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AFLP-Based Analysis of Genetic Diversity, Population Structure, and Relationships with Agronomic Traits in Rice Germplasm from North Region of Iran and World Core Germplasm Set

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Abstract

Analysis of the genetic diversity and population structure of crops is very important for use in breeding programs and for genetic resources conservation. We analyzed the genetic diversity and population structure of 47 rice genotypes from diverse origins using amplified fragment length polymorphism (AFLP) markers and morphological characters. The 47 genotypes, which were composed of four populations: Iranian native varieties, Iranian improved varieties, International Rice Research Institute (IRRI) rice varieties, and world rice collections, were analyzed using ten primer combinations. A total of 221 scorable bands were produced with an average of 22.1 alleles per pair of primers, of which 120 (54.30%) were polymorphic. The polymorphism information content (PIC) values varied from 0.32 to 0.41 with an average of 0.35. The high percentage of polymorphic bands (%PB) was found to be 64.71 and the resolving power (R p) collections were 63.36. UPGMA clustering based on numerical data from AFLP patterns clustered all 47 genotypes into three large groups. The genetic similarity between individuals ranged from 0.54 to 0.94 with an average of 0.74. Population genetic tree showed that Iranian native cultivars formed far distant cluster from the other populations, which may indicate that these varieties had minimal genetic change over time. Analysis of molecular variance (AMOVA) revealed that the largest proportion of the variation (84%) to be within populations showing the inbreeding nature of rice. Therefore, Iranian native varieties (landraces) may have unique genes, which can be used for future breeding programs and there is a need to conserve this unique diversity. Furthermore, crossing of Iranian genotypes with the genetically distant genotypes in the other three populations may result in useful combinations, which can be used as varieties and/or lines for future rice breeding programs.

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Acknowledgments

We thank Shahid Chamran University of Ahwaz, Iran and the Rice Research foundation, Rasht, Iran. The authors would like to thank Mohammad Bagher Mahdieh Najafabadi for his help during phenotypic measurements.

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Authors and Affiliations

  1. Department of Agronomy and Plant Breeding, Faculty of Agriculture, Shahid Chamran University of Ahvaz, P. O. Box 61355/144, Ahvaz, Iran

    Karim Sorkheh

  2. Department of Agronomy and Biotechnology, Faculty of Agriculture, University of Guilan, P.O. Box 41635/3988, Rasht, Iran

    Mohammad Masaeli

  3. Rice Research Institute of Iran, P. O. Box 1658, Rasht, Iran

    Maryam Hosseini Chaleshtori

  4. Melkassa Agricultural Research Center, P.O. Box 1085, Adama, Ethiopia

    Asfaw Adugna

  5. Department of Horticulture, Agricultural Faculty, Ataturk University, 25240, Erzurum, Turkey

    Sezai Ercisli

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  1. Karim Sorkheh
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Sorkheh, K., Masaeli, M., Chaleshtori, M.H. et al. AFLP-Based Analysis of Genetic Diversity, Population Structure, and Relationships with Agronomic Traits in Rice Germplasm from North Region of Iran and World Core Germplasm Set. Biochem Genet 54, 177–193 (2016). https://doi.org/10.1007/s10528-016-9711-7

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