Identification of Partial GDF9 Gene for Genotyping Bligon Goats and Its Origin

Fariz Jordan  Fadillah; Dina  Puspitasari; Nanik Prasetya  Ningrum; Fatimah Az Zahra  Chairunissa; Arif  Irawan; Mifta Pratiwi  Rachman; Kustantinah; Sigit  Bintara; Tety  Hartatik

doi:10.22146/jtbb.26539

Fariz Jordan Fadillah Department of Animal Breeding and Reproduction, Faculty of Animal Science Universitas Gadjah Mada, Yogyakarta, 55281, Indonesia
Dina Puspitasari Department of Animal Breeding and Reproduction, Faculty of Animal Science Universitas Gadjah Mada, Yogyakarta, 55281, Indonesia
Nanik Prasetya Ningrum Department of Animal Breeding and Reproduction, Faculty of Animal Science Universitas Gadjah Mada, Yogyakarta, 55281, Indonesia
Fatimah Az Zahra Chairunissa Department of Animal Breeding and Reproduction, Faculty of Animal Science Universitas Gadjah Mada, Yogyakarta, 55281, Indonesia
Arif Irawan Department of Animal Nutrition and Feed, Faculty of Animal Science Universitas Gadjah Mada, Yogyakarta, 55281, Indonesia
Mifta Pratiwi Rachman Department of Animal Breeding and Reproduction, Faculty of Animal Science Universitas Gadjah Mada, Yogyakarta, 55281, Indonesia https://orcid.org/0000-0002-5577-798X
Kustantinah Department of Animal Nutrition and Feed, Faculty of Animal Science Universitas Gadjah Mada, Yogyakarta, 55281, Indonesia https://orcid.org/0000-0002-5272-1059
Sigit Bintara Department of Animal Breeding and Reproduction, Faculty of Animal Science Universitas Gadjah Mada, Yogyakarta, 55281, Indonesia https://orcid.org/0000-0001-8968-9227
Tety Hartatik Department of Animal Breeding and Reproduction, Faculty of Animal Science Universitas Gadjah Mada, Yogyakarta, 55281, Indonesia

DOI: https://doi.org/10.22146/jtbb.26539

Keywords: Bligon goat, GDF9, PCR-RFLP, Restriction enzymes mapping, SNPs

Abstract

GDF9, a peptide in the TGF-β growth factor family, plays a crucial role in oocyte growth and maturation, affecting reproduction through genetic factors. This makes it valuable for livestock selection via SNPs, which are used in genotyping methods like PCR-RFLP. This study aimed to identify SNPs, map restriction enzyme sites, and perform genotyping to explore reproductive traits in Bligon goats. A total of 91 female goats were analysed, including 36 Bligon goats, 26 Peranakan Etawa goats, and 29 Kacang goats, and all of them had single births. PCR amplification was conducted using two pairs of primers for the GDF9 gene: the forward primer 5'-CTCCTCTTGAGCCTCTGGTG-3' and reverse primer 5'-TCCAGTTGTCCCACTTCAGC-3' for GDF9-3, and forward primer 5'-TGTAAGATCGTCCCGTCACC-3' and reverse primer 5'-CACACTTCCTCTCCCTCTCA-3' for GDF9-6. Sequencing was done after amplification. Six SNPs were identified at positions g.2565C>M, g.2589G>A, g.2634G>A, g.2653G>T, g.2679A>G, and g.2691A>G, with one being synonymous (g.2653G>T) and five non-synonymous, causing amino acid changes. Among these, g.2565C>M was recognized by the restriction enzymes HpaII and MspI, was recommended for use in PCR-RFLP for genotyping with the GDF9-3 primer. The study also found that the genotype frequencies in Bligon, Peranakan Etawa, and Kacang goats were in Hardy-Weinberg equilibrium (HWE), supporting the use of SNP g.2565C>M as a genetic marker. Enzym MspI can be used for genotyping the target gene in exon 2 of the GDF9 gene in three types of goats: Bligon, Peranakan Etawa, and Kacang.

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