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<p>Crucial to research aimed at genetic improvement of the mango fruit crop is the identification of promising diverse and distinct local elites as parents in hybridisation programs, development of genotype-specific unique fingerprints for identifying and documenting different mango genotypes, associations of DNA markers with fruit traits of interest and analysis of population structure and genetic diversity in mangoes from different geographical locations. Considering this, we validated a robust PCR amplicon-based Directed Amplified Minisatellite DNA (PCR-DAMD) marker system for population structure analysis of 58 selected Indian mango genotypes originating in different eco-geographical locations of India and to explore the association of markers with pheno-biochemical fruit traits. DAMD markers proved to be informative for genetic diversity research due to high values of diversity parameters both at the genotype level and population level. As many as 27 out of 58 mango genotypes were identified depending on the presence&#xa0;or&#xa0;absence of genotype-specific unique DAMD amplicons. High bootstrapped Unweighted Pair Group Method with Arithmetic Mean (UPGMA) dendrogram and population structure based on DAMDs moderately discriminated genotypes according to their geographic origin. Analysis of Molecular Variance (AMOVA) accounted for 89% variance within the geographical population and 11% among populations of Indian mangoes, which was further supported by the moderate-to-high levels of genetic differentiation and gene flow. Based on the genetic parameters, the genetic diversity is shown in decreasing order as East India &gt; South India &gt; West India &gt; North India. Bayesian model-based population structure detected 56.8% of individual admixture among genotypes. Multiple Regression Analysis (MRA) analysis revealed the association of a total of 71 DAMD marker bands with different quantitative pheno-biochemical pomological traits positively or negatively. Some of the bands were found to be associated with multiple fruit traits because of the correlation among traits as well as the pleiotropic effect of the closely linked quantitative trait loci (QTL) on different traits. These results could facilitate characterization, marker assisted selection (MAS) and QTL breeding programs towards genetic improvement of this economically important fruit crop.</p>

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Validation of PCR amplicon-based directed amplified minisatellite DNA (DAMD) markers for analysis of population structure and fruit trait association of promising Indian mangoes

  • 期刊论文

  • 发表日期：

    2025年1月27日

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  • Ram Chandra Jena,
  • Pradeep Kumar Chand

摘要

Crucial to research aimed at genetic improvement of the mango fruit crop is the identification of promising diverse and distinct local elites as parents in hybridisation programs, development of genotype-specific unique fingerprints for identifying and documenting different mango genotypes, associations of DNA markers with fruit traits of interest and analysis of population structure and genetic diversity in mangoes from different geographical locations. Considering this, we validated a robust PCR amplicon-based Directed Amplified Minisatellite DNA (PCR-DAMD) marker system for population structure analysis of 58 selected Indian mango genotypes originating in different eco-geographical locations of India and to explore the association of markers with pheno-biochemical fruit traits. DAMD markers proved to be informative for genetic diversity research due to high values of diversity parameters both at the genotype level and population level. As many as 27 out of 58 mango genotypes were identified depending on the presence or absence of genotype-specific unique DAMD amplicons. High bootstrapped Unweighted Pair Group Method with Arithmetic Mean (UPGMA) dendrogram and population structure based on DAMDs moderately discriminated genotypes according to their geographic origin. Analysis of Molecular Variance (AMOVA) accounted for 89% variance within the geographical population and 11% among populations of Indian mangoes, which was further supported by the moderate-to-high levels of genetic differentiation and gene flow. Based on the genetic parameters, the genetic diversity is shown in decreasing order as East India > South India > West India > North India. Bayesian model-based population structure detected 56.8% of individual admixture among genotypes. Multiple Regression Analysis (MRA) analysis revealed the association of a total of 71 DAMD marker bands with different quantitative pheno-biochemical pomological traits positively or negatively. Some of the bands were found to be associated with multiple fruit traits because of the correlation among traits as well as the pleiotropic effect of the closely linked quantitative trait loci (QTL) on different traits. These results could facilitate characterization, marker assisted selection (MAS) and QTL breeding programs towards genetic improvement of this economically important fruit crop.