Most of the commercial papaya genotypes show susceptibility to water deficit stress and require high volumes of irrigation water to yield properly. To tackle this problem, we have collected wild native genotypes of Carica papaya that have proved to show better physiological performance under water deficit stress than the commercial cultivar grown in Mexico. In the present study, plants from a wild Carica papaya genotype and a commercial genotype were subjected to water deficit stress (WDS), and their response was characterized in physiological and molecular terms. The physiological parameters measured (water potential, photosynthesis, Fv/Fm and electrolyte leakage) confirmed that the papaya wild genotype showed better physiological responses than the commercial one when exposed to WDS. Subsequently, RNA-Seq was performed for 4 cDNA libraries in both genotypes (susceptible and tolerant) under well-watered conditions, and when they were subjected to WDS for 14 days. Consistently, differential expression analysis revealed that after 14 days of WDS, the wild tolerant genotype had a higher number of up-regulated genes, and a higher number of transcription factors (TF) that were differentially expressed in response to WDS, than the commercial genotype. Thus, six TF genes (CpHSF, CpMYB, CpNAC, CpNFY-A, CpERF and CpWRKY) were selected for further qRT-PCR analysis as they were highly expressed in response to WDS in the wild papaya genotype. qRT-PCR results confirmed that the wild genotype had higher expression levels (REL) in all 6 TF genes than the commercial genotype. Our transcriptomic analysis should help to unravel candidate genes that may be useful in the development of new drought-tolerant cultivars of this important tropical crop.

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Carica papaya L. is a native fruit from Central America and Mexico and it is an economically important fruit. As a pre-breeding genetic study, the variability of both parents (L7 and M22) and the F1 individuals derived from their crosses (L7 × M22), was evaluated in terms of 32 morphochemical traits, and contrasted with their genetic diversity indicated by amplified fragment length polymorphism (AFLP) markers. According to morphochemical traits, L7 and M22 were grouped in two different clades. The first group included L7 and 13 genotypes from the F1, while a second group included the parent M22 and 15 other genotypes from the F1 progeny. The analysis based on morphochemical traits showed an average correlation of 0.652 among genotypes. For AFLP analysis the combination of the primers E-ACA/M-CTA had the best polymorphic index (72.73%). When they were grouped based on AFLPs markers, it was confirmed that both parents are genetically distant, and they were again grouped in two different clades. Five genotypes from the F1 population were grouped in the same clade as L7 and shared 55% similarity. Twenty six genotypes were grouped in the same clade as M22, showing 63.3% similarity. Another 12 genotypes (mainly female genotypes) were grouped in a third independent clade. This relative general agreement between the grouping based on a large number of morphochemical traits (including both plant and fruit traits) and that based on its genetic diversity using AFLPs, suggests that morphochemical characterization, together with genetic analysis by AFLPs, can be complementary and useful techniques for the identification and assessment of genetic diversity within C. papaya L. genotypes, that should be useful for genetic breeding programs of this important species.