Carrot Genome

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A Complete Genome for the Carrot

Circle of Carrots

Photo compliments of USDA Agricultural Research Service, where researchers have selectively bred carrots with pigments that reflect almost all colours of the rainbow. More importantly, though, they are very good for your health. Photo by Stephen Ausmus, USDA.
Often the evolutionary history of a species can be found in a fossil record. Other times, DNA and genetic fingerprints replace rocks and imprints. That is the case for the carrot, the richest crop source of vitamin A in the American diet, whose full genetic code has been deciphered by a team led by the University of Wisconsin–Madison in collaboration with the University of California, Davis.

May 2016 - Scientists have unveiled the gene in carrots that gives rise to carotenoids, a critical source of Vitamin A and the pigment that turns some fruits and vegetables bright orange or red. The new, high-quality genome assembly, which the researchers established for an orange doubled-haploid carrot (Nantes variety), contains more than 32,000 predicted protein-coding genes. .As the researchers reported  they were able to track down a candidate gene involved in orange carrot pigmentation and gained insight into the evolution of plants in the euasterid II lineage, which contains carrots, lettuce, sunflower, celery, and parsley.

Formally named DCAR_032551, the star gene emerged from the first complete decoding of the carrot genome, published in the scientific journal "Nature Genetics". The gene  which "conditions carotenoid accumulation in carrot taproot," according to the research in the science journal Nature Genetics. The researchers believe the gene "regulates upstream photosystem development and functional processes, including photomorphogenesis and root de-etiolation" of the carrot.

The study reveals how the orange colour occurs and which genes are involved, and also shows that carrot colour is not genetically connected to flavour. It is fortuitous that coloured carrots became popular, because the pigments are what make carrots nutritious, and orange carrots are the most nutritious of all.

University of Wisconsin–Madison horticulture professor and geneticist Phil Simon, who led the research team, said: "Now we have the chance to dig deeper and it's a nice addition to the toolbox for improving the crop."

Co-author Allen Van Deynze, Seed Biotechnology Center director of research at the University of California, Davis, added: "This was an important public-private project, and the genomic information has already been made available to assist in improving carrot traits such as enhanced levels of beta-carotene, drought tolerance and disease resistance. Going forward, the genome will serve as the basis for molecular breeding of the carrot."

The study reveals that genes for colour and genes associated with preferred flavours are not connected, and that early breeders' preference for orange carrots was fortuitous as the beta-carotene pigments are what make them nutritious, Simon explained.

"The accumulation of orange pigments is an accumulation that normally wouldn't happen," he said. "It's a repurposing of genes plants usually use when growing in light."

The researchers also sequenced 35 different types of carrots to compare them to their wild ancestors. They showed that carrots were first domesticated in the Middle East and Central Asia, confirming the Vavilov Center of Diversity theory, which predicts cultivated plants arose from specific regions rather than randomly. Sometime about 1,100 years ago, farmers living in what is now Afghanistan took advantage of a mutation in the Y gene that put it to work down in their carrots' roots. In the process of domesticating the white, wild carrot, they turned it yellow. Six hundred years later in Europe, cultivation took another turn, and carrots deepened in hue from yellow to dark orange.

It's obvious that farmers were selecting for the mutation that concentrated carotenoids in the carrot root. It's a good thing they did so, too, since it made carrots much more nutritious. But health can't have been bygone breeders' motivation - no one in the 9th century knew what a carotenoid was, let alone that it was a source of a vitamin that's good for our eyes, immune systems and other organs.

So Simon examined flavour, to see if colourful carrots tasted better. Again, no dice: Orange carrots and their white counterparts taste pretty much the same. There are other possibilities - perhaps the gene for colour is linked to one for size, or hardiness. Or perhaps historic humans just liked the way yellow and orange carrots looked.

Is it possible that this is one question best answered by people, rather than carrots?

Senior author Phillip Simon, a horticulture researcher affiliated with the University of Wisconsin at Madison and the US Department of Agriculture's Agricultural Research Service said "The motivation was to get as complete a genome for carrot as we could … for basic knowledge reasons and from the standpoint of crop improvement - It gives us a better handle on genomic regions to track when we're in the plant breeding process, and to get a better handle on the process of gene expression in both basic and applied applications."

He also noted that the results are generating interest amongst carrot breeders in the public sector, at academic institutions, and seed companies.

Carotenoids were first discovered in carrots (hence the name), but which among the vegetable’s newly tallied 32,115 genes was most responsible for their formation remained a mystery.

Daucus carota (the Latin name) now joins a select club of about a dozen veggies — including the potato, cucumber, tomato and pepper — whose complete genomes have been sequenced

Laying bare the humble carrot’s genetic secrets will make it easier to enhance disease resistance and nutritive value in other species, the researchers said.

Having identified the mechanism controlling the accumulation of carotenoid, it may be possible - through gene-editing, for example — to import it to other staple root vegetables such as the cassava, native to South American and widely grown in Africa.

“These results will facilitate biological discovery and crop improvement in carrots and other crops,” said Philipp Simon, senior author and a professor at the University of Wisconsin-Madison.

Interestingly, carrots — along with many other plants — have about 20 percent more genes than humans. This enables carrots to better thrive and develop through changing environmental conditions.

Looking back at the plant’s family tree, scientists have been able to determine that it split with the grape about 113 million years ago and from the kiwi about 10 million years after that. The research team traced carrot evolution as far back as the dinosaurs. Sometime between the Cretaceous and Paleogene periods - roughly around the time dinosaurs went extinct - carrots, along with other plants of the era, picked up genetic advantages that allowed them to thrive in differing environmental conditions.

At 32,000 genes, the carrot genome is a good deal longer than that of humans (somewhere between 20,000 and 25,000 genes). It's not actually surprising that a lowly carrot's DNA would have to be more sophisticated than a human's, after all, plants can't choose or change their environments, so they need to prepare for all contingencies, stocking their genome with traits that can be turned on or off depending on changing environmental circumstances.

The Technical Bits

To delve into carrot traits and the history of the euasterid II clade, the researchers performed Illumina paired-end sequencing on libraries with a range of insert sizes on an orange, doubled-haploid, Nantes-type carrot called DH1, which has an estimated genome size of 473 million bases. The sequence data was then combined with bacterial artificial chromosome end reads and linkage map data.

They also sequenced RNA from 20 DH1 carrot tissues and did genome re-sequencing on representatives from 35 carrot accessions spanning several D. carota sub-species or outgroups.

The reference genome assembly spanned 421.5 million bases, with nearly half of assembled sequences stemming from transposable elements and other repetitive sequences. The team's annotation efforts uncovered 32,113 predicted protein-coding genes — including thousands of suspected regulatory genes — along with almost 250 microRNAs, and more than 1,000 more non-coding RNAs.

"It's a relatively small genome," Simon said, "and that certainly played into our ability to be able to say that … it's one of the most complete [plant genomes] in coverage and contiguity."

From the re-sequencing data, the researchers identified almost 1.4 million high-quality SNPs, which they used to cluster the carrot accessions into groups coinciding with plant geography, origins in Central Asia, and cultivation history.

The study confirmed that the “Y” gene is responsible for the difference between white carrots and yellow or orange carrots. It is one of two genes responsible for converting ancestral wild-type white carrots to orange ones. It also identified a new, previously unknown gene that contributes to the accumulation of the colourful compounds. The newly discovered gene is actually a defect in a metabolic pathway that appears to be related to light sensing, the researchers said.

Plants derive their own nutrition through light sensing, or photosynthesis, but roots like carrots aren’t normally exposed to light and do not need photosynthetic pigments like carotenoids. The carrot has, in a sense, repurposed genes that plants usually use when growing in light.

The researchers also compared the carrot genome to sequences from more than a dozen other plants ranging from potato and tomato plants in the euasterid I clade — which diverged from carrot ancestors around 90.5 million years ago — to more distantly related grape and kiwi plants. They saw evidence of two past whole-genome duplications in the carrot lineage, one taking place roughly 70 million years ago, with a more recent duplication occurring an estimated 43 million years ago.

Meanwhile, the researchers' fine mapping search for genes related to key carrot traits led them to a candidate gene called DCAR_032551 on chromosome 5 that appears to influence the accumulation of the carotenoid pigment, turning otherwise white carrots orange. That pigment is mainly found in domestic carrots, Simon explained, and was not documented prior to the 16th century when it first appeared in Europe.

In addition to the "generic" carrot genome, the researchers also sequenced DNA from 35 different wild and cultivated specimens and sub-species to shed light on domestication patterns. The carrot genome would assist the identification of other candidate genes behind "healthy" plant compounds such as flavonoids, as well as mechanisms involved in stress resistance, growth, flowering, seed production and regeneration, said the scientists.

All these properties were said to be "important traits for sustained agricultural production and improved human health".

The team is now following up on this and other leads from the study, including genes that may contribute to the production of anthocyanin, lycopene, and lutein pigments that lend some carrots their purple, red, and yellow colouring, respectively. Simon noted that the researchers are also investigating genes involved in resistance to plant disease or pests such as nematodes, and genes that mediate key plant growth features or response to abiotic stressors such as drought.


Reference - Nature Genetics (2016) doi:10.1038/ng.3565 Received 23 September 2015 Accepted 11 April 2016 Published online 09 May 2016   link here

 

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Reference material here. Also read the Comprehensive Review of Carrot Colors and their properties here.

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