Identification and characterization of microsatellites in ESTs of Rosa species: Insight in development of SSR markers

SAPNA PANWAR; KANWAR PAL SINGH; NAMITA NAMITA; HUMIRA SONAH; RUPESH K DESHMUKH; T R SHARMA

doi:10.56093/ijas.v85i3.47189

Authors

SAPNA PANWAR Scientist, Indian Agricultural Research Institute, New Delhi 110 012
KANWAR PAL SINGH Principal Scientist, Indian Agricultural Research Institute, New Delhi 110 012
NAMITA NAMITA Scientist, Indian Agricultural Research Institute, New Delhi 110 012
HUMIRA SONAH Research Associate,Â Indian Agricultural Research Institute, New Delhi 110 012
RUPESH K DESHMUKH Research Associate, Indian Agricultural Research Institute, New Delhi 110 012
T R SHARMA Director, National Research Centre on Plant Biotechnology, IARI, New Delhi 110 012

https://doi.org/10.56093/ijas.v85i3.47189

Keywords:

Expressed Sequence Tags (ESTs), Markers, Microsatellites, Rosa species, SSR

Abstract

The present investigations were undertaken during the year 2012. In this study, analysis of microsatellites identified in expressed sequence tags (ESTs) of Rosa species was performed. Entire set of ESTs for genus Rosa including 1 792 of Rosa chinensis, 5 495 of R.× hybrida and 1 849 of R. lucieae was retrieved from public database and assembled individually. Furthermore, 668 microsatellites (SSR) were identified in the 5 272 assembled ESTs in which di-nucleotide repeats were most frequent. The highest 55.2 percentage of di-nucleotide was identified in R. chinensis followed by R.× hybrida (50.1%) and R. lucieae (44.3%). Repeats with motif sequences AG/CT and AAG/CTT were observed as most frequent motifs. Moreover, SSRs were also identified in non-EST sequences available for the genus Rosa. The entire sequences were assembled together to develop non-redundant data that was subsequently used to design 293 SSR markers. Analysis of microsatellite and resource of SSR markers developed in present study will help for undertaking the molecular research in Rosa species.

Downloads

Download data is not yet available.

References

Benemann D P, Machado L N, Arge L W P , Bianchi V J, Oliveira A C, Maia L C and Peters J A. 2012. Identification, characterization and validation of SSR markers from the gerbera EST database. Plant Omics Journal 5(2):159–66. DOI: https://doi.org/10.5539/jas.v5n5p35

Bhati J, Sonah H, Jhang T, Singh N K and Sharma T R. 2010. Comparative analysis and EST mining reveals high degree of conservation among five Brassicaceae species. Comparative and Functional Genomics: 5202–38. DOI: https://doi.org/10.1155/2010/520238

Buckler E S and Thornsberry J M. 2002. Plant molecular diversity and applications to genomics. Current Opinion in Plant Biology 5(2): 107–11. DOI: https://doi.org/10.1016/S1369-5266(02)00238-8

Channamallikarjuna V, Sonah H, Prasad M, Rao G J N, Chand S, Upreti H C, Singh N K and Sharma T R. 2010. Identification of major quantitative trait loci qSBR11-1 for sheath blight resistance in rice. Molecular Breeding 25:155–66. DOI: https://doi.org/10.1007/s11032-009-9316-5

Deshmukh R K, Singh A, Jain N, Anand S, Gacche R N, Singh A K, Gaikawad K, Sharma T R, Mohapatra T and Singh N K. 2010. Identification of candidate genes for grain number in rice (Oryza sativa L.). Functional and Integrative Genomics 10: 339–47. DOI: https://doi.org/10.1007/s10142-010-0167-2

Ellis J R and Burke J M. 2007. EST-SSRs as a resource for population genetic analyses. Heredity 99: 125–32. DOI: https://doi.org/10.1038/sj.hdy.6801001

Foote M. 1997. The evolution of morphological diversity. Annual Review of Ecology and Systematics 28: 129–52. DOI: https://doi.org/10.1146/annurev.ecolsys.28.1.129

Gudin S. 2010. Rose: Genetics and breeding. Plant Breeding Reviews. Janick J (Ed). John Wiley and Sons, Inc., Oxford, UK.

Kashyap P, Singh A K, Singh S K and Deshmukh R. 2010. Genetic diversity analysis of indigenous and exotic apple genotypes using inter simple sequence repeat markers. Indian Journal of Horticulture 67:15–20.

Kulkarni K P, Kulkarni S S, Gedda M, Bandevar M, Sonah H, Gacche R N, Deshmukh N K and Deshmukh R K. 2012. Insilico identification of rice gene homologues in brachypodium, sorghum and maize: insight into development of gene specific markers. Webmed Central Bioinformatics 3(4): Wmc003258.

McCouch S R, Chen X, Panaud O, Temnykh S, Xu Y, Cho Y G, Huang N, Ishii T and Blair M. 1997. Microsatellite marker development, mapping and applications in rice genetics and breeding. Plant Molecular Biology 35(1-2): 89–99. DOI: https://doi.org/10.1023/A:1005711431474

Namita, Singh K P, Bharadwaj C, Sharma T R, Sonah H, Raju D V S and Deshmukh R K. 2011. Gene action and combining ability analysis for flower yield and its component traits in interspecific hybrids of marigold (Tagetes spp.). Indian Journal of Agricultural Sciences 81(9): 807–11.

Nybom H. 2004. Comparison of different nuclear DNA markers for estimating intraspecific genetic diversity in plants. Molecular Ecology 13(5):1 143–55. DOI: https://doi.org/10.1111/j.1365-294X.2004.02141.x

Panwar S, Singh K P, Namita and Sonah H. 2010. Genetic divergence analysis in rose (Rosa×hybrida) using morphological markers. Journal of Ornamental Horticulture 13: 122–6.

Rout G R, Samantaray S, Mottley J and Das P. 1999. Biotechnology of the rose: A review of recent progress. Scientia Horticulturae 81: 201–28. DOI: https://doi.org/10.1016/S0304-4238(99)00025-4

Sharma J, Singh A, Pallavi J K, Sonah H and Gupta P. 2010. Assessment of genetic relationship among bread wheat (Triticum aestivum L. em. Thell.) genotypes using microsatellite markers. International Journal of Applied Agricultural Research 5: 575–82.

Shirasawa K, Ishii, K, Kim C, Ban T, Suzuki M, Ito T, Muranaka T, Kobayashi, M, Nagata N, Isobe S and Tabata S. 2013. Development of capsicum EST–SSR markers for species identification and in silico mapping onto the tomato genome sequence. Molecular Breeding 31:101–10. DOI: https://doi.org/10.1007/s11032-012-9774-z

Sonah H, Deshmukh R K, Sharma A, Singh V P, Gupta D K, Gacche R, Rana J C, Singh N K and Sharma T R. 2011. Genome-wide distribution and organization of microsatellite in plants: An insight of microsatellite based marker development in Brachypodium. PLoSONE 6(6): e21298. DOI: https://doi.org/10.1371/journal.pone.0021298

Sonah H, Deshmukh R K, Singh V P, Gupta D K, Singh N K and Sharma T R. 2011b. Genomic resources in horticultural crops: Status, utility and challenges. Biotechnology Advances 29:199– 209. DOI: https://doi.org/10.1016/j.biotechadv.2010.11.002

Tripathi K P, Roy S, Khan F, Shasany A K, Sharma A and Khanuja S P S. 2008. Identification of SSR-ESTs corresponding to alkaloid, phenylpropanoid and terpenoid biosynthesis in MAPs. Online Journal Bioinforma 9:78–91.

Yu H and Li Q. 2008. Exploiting EST databases for the development and characterization of EST–SSRs in the pacific oyster (Crassostrea gigas). Journal of Heredity 99(2): 208–14. DOI: https://doi.org/10.1093/jhered/esm124

Zhang M , Fan L, Liu Q, Song Y, Wei S, Zhang Sand Wu J. 2014. A novel set of EST-derived SSR markers for pear and crossspecies transferability in Rosaceae. Plant Molecular Biology Reporter 32: 290–302. DOI: https://doi.org/10.1007/s11105-013-0638-4

Zhu Y, Queller D C and Strassmann J E. 2000. A phylogenetic perspective on sequence evolution in microsatellite loci. Journal of Molecular Evolution 50(4): 324–38. DOI: https://doi.org/10.1007/s002399910036