EAGER: Clonal propagation of tomato through seeds

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The large-scale use of hybrid seeds over the past century has contributed to a revolution in agriculture. Hybrid crop plants produce high yields, but due to genetic segregation, their progeny have variable and frequently low yields. This means that hybrid seeds have to be generated afresh for every season, using labor-intensive methods such as hand pollination, resulting in substantially higher costs. Consequently, hybrids are underutilized for many crops, especially by farmers in developing countries. Recently a technology called synthetic apomixis has been developed to enable hybrid rice plants to produce seeds that are genetic clones of the parent plant, such that the progeny can produce the same high yields as the parent plant. The method mimics a process called apomixis that occurs naturally in many asexual plant species, and utilizes genome editing together with manipulation of gene expression to bypass both genetic segregation and fertilization. In this project, the method for clonal propagation of hybrid seeds developed for the monocot plant rice will be modified and tested for use in tomato, which is a dicot species. If successful in tomato, the method can be extended to other major crops that are dicots, such as soybean and cotton, with correspondingly large impacts on world agriculture.The first successful propagation of clonal seeds by a sexually reproducing plant has been recently achieved in rice, through the elimination of meiosis by CRISPR-Cas9 genome editing of three meiotic genes, followed by parthenogenesis arising from egg cell expression of an embryogenic transcription factor of the BABY BOOM family. The resulting seeds were clonal and maintained the genome wide heterozygosity of the parent plant. A similar approach will be used in this project on the dicot plant tomato, to enable the propagation of hybrid tomato plants clonally through seeds. Tomato orthologs of the highly conserved meiosis genes REC8, PAIR1 and OSD1 will be genome edited by CRISPR-Cas9 to eliminate meiosis and form unreduced gametes. Parthenogenesis of the unreduced egg cell will be induced by ectopic expression of candidate embryogenic factors identified by orthology to embryonic factors in rice and Arabidopsis, including those of the BABY BOOM transcription factor family. Putative clonal progeny will be identified by their chromosomal ploidy, and validated by whole genome sequencing to confirm maintenance of parental heterozygosity in their genomes.This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.