Papaya (Carica papaya L) is a versatile tropical fruit with its usage ranging from consumption, cosmetics, to pharmaceuticals. In 2020, it was the third most-produced tropical fruit crop in the world. Papaya is a trioecious herbaceous plant with distinct flower and fruit morphological appearances. The fruits from hermaphrodite papaya are favorable for both consumption and processing due to their superior quality. Papaya has a genome size of 372 Mb and chromosome of 2n =18. The male and hermaphrodite papaya have XY and XYh sex chromosomes, respectively, while the female has XX. Using omics and bioinformatics approaches, papaya cultivars with desired fruit quality can be selected and identified from germplasm for incorporation in breeding programs. Papaya production can be done either in open fields or under protected cultivation. Open field cultivation provides for large-scale production, but with the disadvantages of variability in fruit yield, quality, and limitations on growing and harvesting seasons. Under protected cultivation, papaya can be cultivated in all seasons, whilst delivering higher yields. Conversely, multidisciplinary approaches with selected papaya cultivars, good farm management, and suitable conditions provide high yields of quality fruit for both consumption and processing, whilst minimizing the adverse effects related to environmental conditions.

The effects of cultivation conditions on the texture of unripe papaya fruit ‘Khak Nual’ were investigated. Fruit from papaya cultivated using raised bed conditions were crisper than those cultivated under open field conditions. Conversely, fruit cultivated under open field conditions were firmer. In all cases, mesocarp cells and intercellular spaces were larger in papaya fruit cultivated in raised beds, reflecting the higher relative humidity (RH) of the cultivation conditions and greater water availability. At harvest, TIP2–1, TIP4–1, SIP1 and PIP1–3 expression was significantly higher in fruit cultivated under raised bed conditions, which correlated with the larger cells of the mesocarp, the RH and the ready availability of water. There also appeared to be a link between aquaporin gene expression and crispness in papaya fruit from both conditions. Expression of TIP2–1 and TIP4–1 correlated with papaya fruit under open field conditions while SIP1 and PIP2–5 correlated with papaya fruit under raised bed conditions. The results clearly demonstrate the effect of cultivation conditions on fruit texture, with water availability being critical in the production of market-preferred crisp fruit with the optimal conditions. These conditions are reflected in the higher expression of the water transport aquaporins which likely control crispness.

Callus induction (CI) is a critical trait for transforming desirable genes in plants. A genome-wide association study (GWAS) analysis was conducted on the rice germplasms of 110 Indica rice accessions, in which three tissue culture media, B5, MS, and N6, were used for the CI of those rice panels’ mature seeds. Seven quantitative trait loci (QTLs) on rice chromosomes 2, 6, 7, and 11 affected the CI percentage in the three media. For the B5 medium, one QTL (qCI–B5–Chr6) was identified on rice chromosome 6; for the MS medium, two QTLs were identified on rice chromosomes 2 and 6 (qCI–MS–Chr2 and qCI–MS–Chr6, respectively); for the N6 medium, four QTLs were identified on rice chromosomes 6, 7, and 11 (qCI–N6–Chr6.1 and qCI–N6–Chr6.2, qCI–N6–Chr7, and qCI–N6–Chr11, respectively). Fifty-five genes were identified within the haplotype blocks corresponding to these QTLs, thirty-one of which showed haplotypes associated with different CI percentages in those media. qCI–B5–Chr6 was located in the same region as qCI–N6–Chr6.2, and the Caleosin-related family protein was also identified in this region. Analysis of the gene-based haplotype revealed the association of this gene with different CI percentages in both B5 and N6 media, suggesting that the gene may play a critical role in the CI mechanism. Moreover, several genes, including those that encode the beta-tubulin protein, zinc finger protein, RNP–1 domain-containing protein, and lysophosphatidic acid acyltransferase, were associated with different CI percentages in the N6 medium. The results of this study provide insights into the potential QTLs and candidate genes for callus induction in rice that contribute to our understanding of the physiological and biochemical processes involved in callus formation, which is an essential tool in the molecular breeding of rice.

Callus induction (CI) is the critical trait for the transformation of desirable genes in plants. A genome-wide association study (GWAS) analysis was conducted on the rice germplasm of 110 diverse indica rice accessions. Three tissue culture media, including B5, MS, and N6, were used for CI in those rice panels. Seven quantitative trait loci (QTLs) on chromosomes 2, 6, 7, and 11 were found to confer a CI percentage in these three media. For the B5 medium, one QTL (qCI-B5-Chr6) was identified on the rice chromosome 6. For the MS medium, two QTLs were identified on the rice chromosomes 2 and 6 (qCI-MS-Chr2 and qCI-MS-Chr6, respectively). For the N6 medium, four QTLs were identified on the rice chromosomes 6, 7, and 11 (qCI-N6-Chr6.1, qCI-N6-Chr6.2, qCI-N6-Chr7, and qCI-N6-Chr11, respectively). Fifty-five genes were identified within the haplotype blocks corresponding to these QTLs. Thirty-one genes showed haplotypes associated with different CI in those media. The qCI-B5-Chr6 was located in the same region as the qCI-N6-Chr6.2. The caleosin-related family protein was identified in this region. Analysis of the gene-based haplotype reveals the association of this gene with different CI in both B5 and N6 media, suggesting that the gene may play a critical role in the CI mechanism. Moreover, several genes, including the beta-tubulin, the zinc finger proteins, the RNP-1 domain-containing protein, and the Lysophosphatidic acid acyltransferase, were associated with different CI in the N6 media. Results from this study provide insight into the potential QTLs and candidate genes for callus induction in rice that will fulfill the understanding of the physiological and biochemical processes involved in callus formation, which is an essential tool in the molecular breeding of rice.