Citrus genomics

Abstract

Citrus fruits (sweet orange, mandarin, pummelo, grapefruit, lemon, lime and assorted hybrids) are among the most widely grown and economically important fruit tree crops in the world. As fresh fruit, they are an important and nutrient dense food source for human diets; as processed juice products, primarily sweet orange juice, they represent a globally traded commodity. To support genetic improvement efforts for this important crop, the international citrus genetics community has collaborated with international sequencing centers in the development of freely available genomic resources, some of which are described herein. Most notable, two full-length annotated genome assemblies have been produced and made available to the global research community. The first genome, based exclusively on Sanger sequencing, is from a haploid plant derived from 'Clementine' mandarin, to serve as the reference genome for citrus. A second genome assembly was produced from the sweet orange clone 'Ridge Pineapple', this was done primarily with 454 technology. Extensive EST datasets and a number of microarray platforms for exploring the transcriptomic responses of citrus species and hybrids to a wide range of conditions have been shared, to support exploitation and utilization of genome sequence information. As many researchers in the citrus genomics community are also actively engaged in genetic improvement programs, there has been a natural integration of improvement efforts with the rapidly evolving genomic tools. Examples described below include work designed to better understand the control of gene expression in citrus polyploids, which are being used in development of seedless triploid selections or as rootstocks; unraveling the molecular mechanisms of host-pathogen interactions to devise novel genetic strategies to overcome a multitude of devastating diseases that currently threaten citrus production globally; and the mining of SSR and SNP markers for linkage studies to enable marker-assisted parental selection and breeding strategies, illustrated bywork on two citrus traits, nucellar embryony and juvenility, which significantly impact breeding approaches. Citrus genome resources are available through publicly available web portals, through the USDOEJGI (phytozome.net) and Tree Fruit Genome Database Resources (tfGDR, citrusgenomedb.org). Work is continuing to expand and improve the citrus genome sequence resources and tools, to enable application of sequence-derived knowledge in improving citrus plants and to managing better their interactions with biotic and abiotic factors. (Résumé d'auteur

Genome wide selection in Citrus breeding

“…Therefore, there is a delay in the hybridization process and in the selection of desired characteristics in breeding programs. In addition, large areas are required for the development of hybrids, which not only increases the cost of plant maintenance in the field but also limits the number of families and individuals per family that can be evaluated (Talon and Gmitter Junior, 2008;Gmitter Junior et al, 2012). GWS can minimize these undesirable consequences as selection can be performed in juvenile plants, which reduces the interval between generations, increases the intensity of selection and, therefore, the gain per unit time and cost (Resende et al, 2008;Wong and Bernardo, 2008;Heffner et al, 2009;Grattapaglia and Resende, 2011;Kemper and Goddard, 2012).…”

Induction of parthenogenetic haploid plants using gamma irradiated pollens in ‘Hirado Buntan’ pummelo (Citrus grandis [L.] Osbeck)

“…Citrus is the most widely cultivated tropical and subtropical fruit tree with great economic and healthy value in the world (Gmitter et al, 2012). The citrus types are quite rich including oranges, pummelos, mandarins, grapefruits, lemons and their relative species; however the genetic relationship and classification of various kinds of citrus made the scientists perplexed (Moore, 2001).…”

The draft genome of sweet orange (Citrus sinensis)

“…Consequently, somatic embryos grow much more vigorously than the zygotic embryos in seeds such that seedlings are essentially clones of the maternal parent. Such citrus-unique characteristics have hindered the study of citrus genetics and breeding improvement 1,2 . Complete genome sequences would provide valuable genetic resources for improving citrus crops.…”