1000’s of years in the past, individuals in South America started domesticating Solanum pimpinellifolium, a weedy plant with small, intensely flavored fruit. Over time, the plant developed into S. lycopersicum – the trendy cultivated tomato.
Though immediately’s tomatoes are bigger and simpler to farm in contrast with their wild ancestor, in addition they are much less immune to illness and environmental stresses like drought and salty soil.
Researchers from Boyce Thompson Institute, led by Zhangjun Fei, created a high-quality reference genome for S. pimpinellifolium and found sections of the genome that underlie fruit taste, dimension and ripening, stress tolerance and illness resistance. The results were published in Nature Communications on November 16.
“This reference genome will enable researchers and plant breeders to enhance traits like fruit high quality and stress tolerance within the tomato,” mentioned Fei, “for instance, by serving to them uncover new genes within the trendy tomato in addition to by reintroducing genes from S. pimpinellifolium that have been misplaced over time as S. lycopersicum was domesticated.”
Fei is a BTI college member and co-corresponding creator on the paper, in addition to an adjunct professor in Cornell College’s College of Integrative Plant Science (SIPS).
Though different teams had beforehand sequenced S. pimpinellifolium, Fei mentioned this reference genome is extra full and correct, thanks partially to cutting-edge sequencing applied sciences which can be in a position to learn very lengthy items of DNA.
“Older sequencing applied sciences that learn brief items of DNA can determine mutations on the single-base stage,” mentioned Shan Wu, a postdoctoral scientist in Fei’s lab and co-corresponding creator on the paper. “However they are not good at discovering structural variants, like insertions, deletions, inversions or duplications of enormous chunks of DNA.”
“Many identified traits of the tomato are brought on by structural variants, so that’s the reason we targeted on them,” Fei mentioned. “Structural variants are also understudied as a result of they’re harder to determine.”
Fei’s group in contrast their S. pimpinellifolium reference genome to that of the cultivated tomato, known as Heinz 1706, and located greater than 92,000 structural variants.
The researchers then combed the tomato pan-genome, a database with the genomes of greater than 725 cultivated and intently associated wild tomatoes, and found structural variants associated to many vital traits. For instance, the trendy cultivated tomato has some genomic deletions that scale back their ranges of lycopene, a pink pigment with dietary worth, and an insertion that reduces their sucrose content material.
Jim Giovannoni, BTI college member and co-author of the research, notes that many customers are disillusioned within the high quality and taste of contemporary manufacturing tomatoes as a result of previous breeding efforts ignored these traits in favor of efficiency and yield.
“Identification of the extra genetic range captured within the S. pimpinellifolium genome supplies breeders with alternatives to carry a few of these vital options again to store-bought tomatoes,” mentioned Giovannoni, who can be an adjunct professor in SIPS and a scientist with the U.S. Division of Agriculture’s Agricultural Analysis Service.
The researchers discovered many different structural variants that may very well be of curiosity to plant breeders, together with variants in quite a few disease-resistance genes and in genes concerned in fruit dimension, ripening, hormonal regulation, metabolism, and the event of flowers, seeds and leaves.
The group additionally discovered structural variants related to regulating the expression of genes concerned within the biosynthesis of lipids in fruit pores and skin, which might assist enhance the fruit’s post-harvest efficiency.
“A lot genetic range was misplaced throughout tomato domestication,” Fei mentioned. “These knowledge might assist carry a few of that range again and lead to tomatoes that style higher, are extra nutritious and extra resilient.”
Reference: Wang X, Gao L, Jiao C, et al. Genome of Solanum pimpinellifolium supplies insights into structural variants throughout tomato breeding. Nature Communications. 2020;11(1):5817. doi:10.1038/s41467-020-19682-0.
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