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DNA marker based diversity across rice genotypes and advanced breeding lines bred for temperate regions of North-West India

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Abstract

Background

Characterization and evaluation of plant genetic resources play an important role for their utilization in the crop improvement programmes.

Methods and results

This study involves the agro-morphological and cooking quality besides, molecular characterization of 51 genotypes/advance breeding lines of rice from Kashmir Himalayas. Significant variability was observed for all agro-morphological and cooking quality traits among all the studied genotypes. Cluster analysis using UPGMA method divided the genotypes into two major clusters having 15 and 36 genotypes. Thirty eight genotypes screened using 24 SSR markers detected 48 alleles with 2.0 alleles for each locus with average polymorphism information content (PIC) of 0.37. High polymorphism information content (PIC) values was observed for the primers RM263 (0.67), RM159 (0.59) and RM333 (0.50). Furthermore, out of 38 SSR markers screened on 192 temperate rice germpalsm lines, R4M17 accurately differentiated indica and temperate japonica genotypes amplifying 220 bp and 169 bp, respectively. Accordingly, 15 genotypes were reported as indica and 28 temperate japonica in addition to 149 genotypes as intermediate types.

Conclusion

The information on marker-based diversity and performance based on cooking quality and agronomic traits helped to select the most divergent lines for crossing. Also the analysis was useful to classify the temperate germplasm into indica and temperate japonica. The classification could be helpful to devise a strategy for inter-sub species hybridization to breed for improved rice varieties.

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Acknowledgements

The authors acknowledge the Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, (SKUAST-K) Wadura Agriculture College and Mountain Research Centre for Field Crops (MRCFC) Khudwani Anantnag for letting us work in their labs and providing matrial for the study.

Funding

No funds/grants was received for conducting this study.

Author information

Authors and Affiliations

  1. Division of Genetics and Plant Breeding, Faculty of Agriculture, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Wadura, J&K, 193201, India

    Nakeeb-Un-Nisa, Reyaz R. Mir, M. Ashraf Bhat, Sofora Jan & Sumira Rafiqee

  2. Mountain Research Centre for Field Crops, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Khudwani, J&K, 192101, India

    Najeebul Rehman Sofi, Asif B. Shikari, Gazala H. Khan & Shabir H. Wani

  3. Mountain Crop Research Station, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Sagam, J&K, 192202, India

    Showkat A. Waza

  4. Division of Plant Biotechnology, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, (SKUAST-K), Shalimar, J&K, 190025, India

    Aafreen Sakina

Authors
  1. Nakeeb-Un-Nisa
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  2. Aafreen Sakina
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  3. Najeebul Rehman Sofi
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  4. Asif B. Shikari
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  10. Gazala H. Khan
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  11. Shabir H. Wani
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Contributions

NRS and ABS conceived the experiment. Nakeeb-Un-Nisa, SJ, RRM and NRS conducted the DNA marker analysis for estimation of genetic diversity. AS, GHK and ABS carried molecular marker work on indica-japonica differentiation. Materials were maintained by NRS and morphological data was generated by Nakeeb-Un-Nisa, SR and SHW. Analysis was carried out by Nakeeb-Un-Nisa, ABS, RRM and SAW.

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Correspondence to Najeebul Rehman Sofi.

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Nakeeb-Un-Nisa, Sakina, A., Sofi, N.R. et al. DNA marker based diversity across rice genotypes and advanced breeding lines bred for temperate regions of North-West India. Mol Biol Rep 49, 7145–7155 (2022). https://doi.org/10.1007/s11033-022-07609-5

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