar 

  • Group ISMW (2001) A map of human genome sequence variation containing 1.42 million single nucleotide polymorphisms. Nature 409:928

    Article  Google Scholar 

  • Han B, Liang W, Liu L, Li Y, Sun D (2018) Genetic association of the ACACB gene with milk yield and composition traits in dairy cattle. Animal Genet 49:169–177

    Article  CAS  Google Scholar 

  • Hegde NG (2019) Buffalo husbandry for sustainable development of small farmers in India and other developing countries. Asian J Res Animal Vet Sci 3(1):1–20

    Google Scholar 

  • Hohenlohe PA, Bassham S, Etter PD, Stiffler N, Johnson EA, Cresko WA (2010) Population genomics of parallel adaptation in threespine stickleback using sequenced RAD tags. PLoS Genet 6:e1000862

    Article  Google Scholar 

  • Iamartino D, Williams JL, Sonstegard T, Reecy J, Tassell CV, Nicolazzi EL, Biffani S, Biscarini F, Schroeder S, de Oliveira DA (2013) The buffalo genome and the application of genomics in animal management and improvement buffalo. Bulletin 32:151–158

    Google Scholar 

  • Kiplagat SK, Limo MK, Kosgey IS (2012) Genetic improvement of livestock for milk production. In: Chaiyabutr N (ed) Milk production-advanced genetic traits, cellular mechanism. Animal Management and Health. InTechOpen

  • Landegren U, Nilsson M, Kwok P-Y (1998) Reading bits of genetic information: methods for single-nucleotide polymorphism analysis. Genome Res 8:769–776

    Article  CAS  Google Scholar 

  • Langmead B, Salzberg SL (2012) Fast gapped-read alignment with Bowtie 2. Nat Methods 9(4):357

    Article  CAS  Google Scholar 

  • Lee J, Ware B (2002) Open source development with LAMP: using Linux, Apache, MySQL and PHP. Addison-Wesley Professional

  • Lenstra JA, Felius M (2015) Genetic aspects of domestication. In: Garrick DJ, Ruvinski A (eds) The genetics of cattle. CAB International

  • Li Y, Han B, Liu L, Zhao F, Liang W, Jiang J, Yang Y, Ma Z, Sun D (2019) Genetic association of DDIT 3, RPL 23A, SESN 2 and NR 4A1 genes with milk yield and composition in dairy cattle. Animal Genet 50(2):123–135

    Article  CAS  Google Scholar 

  • Liu J, Liang A, Campanile G, Plastow G, Zhang C, Wang Z, Salzano A, Gasparrini B, Cassandro M, Yang L (2018) Genome-wide association studies to identify quantitative trait loci affecting milk production traits in water buffalo. J Dairy Sci 101:433–444

    Article  CAS  Google Scholar 

  • Low WY, Tearle R, Bickhart DM, Rosen BD, Kingan SB, Swale T, Thibaud-Nissen F, Murphy TD, Young R, Lefevre L (2019) Chromosome-level assembly of the water buffalo genome surpasses human and goat genomes in sequence contiguity. Nat Commun 10:260

    Article  Google Scholar 

  • Malik A, Sharma R, Ahlawat S, Deb R, Negi M, Tripathi S (2018) Analysis of genetic relatedness among Indian cattle (Bos indicus) using genotyping-by-sequencing markers. Animal Genet 49:242–245

    Article  CAS  Google Scholar 

  • Matukumalli LK, Lawley CT, Schnabel RD, Taylor JF, Allan MF, Heaton MP, O’Connell J, Moore SS, Smith TP, Sonstegard TS (2009) Development and characterization of a high density SNP genotyping assay for cattle. PloS One 4:e5350

    Article  Google Scholar 

  • Menon R, Patel AB, Joshi C (2016) Comparative analysis of SNP candidates in disparate milk yielding river buffaloes using targeted sequencing. PeerJ 4:e2147

    Article  Google Scholar 

  • Michelizzi VN, Dodson MV, Pan Z, Amaral MEJ, Michal JJ, McLean DJ, Womack JE, Jiang Z (2010) Water buffalo genome science comes of age international. J Biol Sci 6:333

    CAS  Google Scholar 

  • Michelizzi VN, Wu X, Dodson MV, Michal JJ, Zambrano-Varon J, McLean DJ, Jiang Z (2011) A global view of 54,001 single nucleotide polymorphisms (SNPs) on the Illumina BovineSNP50 BeadChip and their transferability to water buffalo. Int J Biol Sci 7:18

    Article  CAS  Google Scholar 

  • Mokhber M, Shahrbabak MM, Sadeghi M, Shahrbabak HM, Stella A, Nicolzzi E, Williams JL (2019) Study of whole genome linkage disequilibrium patterns of Iranian water buffalo breeds using the Axiom Buffalo Genotyping 90K Array. PloS One 14:e0217687

    Article  CAS  Google Scholar 

  • Notter DR (1999) The importance of genetic diversity in livestock populations of the future. J Anim Sci 77:61–69

    Article  CAS  Google Scholar 

  • Peterson BK, Weber JN, Kay EH, Fisher HS, Hoekstra HE (2012) Double digest RADseq: an inexpensive method for de novo SNP discovery and genotyping in model and non-model species. PloS One 7:e37135

    Article  CAS  Google Scholar 

  • Sambrook J, Russell DW (2001) Molecular cloning: a laboratory manual (3-volume set). Immunol 49:895–909

    Google Scholar 

  • Seno L, Cardoso V, El Faro L, Sesana R, Aspilcueta-Borquis R, De Camargo G, Tonhati H (2010) Genetic parameters for milk yield, age at first calving and interval between first and second calving in milk Murrah buffaloes. Livestock Res Rural Dev 22:1–8

    Google Scholar 

  • Sikka P, Nath A, Paul SS, Andonissamy J, Mishra DC, Rao AR, Balhara AK, Chaturvedi KK, Yadav KK, Balhara S (2020) Inferring relationship of blood metabolic changes and average daily gain with feed conversion efficiency in murrah heifers: machine learning approach. Front Vet Sci 7:518

  • Stickney HL, Schmutz J, Woods IG, Holtzer CC, Dickson MC, Kelly PD, Myers RM, Talbot WS (2002) Rapid mapping of zebrafish mutations with SNPs and oligonucleotide microarrays. Genome Res 12:1929–1934

    Article  CAS  Google Scholar 

  • Surya T, Vineeth M, Sivalingam J, Tantia MS, Dixit SP, Niranjan SK, Gupta ID (2018) Genomewide identification and annotation of SNPs in Bubalus bubalis. Genomics 111(6):1695–1698

    Article  Google Scholar 

  • Taneja VK, Bhat PN (1986) Milk and beef production in tropical environments. In: Dickerson GE, Johnson RK (eds) 3rd world congress on genetics applied to livestock production, 4 vols. University of Nebraska Institute of Agriculture and Natural Resources, Lincoln

  • Thiruvenkadan A (2011) Performances of Murrah buffaloes at coastal region of Tamil Nadu. India Indian J Animal Sci 81:1080

    Google Scholar 

  • Vignal A, Milan D, SanCristobal M, Eggen A (2002) A review on SNP and other types of molecular markers and their use in animal genetics. Genet Sel Evol 34:275

    Article  CAS  Google Scholar 

  • Young R, Lefevre L, Bush SJ, Joshi A, Singh SH, Jadhav SK, Dhanikachalam V, Lisowski ZM, Iamartino D, Summers KM (2019) A gene expression atlas of the domestic water buffalo (Bubalus bubalis). Front Genet 10:668

    Article  CAS  Google Scholar 

Download references

Acknowledgements

We acknowledge support from Network Project on Agricultural Bioinformatics and Computational Biology under Centre for Agricultural Bioinformatics Scheme, ICAR-IASRI, Indian Council for Agricultural Research (ICAR), New Delhi, India.

Funding

The financial support for this study has been provided by Centre for Agricultural Bioinformatics (CABin) scheme of Indian Council of Agricultural Research (ICAR), New Delhi, India.

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Authors and Affiliations

  1. ICAR-Indian Agricultural Statistics Research Institute, Library Avenue, New Delhi, 110012, India

    D. C. Mishra, Sunita Yadav, A. R. Rao, Neeraj Budhlakoti, Jyotika Bhati, Anil Rai & K. K. Chaturvedi

  2. ICAR-Central Institute for Research on Buffaloes, Hisar, India

    Poonam Sikka, A. Jerome, S. S. Paul, K. P. Singh, A. K. Balhara & I. Singh

Authors
  1. D. C. Mishra
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  2. Sunita Yadav
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  3. Poonam Sikka
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  4. A. Jerome
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  5. S. S. Paul
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  6. A. R. Rao
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  7. Neeraj Budhlakoti
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  8. Jyotika Bhati
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  9. K. P. Singh
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  10. A. K. Balhara
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  11. I. Singh
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  12. Anil Rai
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  13. K. K. Chaturvedi
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Corresponding author

Correspondence to K. K. Chaturvedi.

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The authors declare that they have no conflict interest.

Ethical approval

The data and samples of buffaloes used in this study were provided by buffalo herd of ICAR-Central Institute for Research on Buffaloes Hisar (Haryana), India. Experiment design and animal treatments were approved by the Institutional Animal Ethics committee (IAEC) of the Institute.

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Mishra, D.C., Yadav, S., Sikka, P. et al. SNPRBb: economically important trait specific SNP resources of buffalo (Bubalus bubalis). Conservation Genet Resour 13, 283–289 (2021). https://doi.org/10.1007/s12686-021-01210-x

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  • DOI: https://doi.org/10.1007/s12686-021-01210-x

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