b'S T R A T E G Y A featured segment designed to help you in the realm of retail seed sales. Better Defense for Better TomatoesAs Tomato Brown Rugose Fruit Virus infects tomato and pepper plants across the globe, seed companies are working on breeding a resistant tomato.Joe FunkTHOUSANDS OFstructural variants, says YEARSago, when farm- pan-genome project leader ers in South America beganZhangjun Fei. Structural vari-domesticating tomatos wildants are understudied because ancestors, Solanum pimpinel- they are more difficult to iden-lifolium, they were workingtify. That is why we focused on with weedy-looking plantsthem. that produced small albeitIn 2019, an interna-intensely flavored fruit. Overtional group of research-time, through continueders constructed a tomato selection, tomatoes evolvedpan-genome using genome into the larger, modern culti- sequences from 725 phyloge-vated tomato. What modernnetically and geographically tomatoes gained in size, theyrepresentative varieties. This lost in disease resistance anddatabase includes 4,873 genes ability to withstand abioticnot found in the original refer-stress. For more than 100ence genome. Present/absent years, plant breeders havevariation analyses revealed been on a continual trek tosubstantial gene loss and improve tomato yield andintense negative selection of disease resistance.genes and promoters during Rich genetic and genomictomato domestication and resources were available toFor more than 100 years, plant breeders have been climbing up hillimprovement. tomato breeders even beforeto improve tomato yield and disease resistance.Feis group compared the inception of the tomatostheir wild variety genome to genomic sequencing projects.ligence, machine learning andpart to cutting-edge sequenc- the genome of Heinz 1706, a Large tomato germplasm col- advanced algorithms to ana- ing technologies that can readcultivated variety included in lections have long been estab- lyze large quantities of geneticvery long pieces of DNA, thethe construction of the original lished in several locations.and phenotypic data.reference genome is moretomato genome. The compari-More than 75,000 tomatocomplete and accurate thanson found more than 92,000 accessions are conserved inTomato Pan-Genome the existing database. structural variants. Many of genebanks around the world.Researchers from the BoyceOlder sequencing technol- these structural variants are One of the largest is the USDAThompson Institute in 2020ogies that read shorter piecesof potential interest to plant genebank at Geneva, NY.created a high-quality ref- of DNA identifies mutations atbreeders. The variants pertain Sequencing of the tomatoerence genome for wildthe single-base level. However,to numerous disease-resist-genome was initiated intomatoes to produce a morethey are not good at findingance genes as well as to genes 2005 as a multinationalcomplete and useful tomatostructural variants such asinvolved in fruit size, ripening, effort between 14 coun- pan-genome. They discoveredinsertions, deletions, inver- hormonal regulation, metabo-tries and completed in 2012.sections of the genome thatsions or duplications of largelism, and the development of These efforts have beenunderlie fruit flavor, size andchunks of DNA. flowers, seeds and leaves.greatly accelerated with theripening, stress tolerance andMany known traits ofOnce a genomic region is application of artificial intel- disease resistance. Thanks inthe tomato are caused byfound, molecular geneticists 60/ SEEDWORLD.COMFEBRUARY 2021'