African Journal of
Agricultural Research

  • Abbreviation: Afr. J. Agric. Res.
  • Language: English
  • ISSN: 1991-637X
  • DOI: 10.5897/AJAR
  • Start Year: 2006
  • Published Articles: 6091

Full Length Research Paper

Genetic diversity of rice (Oryza sativa L.) accessions collected from Sudan and IRRI using SSR markers

Seif Gasim
  • Seif Gasim
  • Department of Agronomy, Faculty of Agriculture, University of Khartoum, Postal code 13314 Shambat, Sudan.
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Ishraka Abuanja
  • Ishraka Abuanja
  • Department of Agronomy, Faculty of Agriculture, Upper Nile University, Malakal, South Sudan.
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Abdel-Wahab Abdalla
  • Abdel-Wahab Abdalla
  • Department of Agronomy, Faculty of Agriculture, University of Khartoum, Postal code 13314 Shambat, Sudan.
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  •  Received: 18 September 2018
  •  Accepted: 05 December 2018
  •  Published: 17 January 2019

Abstract

The assessment of genetic diversity of the traditional rice varieties or landraces is an essential component in germplasm characterization and conservation to identify potential parents. In the present study SSR markers (588 SSR markers) were used for the assessment of genetic diversity and relatedness among 31 rice accessions. These included 18 accessions from Sudan and 13 from IRRI. Among the SSR markers used only 483 generated polymorphic patterns, and showed 1274 alleles. The number of alleles per locus ranged from 2 (about 214 markers) to 5 (RM16820 and AP3206a) with an average of 2.64 alleles per locus. The polymorphic information content (PIC) values ranged from 0.06 (RM3138, RM10671, SKC3, R1M7, R6M30, S07101 and S12041B) to 0.69 (RM7643), with an average of 0.39. The major allele frequency per locus varied from 32% (RM7643) to 97% (RM3138, RM10671, SKC3, R1M7, R6M30, S07101 and S12041B), with an average of 64%. Among the primers used in the present investigation, RM7643 was highly informative as it recorded the highest PIC value (0.69). The UPGMA resulted in allelic richness of four major clusters in which cluster I is composed of a high number of accessions. The pairwise genetic dissimilarity indices revealed the highest genetic dissimilarity of 62.3% between Pipanfary Red1 and FL478. The lowest genetic dissimilarity was found between NBGS3 and NBGS2 (4.1%), but they showed wide dissimilarity with other accessions. The study highlighted the usefulness of the application markers for efficient characterization of the Sudanese rice accessions.

Key words: Rice accessions, genetic diversity, SSR markers, polymorphism.