Characterization and Phylogenetic Analysis of Ancient Italian Landraces of Pear

Abstract

Pear is one of the oldest fruit tree crops and the third most important temperate fruit species. Its domestication took place independently in the Far East (China) and in the Caucasus region. While the origin of Eastern Asian cultivars is clear, that of European cultivars is still in doubt. Italy has a wealth of local varieties and genetic resources safeguarded by several public and private collections to face the erosion caused by the introduction of improved varieties in specialized orchards. The objectives of the present study were: (i) to characterize the existing germplasm through nuclear (SSR) and (ii) to clarify the genetic divergence between local and cultivated populations through chloroplast DNA (cpDNA) markers in order to provide insights into phylogenetic relationships of Pyrus spp. For this reason, 95 entries from five different germplasm collections, including nine European, Mediterranean and Eastern Asian species, were analyzed, and the intergenic accD-psaI sequences were compared to the worldwide distributed dataset encompassing a total of 298 sequences from 26 different Pyrus species. The nine nuclear SSRs were able to identify a total of 179 alleles, with a loci polymorphism P = 0.89. Most of the variation (97%) was found within groups. Five accessions from different sources were confirmed to be the same. Eight out of 20 accessions of unknown origin were identified, and six synonyms were detected. Locus NH030a was found to be monomorphic in all the cultivated accessions and in reference species interfertile with P. communis, leading to hypothesize selection pressures for adaptation to cultivation. The cpDNA sequences of the 95 accessions were represented by 14 haplotypes, six of which (derived from P. communis, P. cossonii and P. ussuriensis) are recorded here for the first time and may suggest the ancient origin of some local varieties. The network analysis of the 298 cpDNA sequences allowed two different haplogroups, Eastern and Western Eurasia, to be defined, supporting recent views of a clear division between Occidental and Oriental species. By combining the results from nuclear and uniparental markers, it was possible to better define many unknown accessions.

Genetic Diversity and Structure of the Portuguese Pear (Pyrus communis L.) Germplasm

“…The majority of cultivated pears are diploid (2n = 2X = 34) but a few cultivars of P. communis are polyploids [28,42] and it is known that the size of the Pyrus genome was influenced by polyploidy [43]. Queiroz et al [15], using six SSRs, verified that "Baguim" (V39), "PerolaAmarela 1" (V66), and "PeraCabaça" (V26) were triploids, which we confirmed in the present work using flow cytometry.…”

Combined Analyses of Chloroplast DNA Haplotypes and Microsatellite Markers Reveal New Insights Into the Origin and Dissemination Route of Cultivated Pears Native to East Asia

“…The congruency of the nuclear DNA- and cpDNA-based genetic structures in the geographic populations might be attributed to the extensive practice of clonal propagation during the domestication of fruit trees, but the incongruence between them would indicate an intensive influence of cross-pollination ( Nikiforova et al, 2013 ). The combination of nuclear SSR and chloroplast DNA has provided new insight into the origin of European pear cultivars ( Ferradini et al, 2017 ). Therefore, the genetic comparison of parental inherited nuclear DNA markers and maternal inherited cpDNA in this study might generate meaningful results for the domestication of cultivated Asian pears.…”

Genetic relationships and polyploid origins in the Lippia alba complex

“…The comparison of gene sequences and SSR data has contributed to a better evolutionary understanding of the Lippia alba complex. Whereas polyploid complexes from the temperate zone have been comparatively analyzed (Garcia‐Mas et al., ; Yang et al., ; Feng et al., ; Ferradini et al., ), this natural tropical polyploid complex is the first to be studied in this manner. SSR analysis showed patterns of similarity among ploidal levels, and the DNA sequence analysis adds further information about polyploid origins.…”

“…The comparison of gene sequences and SSR data has contributed to a better evolutionary understanding of the Lippia alba complex. Whereas polyploid complexes from the temperate zone have been comparatively analyzed (Garcia-Mas et al, 2004;Yang et al, 2006;Feng et al, 2014;Ferradini et al, 2017), this natural tropical polyploid complex is the first to be studied in this manner. SSR analysis showed patterns of similarity among ploidal levels, and the DNA sequence analysis adds further information about 2xSE102 4xNE101 4xCW34 4xSE32 4xNE86 4xCW76 4xNE103 4xNE97 4xCW64 4xCW31 4xSE45 4xN26 4xSE3 4xN61 4xNE87 4xCW15 4xCW70 4xCW6 4xSE35 4xCW47 4xCW36 4xCW7 6xCW42 2xS52 2xSE5 2xSE78 2xCW55 2xCW18 2xCW53 2xCW46 2xCW20 2xN2 2xSE72 2xCW13 2xSE33 2xNE100 2xS38 2xNE90 2xSE40 2xSE69 2xCW14 2xNE81 2xCW51 2xNE89 2xSE68 2xNE82 2xCW50 2xNE67 2xNE91 2xCW9 2xCW73 2xNE88 2xNE99 2xCW12 2xCW22 2xCW19 2xNE94 2xNE65 2xSE43 2xCW48 2xNE80 2xCW11 2xNE95 2xCW56 2xNE84 2xNE21 2xCW74 2xCW58 2xNE57 2xNE98 2xCW29 2xNE96 2xCW30 2xCW63 2xCW77 2xCW71 2xSE66 3xCW8 3xCW49 3xCW10 3xCW37 3xSE59 3xSE24 3xSE62 3xSE4 3xSE41 3xSE28 3xSE23 3xCW60 3xCW1 polyploid origins.…”