Application of Microsatellite Markers for Genetic Diversity Analysis of Indonesian Local Cattle

Dwi Hariyono

Abstract

Animal genetic resources (AnGR), including cattle, have been valuable national assets that need to be preserved and developed. There are at least 16 recognized breeds of cattle that have been registered as local and new breeds by the Ministry of Agriculture of the Republic of Indonesia. Conservation and development programs of these local cattle breeds require basic information regarding their genetic diversity, relationships, and structures. There are several types of DNA markers that can be used for genetic diversity analysis, such as microsatellite markers. Microsatellites or short tandem repeats (STRs) are a group of DNA sequences consisting of tandemly repeated units (1–6 bp), which are abundant throughout the genome and can be found in both coding and non-coding regions. The primary advantages of microsatellites are that they are inherited in a Mendelian pattern (codominant markers), high polymorphism rates, and high abundances throughout the genome. The aim of this review is to discuss the application of microsatellite markers for genetic diversity analysis in Indonesian local cattle based on 3 indices: number alleles per locus, expected heterozygosity (He), and polymorphisms information content (PIC). There are at least 28 microsatellite markers that have been studied in Indonesian local cattle, with the number of alleles per locus ranging from 2 to 32, He values ranging from 0.100 to 0.985, and PIC values from 0.095 to 0.935. Based on the PIC values, several microsatellites are classified as highly informative, e.g. BM1824, ILST6, TGLA126, TGLA53, TGLA227, TGLA122, ETH225, INRA23, SPS113, SPS115, BM1818, CSSM66, ETH10, INRA005, INRA037, ETH185, HEL017, and ILSTS029. Therefore, these microsatellite markers can be potentially used for future genetic diversity analysis of other breeds of cattle.

Keywords

Genetic analysis; DNA marker; microsatellite; local cattle; conservation

Full Text:

PDF

References

Abdul-Muneer PM. 2014. Application of microsatellite markers in conservation genetics and fisheries management: recent advances in population structure analysis and conservation strategies. Genet. Res. Int. 2014: 691759.

Abebe AS, Mikko S, Johansson AM. 2015. Genetic diversity of five local Swedish chicken breeds detected by microsatellite markers. PLoS One 10: 1–13.

Adinata Y, Aryogi, Pamungkas D. 2016. Morphostruktural bangsa Sapi PO, PO Kebumen dan Bali, dasar informasi genetik mendukung ketahanan pangan, in: Prosiding Seminar Nasional Inovasi Teknologi Pertanian. Banjarbaru, pp. 1227–1233.

Agung PP, Saputra F, Zein MSA, Wulandari AS, Putra WPB, Said S, Jakaria J. 2019. Genetic diversity of Indonesian cattle breeds based on microsatellite markers. Asian-Australasian J. Anim. Sci. 32: 467–476.

Ahrestani F. 2018. Bos frontalis and Bos gaurus (Artiodactyla: Bovidae). Mamm. Species. 50: 34–50.

Aitnazarov R, Mishakova T, Yudin N. 2022. Assessment of genetic diversity and phylogenetic relationships in Black Pied cattle in the Novosibirsk Region using microsatellite markers. Vavilov J. Genet. Breed. 25: 831–838.

Al-Samarai FR, Al-Kazaz AA. 2015. Molecular markers: an introduction and applications. Eur. J. Mol. Biotechnol. 9: 118–130.

Anmarkrud JA, Kleven O, Bachmann L, Lifjeld JT. 2008. Microsatellite evolution: Mutations, sequence variation, and homoplasy in the hypervariable avian microsatellite locus HrU10. BMC Evol. Biol. 8: 138.

Aryogi, Pamungkas D, Efendy J. 2020. Formation and phenotypic performance of the new breed POGASI Agrinak cattle. IOP Conf. Ser. Earth Environ. Sci. 492: 12106.

Azimu W, Manatbay B, Li Y, Kaimaerdan D, Wang HE, Reheman A, Muhatai G. 2018. Genetic diversity and population structure analysis of eight local chicken breeds of Southern Xinjiang. Br. Poult. Sci. 59: 629–635.

Botstein D, White RL, Skolnick M, Davis RW. 1980. Construction of a genetic linkage map in man using restriction fragment length polymorphisms. Am. J. Hum. Gen. 32: 314–331.

De Carvalho DA, Martínez AM, Carolino I, Barros MC, Vallejo MEC, Santos-Silva F, Almeida MJDO, Carolino N, Bermejo JVD, Sarmento JLR. 2020. Diversity and genetic relationship of free-range chickens from the northeast region of Brazil. Animals. 10: 1–14.

Direktorat Jenderal Peternakan dan Kesehatan Hewan, Kementerian Pertanian Republik Indonesia (Ditjenpkh). 2022. Jenis Rumpun Sapi [Internet]. Diunduh pada tanggal 25 Maret 2022. Tersedia di: http://bibit.ditjenpkh.pertanian.go.id/jenis-rumpun/sapi.

Faid-Allah E, Ghoneim E, Elbetagy AR, El-Dabour M. 2018. Genetic diversity and structure of native Egyptian cattle populations and French-Egyptian Cross via DNA-microsatellite. Jurnal Ilmu Ternak dan Veteriner. 23: 1-10.

FAO. 2011. Molecular genetic characterization of animal genetic resources, in: FAO Animal Production and Health Guidelines. Cambridge University Press.

Gamarra D, Taniguchi M, Aldai N, Arakawa A, Lopez-Oceja A, de Pancorbo MM. 2020. Genetic characterization of the local pirenaica cattle for parentage and traceability purposes. Animals. 10: 1–13.

Habimana R, Okeno TO, Ngeno K, Mboumba S, Assami P, Gbotto AA, Keambou CT, Nishimwe K, Mahoro J, Yao N. 2020. Genetic diversity and population structure of indigenous chicken in Rwanda using microsatellite markers. PLoS One 15: 1–17.

Hamdani MDI, Adhianto K, Sulastri, Husni A, Renitasari. 2017. Ukuran-ukuran tubuh sapi Krui jantan dan betina di Kabupaten Pesisir Barat Lampung. Jurnal Ilmu Ternak. 17: 97–102.

Hariyono DNH, Maharani D, Cho S, Manjula P, Seo D, Choi N, Sidadolog JHP, Lee JH. 2019. Genetic diversity and phylogenetic relationship analyzed by microsatellite markers in eight Indonesian local duck populations. Asian-Australasian J. Anim. Sci. 32: 31–37.

Hartati, Sumadi, Hartatik T. 2009. The identification of genetic characteristic of Ongole Grade cattle in smallholder farmers. Buletin Peternakan 33: 64–73.

Hartatik T, Hariyono DNH, Adinata Y. 2019. Short communication: Genetic diversity and phylogenetic analysis of two indonesian local cattle breeds based on cytochrome b gene sequences. Biodiversitas. 20: 17–22.

Hikmawaty, Gunawan A, Noor R, Jakaria. 2014. Identification of body size and body shape of Bali cattle in breeding centers on principal componenet analysis. Jurnal Ilmu Produksi dan Teknologi Hasil Peternakan. 2: 231–237.

Ho EKH, MacRae F, Latta LC, Benner MJ, Sun C, Ebert D, Schaack S, Rogers R. 2019. Intraspecific variation in microsatellite mutation profiles in Daphnia magna. Mol. Biol. Evol. 36: 1942–1954.

Jakaria J, Alwiyah A, Saputra F, Baihaqi M, Noor RR. 2020. Genetic diversity between Bali cattle (Bos javanicus) and it’s hybrids using microsatellite markers. Iran. J. Appl. Anim. Sci. 10: 453–460.

Kambanau DH, Kaka A, Hambakodu M. 2022. Sifat kualitatif dan kuantitatif bibit sapi Sumba Ongole Kecamatan Pandawai Kabupaten Sumba Timur. Jurnal Peternakan 6: 1–6.

Kepmentan. 2020. Keputusan Menteri Pertanian Republik Indonesia Nomor 617/KPTS/PK.020/M/09/2020 tentang Penetapan Rumpun Sapi Galekan.

Kuswati, Ali MI, Wahyuni RD. 2022. Morphometric characteristics of Galekan cattle breed base on principle component analysis (PCA). Jurnal Ilmu-Ilmu Peternakan 32: 1–12.

Leffak M, Gadgil R, Barthelemy JLT. 2017. Replication stalling and DNA microsatellite instability. Biophys. Chem. 225: 38–48.

Mansur M, Mahmudi ATB, Dagong MIA, Rahmi L, Bugiwati RSRA, Baco S. 2016. Keragaman genetik sapi Bali di kabupaten Barru berdasarkan karakteristik fenotipe dan DNA penciri mikrosatelit. JITP. 4: 104–111.

Margawati ET, Volkandari SD, Indriawati I, Ridwan M. 2019. Genetic Diversity and Relationship among Bali Cattle from Several Locations in Indonesia Based on ETH10 Microsatellite Marker. Jurnal Ilmu Ternak dan Veteriner. 23: 168.

Masduqi, Sari EM, Abdullah MAN. 2021. Identifikasi sifat kuantitatif dan sifat kualitatif pada Sapi Aceh dalam rangka pelestarian sumber daya genetik ternak lokal. Jurnal Agripet. 21: 141–148.

Maylinda S, NUgroho H, Busono W, 2021. Phenotypic characteristics of local cattle in Madura island. AIP Conf. Proc. 060002.

Merliana MR, Wandia IN, Puja IK. 2014. Polimosfisme lokus mikrosatelit BM1329 dan hubungannya dengan calving interval pada sapi Bali. Jurnal Ilmu dan Kesehatan Hewan 2: 117–125.

Miah G, Rafii MY, Ismail MR, Puteh AB, Rahim HA, Islam NK, Latif MA. 2013. A review of microsatellite markers and their applications in rice breeding programs to improve blast disease resistance. Int. J. Mol. Sci. 14: 22499–22528.

Misrianti R, Mustika RP, Ali A. 2018. Keragaman sifat kualitatif dan kuantitatif sapi Kuantan pada berbagai tingkatan umur di Kecamatan Benai Kabupaten Kuantan Singingi Provinsi Riau. Jurnal Peternakan 15: 55–61.

Mohamad K, Olsson M, van Tol HTA, Mikko S, Vlamings BH, Andersson G, Rodríguez-Martínez H, Purwantara B, Paling RW, Colenbrander B, Lenstra JA. 2009. On the origin of Indonesian cattle. PLoS One 4: e5490.

Mukhtar, Jamaliah, Hendra S. 2015. Keragaman fenotipe sapi Aceh betina pada BPTU-HPT Indrapuri. Jurnal Ilmu Peternakan. 3: 34–38.

Nijman IJ, Otsen M, Verkaar ELC, de Ruijter C, Hanekamp E, Ochieng JW, Shamshad S, Rege JEO, Hanotte O, Barwegen M, Sulawati T, Lenstra JA. 2003. Hybridization of banteng (Bos javanicus) and zebu (Bos indicus) revealed by mitochondrial DNA, satellite DNA, AFLP and microsatellites. Heredity (Edinb). 90: 10–16.

Ningsih SF, Sulastri, Hamdani MDI. 2017. Karakteristik kualitatif sapi Krui di Kabupaten Pesisir Barat Lampung. Jurnal Riset dan Inovasi Peternakan. 1: 5–9.

Norris DE, Shurtleff AC, Toure YT, Lanzaro GC. 2001. Microsatellite DNA polymorphism and heterozygosity among field and laboratory populations of Anopheles gambie s.s. (Diptera: Culicidae). J. Med. Entomol. 38: 336–340.

Nurgiartiningsih V, Budiarto A, Kusmartono K, Suyadi S, 2016. Evaluation of performance in female Madura cattle in Madura island, Indonesia. Animal Production. 18: 125.

Prajapati BM, Gupta JP, Pandey DP, Parmar GA, Chaudhari JD. 2017. Molecular markers for resistance against infectious diseases of economic importance. Vet. World. 10: 112–120.

Prihandini PW, Primasari A, Luthfi M, Efendy J, Pamungkas D. 2020. Genetic diversity of mitochondrial DNA cytochrome b in Indonesian native and local cattle populations. JITV. 25: 39.

Putri AE, Farajallah A, Perwitasari D. 2019. The origin of pesisir cattle based on D-loop mitochondrial DNA. Biodiversitas 20: 2569–2575.

Ramadhan TM, Mulliadi D, Arifin J. 2014. Perbedaan kualitatif dan kuantitatif sapi betina lokal di Majalengka dengan sapi betina Jabres. Students e-Journals 3: 1–11.

Said S, Pintaka W, Putra W, Anwar S, Agung PP, Yuhani H. 2017. Phenotypic, morphometric characterization and population structure of Pasundan cattle at West Java, Indonesia. Biodiversitas. 18: 1638–1645.

Septian WA, Jakaria, Sumantri C. 2015. Genetic diversity of Bali cattle based on microsatellite marker in Indonesian breeding centre. Media Peternakan. 38: 12–17.

Serrote CML, Reiniger LRS, Silva KB, Rabaiolli SM dos S, Stefanel CM. 2020. Determining the polymorphism information content of a molecular marker. Gene. 726: 144175.

Singh U, Deb R, Alyethodi RR, Alex R, Kumar S, Chakraborty S, Dhama K, Sharma A. 2014. Molecular markers and their applications in cattle genetic research: A review. Biomark. Genom. Med. 6: 49–58.

Sudrajad P, Subiharta. 2014. Karakter fenotipik sapi betina Peranakan Ongole (PO) Kebumen. Widyariset 17: 283–290.

Sutarno, Setyawan AD, Lymbery AJ. 2015. Genetic diversity of five Indonesian native cattle breeds at microsatellite loci. Asian J. Anim. Sci. 9:57-64.

Svishcheva G, Babayan O, Lkhasaranov B, Tsendsuren A, Abdurasulov A, Stolpovsky Y. 2020. Microsatellite diversity and phylogenetic relationships among East Eurasian Bos taurus breeds with an emphasis on rare and ancient local cattle. Animals. 10: 1493.

Teneva A, Dimitrov K, Petrović CV, Petrović MP, Dimitrova I, Tyufekchiev N, Petrov N. 2013. Molecular genetics and SSR markers as a new practice in farm animal genomic analysis for breeding and control of disease disorders. Biotechnol. Anim. Husb. 29: 405–431.

Trifena, Budisatria IGS, Hartatik T. 2011. The phenotypic changes of first filial and backcross of Ongole Grade, Simpo, and Limpo cows. Buletin Peternakan. 35: 11–16.

Utomo BN, Noor RR, Sumantri C, Supriatna I, Gurnadi ED. 2011. Keragaman genetik sapi Katingan dan hubungan kekerabatannya dengan beberapa sapi lokal lain menggunakan analisis DNA mikrosatelit. JITV. 16: 112–125.

Wang H, Yang B, Wang H, Xiao H. 2021. Impact of different numbers of microsatellite markers on population genetic results using SLAF-seq data for Rhododendron species. Sci. Rep. 11: Article number 8591.

Widi TS, Baliarti E, Ibrahim A, Koesmara H, Budisatria IGS. 2016. Phenotypic characteristics of Aceh cattle on different sex and age in smallholder farmers. Proceeding at the 3rd Animal Production International Seminar and The 3rd ASEAN Regional Conference on Animal Production. Batu.

Wimmers K, Ponsuksili S, Hardge T, Valle-Zarate A, Mathur PK, Horst P. 2022. Genetic distinctness of African, Asian and South American local chickens. Anim. Genet. 31: 159–165.

Yendraliza, Abadi H, Misrianti R, Ali A, Effendi A. 2019. Body size identification and semen quality of Kuantan cattle. Jurnal Ilmu Peternakan Terpadu 7: 186–191.

Zhang X, He Y, Zhang W, Wang Y, Liu Xinmeng, Cui A, Gong Y, Lu J, Liu Xin, Huo X, Lv J, Guo M, Du X, Han L, Chen H, Chen J, Li C, Chen Z. 2021. Development of microsatellite marker system to determine the genetic diversity of experimental chicken, duck, goose, and pigeon populations. Biomed Res. Int. 2021: Article ID. 8851888.

Zulkharnaim, Baco S, Rahim L, Yusuf M. 2020. Identification of qualitative characteristic Bali polled cattle. Hasanuddin J. Anim. Sci. 2: 70–75.

Refbacks

  • There are currently no refbacks.

Copyright (c)  2022 WARTAZOA. Indonesian Bulletin of Animal and Veterinary Sciences

Creative Commons License
This work is licensed under a Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License.

View My Stats