Abstract
For breeding of salinity tolerant rice, halophytic species Oryza coarctata is considered as a valuable resource. Non-availability of molecular markers in the species is a major limitation and identification of markers applicable with wider gene pool will be resource-saving. Even after the recent advancement in high throughput genoty** techniques, sequence-tagged microsatellite sites (STMS) markers are considered as valuable resource for pre-breeding, especially when usable for a large number of species. Using a novel bioinformatics pipeline for cross transferable marker identification, whole genome sequences of nine Oryza species were surveyed with 23,499 STMS markers of rice. With this highly reproducible strategy, band sizes or polymorphism prediction among different species is possible before in-vitro validation. Only 359 STMS markers were cross-transferable to O. coarctata and 77 of those were common with O. sativa complex. These core markers were distributed over 11 chromosomes and nearly 76% were located within various genes of Oryza. The markers also showed unique genome specific polymorphism pattern with high levels of inter- and intraspecific variations in “AA” genome and complete absence of intra- or inter-population variations in O. coarctata (KKLL). The numbers of microsatellite motifs and the repeat numbers in different motifs were much lesser in O. coarctata leading to the exceptionally high level of polymorphism with all “AA” genome species. Two markers are also useful for species identification. The hyper-variable markers are effective resource for pre-breeding of O. sativa, O. glaberrima and new rice for Africa involving O. coarctata or any other species of O. sativa complex.
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Acknowledgements
The authors acknowledge the support of International Rice Research Institute, Philippines and Punjab Agriculture University, India for providing the germplasm of seven species used in the study. We are grateful to the teams of International Oryza Map Alignment Project, International Rice Genome Sequencing Project, Bei**g Genomics Institute and the Gramene database for making the Oryza genomic resources and analysis tools accessible for advancing research on individual loci. The academic and administrative support from the Director General, ICAR and Director, ICAR-National Rice Research Institute, Cuttack to the entire team and the Vice Chancellor of Utkal University, Bhubaneswar to the first author is also gratefully acknowledged.
Funding
This study was financially supported by institutional funding for Project 1.3 (2017–20) of ICAR-National Rice Research Institute. The University Grants Commission, Government of India supported the first author through Rajiv Gandhi National Fellowship for her Doctoral studies and the paper will be a part of her Ph.D. thesis.
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DD carried out the in-vitro validation; MC conceptualized and designed the experiments, arranged resources, analysed data and prepared draft manuscript; TKM, SR, D and JV carried out the Bioinformatics analyses; MKK and CP supervised the work; KC and KRC conducted salinity screening; DRP, LKB, SKD, BCP and BCM collected, imported and maintaining the germplasm used in the study; SS and MB provided support in wet lab works and preparation of tables and figures; TKM, SR, KC, SS and KRC critically reviewed the data and manuscript; DD, MC, TKM and SR made equal contribution for the work. All authors read and approved the final manuscript.
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Dalai, D., Chakraborti, M., Mondal, T.K. et al. The core set of sequence-tagged microsatellite sites markers between halophytic wild rice Oryza coarctata and Oryza sativa complex. Euphytica 217, 57 (2021). https://doi.org/10.1007/s10681-021-02790-3
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DOI: https://doi.org/10.1007/s10681-021-02790-3