Genetic diversity of local corn (Zea mays) cultivars from South Amarasi, Kupang District, Indonesia by Inter Simple Sequence Repeats marker
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Abstract. Uslan, Jannah N. 2020. Genetic diversity of local corn (Zea mays) cultivars from South Amarasi, Kupang District, Indonesia by Inter Simple Sequence Repeats marker. Biodiversitas 21: 1208-1214. Corn (Zea mays L.) is one of the most important food crops in Indonesia. However, the studies described their genetic variation is relatively poor. Therefore, the aim of this study was to analyze the genetic diversity of local corn cultivars from South Amarasi, Kupang District, East Nusa Tenggara (NTT), Indonesia using ISSR markers. The sampling was conducted in 4 different sites in Sub-district of Amarasi, Kupang District. A total of 11 corn cultivars from Sub-district of South Amarasi was collected. DNA isolation was performed by using CTAB Method. Clustering analysis was conducted on MSVP 3.2 software. It was shown that all ISSR-primers used (UBC 811, UBC 814 and UBC 824) were successfully produced polymorphic bands and represents the high genetic diversity of the local corn cultivars. The genetic distance index indicated that several corn cultivars from two different populations were geographically unclustered, although there are samples from several populations that have a low genetic distance. The genetic variation index also showed high genetic diversity among the populations. Further research on the exhaustive sample collection was needed to give an insight into the genetic diversity of local corn cultivars (Zea mays L.) from South Amarasi, Indonesia. Please write implementation of this research
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References
Ardiyani M, Sulistyaningsih LD and Esthi YN. 2014. Keragaman genetik Tacca leontopetaloides (L.) Kuntze (Taccaceae) dari beberapa provenansi di Indonesia berdasarkan Marka Inter Simple Sequence Repeats (ISSR). Berita Biologi 13(1): 85-96.
Adriansyah F, Hanum L, Muharni M and Windusari Y. 2018. Analisis Polimorfisme Padi Varietas Lokal Sumatera Selatan Berdasarkan Pendekatan PCR-RAPD. Jurnal Lahan Suboptimal: Journal of Suboptimal Lands 7(1): 50-58.
Beyene Y, Botha AM, and Myburg AA. 2005. Genetic diversity in traditional Ethiopian highland maize accessions assessed by AFLP markers and morphological traits. Afr J Biotechnol 4(7): 586-595.
BPS. 2009. Nusa Tenggara Timur Dalam Angka 2009. https://www.bps.go.id/
BPS. 2015. Nusa Tenggara Timur Dalam Angka 2015 https://www.bps.go.id/
Costa R, Pereira G, Garrido I, Tavares-de-Sousa MM and Espinosa F. 2016. Comparison of RAPD, ISSR, and AFLP Molecular Markers to Reveal and Classify Orchardgrass (Dactylis glomerata L.) Germplasm Variations. PloS one 11(4): e0152972
Darrah LL, McMullen MD and Zuber MS. 2019. Breeding, Genetics and Seed Corn Production. Woodhead Publishing, Cambridge.
Djaini V 2014 Respon Pertumbuhan Tanaman Jagung Lokal (Zea mays L.) Varietas Motoro Kiki Berdasarkan Waktu Pemberian Pupuk Kotoran Ayam [Master thesis]. Jurusan Agroteknologi Fakultas Pertanian Universitas Gorontalo, Gorontalo. [Indonesian]
Dar TH, Shakeel R and Verma S. 2018. Comparative Germplasm Characterization of Maize (Zea mays L.) in Rajouri Region of Pir Panjal Himalaya J & K (India), based on Morphological and ISSR Markers. JCSB 21(1): 43-55.
Doyle JJ and Doyle JL. 1990. Isolation of Plant DNA from Fresh Tissue. Focus 12(13): 39-40.
Faesal and Syuryawati S. 2011. Urgensi Koleksi Plasma Nutfah Jagung Lokal di Flores Nusa Tenggara Timur Seminar Nasional Serelia. Balai Penelitian Tanaman Serealia, Maros. [Indonesian]
Guevarra PR, Diaz DC and Canama AO. 2017. Molecular characterization of native corn populations in the Philippines based on SSR markers. Philipp J Crop Sci 42: 111-121.
Gusmiati LH, Hapsari L and Wahyudi D. 2018. Keragaman dan Pengelompokan Morfologi 10 Pisang Olahan (Musa cv. Grup ABB) Koleksi Kebun Raya Purwodadi LIPI. Floribunda 5(8): 299-313.
Hosang H, Kasim EYF, Bora CH and Bhuja P. 2007. Koleksi Jagung Lokal NTT. Balai Pengkajian Teknologi Pertanian (BPTP), Nusa Tenggara Timur. [Indonesian]
Ihwan, Uslan, Widodo and Hakim L 2019 Genetic diversity of Rhizophora mucronata in eastern region of Timor Island, Indonesia as revealed by RAPD. Biodiversitas 20(11): 3364-3371.
Iqbal J, Shinwari ZK and Rabbani MA 2015 Prediction of Grain Yield Losses in Wheat (Triticum aestivum L.) under different densities of wild oat (Avena Fatua L.). Pak J Bot 47: 255-264.
Karuniawan A, Sahala B and Ismail A. 2008. Keanekaragaman genetik mucuna berdasarkan karakter morfologi dan komponen hasil. Zuriat 19(1): 41-59. [Indonesian]
Kusumadewi Y, Poerba YS and Partomihardjo T 2010 Keragaman Genetika Ramin [Gonystylus bancanus (Miq.) Kurz] dari Provinsi Riau Berdasarkan Profil Random Amplified Polymorphic DNA. Jurnal Biologi Indonesia 6(2): 173-183. [Indonesian]
Laurentin H and Karlovsky P. 2007. AFLP fingerprinting of sesame (Sesamum indicum L.) cultivars: Identification, genetic relationship and comparison of AFLP informativeness parameters. Gen Resour Crop Evol 54(7): 1437–1446.
Lopes HM, Bastos CS, Boiteux LS, Foresti J and Suinaga FA. 2017. A RAPD-PCR-based genetic diversity analysis of Helicoverpa armigera and H. zea populations in Brazil. Genet Mol Res 16: 3-9
Murningsih T, Yulita KS Bora CY and Arsal BA 2015 Respon tanaman jagung varietas lokal NTT umur sangat genjah (pena tunu’ana’) terhadap cekaman kekeringan. Berita Biologi 4(1): 49-55. [Indonesian]
Nei M. 1987. Molecular evolutionary genetics. Columbia University Press, New York.
Pharmawati M, Yan G and McFarlane IJ. 2005. Molecular Variation and Fingerprinting of Leucadendron Cultivars (Proteaceae) by ISSR Markers. Aust Syst Bot 17(1): 49-61.
Pharmawati M. 2009. Optimalisasi ekstraksi DNA dan PCR-RAPD pada Grevillea spp. (Proteaceae). Jurnal Biologi XIII 1: 12-16. [Indonesian]
Poerba YS and Martanti D. 2008. Keragaman Genetik Berdasarkan Marka Random Amplified Polymorphic DNA pada Amorphophallus muelleri Blume di Jawa. Biodiversitas 9(4): 245-249. [Indonesian]
Probojati RT, Wahyudi D, Hapsari L. 2019. Clustering Analysis and Genome Inference of Pisang Raja Local Cultivars (Musa spp.) from Java Island by Random Amplified Polymorphic DNA (RAPD) Marker. J Trop Biodiv Biotechnol 4(2): 42-53.
Reni R 2015 Analisis Keragaman Genetik Genotipe Elit Jagung (Zea mays L.) Tahan Bulai Berbasis Marka Simple Sequence Repeats (SSRs) [thesis]. Program Studi Agroteknologi Jurusan Budidaya Pertanian Fakultas Pertanian Universitas Hasanuddin, Makasar. [Indonesian]
Rimbawanto A, Widyatmoko W and Sulistyowati P. 2006. Distribusi Keragman Genetik Populasi Santalum album berdasarkan penanda RAPD. Jurnal Pemuliaan Tanaman Hutan 3: 175-181. [Indonesian]
Roldàn-Ruiz I, Dendauw J, Van BE, Depicker A, de Loose M. 2000. AFLP markers reveal high polymorphic rates in ryegrasses (Lolium spp.). Mol Breeding 6(2): 125-134.
Sambrook J and Russel DW. 2001. Molecular Cloning (A Laboratory Manual), Volume 1, Third Edition. Cold Spring Harbor Laboratory, New York.
Subagio H and Aqil M 2013 Pengembangan Produksi Sorgum di Indonesia Seminar Nasional Inovasi Teknologi Pertanian. BPTP Kalimantan Selatan, Kalimantan Selatan. [Indonesian]
Sundari, Arumingtyas EL, Hakim L, Azrianingsih R and Wahyudi D. 2017. Genetic Variability of Local Durian (Durio zibethinus Murr.) in Ternate Island Based on Rapd Markers. Plant Cell Biotechnol Mol Biol 18(1): 68-75.
Tingey SV, Rafalski J A and Hanafey MK. 1994. Genetic analysis with RAPD markers,” in Plant Molecular Biology. Springer, Berlin.
Uslan and Pharmawati M. 2015 Optimasi Konsentrasi DNA dan MgCl2 pada Reaksi Polymerase Chain Reaction-Random Amplified Polymorphic DNA untuk Analisis Keragaman Genetik Tanaman Faloak (Sterculia quadrifida R.Br) (Optimization of DNA and MgCl2 Concentrations in Polymerase Chain Reaction. Bios Logos 5(1): 26-34. [Indonesian]
Weising K, Nybom H, Pfenninger M, Wolff K and Kahl G. 2005. Principles, methods, and applications DNA fingerprinting,” in Plants. CRC Press, Boca Raton.
Wijayanto T, Dirvamena B and Ente L. 2013. Hubungan kekerabatan aksesi Pisang Kepok (Musa paradisiaca Formatypica) di Kabu-paten Muna berdasarkan karakter morfologi dan penanda RAPD. Jurnal Agroteknos 3(3):163-166. [Indonesian]
Yusuf Y, Pohan A and Syamsuddin S. 2013. Jagung Makanan Pokok Untuk Mendukung Ketahanan Pangan di Provinsi Nusa Tenggara Timur; Prosiding Seminar Nasional Serealia. Balai Penelitian Tanaman Serealia, Maros, 2013. [Indonesian]
Yulita KS and Naiola N. 2013. Keragaman Genetik Beberapa Aksesi Jagung dari Nusa Tenggara Timur Berdasarkan Profil Inter Short Sequence Repeat (ISSR). Jurnal Biologi Indonesia 9(2): 255-264. [Indonesian]
Zulfahmi R. 2013. Genetic Diversity of Eurycoma longifolia Jack Based on Random Amplified Polymorphic DNA Marker. Journal of Tropical Forest Management 3(2): 41-52.
Adriansyah F, Hanum L, Muharni M and Windusari Y. 2018. Analisis Polimorfisme Padi Varietas Lokal Sumatera Selatan Berdasarkan Pendekatan PCR-RAPD. Jurnal Lahan Suboptimal: Journal of Suboptimal Lands 7(1): 50-58.
Beyene Y, Botha AM, and Myburg AA. 2005. Genetic diversity in traditional Ethiopian highland maize accessions assessed by AFLP markers and morphological traits. Afr J Biotechnol 4(7): 586-595.
BPS. 2009. Nusa Tenggara Timur Dalam Angka 2009. https://www.bps.go.id/
BPS. 2015. Nusa Tenggara Timur Dalam Angka 2015 https://www.bps.go.id/
Costa R, Pereira G, Garrido I, Tavares-de-Sousa MM and Espinosa F. 2016. Comparison of RAPD, ISSR, and AFLP Molecular Markers to Reveal and Classify Orchardgrass (Dactylis glomerata L.) Germplasm Variations. PloS one 11(4): e0152972
Darrah LL, McMullen MD and Zuber MS. 2019. Breeding, Genetics and Seed Corn Production. Woodhead Publishing, Cambridge.
Djaini V 2014 Respon Pertumbuhan Tanaman Jagung Lokal (Zea mays L.) Varietas Motoro Kiki Berdasarkan Waktu Pemberian Pupuk Kotoran Ayam [Master thesis]. Jurusan Agroteknologi Fakultas Pertanian Universitas Gorontalo, Gorontalo. [Indonesian]
Dar TH, Shakeel R and Verma S. 2018. Comparative Germplasm Characterization of Maize (Zea mays L.) in Rajouri Region of Pir Panjal Himalaya J & K (India), based on Morphological and ISSR Markers. JCSB 21(1): 43-55.
Doyle JJ and Doyle JL. 1990. Isolation of Plant DNA from Fresh Tissue. Focus 12(13): 39-40.
Faesal and Syuryawati S. 2011. Urgensi Koleksi Plasma Nutfah Jagung Lokal di Flores Nusa Tenggara Timur Seminar Nasional Serelia. Balai Penelitian Tanaman Serealia, Maros. [Indonesian]
Guevarra PR, Diaz DC and Canama AO. 2017. Molecular characterization of native corn populations in the Philippines based on SSR markers. Philipp J Crop Sci 42: 111-121.
Gusmiati LH, Hapsari L and Wahyudi D. 2018. Keragaman dan Pengelompokan Morfologi 10 Pisang Olahan (Musa cv. Grup ABB) Koleksi Kebun Raya Purwodadi LIPI. Floribunda 5(8): 299-313.
Hosang H, Kasim EYF, Bora CH and Bhuja P. 2007. Koleksi Jagung Lokal NTT. Balai Pengkajian Teknologi Pertanian (BPTP), Nusa Tenggara Timur. [Indonesian]
Ihwan, Uslan, Widodo and Hakim L 2019 Genetic diversity of Rhizophora mucronata in eastern region of Timor Island, Indonesia as revealed by RAPD. Biodiversitas 20(11): 3364-3371.
Iqbal J, Shinwari ZK and Rabbani MA 2015 Prediction of Grain Yield Losses in Wheat (Triticum aestivum L.) under different densities of wild oat (Avena Fatua L.). Pak J Bot 47: 255-264.
Karuniawan A, Sahala B and Ismail A. 2008. Keanekaragaman genetik mucuna berdasarkan karakter morfologi dan komponen hasil. Zuriat 19(1): 41-59. [Indonesian]
Kusumadewi Y, Poerba YS and Partomihardjo T 2010 Keragaman Genetika Ramin [Gonystylus bancanus (Miq.) Kurz] dari Provinsi Riau Berdasarkan Profil Random Amplified Polymorphic DNA. Jurnal Biologi Indonesia 6(2): 173-183. [Indonesian]
Laurentin H and Karlovsky P. 2007. AFLP fingerprinting of sesame (Sesamum indicum L.) cultivars: Identification, genetic relationship and comparison of AFLP informativeness parameters. Gen Resour Crop Evol 54(7): 1437–1446.
Lopes HM, Bastos CS, Boiteux LS, Foresti J and Suinaga FA. 2017. A RAPD-PCR-based genetic diversity analysis of Helicoverpa armigera and H. zea populations in Brazil. Genet Mol Res 16: 3-9
Murningsih T, Yulita KS Bora CY and Arsal BA 2015 Respon tanaman jagung varietas lokal NTT umur sangat genjah (pena tunu’ana’) terhadap cekaman kekeringan. Berita Biologi 4(1): 49-55. [Indonesian]
Nei M. 1987. Molecular evolutionary genetics. Columbia University Press, New York.
Pharmawati M, Yan G and McFarlane IJ. 2005. Molecular Variation and Fingerprinting of Leucadendron Cultivars (Proteaceae) by ISSR Markers. Aust Syst Bot 17(1): 49-61.
Pharmawati M. 2009. Optimalisasi ekstraksi DNA dan PCR-RAPD pada Grevillea spp. (Proteaceae). Jurnal Biologi XIII 1: 12-16. [Indonesian]
Poerba YS and Martanti D. 2008. Keragaman Genetik Berdasarkan Marka Random Amplified Polymorphic DNA pada Amorphophallus muelleri Blume di Jawa. Biodiversitas 9(4): 245-249. [Indonesian]
Probojati RT, Wahyudi D, Hapsari L. 2019. Clustering Analysis and Genome Inference of Pisang Raja Local Cultivars (Musa spp.) from Java Island by Random Amplified Polymorphic DNA (RAPD) Marker. J Trop Biodiv Biotechnol 4(2): 42-53.
Reni R 2015 Analisis Keragaman Genetik Genotipe Elit Jagung (Zea mays L.) Tahan Bulai Berbasis Marka Simple Sequence Repeats (SSRs) [thesis]. Program Studi Agroteknologi Jurusan Budidaya Pertanian Fakultas Pertanian Universitas Hasanuddin, Makasar. [Indonesian]
Rimbawanto A, Widyatmoko W and Sulistyowati P. 2006. Distribusi Keragman Genetik Populasi Santalum album berdasarkan penanda RAPD. Jurnal Pemuliaan Tanaman Hutan 3: 175-181. [Indonesian]
Roldàn-Ruiz I, Dendauw J, Van BE, Depicker A, de Loose M. 2000. AFLP markers reveal high polymorphic rates in ryegrasses (Lolium spp.). Mol Breeding 6(2): 125-134.
Sambrook J and Russel DW. 2001. Molecular Cloning (A Laboratory Manual), Volume 1, Third Edition. Cold Spring Harbor Laboratory, New York.
Subagio H and Aqil M 2013 Pengembangan Produksi Sorgum di Indonesia Seminar Nasional Inovasi Teknologi Pertanian. BPTP Kalimantan Selatan, Kalimantan Selatan. [Indonesian]
Sundari, Arumingtyas EL, Hakim L, Azrianingsih R and Wahyudi D. 2017. Genetic Variability of Local Durian (Durio zibethinus Murr.) in Ternate Island Based on Rapd Markers. Plant Cell Biotechnol Mol Biol 18(1): 68-75.
Tingey SV, Rafalski J A and Hanafey MK. 1994. Genetic analysis with RAPD markers,” in Plant Molecular Biology. Springer, Berlin.
Uslan and Pharmawati M. 2015 Optimasi Konsentrasi DNA dan MgCl2 pada Reaksi Polymerase Chain Reaction-Random Amplified Polymorphic DNA untuk Analisis Keragaman Genetik Tanaman Faloak (Sterculia quadrifida R.Br) (Optimization of DNA and MgCl2 Concentrations in Polymerase Chain Reaction. Bios Logos 5(1): 26-34. [Indonesian]
Weising K, Nybom H, Pfenninger M, Wolff K and Kahl G. 2005. Principles, methods, and applications DNA fingerprinting,” in Plants. CRC Press, Boca Raton.
Wijayanto T, Dirvamena B and Ente L. 2013. Hubungan kekerabatan aksesi Pisang Kepok (Musa paradisiaca Formatypica) di Kabu-paten Muna berdasarkan karakter morfologi dan penanda RAPD. Jurnal Agroteknos 3(3):163-166. [Indonesian]
Yusuf Y, Pohan A and Syamsuddin S. 2013. Jagung Makanan Pokok Untuk Mendukung Ketahanan Pangan di Provinsi Nusa Tenggara Timur; Prosiding Seminar Nasional Serealia. Balai Penelitian Tanaman Serealia, Maros, 2013. [Indonesian]
Yulita KS and Naiola N. 2013. Keragaman Genetik Beberapa Aksesi Jagung dari Nusa Tenggara Timur Berdasarkan Profil Inter Short Sequence Repeat (ISSR). Jurnal Biologi Indonesia 9(2): 255-264. [Indonesian]
Zulfahmi R. 2013. Genetic Diversity of Eurycoma longifolia Jack Based on Random Amplified Polymorphic DNA Marker. Journal of Tropical Forest Management 3(2): 41-52.
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