The Molecular Genetics of Crop Domestication

Doebley, John; Gaut, Brandon S.; Smith, Bruce D.

doi:10.1016/j.cell.2006.12.006

Cited by 1,597 publications

(1,278 citation statements)

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“…Cultivation of wild plants always produces genetic bottlenecks and thus results in loss of genetic diversity due to founder effects and unconscious or conscious selections [8]. For example, only 23% of the total chloroplast haplotypes detected in Oryza rufipogon and O. sativa were recovered in the cultivated rice [29].…”

Section: Discussionmentioning

confidence: 99%

“…The strength of genetic bottleneck during cultivation is determined by two interacting factors: the size of the bottlenecked population and the bottleneck's duration [8,45]. Intuitively, cultivated plants of multiple origins (multiple places and multiple events) would hold larger population size and thus most likely maintain greater genetic diversity [46].…”

Section: Discussionmentioning

confidence: 99%

“…Medicinal plant production through cultivation, for example, can reduce the incentives to conserve wild populations [7]. More importantly, founder effects and artificial selections for high yielding or pharmacologically standard individuals would probably result in a narrow genetic range of material in cultivation, resembling the genetic bottleneck during the domestication of cereal species [8]. Furthermore, seed exchange between farmers is much easier due to the highly developed transportation and commercial markets of modern times [9], but migration of seeds from their collection sites to other environments within a species range for cultivation may increase the risk of maladaptation [10,11].…”

Section: Introductionmentioning

confidence: 99%

“…The sharp increase in medicinal plant cultivation may greatly mitigate the pressure on the wild medicinal resources, but also impose profound impacts on the genetic diversity patterns of these medicinal plants. However, studies about genetic impacts of cultivation are mostly concentrated on economically valuable crops with long domestication history (see review in [8]), little is known regarding the genetic impacts of recent cultivation on medicinal plants (but see [15-18]). This issue becomes more important as wild gene pools of many medicinal species have decreased rapidly or become extinct.…”

Section: Introductionmentioning

confidence: 99%

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Impacts of recent cultivation on genetic diversity pattern of a medicinal plant, Scutellaria baicalensis (Lamiaceae)

Yuan

Zhang

et al. 2010

BMC Genet

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BackgroundCultivation of medicinal plants is not only a means for meeting current and future demands for large volume production of plant-based drug and herbal remedies, but also a means of relieving harvest pressure on wild populations. Scutellaria baicalensis Georgi (Huang-qin or Chinese skullcap) is a very important medicinal plant in China. Over the past several decades, wild resource of this species has suffered rapid declines and large-scale cultivation was initiated to meet the increasing demand for its root. However, the genetic impacts of recent cultivation on S. baicalensis have never been evaluated. In this study, the genetic diversity and genetic structure of 28 wild and 22 cultivated populations were estimated using three polymorphic chloroplast fragments. The objectives of this study are to provide baseline data for preserving genetic resource of S. baicalensis and to evaluate the genetic impacts of recent cultivation on medicinal plants, which may be instructive to future cultivation projects of traditional Chinese medicinal plants.ResultsThirty-two haplotypes of S. baicalensis (HapA-Y and Hap1-7) were identified when three chloroplast spacers were combined. These haplotypes constituted a shallow gene tree without obvious clusters for cultivated populations, suggesting multiple origins of cultivated S. baicalensis. Cultivated populations (hT = 0.832) maintained comparable genetic variation with wild populations (hT = 0.888), indicating a slight genetic bottleneck due to multiple origins of cultivation. However, a substantial amount of rare alleles (10 out of 25 haplotypes within wild populations) lost during the course of S. baicalensis cultivation. The genetic differentiation for cultivated group (GST = 0.220) was significantly lower than that of wild group (GST = 0.701). Isolation by distance analysis showed that the effect of geographical isolation on genetic structure was significant in wild populations (r = 0.4346, P < 0.0010), but not in cultivated populations (r = 0.0599, P = 0.2710). These genetic distribution patterns suggest that a transient cultivation history and the extensive seed change among different geographical areas during the course of S. baicalensis cultivation.ConclusionsAlthough cultivated S. baicalensis maintains comparable genetic diversity relative to wild populations, recent cultivation has still imposed profound impacts on genetic diversity patterns of the cultivated S. baicalensis populations, i.e., the loss of rare alleles and homogenization of cultivated populations. This study suggests that conservation-by-cultivation is an effective means for protecting genetic resources of S. baicalensis, however, the wild resources still need to be protected in situ and the evolutionary consequences of extensive seed exchange mediated by human being should be monitored carefully.

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Impacts of recent cultivation on genetic diversity pattern of a medicinal plant, Scutellaria baicalensis (Lamiaceae)

Yuan

Zhang

et al. 2010

BMC Genet

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“…Reduction in genetic diversity has been reported in modern wheat, compared with wild ancestors, which is thought to be due to population bottlenecks (Doebley et al , 2006), and with the domestication of wheat and varieties becoming adapted to local conditions, giving rise to so‐called landrace cultivars, causing even further reduction in genetic variation (Reif et al , 2005). More recent results from studies on changes in genetic diversity of European wheat varieties over time have suggested that genetic diversity has not in fact decreased, but rather that changes have occurred in alleles present in the germplasm (Huang et al , 2007).…”

Section: Introductionmentioning

confidence: 99%

Searching for wheat resistance to aphids and wheat bulb fly in the historical Watkins and Gediflux wheat collections

Aradottir

Martin

Clark

et al. 2016

Annals of Applied Biology

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Insect pests can reduce wheat yield by direct feeding and transmission of plant viruses. Here we report results from laboratory and field phenotyping studies on a wide range of wheat, including landraces from the Watkins collection deriving from before the green revolution, more modern cultivars from the Gediflux collection (north‐western Europe) and modern UK Elite varieties, for resistance to the bird cherry‐oat aphid, Rhopalosiphum padi (Homoptera: Aphididae) and the English grain aphid, Sitobion avenae (Homoptera: Aphididae). A total of 338 lines were screened for R. padi and 340 lines for S. avenae. Field trials were also conducted on 122 Watkins lines to identify wheat bulb fly, Delia coarctata, preference on these landraces. Considerable variation was shown in insect performance among and within different wheat collections, with reduced susceptibility in a number of varieties, but phenotyping did not identify strong resistance to aphids or wheat bulb fly. Field trials showed within collection differences in aphid performance, with fewer aphids populating lines from the Watkins collection. This differs from development data in laboratory bioassays and suggests that there is a pre‐alighting cue deterring aphid settlement and demonstrates differences in aphid preference and performance on older plants in the field compared with seedlings in the laboratory, highlighting the need for phenotyping for aphid resistance at different plant growth stages. No association was identified between performance of the different insect species on individual varieties, potentially suggesting different nutritional requirements or resistance mechanisms.

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The EIL transcription factor family in soybean: Genome‐wide identification, expression profiling and genetic diversity analysis

Shen

Guo

et al. 2019

FEBS Open Bio

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The ETHYLENE INSENSITIVE3‐LIKE (EIL) transcription factor family plays a critical role in the ethylene signaling pathway, which regulates a broad spectrum of plant growth and developmental processes, as well as defenses to myriad stresses. Although genome‐wide analysis of this family has been carried out for several plant species, no comprehensive analysis of the EIL gene family in soybean has been reported so far. Furthermore, there are few studies on the functions of EIL genes in soybean. In this study, we identified 12 soybean (Gm) EIL genes, which we divided into three groups based on their phylogenetic relationships. We then detected their duplication status and found that most of the GmEIL genes have duplicated copies derived from two whole‐genome duplication events. These duplicated genes underwent strong negative selection during evolution. We further analyzed the transcript profiles of GmEIL genes using the transcriptome data and found that their spatio‐temporal and stress expression patterns varied considerably. For example, GmEIL1–GmEIL5 were found to be strongly expressed in almost every sample, while GmEIL8–GmEIL12 exhibited low expression, or were not expressed at all. Additionally, these genes showed different responses to dehydration, salinity and phosphate starvation. Finally, we surveyed genetic variations of these genes in 302 resequenced wild soybeans, landraces and improved soybean cultivars. Our data showed that most GmEIL genes are well conserved, and are not modified in domesticated or improved cultivars. Together, these findings provide a potentially valuable resource for characterizing the GmEIL gene family and lay the basis for further elucidation of their molecular mechanisms.

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The Molecular Genetics of Crop Domestication

Cited by 1,597 publications

References 69 publications

Impacts of recent cultivation on genetic diversity pattern of a medicinal plant, Scutellaria baicalensis (Lamiaceae)

Impacts of recent cultivation on genetic diversity pattern of a medicinal plant, Scutellaria baicalensis (Lamiaceae)

Searching for wheat resistance to aphids and wheat bulb fly in the historical Watkins and Gediflux wheat collections

The EIL transcription factor family in soybean: Genome‐wide identification, expression profiling and genetic diversity analysis

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