Genetic diversity and structure of Pyrus accessions of Indian Himalayan region based on morphological and SSR markers

Abstract

Genetic diversity and phylogenetic relationships among 48 pear accessions belonging to six species were determined using 23 morphological traits and 20 simple sequence repeat (SSR) primers. To assess the genetic diversity, data on morphological (both quantitative and qualitative) traits were recorded during 2010-2012 using standard pear descriptors. It was observed that the traits ratio of fruit length to diameter, persistency of calyx on mature fruits and fruit surface and pulp texture were important in detecting variation across pear species. At molecular level, 20 SSR primers amplified 190 polymorphic alleles with an average of 9.5 alleles per primer. Size of amplified alleles ranged from 85 to 450 bp. Mean polymorphic information content (PIC) was 0.80 showing high level of SSR polymorphism. Bayesian model-based STRUCTURE analysis assigned genotypes into five clusters and also showed the extent of admixture within individuals. Genotypes belonging to Pyrus pyrifolia were clustered into two different clusters indicating broad genetic base for this species while Pyrus communis genotypes appeared to have conserved genetic makeup. Dendrogram-based on Jaccard's similarity coefficient and neighbor-joining tree showed two major groups of Asiatic (P. pyrifolia, Pyrus pashia, Pyrus serotina and Pyrus jacquemontiana) and European (P. communis) pears. However, accessions belonging to P. pyrifolia were further divided into subgroups. Cluster analysis based on morphological traits was in agreement with the dendrogram and structure clusters obtained with SSR data. The Mantel matrix correspondence test was used to further compare the molecular and morphological similarity matrices and positive correlation coefficient (r=0.164; P=0.001) was observed. Results of this study present important information about genetic structure of Indian pear accessions which can contribute significantly to future breeding and improvement programmes in this species.

Development of novel SSR markers for evaluation of genetic diversity and population structure in Tribulus terrestris L. (Zygophyllaceae)

“…DNA markers offer more accurate information on genetic diversity, as they are rarely influenced by environmental factors of a region (Sharma et al 2008 ). Furthermore, SSR markers specifically possess many desirable useful properties which makes them most preffered DNA markers (Powell et al 1996 ; Rana et al 2015 ; Sharma et al 2015 ). The newly developed SSR markers appeared valuable in detecting diversity in studied germplasm of T. terrestris .…”

Elucidating the contribution of wild related species on autochthonous pear germplasm: A case study from Mount Etna

“…In addition to these markers, SSRs, in particular, have been widely used for genetic relationship and diversity studies given their hyper-variability, co-dominant nature, prevalent locus-specificity, and random genome-wide distributions. A large set of SSR markers has been developed from Japanese and European pear [ 16 – 18 ] and subsequently used for genetic characterization and identification of different Pyrus species [ 19 – 22 ]. In addition, SSR markers present a high transferability between related species and genera.…”

Phenotyping the Genetic Diversity of Wild Agave Species that Coexist in the Same Spatial Region

“…3). A similar study was conducted by Rana et al (2015) where they observed that the ratio of length and diameter of the fruits, persistent calyx in mature fruit, fruit surface and texture of the flesh were important in detecting the morphological variations between pear species.…”