Researchers Complete Mapping of Frantoio, Leccino Genomes

Summary

An inter­na­tional team of researchers has mapped the com­plete genome of the Leccino and Frantoio olive tree vari­eties, pro­vid­ing valu­able infor­ma­tion for under­stand­ing olive tree genet­ics and devel­op­ing more resilient trees in the face of cli­mate change. By com­par­ing the genomes of these two cul­ti­vars, researchers aim to iden­tify genes related to stress responses and poten­tially use gene edit­ing tech­niques to enhance traits such as salt tol­er­ance. This genomic research could rev­o­lu­tion­ize olive tree farm­ing, lead­ing to more pro­duc­tive and inno­v­a­tive solu­tions for grow­ers fac­ing chal­lenges in the Mediterranean cli­mate.

An inter­na­tional team of researchers has mapped the com­plete genome of the Leccino and Frantoio olive tree vari­eties.

The genomic map­ping of the two native Italian cul­ti­vars, now grown in dozens of coun­tries, will enable researchers to com­pare them and pave the way for a deeper under­stand­ing of olive tree genet­ics.

“In times of cli­mate change, know­ing more about olive trees’ genomics means know­ing more about how those trees react to major and some­times new envi­ron­men­tal stres­sors,” said Luca Sebastiani. 

The study’s coor­di­na­tor, who is also a full pro­fes­sor of hor­ti­cul­tural sci­ences at the Scuola Superiore Sant’Anna di Pisa, told Olive Oil Times that genomics could yield more resilient olive groves in the Mediterranean basin.

“To adapt to cli­mate change, we need resis­tant geno­types, as well as suit­able agro­nomic tech­niques,” Sebastiani said. ​“If water is lack­ing, there will be a need for irri­ga­tion, but also cul­ti­vars that use water effi­ciently. There are also chal­lenges related to higher tem­per­a­tures, new pathogen sen­si­tiv­ity and insect attacks.” 

“Gene map­ping is one of the tools that can allow us to find solu­tions more quickly,” he added.

While olive tree gene edit­ing is still in its infancy, com­par­ing the genomes of the two cul­ti­vars could yield more resilient trees more quickly than tra­di­tional breed­ing pro­grams. 

Both Frantoio and Leccino are well doc­u­mented in the sci­en­tific lit­er­a­ture, as is their behav­ior when cop­ing with envi­ron­men­tal stress.

“Their responses to stress, both drought and espe­cially salin­ity, are very inter­est­ing mod­els, because Frantoio is tol­er­ant, while Leccino is less so,” Sebastiani said.

“We have been work­ing for years to explain the mech­a­nism behind this dif­fer­ence, but with­out genomic data, it was always dif­fi­cult to fully under­stand which genes might be involved,” he added.

“Sequencing allows us to have a vocab­u­lary with which to under­stand why these two cul­ti­vars are dif­fer­ent,” Sebastiani noted.

According to the researchers, the com­mon prac­tice of select­ing olive vari­eties through tra­di­tional breed­ing is time-con­sum­ing and does not always yield the best results.

In their paper, researchers noted that mixed results occur since ​“pre­cise mol­e­c­u­lar infor­ma­tion on gene loca­tion and struc­ture is largely miss­ing.” It took the sci­en­tists more than two years to com­plete the map­ping. 

“We made it thanks to the funds from Italy’s National Recovery and Resilience Plan and thanks to the fact that we are a fairly large group,” Sebastiani said, which also included col­leagues from the University of Arizona and King Abdullah University of Science and Technology in Saudi Arabia.

A high per­cent­age of Long Terminal Repeats was found in both cul­ti­vars, indi­cat­ing a sig­nif­i­cant sim­i­lar­ity in their genome.

Repeated DNA sequences are not ran­dom, as they are shaped by evo­lu­tion and may play impor­tant roles, such as help­ing main­tain the sta­bil­ity and integrity of the genome.

“We do not know very well yet how the dif­fer­ent parts of the genome inter­act,” Sebastiani said. ​“Now that we have this infor­ma­tion in dif­fer­ent cul­ti­vars, we can begin to see those dif­fer­ences, and this could help us under­stand the species bet­ter in the com­ing years.” 

He com­pared the chal­lenge the researchers faced in map­ping the genomes of the two cul­ti­vars to com­plet­ing a jig­saw puz­zle, where half of the pieces are of a clear blue sky.

“In such a case, con­nect­ing the puz­zle pieces is way more com­pli­cated com­pared to one that presents a lot of vari­a­tions,” he said. ​“This is a prob­lem in olives, because we have many highly repet­i­tive regions.” 

Locating the posi­tion of genes within a genome is fun­da­men­tal to trans­form­ing raw DNA sequences into prac­ti­cal knowl­edge, and it helps researchers link a gene to a spe­cific trait, such as yield, oil com­po­si­tion, or resis­tance to pests and dis­eases. 

This knowl­edge accel­er­ates breed­ing pro­grams, replac­ing slow, ran­dom selec­tion with tar­geted approaches. 

Gene posi­tion also reveals how they are reg­u­lated and inter­act, offer­ing insights into adap­ta­tion and domes­ti­ca­tion. 

In olives, accu­rate maps enable sci­en­tists to com­pare cul­ti­vars, trace evo­lu­tion­ary changes, and design pre­ci­sion tools such as marker-assisted breed­ing or gene edit­ing to develop more resilient and high-qual­ity vari­eties.

“This high-qual­ity map­ping can only be done when you have tech­niques that sequence very large frag­ments, which makes it eas­ier,” Sebastiani said.

“Over the years, there has been a huge evo­lu­tion in tech­niques,” he added. ​“Today we have PacBio, which allows the sequenc­ing of longer DNA frag­ments, some­thing that was not pos­si­ble before.”

In a state of stress, such as that induced by soil salin­ity or drought, only a hand­ful of genes may be involved, with dif­fer­ences observed between the two cul­ti­vars.

“A small dif­fer­ence in gene struc­ture, or even in the pro­moter region that reg­u­lates how much the gene func­tions, may cause a gene not to work at all, or to be less active, or to be more active,” Sebastiani said.

He added that iden­ti­fy­ing and under­stand­ing the dif­fer­ences is cru­cial.

“If I under­stand that a gene involved in a cer­tain type of stress has one struc­ture in Frantoio and another in Leccino, and it works bet­ter in Frantoio and worse in Leccino, I can then also use gene expres­sion analy­sis tech­niques, with RNA sequenc­ing or other tech­nolo­gies, to see if that struc­tural vari­a­tion affects activ­ity,” Sebastiani said.

“If I dis­cover that it does, we also now have genetic edit­ing,” he added. ​“In olives, it’s not yet very effec­tive, but I could rewrite the Leccino gene to mimic the form of the Frantoio gene, trans­fer­ring that infor­ma­tion so it works dif­fer­ently.”

However, Sebastiani explained that research into edit­ing olive tree genes is still in its early stages of exper­i­men­ta­tion com­pared to other species. 

“I also work on poplar [the genus of 35 species of wil­low trees] with my group,” Sebastiani said. ​“In poplar, we can already do it. In olive trees, the prob­lem is still trans­for­ma­tion dif­fi­cul­ties with these edit­ing tech­niques; it might take years.”

While there have been rapid advances in gene edit­ing tech­nol­ogy, Sebastiani acknowl­edged that it was impos­si­ble to esti­mate how long this might take. 

Still, he expects the quick devel­op­ment of genomics and related tech­nolo­gies might have an impact in a rel­a­tively short time com­pared to pre­vi­ous approaches.

“Today, even using tra­di­tional tech­niques but assisted by mol­e­c­u­lar biol­ogy, if I cross Leccino and Frantoio to trans­fer salt tol­er­ance, I would have to wait until the plant grows and then test it. That takes a very long time,” he said.

“If instead I look directly for the gene struc­ture, I can already track it with genomics or other tech­niques,” Sebastiani added. ​“Today I can even sequence the whole genome at reduced cost, and since I already have the ref­er­ence genome, I can see exactly where that gene is and in what posi­tion.”

“I could take Leccino, know­ing that two or three genes increase tol­er­ance, and mod­ify only those,” he noted. ​“With edit­ing, if every­thing worked, in one or two years, it could be done in the lab. That would be a big step for­ward.”

Genomics and map­ping the olive tree genes could pave the way to a new approach to olive tree farm­ing. 

While tra­di­tional farm­ing often involves cen­tury-old olive orchards, new groves planted with the gene-edited olive vari­eties could prove cru­cial in sup­port­ing pro­duc­tion against the back­drop of a hot­ter and drier Mediterranean cli­mate.

“Such new knowl­edge could trans­late into changes in pro­duc­tiv­ity, inno­va­tion and solu­tions for grow­ers,” Sebastiani said. 

The research team will uti­lize the new genomic infor­ma­tion to gain a deeper under­stand­ing of the dif­fer­ences between the two cul­ti­vars in response to salt stress. 

“We also plan, if pos­si­ble, to sequence more vari­eties that inter­est us for their responses to other stresses, includ­ing pol­lu­tants,” Sebastiani con­cluded. ​“We’ll def­i­nitely use genomics to under­stand mech­a­nisms bet­ter.”