The full genome sequence of the carrot has finally been reported for the first time in a paper published this week in Nature Genetics (“A high-quality carrot genome assembly provides new insights into carotenoid accumulation and asterid genome evolution”, http://www.nature.com/ng/journal/vaop/ncurrent/full/ng.3565.html#contrib-auth) representing one of the most complete vegetable genome assemblies known to date. The genome sequence sheds light on the evolutionary origin of the carrot, the distinctive orange colour of its root and its nutritious value. To our knowledge, man first experimented with carrot 1,100 years ago when these were mainly yellow and purple. By the sixteenth century, Europeans, and more specifically the Dutch, began to cross the most orange varieties to achieve the classic orange carrot we know today.
The international research group we joined, led by Philipp Simon from the Department of Horticulture, University of Wisconsin–Madison, Madison, Wisconsin, USA assembled a high-quality reference genome, identifying 26,320 genes, with 10,530 genes unique to carrot. Then we sequenced 35 different carrot specimens and subspecies, both wild and cultivated, to understand domestication patterns. We then compared the carrot sequence to other plant genomes and determined when carrots diverged from grapes, kiwis and tomatoes. Eventually, we found a gene responsible for the uncommonly high accumulation of beta-carotene, a vitamin A precursor, in the carrot root.
This news is relevant in terms of the nutritional role of carrot. FAO notes that between 1976 and 2013, the production of this vegetable has quadrupled, and not only in developing countries. In the United States, carrots are the leading source of pro-vitamin A.
In only 40 years the amount of beta carotene in carrots has increased by 50% just by cross-breeding. The information discovered in our study can be used to help breeders improve the nutritional quality of not only carrots but other diverse crops as well.
“The carrot is the first published genome of a group of plants called Euastéridas II, which is very important because this group also includes lettuce, celery and sunflower,” says Walter Sanseverino, Sequentia Biotech’s CEO. “Having a reference genome sequenced will aid in the future development of new varieties and improve cross-breeds within this branch of fundamental food plants.”
How did Sequentia Biotech contribute to this research?
“We developed a tool that is able to search all the well known plant resistance genes (R-Genes) whose roles are very important in plants because they protect them naturally from pathogenic microorganisms or bacteria,” continues Walter Sanseverino. “We have been waiting for a good tool that enables us to study and understand these genes very well. In the end, we created this tool in Barcelona and it allowed us to find which of the 32,113 carrot genes serve to protect the plant. Our tool is now becoming a reference in the world of genomics to search these types of genes, and has been used for tomato, melon and wild potato.”
The tool we are talking about, known as Matrix-R, has been recently updated, thus becoming an even more powerful instrument to analyze pest and disease resistance genes, giving rise to its new name: DRAGO2.
Thanks to this tool we predicted 634 putative pest and disease resistance (R) genes in carrot (Supplementary Tables 29–34 and Supplementary Note). Most R gene classes were under-represented in carrot. The expanded orthologous subgroups included classes containing the NBS and LRR protein domains (NL) and coiled-coil NBS and LRR domains (CNL). Lineage-specific duplications contributed to the expansion and diversification of these R gene families in carrot and other genomes (Supplementary Fig. 21 and Supplementary Table 35). Many R genes (206) were located in clusters, and these clusters tended to harbour genes from multiple R gene classes (Supplementary Tables 36 and 37). The expansion of the NL and CNL families might reflect evolutionary events by generating tandem duplications, resulting in preferential clustering on chromosomes 2 and 3–7 respectively (Supplementary Fig. 22). One cluster containing three RLK genes and one LRR gene, spanning only 50 kb, colocalized with the Mj-1 carrot region, which controls resistance to Meloidogyne javanica, a major carrot pest39 (Supplementary Fig. 22). This analysis demonstrates the important role of tandem duplications in the expansion of R genes in carrot. Additionally, R gene clusters may provide a reservoir of genetic diversity for newly evolving plant–pathogen interactions.
Moreover, following the company’s philosophy of using science in a socially-conscious, sustainable and effective way, Sequentia has put all the genomics data available on R-genes on the web (www.prgdb.org), so that anyone interested can download them. “These genes are very important because if we know where they are, we can improve plants in a natural way, just by knowing what genes must be present in the progeny.”