USING FUNCTIONAL AND APPLIED GENOMICS TO IMPROVE STRESS AND DISEASE RESISTANCE IN FRUIT TREES
Location: Appalachian Fruit Research Laboratory: Innovative Fruit Production, Improvement and Protection
Title: Gene expression is highly regulated in early developing fruit of apple
| Soria-Guerra, Ruth Elena - |
| Rosales-Mendoza, Sergio - |
| Gasic, Ksenija - |
| Korban, Schuyler - |
| Band, Mark - |
Submitted to: Plant Molecular Biology Reporter
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: October 15, 2010
Publication Date: March 30, 2011
Citation: Soria-Guerra, R., Rosales-Mendoza, S., Gasic, K., Wisniewski, M.E., Korban, S.S., Band, M. 2011. Gene expression is highly regulated in early developing fruit of apple. Plant Molecular Biology Reporter. DOI 10.1007/s 11105-011-0300-y.
Interpretive Summary: Global studies of gene expression in plants provide an opportunity to study changes in hundreds of genes simultaneously. This is accomplished by attaching thousands of genes on to a glass slide known as a microarray and probing the slide with samples of DNA obtained from the plant of interest. Using this technique, one can study a plant’s response to biotic or abiotic stress, and also identify pathways responsible for economically important traits such as fruit size, texture, taste, etc. This research describes the development of microarray for use in apple and related crops such as pear, stone fruit, and strawberry. It was developed using over 40,000 apple gene sequences. The quality of the microarray was assessed by evaluating gene expression in fruit from three different apple cultivars at the same stage of maturity. Approximately 3,000 genes were identified as being expressed in the fruit and grouped into 19 functional groups such as metabolism, photosynthesis, cellular transport, etc. Using another method (PCR) to confirm the expression levels of a subset of the genes identified on the microarray validated the quality of the microarray. The microarray, developed jointly by the University of Illinois and USDA-ARS, provides an important resource for genetic studies of temperate tree fruit crops belonging to the Rose family (Rosaceae) that will aid breeders in developing new cultivars that are resistant to environmental stresses, insects, and disease.
An oligonucleotide-based microarray for apple was developed using over 40,000 sequences, along with positive and negative controls, obtained from 34 cDNA libraries constructed from both vegetative and reproductive tissues at different stages of development, varying genotypes, and under different biotic and abiotic stresses. The apple microarray was used to conduct a global analysis of gene expression in fruit collected, at the same stage of maturity, from three apple genotypes, including 'Golden Delicious', 'Gala', and 'Fuji'. A set of 2,896 genes demonstrating statistically significant differential expression profiles among the three different genotypes was identified. This set included genes encoding enzymes involved in primary metabolism, followed by genes related to cellular communication, cell proliferation, differentiation, proteins with binding functions, and cellular transport. Differentially expressed genes were grouped into 19 functional categories. Quantitative real-time reverse-transcription polymerase chain reaction (qRT-PCR) confirmed differential expression for most of the genes detected in the microarray analysis. This simultaneous genome-wide analysis of gene expression changes in ripening fruit provides new insights into biological changes occurring among different apple genotypes.