Abstract
Polymorphisms in growth differentiation factor 9 (GDF9) and bone morphogenetic protein 15 (BMP15) genes have been found to be associated with litter size in goats across the globe. Our previous study detected single-nucleotide polymorphisms (SNPs) in GDF9 and BMP15 genes associated with litter size in Black Bengal, Bangladesh’s primary native goat breed. However, Jamunapari and crossbred goats in Bangladesh are yet to be investigated for litter size–associated polymorphisms. In this study, we screened Jamunapari and crossbred (50% Black Bengal × 50% Jamunapari) goats to identify polymorphisms in the GDF9 and BMP15 genes and to assess the association between identified SNPs and litter size. The genomic DNA from 100 female goats (50 Jamunapari and 50 crossbred) was used in polymerase chain reactions (PCRs) to amplify exon 2 of the GDF9 and exon 2 of the BMP15 genes. PCR products were sequenced employing the BigDye Terminator cycle sequencing protocol to identify SNPs. We used a generalized linear model to perform the association analysis for identified SNPs and litter size. Seven SNPs were identified, of which four, C818CT, G1073A, G1189A, and G1330T, were in the GDF9 gene and three, G616T, G735A, and G811A, were in the BMP15 gene. G735A was a synonymous SNP, whereas the remaining were non-synonymous SNPs. Identified SNP loci in GDF9 were low polymorphic (PIC < 0.25), while loci in BMP15 were moderately polymorphic (PIC ≥ 0.25). The genotypes at the G1330T locus had a significant (p < 0.05) difference in litter size in Jamunapari goats, but no significant difference was observed for all genotypes at other loci. Therefore, the G1330T loci could be useful as a marker in marker-assisted selection for litter size traits in goats of Bangladesh.
Similar content being viewed by others
Data availability
The data that support the findings of this study are available from the corresponding author on reasonable request.
Code availability
Not applicable.
References
Abadi, M.R. and Zakizadeh, S. 2010. Exon 2 of BMP15 gene polymorphism in Jabal Barez Red Goat. Journal of Agricultural Biotechnology, 2 (1), 69-80
Ahlawat, S., Sharma, R. and Maitra, A., 2013. Screening of indigenous goats for prolificacy associated DNA markers of sheep. Gene, 517, 128-131.
Ahlawat, S., Sharma, R., Maitra, A. and Tantia, M., 2015a. Current status of molecular genetics research of goat fecundity. Small Ruminant Research, 125, 34-42.
Ahlawat, S., Sharma, R., Roy, M., Tantia, M. and Prakash, V., 2015b. Association analysis of novel SNPs in BMPR1B, BMP15 and GDF9 genes with reproductive traits in Black Bengal goats. Small Ruminant Research, 132, 92-98.
Ahlawat, S., Sharma, R., Roy, M., Mandakmale, S., Prakash, V. and Tantia, M. 2016. Genoty** of novel SNPs in BMPR1B, BMP15, and GDF9 genes for association with prolificacy in seven Indian goat breeds. Animal Biotechnology, 27, 199-207.
Ahsani, M.R., Mohammadabadi, M.R. and Shamsaddini, M.B., 2010. Clostridium perfringens isolate ty** by multiplex PCR. Journal of Venomous Animals and Toxins including Tropical Diseases 16 (4): 573-578.
Ahsani, M.R., Bafti, M.S., Esmailizadeh, A.K. and Mohammadabadi, M.R. 2011. Genoty** of isolates of Clostridium perfringens from vaccinated and unvaccinated sheep. Small Ruminant Research, 95 (1), 65-69.
An, X., Hou, J., Zhao, H., Li, G., Bai, L., Peng, J., M Yan, Q., Song, Y., Wang, J., and Cao, B., 2013. Polymorphism identification in goat GNRH1 and GDF9 genes and their association analysis with litter size. Animal Genetics, 44, 234-238.
Bhuiyan, A., 2014. Farm animal genetic resources in Bangladesh: diversity, conservation and management. Farm animal genetic resources in SAARC countries: diversity, conservation and management. Publisher: SAARC Agriculture Centre (SAC), Dhaka 1215, 1-74.
Bi, Y., Li, J., Wang, X., He, L., Lan, K., Qu, L., Lan, X., Song, X. and Pan, C., 2020. Two novel rare strongly linked missense SNPs (P27R and A85G) within the GDF9 gene were significantly associated with litter size in Shaanbei White Cashmere (SBWC) goats. Frontiers in Veterinary Science, 7, 407.
Das, A., Shaha, M., Gupta, M.D., Dutta, A. and Miazi, O.F., 2021. Polymorphism of fecundity genes (BMP15 and GDF9) and their association with litter size in Bangladeshi Prolific Black Bengal goat. Tropical Animal Health and Production, 53, 1-8.
Drouilhet, L., Mansanet, C., Sarry, J., Tabet, K., Bardou, P., Woloszyn, F., Lluch, J., Harichaux, G., Viguié, C. and Monniaux, D., 2013. The highly prolific phenotype of Lacaune sheep is associated with an ectopic expression of the B4GALNT2 gene within the ovary. PLoS Genetics, 9, e1003809.
Ebrahimi Hoseinzadeh, Z., Mohammadabadi, M.R., Esmailizadeh, A., Khezri, A. and Noori A. N., 2015. Association of PIT1 gene with milk fat percentage in Holstein cattle. Iranian Journal of Applied Animal Science, 5 (3), 575-582
Feng, T., Geng, C., Lang, X., Chu, M., Cao, G., Di, R., Fang, L., Chen, H., Liu, X. and Li, N., 2011. Polymorphisms of caprine GDF9 gene and their association with litter size in **ing Grey goats. Molecular Biology Reports, 38, 5189-5197.
Gooki, F.G., Mohammadabadi, M. R. and Fozi, M. A., 2018. Polymorphism of the growth hormone gene and its effect on production and reproduction traits in goat. Iranian Journal of Applied Animal Science, 8 (4), 653-659.
Gooki, F.G., Mohammadabadi, M., Fozi, M.A. and Soflaei, M. 2019 Association of biometric traits with growth hormone gene diversity in Raini Cashmere goats. Walailak Journal of Science and Technology, 16 (7), 499-508
Gootwine, E., 2020. Invited review: Opportunities for genetic improvement toward higher prolificacy in sheep. Small Ruminant Research, 186, 106090.
Hadizadeh, M., Mohammadbadi, M.R., Niazi, A., Esmailizadeh, A. and Gazooei, Y.M., 2014. Search for polymorphism in growth and differentiation factor 9 (GDF9) gene in prolific Beetal and Tali goats (Capra hircus). Journal of Biodiversity and Environmental Sciences, 4, 186-191.
Hassan, M.M., Mahmud, S.N., Islam, S.A. and Miazi, O.F., 2007. A comparative study on reproductive performance and productivity of the Black Bengal and Crossbred goat at Atrai, Bangladesh. University Journal of Zoology, Rajshahi University, 26, 55-57.
Koopaei H.K., Abadi M.R.M., Mahyari S.A., Tarang A.R., Potki P. and Esmailizadeh. A., 2012. Effect of DGAT1 variants on milk composition traits in Iranian Holstein cattle population. Animal Science Papers & Reports 30 (3), 231-240.
Kumar, S., Stecher, G. and Tamura, K., 2016. MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Molecular Biology and Evolution 33, 1870-1874.
Department of Livestock Services (DLS), 2020. Livestock population of Bangladesh: In: Livestock economy at a glance. http://www.dls.gov.bd/site/page/22b1143b-9323-44f8-bfd8-647087828c9b/Livestock-Economy/. Accessed 15 October 2021.
Maitra, A., Sharma, R., Ahlawat, S., Borana, K. and Tantia, M., 2016. Fecundity gene SNPs as informative markers for assessment of Indian goat genetic architecture. Indian Journal of Animal Research, 50, 349-356.
McNatty, K.P., Heath, D.A., Clark, Z., Reader, K., Juengel, J.L. and Pitman, J.L., 2017. Ovarian characteristics in sheep with multiple fecundity genes. Reproduction, 153, e40.
Miah, G., Das, A., Bilkis, T., Momin, M.M., Uddin, M.A., Alim, M.A., Mahmud, M.S. and Miazi, O.F., 2016. Comparative study on productive and reproductive traits of Black Bengal and Jamnapari goats under semi-intensive condition. Scientific Research Journal, 4, 1-7.
Mishra, C., Rout, M., Mishra, S.P., Sahoo, S.S., Nayak, G. and Patra, R.C., 2017. Genetic polymorphism of prolific genes in goat—a brief review. Exploratory Animal and Medical Reseach, 7, 132-141.
Moghadaszadeh, M., Mohammadabadi, M.R. and Esmailizadeh, A.K. 2015. Association of exon 2 of BMP15 gene with the litter size in the Raini Cashmere goat. Genetics in the 3rd Millennium, 13 (3), 4062–4067.
Mohammadabadi, M. and Soflaei, M. 2020. Tissue-specific mRNA expression profile of BMP15 gene in goat. Agricultural Biotechnology Journal, 12 (3), 191-208.
Mohammadabadi, M.R., Nikbakhti, M., Mirzaee, H.R., Shandi, A., Saghi, D.A., Romanov, M.N. and Moiseyeva, I.G., 2010a. Genetic variability in three native Iranian chicken populations of the Khorasan province based on microsatellite markers. Russian Journal of Genetics 46 (4), 505-509
Mohammadabadi, M.R., Torabi, A., Tahmourespoor, M., Baghizadeh, A., Esmailizadeh, A. and Mohammadi, A., 2010b. Analysis of bovine growth hormone gene polymorphism of local and Holstein cattle breeds in Kerman province of Iran using polymerase chain reaction restriction fragment length polymorphism (PCR-RFLP). African Journal of Biotechnology, 9 (41), 6848-6852.
Mohammadabadi, M.R., Jafari, A.H.D. and Bordbar, F. (2017). Molecular analysis of CIB4 gene and protein in Kermani sheep. Brazilian Journal of Medical and Biological Research, 50, e6177.
Mohammadi, A., Nassiry, M.R., Mosafer, J. and Mohammadabadi, M.R., 2009. Distribution of BoLA-DRB3 allelic frequencies and identification of a new allele in the Iranian cattle breed Sistani (Bos indicus). Russian Journal of Genetics, 45 (2), 198-202
Nassiry, M.R., Shahroodi, F.E., Mosafer, J., Mohammadi, A., Manshad, E., Ghazanfari, S., Mohammad, Abadi, M.R. and Sulimova, G.E., 2005. Analysis and frequency of bovine lymphocyte antigen (BoLA-DRB3) alleles in Iranian Holstein cattle. Russian Journal of Genetics, 41 (6), 664-668.
Norouzy, A., Nassiry, M.R., Shahrody, F.E., Javadmanesh, A., Abadi, M.R.M. and Sulimova, G.E., 2005 Identification of bovine leucocyte adhesion deficiency (BLAD) carriers in Holstein and Brown Swiss AI bulls in Iran. Russian Journal of Genetics, 41 (12), 1409-1413.
Plakkot, B., Mohanan, A. and Kanakkaparambil, R., 2020. Prolificacy in small ruminants. Journal of Dairy, Veterinary and Animal Research, 9, 85-90.
Sasi, R., Kanakkaparambil, R. and Thazhathuveettil, A., 2020. Polymorphism of fecundity genes, BMPR1B, BMP15 and GDF9, in tropical goat breeds of Kerala. Gene Reports, 21, 100944.
Shaha, M., 2019. Screening for polymorphisms in litter size trait associated genes in goats of Bangladesh. Unpublished MS thesis, Chattogram Veterinary and Animal Sciences University, Chattogram, Bangladesh.
Shokrollahi, B., 2014. Investigation of BMP15 gene polymorphisms associated with twining in Markhoz goat. Biharean Biologist, 9, 1-4.
Shokrollahi, B. and Morammazi, S., 2018. Polymorphism of GDF 9 and BMPR 1B genes and their association with litter size in Markhoz goats. Reproduction in Domestic Animals, 53, 971-978.
Siddiky, N., A, ed. 2017. Sustainable goat farming for livelihood improvement in South Asia. SAARC Agriculture Centre, Dhaka-1215, Bangladesh, p.190
Wang, Y., Zhang, X. and Chu, M., 2013. Polymorphisms of caprine GDF9 gene and their association with litter size in Henan dairy goat. Journal of Animal and Veterinary Advances, 12, 1590-1596.
Wang, X., Yang, Q., Wang, K., Yan, H., Pan, C., Chen, H., Liu, J., Zhu, H., Qu, L. and Lan, X., 2019a. Two strongly linked single nucleotide polymorphisms (Q320P and V397I) in GDF9 gene are associated with litter size in cashmere goats. Theriogenology, 125, 115-121.
Wang, X., Yang, Q., Zhang, S., Zhang, X., Pan, C., Chen, H., Zhu, H. and Lan, X., 2019b. Genetic effects of single nucleotide polymorphisms in the goat GDF9 gene on prolificacy: True or false positive? Animals, 9, 886.
Zheng, J., Wang, Z., Yang, H., Yao, X., Yang, P., Ren, C., Wang, F. and Zhang, Y., 2019. Pituitary transcriptomic study reveals the differential regulation of lncRNAs and mRNAs related to prolificacy in different FecB genoty** sheep. Genes, 10, 157.
Acknowledgements
The authors thank Chattogram Veterinary and Animal Sciences University for providing research facilities and funds for the conduct of research. The support from the farmers is also acknowledged.
Funding
This work was financially supported by the National Science and Technology Fellowship, fund from the Ministry of Science and Technology.
Author information
Authors and Affiliations
Contributions
M.S.: data collection, investigation, methodology, funding acquisition, and writing—review. G.M.: supervision and editing original draft. A.L.: investigation and methodology. O.F.M.: investigation and writing—review. M.D.G.: data curation, editing and finalizing draft. A.D.: conceptualization, methodology, data curation, formal analysis, funding acquisition, project administration, supervision, writing—original draft, editing and finalizing draft.
Corresponding author
Ethics declarations
Ethics approval
All the techniques employed on the experimental animals were approved by the Animal Experimentation Ethics Committee (CVASU/Dir(R&E)EC/2020/169/8) at Chattogram Veterinary and Animal Sciences University.
Consent to participate
Not applicable.
Consent for publication
Not applicable.
Conflict of interest
The authors declare no competing interests.
Additional information
Publisher's note
Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
Rights and permissions
Springer Nature or its licensor (e.g. a society or other partner) holds exclusive rights to this article under a publishing agreement with the author(s) or other rightsholder(s); author self-archiving of the accepted manuscript version of this article is solely governed by the terms of such publishing agreement and applicable law.
About this article
Cite this article
Shaha, M., Miah, G., Lima, A. et al. Identification of polymorphisms in GDF9 and BMP15 genes in Jamunapari and crossbred goats in Bangladesh. Trop Anim Health Prod 54, 350 (2022). https://doi.org/10.1007/s11250-022-03347-9
Received:
Accepted:
Published:
DOI: https://doi.org/10.1007/s11250-022-03347-9