Sequencing

11th Annual Sequencing, Finishing, and Analysis in the Future Meeting
A GENOME IN THE SUGAR BEET FIELD
Friday, 3rd June 12:00 La Fonda Ballroom Talk (OS‐8.02)
Mitch McGrath 1 , Belinda Townsend 2 , Karen Davenport 3 , Hajnalka Daligault 3 ,
Shannon Johnson 3 , Alex Hastie 4 , Sven Bockland 4 , Aude Darracq 5 , Glenda Willems 5 ,
Steve Barnes 5 , Paul Galewski 6 , Andy Funk 6 , Jane Pulman 6 , Tiffany Liu 6 , Kevin Childs 6 ,
Robert Bogden 7 , Jon Wittendorp 7
1 USDA‐ARS & Michigan State University, 2 Rothamsted Research,
3 Los Alamos National Laboratory, 4 BioNano Genomics, 5 SES Vanderhave,
6 Michigan State University, 7 Amplicon Express
Beets (Beta vulgaris) have been, and are, widely consumed food and fodder crops over the past
three millennia, most recently for their luxurious production of the sweetener sucrose, and perhaps
transitioning to a burgeoning energy and industrial crop that would hearken to its days fueling draft
animals during pre‐industrial times. As a member of the Carophyllales, a group of plant taxa known
for their habitation in stressful and unusual environments, their unusual chemo‐systematics, and
as a sister eudicot lineage to the asterid and rosid clades, beets occupy a niche in crop production
in cooler, northern temperate climates with remarkable ability to produce biomass and accumulate
solutes on an annual cycle. The capacity of beets to meet growing needs is prodigious. Promises of
productivity depend on the ability to engineer products, for which a schematic would be useful.
Such a resource is available through the genome, which in this case, was assembled during 2015
from raw reads to contigs (PacBio, Illumina) to scaffolds (BioNano, Dovetail), resulting in 86 superscaffolds
in 566 Mb with 6% N’s and collapsing to 9 pseudo‐molecules plus 5 super‐scaffolds (4.5
Mb) unassigned. Plant breeding only has two goals: Improvement in quality traits and protection of
existing traits. This schematic is being explored for features of trait construction (accumulation of
small molecules such as betalain pigments and sucrose), development, and genetic indicators of crop
diversity (leafy chards vs roots of vegetable and industrial beets) as well as disease resistance traits
(rhizomania “crazy root” disease, resistance gene analogs). Such a resource, tied to a host of inbred
genetic populations which themselves are a novel and unique resource for discovering genes through
traditional and new comparative approaches, now gives the ability to dissect the genetic architecture
of beets, and the phenology of agronomic trait development in general, in a species where
traditional genetic analyses have not been possible due to the out‐crossing nature of its breeding
system. Assembly of a high quality genome was relatively affordable from a deeply inbred individual.
With a defined genetic architecture, variants detected at the population level, the level for which
beet breeding has been most successful, are being identified with specific traits to gain insight into
the biochemical and physiological processes contributing. Paired with gene expression changes
across developmental transitions, specific genes responsible for bulk life‐stage properties may be
uncovered. Such phyto‐centric information has never been available for beets, and plants in general,
and strategies to exploit this information will likely still remain in the realm of particular crop
idiosyncrasies. And beets do have many idiosyncrasies, which ideally, will be better interpreted and
manipulated through close inspection of the beet genome.
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