A Novel SNPs of KISS1 Gene Strongly Associated with Litter Size in Indonesian Goat Breeds

A. Febriana, S. Sutopo, E. Kurnianto, W. Widiyanto


Kisspeptin is a protein encoded by the KISS1 gene which behaves as a key role by stimulating gonadotropin releasing hormone (GnRH) neuron activity directly in the reproductive axis. The objective of the present study was to determine the genetic diversity within intron 1 of KISS1 gene and to verify their association with fecundity traits which can be devoted as a marker assisted selection (MAS) for breeding selection. This study was established on three Indonesian native goat populations (Kacang, Kejobong, and Senduro). The PCR products were then sequenced in both directions. The DNA sequencing alignment resulted fifteen variants (one indel and fourteen SNPs), with SNP1, SNP2, SNP3, and SNP9 being novel single nucleotide polymorphisms (SNPs) of KISS1 gene intron 1. Genotype, haplotype, and parity were significantly associated with litter size. SNP8, SNP9, and SNP10 were correlated with overall means of litter size (LS) and LS at the first and the third parities (p<0.05). Additionally, novel SNP9 were in remarkably strong linkage disequilibrium with SNP8 and SNP10 (D’=1.00; r≥0.58; χ2≥13.38), and allele A had putative binding sites for the NFIC which plays an important role in activating the expression of KISS1 gene. The H2 haplotype (CATAGCGCAACGCT) was found to have the highest litter size (p<0.0001). CC genotype at SNP8, AA genotype at novel SNP9, GA genotype at SNP10, and H2 haplotype were the excellent genotypes and haplotype that associated with the superior LS (p<0.05). Therefore, this result led to presume that these three SNPs and H2 haplotype can be acknowledged as prominent genetic markers for goat- breeding selection.


Abdel-Aziem, S. H., K. F. Mahrous, M. A. M. Abd El-Hafez, & M. Abdel Mordy. 2018. Genetic variability of myostatin and prolactin genes in popular goat breeds in Egypt. J. Genet. Eng. Biotechnol. 16:89-97. https://doi.org/10.1016/j.jgeb.2017.10.005
Ahlawat, S., R. Sharma, A. Maitra, & M. S. Tantia. 2015. Current status of molecular genetics research of goat fecundity. Small. Rumin. Res. 125:34–42. https://doi.org/10.1016/j.smallrumres.2015.01.027
An, X., T. Ma, J. Hou, F. Fang, P. Han, Y. Yan, H. Zhao, Y. Song, J. Wang, & B. Cao. 2013. Association analysis between variants in KISS1 gene and litter size in goats. BMC Genet. 14:1-6. https://doi.org/10.1186/1471-2156-14-63
An, X. P., J. X. Hou, T. Y. Gao, Y. N. Lei, Y. X. Song, J. G. Wang, & B. Y. Cao. 2015a. Association analysis between variants in KITLG gene and litter size in goats. Gene. 558:126-130. https://doi.org/10.1016/j.gene.2014.12.058
An, X. P., J. X. Hou, Y. N. Lei, T. Y. Gao, & B. Y. Cao. 2015b. Polymorphism and DNA methylation in the promoter modulate KISS1 gene expression and are associated with litter size in goats. Anim. Reprod. Sci. 155:36-41. https://doi.org/10.1016/j.anireprosci.2015.01.013
Antonius, A., S. P. Ginting, S. Elieser, A. Tarigan, S. Solehudin, I. G. S. Budisatria, A. P. Z. N. L. Sari, D. N. H. Hariyono, & D. Maharani. 2020. The association of Single Nucleotide Polymorphism (SNP) g.281G > A of CAST Gene with meat quality of Boerka goat. Iran J. Appl. Anim. Sci. 10:303-309.
Cao, G. L., M. X. Chu, L. Fang, R. Di, T. Feng, & N. Li. 2010. Analysis on DNA sequence of KiSS-1 gene and its association with litter size in goats. Mol. Biol. Rep. 37:3921-3929. https://doi.org/10.1007/s11033-010-0049-7
Cartegni, L., S. L. Chew, & A. R. Krainer. 2002. Listening to silence and understanding nonsense: exonic mutations that affect splicing. Nat. Rev. Genet. 3: 285-298. https://doi.org/10.1038/nrg775
Chen, M., H. Yan, K. Wang, Y. Cui, R. Chen, J. W. Liu, Z. Haijing, Q. Lei, & P. Chuanying. 2019. Goat SPEF2: Expression profile, indel variants identification and association analysis with litter size. Theriogenology 139:147-155. https://doi.org/10.1016/j.theriogenology.2019.08.007
Ciptadi, G., M. N. Ihsan, A. Budiarto, M. Mudawamah, A. I. Putri, & M. N. A. Naufal. 2019. Reproductive characters of Senduro goat at Lumajang district East Java. J. Phys. Conf. Ser. 1146:012033. https://doi.org/10.1088/1742-6596/1146/1/012033
Cui, Y., H. Yan, K. Wang, H. Xu, X. Zhang, H. Zhu, J. Liu, L. Qu, X. Lan, & C. Pan. 2018. Insertion/deletion within the KDM6A gene is significantly associated with litter size in goat. Front. Genet. 9:1-23. https://doi.org/10.3389/fgene.2018.00091
de Lima, L. G., N. O. B. de Souza, R. R. Rios, B. A. de Melo, L. T. A. dos Santos, K. de Moraes Silva, T. W. Murphy, & A. B. Fraga. 2020. Advances in molecular genetic techniques applied to selection for litter size in goats (Capra hircus): A review. J. Appl. Anim. Res. 48:38-44. https://doi.org/10.1080/09712119.2020.1717497
Dong, C. H. & L. X. Du. 2011. Research on polymorphism analysis of GDF9 gene related to reproductive traits of goat. Journal of Shandong Agricultural University 42:227-237.
Douhovnikoff, V. & M. Leventhal. 2016. The use of Hardy–Weinberg Equilibrium in clonal plant systems. BMC Ecol. Evol. 6:1173–1180. https://doi.org/10.1002/ece3.1946
El-Komy, S. M., A. A. Saleh, R. M. Abd El-Aziz, & M. A. El-Magd. 2021. Association of GH polymorphisms with growth traits in buffaloes. Domest. Anim. Endocrinol. 74:1-13. https://doi.org/10.1016/j.domaniend.2020.106541
El-Tarabany, M. S., A. W. Zagloola, A. A. El-Tarabany, & A. Awad. 2017. Association analysis of polymorphism in KiSS1 gene with reproductive traits in goats. Anim. Reprod. Sci. 180:92–99. https://doi.org/10.1016/j.anireprosci.2017.03.006
Evans, J., J. Kim, K. L. Childs, B. Vaillancourt, E. Crisovan, A. Nandety, D. J. Gerhardt, T. A. Richmond, J. A. Jeddeloh, S. M. Kaeppler, M. D. Casler, & C. R. Buell. 2014. Nucleotide polymorphism and copy number variant detection using exome capture and next generation sequencing in the polyploid grass Panicum virgatum. Plant Journal 79:993–1008. https://doi.org/10.1111/tpj.12601
Excoffier, L. & H. E. L. Lischer. 2010. Arlequin suite ver 3.5: a new series of programs to perform population genetics analyses under Linux and Windows. Mol. Ecol. Resour. 10: 564–567. https://doi.org/10.1111/j.1755-0998.2010.02847.x
FAOSTAT. 2019. Retrieved from: http://www.fao.org/faostat/en/#data/QL.
Feng, T., Y. Z. Zhao, M. X. Chu, Y. J. Zhang, L. Fang, R. Di, G. L. Cao, & N. Li. 2009. Association between sexual precocity and alleles of KISS-1 and GPR54 genes in goats. Anim. Biotechnol. 20:172–176. https://doi.org/10.1080/10495390903004493
Ferreira, L., M. A. M. Soares, M. T. Rodrigues, J. L. S. Araujo, A. L. P. de Melo, E. Gasparino, & O. S. R. Garcia. 2020. UCP2 and PPARG gene polymorphisms and their association with milk yield and composition traits in goats. Small Rumin. Res. 192:106210. https://doi.org/10.1016/j.smallrumres.2020.106210
Fu, G., G. Saunders, & J. Stevens. 2014. Holm multiple correction for large-scale geneshape association mapping. BMC Genet. 15:1-8. http://www.biomedcentral.com/1471-2156/15/S1/S5
Gama, L. T. & M. C. Bressana. 2011. Biotechnology applications for the sustainable management of goat genetic resources. Small Rumin. Res. 98:133–146. https://doi.org/10.1016/j.smallrumres.2011.03.031
Hardyta, G., D. T. Widayati, & D. Maharani. 2020. Association of SNP T125A on KiSS1 gene with reproduction hormone levels in Kaligesing goat. J. Indones. Trop. Anim. Agric. 45:253-260. https://doi.org/10.14710/jitaa.45.4.253-260
Hernandez, X., L. Bodin, D. Chesneaua, D. Guillaumea, P. Chemineaua, B. Malpauxa, & M. Migaud. 2005. Relationship between MT1 melatonin receptor gene polymorphism and seasonal physiological responses in Île-de-France ewes. Reprod. Nutr. Dev. 45:151–162. https://doi.org/10.1051/rnd:2005012
Hou, J. X., X. P. An, J. G. Wang, Y. X. Song, Y. H. Cui, Y. F. Wang, Q. J. Chen, & B. Y. Cao. 2011. New genetic polymorphisms of KiSS-1 gene and their association with litter size in goats. Small Rumin. Res. 96:106–110. https://doi.org/10.1016/j.smallrumres.2010.11.013
Hu, H., Y. Miao, L. Jia, Q. Yu, Q. Zhang, & A. Guo. 2018. Animal TFDB 3.0: a comprehensive resource for annotation and prediction of animal transcription factors. Nucl. Acids Res. 47:D33-D38. https://doi.org/10.1093/nar/gky822
Hui, Y., Y. Zhang, K. Wang, C. Pan, H. Chen, L. Qu, X. Song, & X. Lan. 2020. Goat DNMT3B: An indel mutation detection, association analysis with litter size and mRNA expression in gonads. Theriogenology. 147:108–115. https://doi.org/10.1016/j.theriogenology.2020.02.025
Jeet, V., A. Magotraa, Y. C. Banga, S. Kumar, A. R. Garga, A. S. Yadava, & P. Bahurupi. 2022. Evaluation of candidate point mutation of Kisspeptin 1 gene associated with litter size in Indian Goat breeds and its effect on transcription factor binding sites. Domest. Anim. Endocrinol. 78:106676. https://doi.org/10.1016/j.domaniend.2021.106676
Jo, B. S. & S. S. Choi. 2015. Introns: the functional benefits of introns in genomes. Genomics Inform. 13:12-118. https://doi.org/10.5808/GI.2015.13.4.112
Kaumbata, W., L. Banda, G. Mészáros, T. Gondwea, M. J. Woodward-Greenec, B. D. Rosen, C. P. Van Tassell, J. Sölkner, & M. Wurzinger. 2020. Tangible and intangible benefits of local goats rearing in smallholder farms in Malawi. Small Rumin. Res. 187:1-8. https://doi.org/10.1016/j.smallrumres.2020.106095
Kumar, S., G. Stecher, M. Li, C. Knyaz, & K. Tamura. 2018. MEGA X: Molecular Evolutionary Genetics Analysis across computing platforms. Mol. Biol. Evol. 35:1547-1549. https://doi.org/10.1093/molbev/msy096
Kurnianto, E., S. Sutopo, E. Purbowati, E. T. Setiatin, D. Samsudewa, & T. Permatasari. 2013. Multivariate analysis of morphological traits of local goats in Central Java, Indonesia. Iranian J. Appl. Anim. Sci. 3:361-367.
Lestari, D. A., E. Purbowati, S. Sutopo, & E. Kurnianto. 2018. Phylogenetical relationships between Kejobong goat and other goats based on Mt-DNA D-loop sequence analysis. Trop. Anim. Sci. J. 41:85-93. https://doi.org/10.5398/tasj.2018.41.2.85
Liu, G., Q. Zhao, J. Lu, F. Sun, X. Han, J. Zhao, H. Feng, K. Wang, & C. Liu. 2019. Insights into the genetic diversity of indigenous goats and their conservation priorities. Asian-Australas. J. Anim. Sci. 32:1501-1510. https://doi.org/10.5713/ajas.18.0737
Maitra, A., R. Sharma, S. Ahlawat, M. S. Tantia, M. Roy, & V. Prakas. 2014. Association analysis of polymorphisms in caprine KISS1 gene with reproductive traits. Anim. Reprod. Sci. 151:71–77. https://doi.org/10.1016/j.anireprosci.2014.09.013
Majd, S. A., A. Ahmad, R. Talebi, P. M. Koohi, S. Fabre, & S. Qanbari. 2019. Polymorphism identification in ovine KISS1R/GPR54 gene among pure and crossbreeds of Iranian sheep. Small Rumin. Res. 173:23–29. https://doi.org/10.1016/j.smallrumres.2019.02.005
Martínez-Royo, A., B. Lahoz, J. L. Alabar, J. Folch, & J. H. Calvo. 2012. Characterisation of the melatonin receptor 1A (MTNR1A) gene in the rasa aragonesa sheep breed: Association with reproductive seasonality. Anim. Reprod. Sci. 133:169-175. https://doi.org/10.1016/j.anireprosci.2012.06.018
Mekuriaw, G., J. M. Mwacharo, T. Dessie, O. Mwai, A. Djikeng, S. Osama, G. Gebreyesus, A. Kidane, S. Abega, & K. Tesfaye. 2017. Polymorphism analysis of kisspeptin (KISS1) gene and its association with litter size in Ethiopian indigenous goat populations. Afr. J. Biotechnol. 16:1254-1264.
Miller, B. A., J. Dubeuf, J. Luginbuhl, & J. Capote. 2012. Scaling up goat based interventions to benefit the poor. Retrieved from: http://www.igagoatworld.com/uploads/6/1/6/2/6162024/scaling_up_goat_based_interventions.pdf.
Ministry of Agriculture. 2020. The Statistic Book on Livestock and Animal Health Services. Directorate General of Livestock and Animal Health Services. Jakarta.
Mulyono, R. H., C. Sumantri, R. R. Noor, J. Jakaria, & D. A. Astuti. 2019. Analysis of the linkage of BMP15, BMPR1B and KISS1 genes with fecundity traits in female etawah crossbreed goats. Jurnal Ilmu Pertanian Indonesia 24:83-92. https://doi.org/10.18343/jipi.24.2.83
Nackley, A. G., S. A. Shabalina, I. E. Tchivileva, & K. Satterfield. 2006. Human catechol-O-methyltransferase haplotypes modulate protein expression by altering mRNA secondary structure. Science. 314:1930–1933. https://doi.org/10.1126/science.1131262
Nakaoka, H., A. Gurumurthy, T. Hayano, S. Ahmadloo, W. H. Omer, K. Yoshihara, A. Yamamoto, K. Kurose, T. Enomoto, S. Akira, K. Hosomichi, & I. Inoue. 2016. Allelic imbalance in regulation of ANRIL through chromatin interaction at 9p21 endometriosis risk locus. PLoS Genet. 12:1-23. https://doi.org/10.1371/journal.pgen.1005893
Nei, M. & S. Kumar. 2000. Molecular Evaluation and Phylogenetiks. Oxford University Press, New York.
Notter, D. R. 2012. Genetic improvemnet of reproductive efficiency of sheep and goats. Anim. Reprod. Sci. 130:147-151. https://doi.org/10.1016/j.anireprosci.2012.01.008
Parenteau, J. & S. A. Elela. 2019. Introns: good day junk is bad day treasure. Trends Genet. 35:923-934. https://doi.org/10.1016/j.tig.2019.09.010
Periasamy, K., S. M. F. Vahidi, P. Silva, M. O. Faruque, A. N. Naqvi, M. Basar, J. Cao, S. H. Zhao, L. T. Thuy, R. Pichler, M. G. Podesta, M. Shamsuddin, P. Boettcher, J. F. Garcia, J. L. Han, P. A. Marsan, A. Diallo, & G. J. Viljoen. 2017. Mapping molecular diversity of indigenous goat genetic resources of Asia. Small Rumin. Res. 148:2-10. https://doi.org/10.1016/j.smallrumres.2016.12.035
Pillai, H. B. & R. T. Venkatachalapathy. 2020. Association of inhibin alpha gene polymorphism with litter size and growth in Malabari goats of India. Small Rumin. Res. 192:1-8. https://doi.org/10.1016/j.smallrumres.2020.106188
Pinilla, L., E. Aguilar, C. Diegue, R. P. Millar, & M. Tena-Sempere. 2012. Kisspeptins and reproduction: physiological roles and regulatory mechanisms. Physiol. Rev. 92:1235–1316. https://doi.org/10.1152/physrev.00037.2010
Pjanic, M., P. Pjanic, C. Schmid, G. Ambrosini, A. Gaussin, G. Plasari, C. Mazza, P. Bucher, & N. Mermod. 2011. Nuclear factor I revealed as family of promoter binding transcription activators. BMC Genomics 12:181. https://doi.org/10.1186/1471-2164-12-181
Rahmatalla, S. A., D. Arends, A. S. Ahmed, M. Reissmann, & G. A. Brockmann. 2020. Whey protein polymorphisms in Sudanese goat breeds. Trop. Anim. Health Prod. 52:1211-1222. https://doi.org/10.1007/s11250-019-02119-2
Rossi, U. A., F. C. Hasenauer, M. E. Caffaro, R. Neumann, A. Salatin, M. A. Poli, & C. A. Rossetti. 2017. A haplotype at intron 8 of PTPRT gene is associated with resistance to Brucella infection in Argentinian creole goats. Vet. Microbiol. 207:133–137. https://doi.org/10.1016/j.vetmic.2017.06.001
Rozas, J., A. Ferrer-Mata, J. C. Sánchez-DelBarrio, S. Guirao-Rico, P. Librado, S. E. Ramos-Onsins, & A. Sánchez-Gracia. 2017. DnaSP 6: DNA sequence polymorphism analysis of large data sets. Mol. Biol. Evol. 34:3299-3302. https://doi.org/10.1093/molbev/msx248
Rupp, R., S. Mucha, H. Larroque, J. McEwan, & J. Conington. 2016. Genomic application in sheep and goat breeding. Anim. Front. 61:39–44. https://hal.inrae.fr/hal-02637118 https://doi.org/10.2527/af.2016-0006
SAS® University Edition. Software 3.8. 2018. SAS Institute Inc.
Sasi, R., R. Kanakkaparambil, & A. Thazhathuveettil. 2020. Polymorphism of fecundity genes, BMPR1B, BMP15 and GDF9, in tropical goat breeds of Kerala. Gene Rep. 21:100944. https://doi.org/10.1016/j.genrep.2020.100944
Spielmann, M., L. Daríog, & M. Stefan. 2018. Structural variation in the 3D genome. Nat. Rev. Genet. 19:453-467. https://doi.org/10.1038/s41576-018-0007-0
Starič, J., F. Farci, S. Luridiana, M. C. Mura, L. Pulinas, G. Cosso, & V. Carcangiu. 2020. Reproductive performance in three Slovenian sheep breeds with different alleles for the MTNR1A gene. Anim. Reprod. Sci. 216:106352. https://doi.org/10.1016/j.anireprosci.2020.106352
Swain, L. L., C. Mishra, S. S. Sahoo, G. Nayak, S. K. Pradhan, S. R. Mishra, & M. Dige. 2020. An in vivo and in silico analysis of novel variation in TMBIM6 gene affecting cardiopulmonary traits of Indian goats. J. Therm. Biol. 88:1-11. https://doi.org/10.1016/j.jtherbio.2019.102491
Tsukahara, Y., Y. Chomei, K. Oishi, A. K. Kahi, J. M. Panandam, T. K. Mukherjee, & H. Hirooka. 2008. Analysis of growth patterns in purebred Kambing Katjang goat and its crosses with the German Fawn. Small Rumin. Res. 80:8–15. https://doi.org/10.1016/j.smallrumres.2008.07.030
Van Laere, A. S., M. Nguyen, M. Braunschweig, C. Nezer, C. Collette, L. Moreau, A. L. Archibald, C. S. Haley, N. Buys, M. Tally, G. Andersson, M. Georges, & L. Andersson. 2003. A regulatory mutation in IGF2 causes a major QTL effect on muscle growth in the pig. Nature 425:832-836. https://doi.org/10.1038/nature02064
Wang, K., Y. Hailong, H. Xua, Q. Yang, S. Zhang, C. Pan, H. Chen, H. Zhu, J. Liu, L. Qu, & X. Lan. 2018. A novel indel within goat casein alpha S1 gene is significantly associated with litter size. Gene. 671:161–169. https://doi.org/10.1016/j.gene.2018.05.119
Wang, X., Q. Yang, K. Wang, H. Yan, C. Pan, H. Chen, J. Liu, H. Zhu, L. Qu, & X. Lan. 2019. Two strongly linked single nucleotide polymorphisms (Q320P and V397I) in GDF9 gene are associated with litter size in cashmere goats. Theriogenology. 125:115-121. https://doi.org/10.1016/j.theriogenology.2018.10.013
Waples, R. S. 2015. Testing for hardy–weinberg proportions: Have we lost the plot? J. Hered. 106:1–19. https://doi.org/10.1093/jhered/esu062
Wray, G. A. 2007. The evolutionary significance of cis-regulatory mutations. Nat. Rev. Genet. 8:206–16. https://doi.org/10.1038/nrg2063
Xu, N, C. Y. Chen, & A. B. Shyu. 1997. Modulation of the fate of cytoplasmic mRNA by AU-rich elements: key sequence features controlling mRNA deadenylation and decay. Mol. Cell. Biol. 17:4611–4621. https://doi.org/10.1128/MCB.17.8.4611
Yang, Q., S. L. Zhang, J. Li, X. Y. Wang, K. Peng, X. Y. Lan, & C. Pan. 2018. Development of a touch-down multiplex PCR method for simultaneously rapidly detecting three novel insertion/deletions (indels) within one gene: an example for goat GHR gene. Anim. Biotechnol. 30:366-371. https://doi.org/10.1080/10495398.2018.1517770
Yang, Y., X. Sun, W. Cui, N. Liu, K. Wang, L. Qu, & C. Pan. 2021. The detection of mutation within goat cell division cycle 25 A and its effect on kidding number. Anim. Biotechnol. https://doi.org/10.1080/10495398.2021.1910519
Yue, C., W. L. Bai, Y. Y. Zheng, T. Y. Hui, J. M. Sun, D. Guo, S. L. Guo, & Z. Y. Wang. 2019. Correlation analysis of candidate gene SNP for high-yield in Liaoning cashmere goats with litter size and cashmere performance. Anim. Biotechnol. 30:1-7. https://doi.org/10.1080/10495398.2019.1652188


A. Febriana
S. Sutopo
drsutopo36@gmail.com (Primary Contact)
E. Kurnianto
W. Widiyanto
Author Biographies

A. Febriana, Faculty of Animal and Agricultural Sciences, Diponegoro University

Febriana is a PhD student in  Faculty of Animal and Agricultural Sciences, Diponegoro University, also a state employee in Indonesian Center of Livestock Training (ICLT) Batu Ministry of Agriculture of Indonesia

E. Kurnianto, Faculty of Animal and Agricultural Sciences, Diponegoro University

A Professor in breeding and genetics 

W. Widiyanto, Faculty of Animal and Agricultural Sciences, Diponegoro University

A Professor in feed nutrition and biochemistry 

FebrianaA., SutopoS., KurniantoE., & WidiyantoW. (2022). A Novel SNPs of KISS1 Gene Strongly Associated with Litter Size in Indonesian Goat Breeds. Tropical Animal Science Journal, 45(3), 255-269. https://doi.org/10.5398/tasj.2022.45.3.255

Article Details

List of Cited By :

Crossref logo