The Genetics and Genomics of Plant Domestication

Kantar, Michael B.; Nashoba, Amber R.; Anderson, Justin; Blackman, Benjamin K.; Rieseberg, Loren H.

doi:10.1093/biosci/bix114

Cited by 88 publications

(80 citation statements)

References 66 publications

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“…In short, these identified genes involved in certain pathways likely play a critical role in genetically distinguishing trees from nontree plants (Neale et al, ), providing new insights into understanding the unique features, complexity, and domestication of tree genomes. It should be noted that more wild and cultivated lines should be selected for genome resequencing to better understand the origin and domestication process of castor bean tree genomes (Kantar, Nashoba, Anderson, Blackman, & Rieseberg, ).…”

Section: Discussionmentioning

confidence: 99%

Genomic analysis reveals rich genetic variation and potential targets of selection during domestication of castor bean from perennial woody tree to annual semi‐woody crop

Yang

Qiu

et al. 2019

Plant Direct

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Relatively, little is known about the genetic variation of woody trees during domestication. Castor bean (Ricinus communis L. Euphorbiaceae) is a commercially important nonedible annual oilseed crop and differs from its wild progenitors that have a perennial woody habit. Although castor bean is one of the oldest cultivated crops, its domestication origin, genomic variation, and potential targets of selection underlying domestication traits remain unknown. Here, we performed a phylogenetic analysis, which suggests that the wild accessions were distinctively separated from the cultivated accessions. Genome sequencing of three accessions (one each wild, landrace, and cultivar) showed a large number of genetic variants between wild and cultivated castor bean (ZB306 or Hale), and relatively few variants between cultivar ZB306 and Hale. Comparative genome analysis revealed many candidate genes of selection and key pathways potentially involved in the transition from a perennial woody tree to annual crop. Interestingly, among 16 oil‐related genes only three showed evidence of selection and the remainder showed low genetic variation at the population level, suggesting strong purifying selection in both the wild and domesticated gene pools. These results extend our understanding of the origin, genomic variation, and domestication, and provide a valuable resource for future gene–trait associations and castor bean breeding.

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Section: Discussionmentioning

confidence: 99%

Genomic analysis reveals rich genetic variation and potential targets of selection during domestication of castor bean from perennial woody tree to annual semi‐woody crop

Yang

Qiu

et al. 2019

Plant Direct

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“…The wild species from which a crop plant was derived in some cases may be well known and easily identified in current wild plant populations, while others have arisen via hybridization and polyploidization [45][46][47]. Based on reproductive isolation, the concept of genepools has been established [18], where the closest crop wild relatives that are fully interfertile with the crop species represent an easily accessible or primary gene pool for crop improvement, while more distant relatives from which genes can be accessed with increasing degrees of difficulty form secondary and tertiary gene pools.…”

Section: Domestication Has Left Signatures Both On Morphological As Wmentioning

confidence: 99%

“…Recently, the concept of gene networks changing under domestication, leading to multiple phenotypes with different plant and inflorescence architecture, was demonstrated in maize [91]. This might not be unexpected given that transcription factors orchestrate the activity of numerous other genes, and consequently, their alteration can potentially modify an entire suite of characters, leading to drastic phenotypic changes in relatively short time scales [45,92].…”

Section: Domestication Has Left Signatures Both On Morphological As Wmentioning

confidence: 99%

The Impact of Genetic Changes during Crop Domestication

et al. 2018

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Abstract:Humans have domesticated hundreds of plant and animal species as sources of food, fiber, forage, and tools over the past 12,000 years, with manifold effects on both human society and the genetic structure of the domesticated species. The outcomes of crop domestication were shaped by selection driven by human preferences, cultivation practices, and agricultural environments, as well as other population genetic processes flowing from the ensuing reduction in effective population size. It is obvious that any selection imposes a reduction of diversity, favoring preferred genotypes, such as nonshattering seeds or increased palatability. Furthermore, agricultural practices greatly reduced effective population sizes of crops, allowing genetic drift to alter genotype frequencies. Current advances in molecular technologies, particularly of genome sequencing, provide evidence of human selection acting on numerous loci during and after crop domestication. Population-level molecular analyses also enable us to clarify the demographic histories of the domestication process itself, which, together with expanded archaeological studies, can illuminate the origins of crops. Domesticated plant species are found in 160 taxonomic families. Approximately 2500 species have undergone some degree of domestication, and 250 species are considered to be fully domesticated. The evolutionary trajectory from wild to crop species is a complex process. Archaeological records suggest that there was a period of predomestication cultivation while humans first began the deliberate planting of wild stands that had favorable traits. Later, crops likely diversified as they were grown in new areas, sometimes beyond the climatic niche of their wild relatives. However, the speed and level of human intentionality during domestication remains a topic of active discussion. These processes led to the so-called domestication syndrome, that is, a group of traits that can arise through human preferences for ease of harvest and growth advantages under human propagation. These traits included reduced dispersal ability of seeds and fruits, changes to plant structure, and changes to plant defensive characteristics and palatability. Domestication implies the action of selective sweeps on standing genetic variation, as well as new genetic variation introduced via mutation or introgression. Furthermore, genetic bottlenecks during domestication or during founding events as crops moved away from their centers of origin may have further altered gene pools. To date, a few hundred genes and loci have been identified by classical genetic and association mapping as targets of domestication and postdomestication divergence. However, only a few of these have been characterized, and for even fewer is the role of the wild-type allele in natural populations understood. After domestication, only favorable haplotypes are retained around selected genes, which creates a genetic valley with extremely low genetic diversity. These "selective sweeps" can allow mildly deleterious...

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“…In particular, breeding might focus on classic domestication syndrome traits such as non-shattering, lack of dormancy, and flowering time [19]. Most of these traits have a well-known genetic basis [20,21]. Leveraging these abilities to improve seed yields may reduce land use impacts, provide economic benefits to seed producers, and improve access to cover crop seed.…”

Section: Main Textmentioning

confidence: 99%