Crop domestication is the process of artificially selecting plants to improve their adaptability to human needs. Long ago all major crops in the world were domesticated from wild ancestral species, often with multiple rounds of domestication and/or breeding, in which the initial domestication events produced primitive local varieties with moderate levels of domestication, while modern plant breeding produces varieties or cultivars that conform to modern desirable phenotypes. At each step of domestication and breeding, germplasm undergoes profound changes, with domesticated germplasm pools having a narrower range of genotypic diversity. In some cases, domesticated crops have broader phenotypic diversity, such as fruit shape, size, and color in tomatos. In addition to the phenotypic changes of the domestication syndrome, the genomes of species also change during domestication.
Fig. 1. The domestication history of barley (Hordeum vulgare ssp. vulgare) from its wild ancestor (Hordeum vulgare ssp. spontaneum), shown as a continuous process along a timeline. (Meyer et al., 2012)
Our solution for Crop Domestication
By improving our understanding of domestication-related events, we can help expand the available gene pool to include genes from increasingly distant relatives. CD Genomics offers next-generation sequencing (NGS) allowing whole genome analyses to discover domestication genes in crops and their wild relatives. We also offer resequencing of domestication genotypes to identify regions of low diversity associated with domestication. With whole genome sequencing, we help you obtain species-specific data from related wild species. This sequence data can be used to design species-specific polymerase chain reaction (PCR) primers. Sequencing the PCR amplification products of target genes can be used to explore genetic variation in a large number of genes and gene families. Novel allelic variation in close or distant relatives can also be characterized by NGS.
Crop domestication also relies on high-quality reference genome sequences for related plant species. CD Genomics provides long-read sequencing to generate reference genome sequences for hundreds of plant species, such as maize, wheat, potato, cotton, and peanut. In addition, we are committed to constructing crop pangenomes by long-read sequencing, which enables the integration of complex variation from multiple genomes of a target species in a single representation and can be feasibly used for subsequent population genetic analyses.
During plant domestication, significant genomic changes have occurred, driven by evolutionary forces such as genetic drift and artificial selection. CD Genomics provides crop population genomics analyses through high-throughput sequencing to study factors such as the diversity of wild population substructures, the relative genetic contribution of different wild subpopulations to cultivated populations, and the timing of the decline in diversity, to help you better address the process of domestication selection of target genes. Combined with quantitative trait locus (QTL) mapping and whole genome association studies (GWAS), we can help you identify the genes responsible for domestication-related traits and explore the selection processes and functions of these genes.
Advantages of our crop domestication solution
By understanding the molecular events associated with crop domestication, it will become easier to capture new genes from wild species.
Re-sequencing of domesticated species can identify regions of low diversity generated by selection during domestication.
Low-coverage birdshot NGS of whole genomes of wild relatives can be used to identify gene-specific sequences to help clone homologs of key domestication genes in wild relatives.
NGS of amplicons from a large number of candidate genes from wild and domesticated plant populations can define the diversity of target genes in wild populations and identify key genes for important traits through association analysis.
CD Genomics is committed to finding beneficial alleles and enriching multiple target alleles for crop domestication. Our NGS supports the rapid domestication of new plant species as well as the efficient identification and capture of new genetic variation in related species. If you are interested, please feel free to contact us.
Reference
Meyer, Rachel S., Ashley E. DuVal, and Helen R. Jensen. Patterns and processes in crop domestication: an historical review and quantitative analysis of 203 global food crops. New Phytologist. 196.1 (2012): 29-48.
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CD Genomics is propelling the future of agriculture by employing cutting-edge sequencing and genotyping technologies to predict and enhance multiple complex polygenic traits within breeding populations.
Fig. 1. The domestication history of barley (Hordeum vulgare ssp. vulgare) from its wild ancestor (Hordeum vulgare ssp. spontaneum), shown as a continuous process along a timeline. (Meyer et al., 2012)
