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Artificial intelligence accelerates search for markers of resistance to sugarcane yellow leaf disease

Publicado em 29 outubro 2021

Yellow leaf illness, a serious sugarcane pest in Brazil, is attributable to a virus proof against thermal remedy. An contaminated plantation may be saved solely by rising plantlets in tissue tradition within the laboratory and planting them out, a time-consuming course of that requires specialised infrastructure and personnel. According to a bunch of scientists who’ve lengthy studied the issue, the simplest method to management the illness is to develop varieties which are proof against the sugarcane yellow leaf virus. This is the aim of a undertaking that’s being carried out with FAPESP’s help.

The scientists are affiliated with universities (University of Campinas – UNICAMP, São Paulo State University – UNESP), and state-run agribusiness analysis institutes (Campinas Agronomic Institute – IAC, Biological Institute – IB) from São Paulo state, Brazil, and with Ecuador’s ESPOL Polytechnic. In an article published recently within the journal Scientific Reports, they describe how they used genomics, machine studying, and statistics to refine and speed up the seek for molecular markers of resistance to the illness.

The group discovered that resistant varieties are principally kinds of so-called power cane, with greater fiber content material and fewer sugar content material than typical cane, and therefore fittest for second-generation or cellulosic ethanol manufacturing, though a minimum of one is match for sugar or typical ethanol manufacturing – a lot in order that it has simply been commercially launched by IAC.

The researchers evaluated 97 sugarcane genotypes, together with wild germplasms of Saccharum officinarum, S. spontaneum and S. robustum, conventional sugar and power cane clones, and industrial varieties developed by Brazilian breeding applications.

“We analyzed the resistance of each of these varieties to yellow leaf disease. The aim was to associate disease resistance with genetic traits. We used several different molecular markers, which are DNA variations, deploying next-generation sequencing to access this information,” mentioned Ricardo Pimenta, a doctoral researcher at UNICAMP’s Center for Molecular Biology and Genetic Engineering (CBMEG).

The varieties have been chosen by IAC’s cane breeding program. Most have been a part of this system, however there have been additionally specimens from the Inter-University Network for Development of the Sugar and Ethanol Industry (RIDESA) and the Sugarcane Technology Center (CTC).

“The collection was representative of the variability of Brazilian cane, both planted and used in cross-breeding to produce other varieties,” mentioned Anete Pereira de Souza, a professor within the Department of Plant Biology at UNICAMP’s Institute of Biology and undertaking coordinator at CBMEG.

The signs of sugarcane yellow leaf illness sometimes seem within the later phases of the plant’s improvement. The foremost symptom is intense yellowing of leaf midribs. The illness alters photosynthetic effectivity in addition to sucrose metabolism and transport, impairing progress and yield.

Methods

According to Pimenta, the article describes an experimental process that had by no means been tried earlier than. “The yellow leaf virus is transmitted by the sugarcane aphid Melanaphis sacchari,” he mentioned. “The IAC team planted experimental plots and at the same time reared aphids on plants already infected by the virus. The aphids were then released into the uninfected plantations and monitored in a controlled process of inoculation and infection. Previous studies used a similar approach, except that they planted the cane and left it to be infected naturally, as it were, in a less controlled inoculation process.”

Viral load was measured by reverse transcription-quantitative polymerase chain response (RT-qPCR). “We used PCR to quantify the virus in the entire set of cane varieties analyzed,” Pimenta defined. Disease severity was assessed by observing leaf yellowing depth and different signs, which might typically be elusive.

To set up associations between illness resistance and genetic traits, the researchers used genomic strategies, machine studying (a synthetic intelligence process based mostly on sample recognition), function choice, and marker-trait affiliation strategies.

“What we normally find in genomic association studies is markers that strongly influence the phenotype [ observable characteristics ]. That’s a problem because you can’t find the others that have less influence on the phenotype. Feature selection captures markers that influence the phenotype in a narrower sense, so we used the technique to screen molecular markers more efficiently,” mentioned Alexandre Hild Aono, additionally a researcher at CBMEG.

Machine studying was used to assemble a mannequin that predicted whether or not a range was resistant or prone to the virus, given the required genetic markers. “To do this, the algorithms first have to rate markers ‘highly important’ or ‘less significant’ for predictive purposes. The question therefore was this: If the system rates certain markers highly, do they also influence the phenotype? Our investigation confirmed this was indeed the case,” Aono mentioned. “We combined the various methodologies and succeeded in filtering and selecting markers with the most potential to influence configuration of the disease directly, even though they may not be especially conspicuous [ in terms of influencing the phenotype ].”

One of the goals of the research, Souza recalled, was to match the outcomes of the methodological strategies with the intention to see in the event that they converged. “We found a larger set of markers with the methodology proposed, but it was also validated by traditional statistics. They talk to each other, and by using them in association we were able to obtain a much broader dataset for analysis and a richer basis for genetic improvement,” she mentioned.

The multidisciplinary workforce achieved an unprecedented stage of element on this research, she added: “We compared the methodologies and demonstrated the efficiency and necessity of using a more refined statistical approach. Nothing in the literature suggests anyone had ever done this type of analysis, or reared the aphids, infected the plants, and then measured viral load with quantitative PCR. The results serve as a foundation and guide for future research, contributing to a better understanding of the molecular mechanism involved in the disease.”

The research was supported by FAPESP by way of a master’s scholarship and a direct doctorate scholarship awarded to Pimenta; a direct doctorate scholarship awarded to Aono; and a postdoctorate scholarship awarded to Carla Cristina da Silva, one other co-author of the article.

Disease resistance

According to Pimenta, genuinely resistant crops that don’t manifest signs or accumulate viral load account for a small proportion of the whole. “Few are really resistant. Most plants don’t display symptoms but accumulate viral load, which eventually becomes a problem because the pathogen is there without the producer being aware of it. Our findings can help eliminate susceptible varieties as well as tolerant varieties, which accumulate viral load without displaying symptoms and can become a viral reservoir,” he mentioned, stressing that the principle problem in crop breeding is selecting the right varieties with out dropping an excessive amount of variability.

Many resistant varieties are representatives of power cane. “They have a recent ‘wild’ ancestor that’s more disease resistant, so this result isn’t a surprise. But we also discovered more commercial varieties that proved resistant, and these are more interesting. One of them, IACSP04-6007, proved so promising that it’s just been launched by IAC’s breeding program,” Pimenta mentioned.

Besides this one, the next varieties have been additionally discovered to be most proof against yellow leaf illness (no signs and low viral masses): IACBIO241, IACBIO257, IACBIO266, IACBIO270, IACBIO271, IACBIO273, IACBIO275, IACBIO279, IACCTC 05-3616, IACSP04-2510, IACSP98-5046, IJ76293, IN8482, IN8488, and Krakatau.

Pimenta additionally famous the significance of the genes related to the markers recognized. “Some of the most striking examples include the gene for a peroxidase, an enzyme previously associated with resistance to this disease; the gene for a Dicer, a very important enzyme in plants’ viral response mechanism; and several genes containing leukin-rich repeats widely involved in plants’ immune responses to pathogens,” he mentioned.

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About São Paulo Research Foundation (FAPESP)

The São Paulo Research Foundation (FAPESP) is a public establishment with the mission of supporting scientific analysis in all fields of information by awarding scholarships, fellowships and grants to investigators linked with greater schooling and analysis establishments within the State of São Paulo, Brazil. FAPESP is conscious that the perfect analysis can solely be carried out by working with the most effective researchers internationally. Therefore, it has established partnerships with funding companies, greater schooling, non-public firms, and analysis organizations in different international locations recognized for the standard of their analysis and has been encouraging scientists funded by its grants to additional develop their worldwide collaboration. You can be taught extra about FAPESP at http://www.FAPESP.br/en and go to FAPESP information company at http://www.agencia.FAPESP.br/en to maintain up to date with the most recent scientific breakthroughs FAPESP helps obtain via its many applications, awards and analysis facilities. You may additionally subscribe to FAPESP information company at http://agencia.FAPESP.br/subscribe.