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A genomic atlas of gene switches in plants provides a roadmap for crop research

June 30, 2013

Canadian-led study will help scientists identify key genomic regions in canola, other food plants

TORONTO, ON — What allows cer­tain plants to sur­vive freez­ing and thrive in the Cana­di­an cli­mate, while oth­ers are sen­si­tive to the slight­est drop in tem­per­a­ture? Those that flour­ish acti­vate spe­cif­ic genes at just the right time — but the way gene acti­va­tion is con­trolled remains poor­ly under­stood.

A major step for­ward in under­stand­ing this process lies in a genom­ic map pro­duced by an inter­na­tion­al con­sor­tium led by sci­en­tists from the Uni­ver­si­ty of Toron­to (U of T) and McGill Uni­ver­si­ty and pub­lished online today in the jour­nal Nature Genet­ics.

The map, which is the first of its kind in plants, will help sci­en­tists to local­ize reg­u­la­to­ry regions in the genomes of crop species such as canola, a major crop in Cana­da, accord­ing to researchers who worked on the project. The team has sequenced the genomes of sev­er­al cru­cifers (a large plant fam­i­ly that includes a num­ber of oth­er food crops) and ana­lyzed them along with pre­vi­ous­ly pub­lished genomes to map more than 90,000 genom­ic regions that have been high­ly con­served but that do not appear to encode pro­teins.

“Plants are com­pli­cat­ed organ­isms, and they have many types of cells and struc­tures,” said Dr. Annabelle Haudry, one of the study’s lead authors and for­mer U of T post­doc­tor­al fel­low. “We found that genes involved in defin­ing how these cells and struc­tures grow as the plant devel­ops from a seed and how it responds to envi­ron­men­t’s stim­uli are sur­round­ed by many of these switch­es.”

“Amaz­ing­ly, sim­i­lar orga­ni­za­tion of switch­es was found for the genes that con­trol ear­ly human devel­op­ment from an embryo – an exam­ple of con­ver­gent evo­lu­tion,” says Robert Williamson, U of T PhD stu­dent and study coau­thor. (Con­ver­gent evo­lu­tion is the sci­en­tif­ic term for bio­log­i­cal traits that arrive through dif­fer­ent evo­lu­tion­ary lin­eages.) Work is cur­rent­ly under­way to iden­ti­fy which of those regions may be involved in con­trol­ling traits of par­tic­u­lar impor­tance to farm­ers.

“The study also weighs in on a major debate among biol­o­gists, con­cern­ing how much of an organ­is­m’s genome has impor­tant func­tions in a cell, and how much is ‘junk DNA,’ mere­ly along for the ride,” says U of T’s Pro­fes­sor Alan Moses, also involved in the study. While stretch­es of the genome that code for pro­teins are rel­a­tive­ly easy to iden­ti­fy, many oth­er ‘non­cod­ing’ regions may be impor­tant for reg­u­lat­ing genes, acti­vat­ing them in the right tis­sue and under the right con­di­tions.

While humans and plants have very sim­i­lar num­bers of pro­tein-cod­ing genes, the map pub­lished in Nature Genet­ics fur­ther sug­gests that the reg­u­la­to­ry sequences con­trol­ling plant genes are far sim­pler, with a lev­el of com­plex­i­ty between that of fun­gi and micro­scop­ic worms. “Plants seem to have a large frac­tion of their genome that is junk DNA,” says U of T’s Pro­fes­sor Stephen Wright, anoth­er leader of the study. “But our analy­sis allows for iden­ti­fi­ca­tion of the tens of thou­sands of ‘nee­dles in the haystack’ that are impor­tant for gene reg­u­la­tion.”

Fund­ing for the research was pro­vid­ed by Genome Cana­da and Génome Québec, along with the Euro­pean Region­al Devel­op­ment Fund, the Czech Sci­ence Foun­da­tion, and the Nation­al Sci­ence Foun­da­tion.


For more infor­ma­tion, con­tact:

Alan Moses, Assis­tant Pro­fes­sor
Depart­ment of Cell and Sys­tems Biol­o­gy
Uni­ver­si­ty of Toron­to
Cell: +1–416-709‑7566

Stephen Wright, Asso­ciate Pro­fes­sor
Depart­ment of Ecol­o­gy & Evo­lu­tion­ary Biol­o­gy
Uni­ver­si­ty of Toron­to
Lab: +1–416-946‑0686
Office: +1–416-946‑8508

Uni­ver­si­ty of Toron­to Media Rela­tions
Tel: +1–416-978‑0100