Amplified fragment length polymorphism as a tool for molecular characterization of almond germplasm: genetic diversity among cultivated genotypes and related wild species of almond, and its relationships with agronomic traits

Abstract

Amplified fragment length polymorphism (AFLP) analysis is a rapid and efficient method for producing DNA fingerprints and molecular characterization. Our objectives were to: estimate genetic similarities (GS), marker indices, and polymorphic information contents (PICs) for AFLP markers in almond cultivars; assess the genetic diversity of almond cultivars and wild species, using GS estimated from AFLP fingerprints and molecular characterization; and facilitate the use of markers in inter-specific introgression and cultivar improvement. The genetic diversity of 45 almond cultivars from Iran, Europe, and America, were studied assaying 19 primer combinations. In addition, several agronomic traits were evaluated, including flowering and maturity times, self-incompatibility, and kernel and fruit properties. Out of the 813 polymerase chain reaction fragments that were scored, 781 (96.23%) were polymorphic. GS ranged from 0.5 to 0.96, marker indices ranged from 51.37 to 78.79, and PICs ranged from 0.56 to 0.86. Results allowed the unique molecular identification of all assayed genotypes. However, the correlation between genetic similarity clustering as based on AFLP and clustering for agronomic traits was low. Cluster analysis based on AFLP data clearly differentiated the genotypes and wild species according to their origin and pedigree, whereas, cluster analysis based on agronomic data differentiated according the pomological characterization. Our results showed the great genetic diversity of the almond cultivars and their interest for almond breeding.

Molecular characterisation and similarity relationships among iranian basil (Ocimum basilicum L.) accessions using inter simple sequence repeat markers

“…Our results showed that the PCoA data approximately corresponded to those obtained through cluster analysis. This is in agreement with other findings (DARVISHZADEH et al, 2010;KUMAR et al, 2009;SORKHE et al, 2007). Table 1 Conclusions 1.…”

Fingerprinting of Vaccinium corymbosum cultivars using DNA of fruits

“…The PIC parameter is used in genetics as a measure of polymorphism for a marker locus (Roldán-Luiz et al 2000), the MI parameter is used to estimate the overall utility of each marker system (Sorkheh et al 2007) and EMR is used to evaluate whether a primer is effective (Powell et al 1996). The most appropriate primers to differentiate species/cultivars were the OPE01 in RAPDs and UBC844 in ISSRs since both presented the highest value of PIC, MI and EMR in both tissues (fruits and leaves).…”

“…and Ib is band informativeness and p i is the proportion of the accessions containing band; the polymorphism information content (PIC) according to Roldán-Ruiz et al (2000) where PIC i = 2f i (1 -f i ) (f i is the frequency of amplified allele and 1 -f i is the frequency of null allele of marker i); the effective multiplex ratio (EMR) following Powell et al (1996) where EMR is number of polymorphic products from a single amplification reaction; and the marker index (MI) following Sorkheh et al (2007) defined as the product of polymorphism percentage and PIC. Cluster analysis was done, applying an unweighted pairgroup method with arithmetic averages (UPGMA) based on a simple matching similarity matrix and SAHN subroutine to compute a principal coordinate (PCO) analysis through the NTSYS-pc Ver.…”

Molecular variance of the Tunisian almond germplasm assessed by simple sequence repeat (SSR) markers

“…Recently, various molecular markers such as sequence related amplified polymorphism (SRAP), amplified fragment length polymorphism (AFLP) and single nucleotide polymorphisms (SNP) have been used for almond genetic diversity assessment (Jing et al, 2013;Sorkheh et al, 2007;Wu et al, 2008). Microsatellites or simple sequence repeat markers (SSRs) are the preferred marker for a wide range of applications in genetics and plant breeding.…”