The extent of adaptive wild introgression in crops

Abstract

The study of crop evolution has focused primarily on the process of initial domestication. Postdomestication adaptation during the expansion of crops from their centers of origin has received considerably less attention. Recent research has revealed that, in at least some instances, crops have received introgression from their wild relatives that has facilitated adaptation to novel conditions encountered during expansion. Such adaptive introgression could have an important impact on the basic study of domestication, affecting estimates of several evolutionary processes of interest (e.g. the strength of the domestication bottleneck, the timing of domestication, the targets of selection during domestication). Identification of haplotypes introgressed from the wild may also help in the identification of alleles that are beneficial under particular environmental conditions. Here we review mounting evidence for substantial adaptive wild introgression in several crops and consider the implications of such gene flow to our understanding of crop histories.

Genomics of Evolutionary Novelty in Hybrids and Polyploids

“…Many of these genes are connected to biotic resistance such as downy mildew resistance, implicating selection for disease resistance as being responsible for adaptive interspecific gene flow. Similar examples of either intentional or unintentional adaptive introgression are common in our major cultivated crops (Janzen et al, 2019).…”

“…The preceding examples of adaptive genic introgression represent the unusual cases where adaptation has been at least arguably causally connected to specific genes. Far more numerous are examples where genomic evidence for adaptive introgression is convincing, but either the responsible genes have not been identified or they have not been directly linked to phenotypes that are unequivocally connected to adaptation (Suarez-Gonzalez et al, 2016Hübner et al, 2019;Janzen et al, 2019;Mitchell et al, 2019). A recent case in point is for cultivated sunflowers (Hübner et al, 2019), where genomic resequencing of about 400 cultivated lines, Native American landraces and wild accessions from 11 wild species demonstrated that 1.5% of the genes in cultivated sunflower arose via interspecific introgression from wild species.…”

Convergent seed color adaptation during repeated domestication of an ancient new world grain

“…Crops and their wild relatives can often intercross in the wild and exchange adaptive traits (Janzen et al 2018). In a number of major crops such as maize (Hufford et al 2013), barley (Poets et al 2015), rice Meyer et al 2016) and pearl millet (Burgarella et al 2018) adaptive introgression from wild relatives has been observed.…”

“…In a number of major crops such as maize (Hufford et al 2013), barley (Poets et al 2015), rice Meyer et al 2016) and pearl millet (Burgarella et al 2018) adaptive introgression from wild relatives has been observed. Adaptive introgression requires several generations of backcrossing to the crop in order to remove linkage drag (reviewed in Janzen et al 2018).…”

Genomic, Transcriptomic and Epigenomic Tools to Study the Domestication of Plants and Animals: A Field Guide for Beginners

“…These methods use the data obtained from linkage disequilibrium between loci to assign ancestry in each portion of the genome in comparison to reference populations that depict ancestral source populations, requiring an a priori assignation of unadmixed reference populations in order to assign local ancestry to the populations of interest (Price et al, 2009). The analysis reveals chromosomic blocks that can be assigned to either a wild or a domesticated ancestry in hybrid populations, which may reveal historical processes of introgression and local adaptation in modern domesticated populations, as well as potential targets for selective breeding (Janzen et al, 2019).…”