Threat to Asian wild apple trees posed by gene flow from domesticated apple trees and their “pestified” pathogens

Abstract

Secondary contact between crops and their wild relatives poses a threat to wild species, not only through gene flow between plants, but also through the dispersal of crop pathogens and genetic exchanges involving these pathogens, particularly those that have become more virulent by indirect selection on resistant crops, a phenomenon known as "pestification." Joint analyses of wild and domesticated hosts and their pathogens are essential to address this issue, but such analyses remain rare. We used population genetics approaches, demographic inference and pathogenicity tests on host-pathogen pairs of wild or domesticated apple trees from Central Asia and their main fungal pathogen, Venturia inaequalis, which itself has differentiated agricultural and wild-type populations. We confirmed the occurrence of gene flow from cultivated (Malus domestica) to wild (Malus sieversii) apple trees in Asian forests,

Convergence in domesticated fungi used for cheese and dry-cured meat maturation: beneficial traits, genomic mechanisms, and degeneration

“…Fungal pathogens on crops have also evolved under indirect human pressure, leading to specific phenotypes on crops, e.g. being more aggressive or more virulent, and with also often bottlenecks and horizontal gene transfers [56,57] ; this process has been called pestification [57].…”

Gene flow between wild trees and cultivated varieties shapes the genetic structure of sweet chestnut (Castanea sativa Mill.) populations

“…Similar genetic interactions between cultivated and wild populations are not uncommon and have previously been noted for 12 of the 13 most important food crops in the world 76 , as well as genera Beta L. 77 , Malus Mill. 10 , Medicago L. 78 , Cichorium L. 8 , Lactuca L. 79 and Solanum L. 80 . Although some authors express concerns about the negative impact of this gene flow on the extinction of the wild populations 4 , 81 – 83 , the occurrence of “pestification” 10 , 84 , 85 and the spread of transgenes from the cultivated crops to wild populations 79 , hybridization may, in contrast, increase genetic variability of a population and promote the emergence of beneficial adaptations 11 .…”

“… 10 , Medicago L. 78 , Cichorium L. 8 , Lactuca L. 79 and Solanum L. 80 . Although some authors express concerns about the negative impact of this gene flow on the extinction of the wild populations 4 , 81 – 83 , the occurrence of “pestification” 10 , 84 , 85 and the spread of transgenes from the cultivated crops to wild populations 79 , hybridization may, in contrast, increase genetic variability of a population and promote the emergence of beneficial adaptations 11 . A similar occurrence has been previously reported for cultivated apple ( Malus domestica Borkh.)…”

“…This gene flow between wild populations and cultivated varieties of the same or closely related species is well-known 4 and has been observed when cultivated varieties are planted within the natural range of their wild relatives 5 – 7 , with spontaneous hybrids known to form their own distinct populations and persist in the wild 8 , 9 . While this introgression can lead to the extinction of the wild lineages 10 , alternatively it may cause increase of genetic variation and the creation of novel adaptations 11 .…”

CRISPR-Cas9 gene editing and rapid detection of gene-edited mutants using high-resolution melting in the apple scab fungus,Venturia inaequalis

“…A key development over recent years has been the availability of several V. inaequalis genome sequences and gene catalogues (2, 5–9), as well as the development of both polyethylene glycol (PEG)-mediated protoplast and Agrobacterium tumefaciens -mediated transformation protocols for use with this fungus (10). However, while several V. inaequalis genes of interest that are putatively involved in the infection process of apple have been identified (5, 11–15), none have been functionally characterized to date using traditional gene deletion or disruption techniques. Indeed, no gene deletions or disruptions, based on homologous recombination, have yet been reported for V. inaequalis in the literature.…”