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Genetic Diversity and Population Structure Analysis of Apple (Malus × domestica Borkh.) Germplasm Collected from North Kashmir, India, Using SSR Markers

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Abstract

Detailed characterization and documentation of apple genetic resources are crucial for genetic amelioration and germplasm management. This study was carried out to fill the missing gap in information on the genetic diversity of cultivated apple (Malus × domestica Borkh.) germplasm maintained in different orchards and fruit nurseries in different areas of the North Kashmir region. In this study, 62 genotypes collected from the North Kashmir region were screened using ten microsatellite markers. Allelic data were used to elucidate the population structure, genetic relationships, and molecular variance to define the genetic structure of the collection of diverse apple genotypes. A total of 77 alleles were amplified with an average polymorphism percentage of 87.5%, polymorphic information content (PIC) of 0.71, and resolving power (RP) of 3.58. The average genetic diversity indices observed for number of alleles (Na) = 1.67, effective number of alleles (Ne) = 1.47, Shannon’s information index (I) = 0.43, expected heterozygosity (Ho) = 0.29, and unbiased heterozygosity (µ He) = 0.3 per assay indicated a moderate level of genetic diversity. Based on Jaccardʼs similarity coefficient, a UPGMA dendrogram, and principal coordinate analysis, a widespread dispersal of genotypes into three sub-clusters showing a high degree of genetic variability within the groups was obtained. STRUCTURE analysis divided the collection into two (K = 2) sub-populations that were more or less grouped on the basis of traditionally cultivated and recently introduced genotypes mixed with a few indigenous genotypes. Analysis of molecular variance (AMOVA) showed significant variation within the populations (81%), indicating that the genotypes were the primary source of wide variation and that there was a limited genetic exchange between the genotypes, which aligns with the findings of the cluster analysis. The apple germplasm analyzed in the North Kashmir region represents an important source of genetic diversity, which can contribute significantly to germplasm management and future apple breeding programs both inside and outside the region.

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Acknowledgements

Zahid Hussain acknowledges financial support from the University Grants Commission, New Delhi, India for providing a teacher fellowship to carry out the study as a part of PhD study under Letter No. 27-14 (TF)/2016 (NRCB dated 3 February 2017). The authors would like to thank the Director Horticulture Kashmir Division and various orchardists for their necessary permission and support during field surveys and collection of samples needed for the study.

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  1. Cytogenetics and Molecular Biology Laboratory, Department of Botany, University of Kashmir, 190006, Srinagar, Jammu and Kashmir, India

    Zahid Hussain Najar, Showkat A. Zargar, Mahpara Kashtwari & Aijaz A. Wani

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  1. Zahid Hussain Najar
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Correspondence to Zahid Hussain Najar.

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Z.H. Najar, S.A. Zargar, M. Kashtwari and A.A. Wani declare that they have no competing interests.

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10341_2023_974_MOESM1_ESM.docx

Supplementary Table S1: List of SSR Primers used for the genetic diversity analysis of 62 apple genotypes. Supplementary Table S2: Table S2: Assignment of individuals to the sub populations (K) based on probability.

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Najar, Z.H., Zargar, S.A., Kashtwari, M. et al. Genetic Diversity and Population Structure Analysis of Apple (Malus × domestica Borkh.) Germplasm Collected from North Kashmir, India, Using SSR Markers. Erwerbs-Obstbau 65, 2207–2218 (2023). https://doi.org/10.1007/s10341-023-00974-w

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