Genetic Diversity Analysis of 53 Indonesian Rice Genotypes using 6K Single Nucleotide Polymorphism Markers
Abstract
Indonesia is rich in rice genetic resources, however, only a small number has been used in variety improvement programs. This study aimed to determine the genetic diversity of Indonesian rice varieties using 6K SNP markers. The study was conducted at ICABIOGRAD for DNA isolation and IRRI for SNP marker analysis. Genetic materials were 53 rice genotypes consisting of 49 varieties and 4 check genotypes. SNP markers used were 6K loci. Results showed that among the markers analyzed, only 4,606 SNPs (76.77%) were successfully read. The SNP markers covered all twelve rice chromosomes of 945,178.27 bp. The most common allele observed was GG, whereas the least allele was TG. Dendrograms of the 53 rice varieties analyzed with 4,606 SNPs demonstrated several small groups containing genotypic mixtures between indica and japonica rice, and no groups were found to contain firmly indica or japonica type. Structure analysis (K = 2) with value of 0.8 showed that the 53 rice varieties were divided into several groups and each group consisted of 4 japonica, 2 tropical japonica, 46 indica, and 1 aus rice type, respectively. IR64 and Ciherang proved to have an indica genome, while Rojolele has japonica one. Dupa and Hawara Bunar, usually grouped into tropical japonica rice, were classified as indica type, and Hawara Bunar has perfectly 100% indica type. The results of this study indicated that rice classification (indica-japonica) which is usually classified based only on morphological characters, e.g. grain and leaf shapes, is not enough and classification based on SNP markers should be considered for that purpose.
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Botstein, D., White, R.L., Skolnick, M., Davis, R.W. (1980)
Construction of a genetic linkage map in man using
restriction fragment length polymorphisms. American
Journal of Human Genetics, 32 (3), 314–331.
Chen, H., He, H., Zou, Y., Chen, W., Yu, R., Liu, X., Yang,
Y., Gao, Y.M., Xu, J.L., Fan, L.M., Li, Y., Li, Z.K. &
Deng, X.W. (2011) Development and application of a
set of breeder-friendly SNP markers for genetic
analyses and molecular breeding of rice (Oryza sativa
L.). Theoretical and Applied Genetics, 123 (6), 869–
Chen, H., Xie, W., He, H., Yu, H., Chen, W., Li, J., Yu., R.,
Yao, Y., Zhang, W., He, Y., Tang, X., Zhou, F., Deng,
X.W. & Zhang, Q. (2014) A high-density SNP
genotyping array for rice biology and molecular
breeding. Molecular Plant, 7 (3), 541–553.
Dellaporta, S.L., Wood, J. & Hicks, J.B. (1983) A plant DNA
minipreparation: Version II. Plant Molecular Biology
Reporter, 1 (4), 19–21.
Gamuyao, R., Chin, J.H., Pariasca-Tanaka, J., Pesaresi, P.,
Catausan, S., Dalid, C., Loedin, I.S., Mendoza, E.M.T.,
Wissuwa, M. & Heuer, S. (2012) The protein kinase
Pstol1 from traditional rice confers tolerance of
phosphorus deficiency. Nature, 488, 535–539.
Ge, S., Oliveira, G.C.X., Schaal, B.A., Gao, L.Z. & Hong,
D.Y. (1999) RAPD variation within and between natural
populations of the wild rice Oryza rufipogon from China
and Brazil. Heredity, 82, 638–644.
Gonzaga, Z.J., Aslam, K., Septiningsih, E.M. & Collard
B.C.Y. (2015) Evaluation of SSR and SNP markers for
molecular breeding in rice. Plant Breeding and
Biotechnology, 3 (2), 139–152.
Hairmansis, A., Aswidinnoor, H., Trikoesoemaningtyas &
Suwarno (2005) Evaluasi daya pemulih kesuburan
padi lokal dari kelompok tropical japonica. Buletin
Agronomi, 33 (3), 1–6.
Hu, W., Wen, M., Han, Z., Tan, C. & Xing, Y. (2013)
Scanning QTLs for grain shape using a whole genome
SNP array in rice. Journal of Plant Biochemistry and
Physiology, 1 (1), 1–5.
IRRI (2017) The International Rice Genebank. [Online]
Available from: http://irri.org/our-work/research/geneticdiversity/
international-rice-genebank [Accessed 25
October 2017].
IRRI Genotyping Services Laboratory (2017) 7k Infinium
SNP genotyping. [Online] Available from:
http://gsl.irri.org/genotyping/infinium-7k [Accessed 25
October 2017].
Jeong, I.S., Yoon, U.H., Lee, G.S., Ji, H.S., Lee, H.J., Han,
C.D., Hahn, J.H., An, G. & Kim, T.H. (2013) SNPbased
analysis of genetic diversity in anther-derived
rice by whole genome sequencing. Rice, 6 (6), 1–12.
doi: 10.1186/1939-8433-6-6.
Kim, C.K., Yoon, U.H., Lee, G.S., Lee, H.K., Kim, Y.H. &
Hahn, J.H. (2009) Rice genetic marker database: An
identification of single nucleotide polymorphism (SNP)
and quantitative trait loci (QTL) markers. African
Journal of Biotechnology, 8 (13), 2963–2967.
Kim, S.I. & Tai, T.H. (2013) Identification of SNPs in closely
related temperate japonica rice cultivars using
restriction enzyme-phased sequencing. PLoS One, 8
(3), e60176. doi: 10.1371/journal.pone.0060176.
Lestari, P., Utami, D.W., Rosdianti, I. & Sabran, M. (2016)
Morphological variability of Indonesian rice germplasm
and the associated SNP markers. Emirates Journal of
Food and Agriculture, 28 (9), 660–670.
Liu, K. & Muse, S.V. (2005) PowerMarker: An integrated
analysis environment for genetic maker analysis.
Bioinformatics, 21 (9), 2128–2129.
Mammadov, J., Aggarwal, R., Buyyarapu, R. & Kumpatla, S.
(2012) SNP markers and their impact on plant
breeding. International Journal of Plant Genomics,
doi: 10.1155/2012/728398.
Masuduzzaman, A., Haque, M., Ahmed, M.M.E. &
Mohapatra, C.K. (2016) SSR marker-based genetic
diversity analysis of tidal and flood prone areas in rice
(Oryza sativa L.). Journal of Biotechnology and
Biomaterials, 6 (3), 1–9. doi: 10.4172/2155-
X.1000241.
McCouch, S.R., Zhao, K., Wright, M., Tung, C.W., Ebana,
K., Thomson, M., Reynolds, A., Wang, D., DeClerck,
G., Ali, Md.L., McClung, A., Eizenga, G. & Bustamante,
C. (2010) Development of genome-wide SNP assays
for rice. Breeding Science, 60 (5), 524–535.
McNally, K.L., Childs, K.L., Bohnert, R., Davidson, R.M.,
Zhao, K., Ulat, V.J., Zeller, G., Clark, R.M., Hoen, D.R.,
Bureau, T.E., Stokowski, R., Ballinger, D.G., Frazer,
K.A., Cox, D.R., Padhukasahasram, B., Bustamante,
C.D., Weigel, D., Mackill, D.J., Bruskiewich, R.M.,
Rätsch, G., Buell, C.R., Leung, H. & Leach, J.E. (2009)
Genome-wide SNP variation reveals relationships
among landraces and modern varieties of rice.
Proceedings of the National Academy of Sciences, 106
(30), 12273–12278.
Milne, I., Shaw, P., Stephen, G., Bayer, M., Cardle, L.,
Thomas, W.T.B., Flavell, A.J. & Marshall, D. (2010)
Flapjack–graphical genotype visualization.
Bioinformatics, 26 (24), 3133–3134.
Nei, M., Tajima, F. & Tateno, Y. (1983) Accuracy of
estimated phylogenetic trees from molecular data. II.
Gene frequency data. Journal of Molecular Evolution,
(2), 153–170.
Parida, S.K., Mukerji, M., Singh, A.K, Singh, N.K. &
Mohapatra, T. (2012) SNPs in stress-responsive rice
genes: Validation, genotyping, functional relevance,
and population structure. BMC Genomics, 13, 426. doi:
1186/1471-2164-13-426.
Prasetiyono, J. & Hidayatun, N. (2017) Keragaman genetik
padi lokal Indonesia toleran keracunan aluminium
menggunakan marka Single Nucleotide Polymorphism.
Dalam: Rosmaina, Isnaini, Fitmawati, Hidayati & Isda,
M.N. (editor) Strategi Pemuliaan dalam Mengantisipasi
Perubahan Iklim Global. Prosiding Seminar Nasional
Perhimpunan Ilmu Pemuliaan Indonesia (Peripi),
Pekanbaru, 20 Juli 2016. hlm. 417−424.
Romdon, A.S., Kurniyati, E., Bahri, S. & Pramono, J. (2014)
Kumpulan deskripsi varietas padi. Jawa Tengah, Balai
Pengkajian Teknologi Jawa Tengah.
Salgotra, R.K., Gupta, B.B., Bhat, J.A. & Sharma, S. (2015)
Genetic diversity and population structure of basmati
rice (Oryza sativa L.) Germplasm collected from North
Western Himalayas using trait linked SSR markers.
PLoS One, 10 (7), e0131858. doi:
1371/journal.pone.0131858.
Singh, N., Choudhury, D.R., Singh, A.K., Kumar, S.,
Srinivasan, K., Tyagi, R.K., Singh, N.K. & Singh, R.
(2013) Comparison of SSR and SNP markers in
estimation of genetic diversity and population structure
of Indian rice varieties. PLoS One, 8 (12), e84136. doi:
1371/journal.pone.0084136.
Singh, N., Jayaswal, P.K., Panda, K., Mandal, P., Kumar,
V., Singh, B., Mishra, S., Singh, Y., Singh, R., Rai, V.,
Gupta, A., Sharma, T.R. & Singh, N.K. (2015) Singlecopy
gene based 50K SNP chip for genetic studies
and molecular breeding in rice. Scientific Reports, 5,
doi: 10.1038/srep11600.
Stanford University (2012) Structure 2.3.4. [Online]
Available from: https:// web.stanford.edu/group/
pritchardlab/structure_software/release_versions/v2.3.
/html/structure.html [Accessed 5 October 2014].
Tasliah, Prasetiyono, J., Dadang, A., Bustamam, M. &
Moeljopawiro, S. (2011) Studi agronomis dan
molekuler padi umur genjah dan sedang. Berita
Biologi, 10 (5), 663–673.
Tasma, I.M. (2014) Single Nucleotide Polymorphism (SNP)
sebagai marka DNA masa depan. Warta , 10
(3), 7–10.
Utami, D.W. & Hanarida, I. (2014) Evaluasi lapang dan
identifikasi molekuler plasma nutfah padi terhadap
keracunan Fe. Jurnal AgroBiogen, 10 (1), 9−17.
Utami, D.W., Rosdianti, I., Lestari, P., Satyawan, D.,
Rijzaani, H. & Tasma, I.M. (2013) Development and
application of 1536-plex single nucleotide
polymorphism marker chip for genome-wide scanning
of Indonesian rice germplasm. Indonesian Journal of
Agricultural Science, 14 (2), 71–78.
Wahab, M.I., Satoto, Rachmat, R., Guswara, A. & Suharno
(2017) Deskripsi varietas unggul baru padi. Jakarta,
Badan Penelitian dan Pengembangan .
Wang, L., Hao, L., Li, X., Hu, S., Ge, S. & Yu, J. (2009) SNP
deserts of Asian cultivated rice: Genomic regions
under domestication. Journal of Evolutionary Biology,
(4), 751–761.
Yu, H., Xie, W., Li, J., Zhou, F. & Zhang, Q. (2014) A wholegenome
SNP array (RICE6K) for genomic breeding in
rice. Plant Biotechnology Journal, 12 (1), 28–37.
Zhang, P., Li, J., Li, X., Liu, X., Zhao, X. & Lu, Y. (2011)
Population structure and genetic diversity in a rice core
collection (Oryza sativa L.) investigated with SSR
markers. PLoS One, 6 (12), e27565. doi:
1371/journal.pone.0027565
DOI: http://dx.doi.org/10.21082/jbio.v14n1.2018.p1-10
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