Keragaman genetik koleksi plasma nutfah jewawut sister line dan lokal menggunakan marka SSR

Karlina Syahruddin; Muhammad Azrai; Marcia Bunga Pabendon; Muhammad Abid; Amin Nur

doi:10.24198/kultivasi.v20i3.34843

Keragaman genetik koleksi plasma nutfah jewawut sister line dan lokal menggunakan marka SSR

Karlina Syahruddin, Muhammad Azrai, Marcia Bunga Pabendon, Muhammad Abid, Amin Nur

Abstract

Abstrak

Keragaman genetik sangat penting dalam pemuliaan tanaman, oleh karena itu informasi genetik sangat dibutuhkan dalam proses seleksi. Teknologi molekuler dengan menggunakan marka Simple Sequence Repeat (SSR) saat ini banyak digunakan karena keakuratan informasi dan polimorfik untuk spesies atau galur yang berkerabat dekat. Penelitian ini dilakukan untuk mengidentifikasi keragaman genetik dari 14 koleksi plasmanutfah jewawut berkerabat dekat dengan menggunakan 27 marka SSR yang menyebar pada semua kromosom jewawut. Hasil penelitian menunjukkan bahwa koleksi plasmanutfah jewawut berkerabat dekat mengelompok pada klaster yang sama, kecuali pada koleksi aksesi Wete dari Nusa Tenggara Timur (NTT) yang menyebar pada kelompok yang berbeda pada kisaran nilai koefisien kemiripan genetik 0,28 – 0,85 dengan nilai matriks korelasi (r) sebesar 0,954. Koleksi Jewawut yang memiliki koefisien kemiripan genetik yang tinggi (0,85) ditunjukkan pada koleksi ICE-276-11A dengan ICE-276-12A dan yang memiliki koefisien kemiripan terkecil (0,61) ditujukkan pada koleksi 2007-ICE-1335 dan 2007-ICE-1335B. Koleksi jewawut yang berasal dari NTT (Wete Gha Gero Phere dan Wete Wolowea) dan introduksi (2007-ICE-1335B dan 2007-ICE-1335) memiliki tingkat variasi genetik tinggi yang ditunjukkan oleh penyebaran aksesi pada klaster yang berbeda dengan nilai jarak genetik rata-rata yang cukup tinggi terhadap aksesi koleksi. Adanya keragaman yang tinggi memberikan peluang keberhasilan program pemuliaan tanaman jewawut.

Kata kunci: Aksesi introduksi ∙ Jewawut ∙ Nusa Tenggara Timur ∙ Variasi

Abstract

Genetic diversity is very important in plant breeding, thus genetic information is needed in plant breeding activities, especially for selection process. Molecular technology using Simple Sequence Repeat (SSR) marker is widely used for genetic diversity research due to the high accuracy of information and highly polymorphic for closely related species. This study was conducted to identify the genetic diversity of 14 millet germplasms using 27 SSR markers. The results showed that the collection of closely related millet germplasm was grouped in the same cluster, except for the Wete accessions from Nusa Tenggara Timur (NTT) that spread to different groups in the range of the genetic similarity coefficient of 0.28 – 0.85 with a correlation matrix value (r) of 0.954. The millet collections which had a high genetic similarity coefficient (0.85) was shown in ICE-276-11A and ICE-276-12A, while the smallest similarity coefficient (0.61) was shown in 2007-ICE-1335 and 2007-ICE-1335B. The accessions from NTT (Wete Gha Gero Phere and Wete Wolowea) and introduction accesions (2007-ICE-1335B and 2007-ICE-1335) showed a high level of genetic variation as indicated by the spread of accessions in different clusters with sufficient high average genetic distance values against the accession of the collections. A wide diversity of germplasm provided greater opportunity of success for millet breeding.

Keywords: Introduction accession ∙ Foxtail millet ∙ Variation ∙ Nusa Tenggara Timur

Keywords

Aksesi introduksi; Jewawut; Nusa Tenggara Timur; Variasi

Full Text:

PDF (Bahasa Indonesia)

References

Al-Badeiry, N.A., A.H. Al-Saadi, and T.K. Merza. 2014. Analysis of Genetic Diversity in Maize (Zea mays L.) Varieties Using Simple Sequence Repeat (SSR) Markers. Pure & Applied Science, 6, 1768-1774.

Anderson, J.A., G.A. Churchill, J.E. Autrique, S.D. Tanksley, and M.E. Sorrells. 1993. Optimizing parental selection for genetic linkage maps. Genome 36, 181–186.

Benabdelmouna, A., M. Abirached-Darmency and H. Darmency. 2001. Phylogenetic and genomic relationships in Setaria italica and its close relatives based on the molecular diversity and chromosomal organization of 5S and 18S-5.8S-25S rDNA genes. Theor Appl Genet 103, 668–677.

Cholastova, T., M. Soldanoa and R. Pokorny. 2011. Random amplified polymorphic DNA (RAPD) and simple sequence repeats (SSR) marker efficacy for maize hybrid identification. Afr. J. Biotech 10(24: 4794-4801.

CIMMYT. 2004. Protokol untuk Karakterisasi Jagung secara Genotipik menggunakan Marka SSR serta Analisis Data. Metro Manila, Philippines.

Doyle, J.J. and J.L. Doyle. 1990. Isolation of plant DNA from fresh tissue. Focus, v.12, p.13-15.

Ellegren, H. and N. Galtier. 2016. Determinants of genetic diversity. Nature Reviews Genetics, Nature Publishing Group, 17 (7), pp.422 - 433.

George, M.L.C., E. Regalado, W. Li, M. Cao, M. Dahlan, M.B. Pabendon, Warbuton, X. Xianchun, D. Hoisington. 2004. Molecular Characterization of Asians maize inbred lines by multiple laboratories. Theor Appl Genet 109:80- 91.

Ghimire, B.K., C.Y. Yu, S.-H. Kim, I.-M. Chung. 2019. Assessment of Diversity in the Accessions of Setaria italica L. Based on Phytochemical and Morphological Traits and ISSR Markers Molecules 2019, 24, 1486.

Govindaraj, M., M. Vetriventhan, and M. Srinivasan. 2014. Importance of Genetic Diversity Assessment in Crop Plants and Its Recent Advances: An Overview of Its Analytical Perspectives. Hindawi Publishing Corporation Genetics Research International Volume 2015, Article ID 431487, 14 pages.

Gupta, S., K. Kumari, and P.P. Sahu. 2012. Sequence-based novel genomic microsatellite markers for robust genotyping purposes in foxtail millet [Setaria italica (L.) P. Beauv.]. Plant Cell Rep 31, 323–337. https://doi.org/10.1007/ s00299-011-1168-x.

Hoxha, S., M.R. Shariflou, and P. Sharp. 2004. Evaluation of genetic diversity in Albanian Maize using SSR markers. Journal Maydica 49:97-103.

Kellogg, E.A., S.S. Aliscioni, O. Morrone, J. Pensiero, and F. Zuloaga. 2009. A phylogeny of Setaria (Poaceae, Panicoideae, Paniceae) and related genera based on the chloroplast gene ndhF. International Journal of Plant Sciences, 170(1), 117-131.

Kumari R., N. Dikshit, D. Sharma, and K.V. Bhat. 2011. Analysis of molecular genetic diversity in a representative collection of foxtail millet [Setaria italica (L.) P. Beauv.] from different agro-ecological regions of India. Physiol. Mol. Biol. Plants 17(4):363–374.

Lin, H.S., C.Y. Chiang, S.B. Chang, G.I. Liao, and C.S.S. Kuoh. 2012. Genetic Diversity in The Foxtail Millet (setaria italica) germplashas determined by agronomic traits and microsatellite markers. Australian Journal of Crop Science (AJCS) 6 (2) 342-349.

Mulsanti, W. Indria, M. Surahman, S. Wahyuni, dan D.W. Utami. 2013. Identifikasi galur tetua padi hibrida dengan marka SSR spesifik dan pemanfaatannya dalam uji kemurnian benih. Jurnal Penelitian Pertanian Tanaman Pangan. 32 (1): 1- 8

Nirmalakumari, A. and M. Vetriventhan. 2010. Characterization of foxtail millet plasmanutfah collections for yield contributing traits. Electronic Journal of Plant Breeding , 1(2): 140-147

Ramanatha, R.V. and T. Hodgkin. 2002. Genetic diversity and conservation and utilization of plant genetic resources. Plant Cell, Tissue and Organ Culture 68: 1–19. Kluwer Academic Publishers. Netherlands.

Randall, A., Y. Yuwariah, A. Nuraini, T. Nurmala, A.W. Irwan, dan W.A. Qosim. 2016. Karakterisasi dan kekerabatan 23 genotip Jawawut (Setaria italic L. Beauv) yang ditanam tumpangsari dengan ubi jalar berdasarkan karakter agromorfologi. Pangan, Vol. 25 No. 1 April 2016 : 21 - 32

Rini, D.W. 2018. Potensi aksesi lokal jewawut (setaria italica (l.) p. beauv) sebagai pangan alternatif di lahan kering pulau sumba ntt. Seminar Nasional Pendidikan Biologi dan Saintek III. ISSN: 2527–533x :558-564.

Rohlf, F.J. 2000. NTSYSpc Numerical Taxonomy and Multivariate Analysis System Version 2.1. Applied Biostatistics Inc.

Sharma, N. and K. Niranjan. 2018. Foxtail millet: Properties, processing, health benefits, and uses, Food Reviews International, 34:4, 329-363.

Vetriventhan, M., H.D. Upadhyaya, C.R. Anandakumar, S. Senthilvel, H.K. Parzies, A. Bharathi, R.K. Varshney, and C.L.L. Gowda. 2012. Assessing genetic diversity, allelic richness and genetic relationship among races in ICRISAT foxtail millet core collection Plant Genetic Resources: Characterization and Utilization, 10(3); 214–223.

DOI: https://doi.org/10.24198/kultivasi.v20i3.34843