Whole-genome duplication as a key factor in crop domestication

Abstract

Polyploidy is commonly thought to be associated with the domestication process because of its concurrence with agriculturally favourable traits and because it is widespread among the major plant crops(1-4). Furthermore, the genetic consequences of polyploidy(5-7) might have increased the adaptive plasticity of those plants, enabling successful domestication(6-8). Nevertheless, a detailed phylogenetic analysis regarding the association of polyploidy with the domestication process, and the temporal order of these distinct events, has been lacking(3). Here, we have gathered a comprehensive data set including dozens of genera, each containing one or more major crop species and for which sufficient sequence and chromosome number data exist. Using probabilistic inference of ploidy levels conducted within a phylogenetic framework, we have examined the incidence of polyploidization events within each genus. We found that domesticated plants have gone through more polyploidy events than their wild relatives, with monocots exhibiting the most profound difference: 54% of the crops are polyploids versus 40% of the wild species. We then examined whether the preponderance of polyploidy among crop species is the result of two, non-mutually-exclusive hypotheses: (1) polyploidy followed by domestication, and (2) domestication followed by polyploidy. We found support for the first hypothesis, whereby polyploid species were more likely to be domesticated than their wild relatives, suggesting that the genetic consequences of polyploidy have conferred genetic preconditions for successful domestication on many of these plants.

The draft genome of tropical fruit durian (Durio zibethinus)

“…First, other subfamilies within Malvaceae, after divergence from the Byttnerioideae subfamily (including cacao), are also likely to have the cotton-specific WGD. Second, this WGD event, which has been proposed to have driven the evolution of unique Gossypium traits 26 , may also have been involved in driving the evolution of unique durian traits, as well as the radiation of different Malvaceae subfamilies around the same time 47,48 .…”

Genetic mapping in polyploids

“…Polyploids are particularly common among domesticated crops (Salman-Minkov et al, 2016), a fact that has helped drive interest to better understand these species. In many cases polyploidy is deliberately induced -for example modern ornamental breeding often relies on inter-specific hybrids to create novel varieties, which are often "polyploidised"…”

“…Polyploids, which carry more than the usual two copies of each chromosome, are an important group of organisms that occur widely among plants, particularly domesticated ones (Salman-Minkov et al, 2016). Many theories to explain their prevalence among crop species have been proposed, identifying features which may have appealed to early farmers in their domestication of wild species.…”

The Impact of Genetic Changes during Crop Domestication

“…There is higher prevalence of recent polyploidy among major domestic crop species (34%) than among wild plant species (24%), with monocots exhibiting the most profound difference: 54% of the crops are recent polyploids versus 40% of the wild species [98]. Domesticated plants benefitted from the versatility of polyploids [99], such as broadening of adaptation, increase in harvested organ size (gigantism), fixation of heterozygosity, and the appearance of novel traits due to epistatic interactions.…”