Epigenetic patterns newly established after interspecific hybridization in natural populations of Solanum

Abstract

Interspecific hybridization is known for triggering genetic and epigenetic changes, such as modifications on DNA methylation patterns and impact on phenotypic plasticity and ecological adaptation. Wild potatoes (Solanum, section Petota) are adapted to multiple habitats along the Andes, and natural hybridizations have proven to be a common feature among species of this group. Solanum × rechei, a recently formed hybrid that grows sympatrically with the parental species S. kurtzianum and S. microdontum, represents an ideal model for studying the ecologically and evolutionary importance of hybridization in generating of epigenetic variability. Genetic and epigenetic variability and their correlation with morphological variation were investigated in wild and ex situ conserved populations of these three wild potato species using amplified fragment length polymorphism (AFLP) and methylation-sensitive amplified polymorphism (MSAP) techniques. We observed that novel methylation patterns doubled the number of novel genetic patterns in the hybrid and that the morphological variability measured on 30 characters had a higher correlation with the epigenetic than with the genetic variability. Statistical comparison of methylation levels suggested that the interspecific hybridization induces genome demethylation in the hybrids. A Bayesian analysis of the genetic data reveled the hybrid nature of S. × rechei, with genotypes displaying high levels of admixture with the parental species, while the epigenetic information assigned S. × rechei to its own cluster with low admixture. These findings suggested that after the hybridization event, a novel epigenetic pattern was rapidly established, which might influence the phenotypic plasticity and adaptation of the hybrid to new environments.

Beyond population genetics: natural epigenetic variation in wild cherry (Prunus avium)

“…Considerable epigenetic differences between natural populations have been reported in other studies, for instance in white poplar (Ma et al 2013), wild potato (Cara et al 2013), and wild barley (Li et al 2008), where epigenetic differentiation of F ST =0.10-0.30 was found. Chwedorzewska and Bednarek (2012) found marked epigenetic differentiation (F ST = 0.5) among Polish and Antarctic annual bluegrass (Poa annua) populations, and Richards et al (2012) reported strong epigenetic differentiation (F ST =0.5-0.8) of Japanese knotweed (Fallopia japonica) populations during invasion into different environments.…”

Epigenetic consequences of interploidal hybridisation in synthetic and natural interspecific potato hybrids

“…These results could be explained by assuming: (1) genetic differences between the diploid and triploid S. microdontum cytotypes, which could have possibly affected nuclear‐cytoplasmic interactions, or (2) aneuploidy in the T×D hybrid progeny. In a previous work (Cara et al ., ), we demonstrated that there were no apparent genetic or epigenetic differences between diploid and triploid S. microdontum cytotypes. Since the same genotypes were used in the present work, the first alternative can be excluded.…”

“…& W. (2n = 29 = 24; 2 EBN) and Solanum microdontum B. (2n = 29 = 24; 2 EBN and 2n = 39 = 36), within the limits of their geographic range (Okada & Hawkes, 1978;Cara et al, 2013). Although most S. microdontum populations are diploid, triploid populations have been recorded at the southern end of their range in Argentina (Okada & Hawkes, 1978;Okada, 1981; this work), where they can hybridise with S. kurtzianum.…”

Increased transgenerational epigenetic variation, but not predictable epigenetic variants, after environmental exposure in two apomictic dandelion lineages

“…Loci were discarded if they were monomorphic or if they contained fragments that showed up in any of the negative controls. Following other MS‐AFLP studies (Alonso, Pérez, Bazaga, Medrano, & Herrera, ; Cara, Marfil, & Masuelli, ; also see Zhang & Hare, ), loci were also discarded if they showed too many mismatches among technical duplicates: We allowed a maximum of three mismatches among the set of 24 pairs of technical duplicates. The averaged mismatch error rate (±standard deviation) across all primer combinations used was before purging for T. alatum 8.46 ± 1.70% ( N = 65) and for T. hemicyclum 9.20% ± 1.39% ( N = 72).…”