Yun J. Zhu

The draft genome of the transgenic tropical fruit tree papaya (Carica papaya Linnaeus)

Papaya, a fruit crop cultivated in tropical and subtropical regions, is known for its nutritional benefits and medicinal applications. Here we report a 3× draft genome sequence of ‘SunUp’ papaya, the first commercial virus-resistant transgenic fruit tree to be sequenced. The papaya genome is three times the size of the Arabidopsis genome, but contains fewer genes, including significantly fewer disease-resistance gene analogues. Comparison of the five sequenced genomes suggests a minimal angiosperm gene set of 13,311. A lack of recent genome duplication, atypical of other angiosperm genomes sequenced so far, may account for the smaller papaya gene number in most functional groups. Nonetheless, striking amplifications in gene number within particular functional groups suggest roles in the evolution of tree-like habit, deposition and remobilization of starch reserves, attraction of seed dispersal agents, and adaptation to tropical daylengths. Transgenesis at three locations is closely associated with chloroplast insertions into the nuclear genome, and with topoisomerase I recognition sites. Papaya offers numerous advantages as a system for fruit-tree functional genomics, and this draft genome sequence provides the foundation for revealing the basis of Carica’s distinguishing morpho-physiological, medicinal and nutritional properties.

Sucrose Accumulation in the Sugarcane Stem Is Regulated by the Difference between the Activities of Soluble Acid Invertase and Sucrose Phosphate Synthase.

To assess the relative importance of morphological and biochemical factors in the regulation of sucrose (Suc) accumulation in the sugarcane (Saccharum spp. hybrids) stem, we investigated morphological and biochemical correlates of Suc accumulation among parents and progeny of a family segregating for differences. In contrast to the parents, no relationship was observed between morphology and the level of Suc accumulation among the progeny. The level and timing of Suc accumulation in the whole stalk and within individual internodes was correlated with the down-regulation of soluble acid invertase (SAI) activity. High SAI activity prevented most, but not all, Suc accumulation. There was a critical threshold of SAI activity above which high concentrations of Suc did not accumulate. This low level of SAI activity was always exceeded in the internodes of the lower-Suc-storing genotypes. However, low activity of SAI was not sufficient by itself to account for the Suc accumulation in the higher-Suc-storing genotypes. Major differences in Suc accumulation among the population were attributed to the difference between activities of SAI and Suc phosphate synthase, provided SAI is below the critical threshold concentration. This result is not unexpected, since the pathway of Suc transport for storage involves Suc hydrolysis and resynthesis.

Genome-wide analysis of Carica papaya reveals a small NBS resistance gene family

The majority of plant disease resistance proteins identified to date belong to a limited number of structural classes, of which those containing nucleotide-binding site (NBS) motifs are the most common. This study provides a detailed analysis of the NBS-encoding genes of the fifth sequenced angiosperm, Carica papaya. Despite having a significantly larger genome than Arabidopsis thaliana, papaya has fewer NBS genes. Nevertheless, papaya maintains genes belonging to both Toll/interleukin-1 receptor (TIR) and non-TIR subclasses. Papaya’s NBS gene family shares most similarity with Vitis vinifera homologs, but seven non-TIR members with distinct motif sequence represent a novel subgroup. Transcript splice variants and adjacent genes encoding resistance-associated proteins may provide functional compensation for the apparent scarcity of NBS class resistance genes. Looking forward, the papaya NBS gene family is uniquely small in size but structurally diverse, making it suitable for functional studies aimed at a broader understanding of plant resistance genes.

Effective selection of transgenic papaya plants with the PMI/Man selection system.

The selectable marker gene phospho-mannose isomerase (pmi), which encodes the enzyme phospho-mannose isomerase (PMI) to enable selection of transformed cell lines on media containing mannose (Man), was evaluated for genetic transformation of papaya (Carica papaya L.). We found that papaya embryogenic calli have little or no PMI activity and cannot utilize Man as a carbon source; however, when calli were transformed with a pmi gene, the PMI activity was greatly increased and they could utilize Man as efficiently as sucrose. Plants regenerated from selected callus lines also exhibited PMI activity but at a lower specific activity level. Our transformation efficiency with Man selection was higher than that reported using antibiotic selection or with a visual marker. For papaya, the PMI/Man selection system for producing transgenic plants is a highly efficient addition to previously published methods for selection and may facilitate the stacking of multiple transgenes of interest. Additionally, since the PMI/Man selection system does not involve antibiotic or herbicide resistance genes, its use might reduce environmental concerns about the potential flow of those genes into related plant populations.

Ectopic expression of Dahlia merckii defensin DmAMP1 improves papaya resistance to Phytophthora palmivora by reducing pathogen vigor

Phytophthora spp., some of the more important casual agents of plant diseases, are responsible for heavy economic losses worldwide. Plant defensins have been introduced as transgenes into a range of species to increase host resistance to pathogens to which they were originally susceptible. However, the effectiveness and mechanism of interaction of the defensins with Phytophthora spp. have not been clearly characterized in planta. In this study, we expressed the Dahlia merckii defensin, DmAMP1, in papaya (Carica papaya L.), a plant highly susceptible to a root, stem, and fruit rot disease caused by Phytophthora palmivora. Extracts of total leaf proteins from transformed plants inhibited growth of Phytophthora in vitro and discs cut from the leaves of transformed plants inhibited growth of Phytophthora in a bioassay. Results from our greenhouse inoculation experiments demonstrate that expressing the DmAMP1 gene in papaya plants increased resistance against P. palmivora and that this increased resistance was associated with reduced hyphae growth of P. palmivora at the infection sites. The inhibitory effects of DmAMP1 expression in papaya suggest this approach has good potential to impart transgenic resistance against Phytophthora in papaya.

Differential expression of soluble acid invertase genes in the shoots of high-sucrose and low-sucrose species of Saccharum and their hybrids

The hydrolytic activity of soluble acid invertase (SAI) is strongly correlated to sucrose accumulation in sugarcane (Saccharum spp.). Plants exhibiting SAI activity above a low threshold level do not accumulate high concentrations of sucrose. The present work investigates the basis for the difference in SAI activity observed between high- and low-sucrose-accumulating sugarcane lines. SAI-encoding cDNAs were isolated from two high- and one low-sucrose lines. All of these cDNAs were highly similar, with deduced proteins at least 98% identical. Expression of SAI in the stem of sugarcane was developmentally regulated, with relatively larger pools of SAI protein and mRNA in the apex and young internodes, which declined rapidly in the maturing internodes where sucroseaccumulation occurs. This developmental pattern, while qualitatively similar, was quantitatively quite different between low- and high-sucrose lines. SAI protein and mRNA pools started substantially higher, declined later, and stabilized at a significantly higher level in a low-sucrose line than in a high-sucrose line. These data indicate that differences in SAI activity between high- and low-sucrose sugarcane lines are due, at least in part, to differences inthe level of expression of essentially identical SAI genes.

Improved Carica papaya tolerance to carmine spider mite by the expression of Manduca sexta chitinase transgene.

Papaya plants producing the tobacco hornworm (Manduca sexta) chitinase protein were obtained following microprojectile bombardment of embryogenic calli derived from the hypocotyls of the cultivar Kapoho. Polymerase chain reaction (PCR) was carried out to confirm the presence of the transgene. RT-PCR and a quantitative chitinase assay showed increased levels of chitinase activity in every selected transgenic line. Insect bioassays in the laboratory showed that plants expressing the Manduca sexta chitinase gene significantly inhibited multiplication of carmine spider mites (Tetranychus cinnabarinus Boisd.). Experiments conducted to evaluate reaction of the transgenic plants to natural infection by carmine spider mites showed that the Manduca sexta chitinase gene provided increased tolerance under field conditions.

RT-PCR and quantitative real-time RT-PCR detection of Sugarcane Yellow Leaf Virus (SCYLV) in symptomatic and asymptomatic plants of Hawaiian sugarcane cultivars and the correlation of SCYLV titre to yield

Sugarcane yellow leaf virus (SCYLV) has been reported worldwide to infect sugarcane and to cause significant yield losses. Current detection methods include tissue blot immunoassay (TBIA), reverse transcription-polymerase chain reaction (RT-PCR) and quantitative real-time RT-PCR assay (qRT-PCR). In this paper, we report the use and comparison of these detection methods for the study of SCYLV in Hawaiian cultivars. We observed positive RT-PCR and qRT-PCR reactions in cultivars previously thought (based on TBIA) to be immune to virus infection. The semi-quantitative virus titre in these cultivars was however at least 106-fold lower than in the cultivars which were known to be SCYLV-susceptible. The RT-PCR methods also revealed that plants of the cultivar H65-7052, which were previously shown to vary strongly between TBIA-positive and TBIA-negative, indeed exhibited fluctuating SCYLV-titres in a range of 103–104-fold. The virus titre was carried through to the next vegetative generation, i. e. plants grown from seed pieces with low virus titre had low virus titre and plants grown from seed pieces with high virus titre contained high virus titre. A small field trial comparing plants of cv. H65-7052 of low and high SCYLV-titre showed that the field plots with plants of high virus titre developed Yellow Leaf symptoms and yielded only 54–60% of cane and sugar tonnage compared to plots with plants of low virus titre.

Novel thigmomorphogenetic responses in Carica papaya: touch decreases anthocyanin levels and stimulates petiole cork outgrowths.

BACKGROUND AND AIMS Because of its rapid growth rate, relative ease of transformation, sequenced genome and low gene number relative to Arabidopsis, the tropical fruit tree, Carica papaya, can serve as a complementary genetic model for complex traits. Here, new phenotypes and touch-regulated gene homologues have been identified that can be used to advance the understanding of thigmomorphogenesis, a multigenic response involving mechanoreception and morphological change. METHODS Morphological alterations were quantified, and microscopy of tissue was conducted. Assays for hypocotyl anthocyanins, lignin and chlorophyll were performed, and predicted genes from C. papaya were compared with Arabidopsis touch-inducible (TCH) and Mechanosensitive channel of Small conductance-like genes (MscS-like or MSL). In addition, the expression of two papaya TCH1 homologues was characterized. KEY RESULTS On the abaxial side of petioles, treated plants were found to have novel, hypertrophic outgrowths associated with periderm and suberin. Touched plants also had higher lignin, dramatically less hypocotyl anthocyanins and chlorophyll, increased hypocotyl diameter, and decreased leaf width, stem length and root fresh weight. Papaya was found to have fewer MSL genes than Arabidopsis, and four touch-regulated genes in Arabidopsis had no counterparts in papaya. Water-spray treatment was found to enhance the expression of two papaya TCH1 homologues whereas induction following touch was only slightly correlated. CONCLUSIONS The novel petiole outgrowths caused by non-wounding, mechanical perturbation may be the result of hardening mechanisms, including added lignin, providing resistance against petiole movement. Inhibition of anthocyanin accumulation following touch, a new phenotypic association, may be caused by diversion of p-coumaroyl CoA away from chalcone synthase for lignin synthesis. The absence of MSL and touch-gene homologues indicates that papaya may have a smaller set of touch-regulated genes. The genes and novel touch-regulated phenotypes identified here will contribute to a more comprehensive view of thigmomorphogenesis in plants.

Genetic transformation with untranslatable coat protein gene of sugarcane yellow leaf virus reduces virus titers in sugarcane

Sugarcane yellow leaf syndrome, characterized by a yellowing of the leaf midrib followed by leaf necrosis and growth suppression, is caused by sugarcane yellow leaf virus (SCYLV). We produced SCYLV-resistant transgenic sugarcane from a susceptible cultivar (H62-4671) and determined the amount of virus present following inoculation. The transgenic plants were produced through biolistic bombardment of cell cultures with an untranslatable coat protein gene. Presence of the transgene in regenerated plants was confirmed using PCR and Southern blot analysis. The transgenic lines were inoculated by viruliferous aphids and the level of SCYLV in the plants was determined. Six out of nine transgenic lines had at least 103-fold lower virus titer than the non-transformed, susceptible parent line. This resistance level, as measured by virus titer and symptom development, was similar to that of a resistant cultivar (H78-4153). The selected SCYLV-resistant transgenic sugarcane lines will be available for integration of the resistance gene into other commercial cultivars and for quantification of viral effects on yield.