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Title: Comparative transcriptome analysis during early fruit development between three seedy citrus genotypes and their seedless mutants

Author
item ZHANG, SHUJIAN
item SHI, QINGCHUN
item ALBRECHT, UTE - FORMER ARS EMPLOYEE
item Shatters, Robert - Bob
item Stange, Richard
item MCCOLLUM, THOMAS
item ZHANG, SHUO - NORTH CAROLINA STATE UNIVERSITY
item FAN, CHENGMING - CHINESE ACADEMY OF SCIENCES
item STOVER, EDDIE

Submitted to: Horticulture Research
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 7/11/2017
Publication Date: 9/15/2017
Citation: Zhang, S., Shi, Q., Albrecht, U., Shatters, R.G., Stange Jr, R.R., McCollum, T.G., Zhang, S., Fan, C., Stover, E.W. 2017. Comparative transcriptome analysis during early fruit development between three seedy citrus genotypes and their seedless mutants. Horticulture Research. 4:17041.

Interpretive Summary: Citrus is the most widely cultivated fruit in the world. Seedlessness is an important trait in relation to fruit quality, and consumers’ interest in seedless citrus such as oranges, mandarins and lemons has increased. Therefore, breeding seedless citrus varieties is a major objective. In this study, we compared the transcriptome profiles of three seedy citrus genotypes: ‘Fallglo’ mandarin hybrid, ‘Pineapple’ sweet orange and ‘Duncan’-like seedy grapefruit and associated seedless mutants during early fruit development. The objective of this work was to identify differentially expressed genes in seedless vs. seedy fruits at critical time points in seed development across all three citrus genotypes. Ultimately, it is hoped the genes identified will be useful in development of seedless varieties.

Technical Abstract: Identification of genes with differential transcript abundance (GDTA) in seedless mutants may enhance understanding of seedless citrus development. Transcriptome analysis was conducted at three time points during early fruit development (Phase 1) of three seedy citrus genotypes: Fallglo [Bower citrus hybrid (Citrus reticulata × C. reticulata × C. paradisi) × Temple (C. reticulata × C. sinensis)], grapefruit (C. paradisi), Pineapple sweet orange (C. sinensis), and their seedless mutants. Seed abortion in seedless mutants was observed at 26 days post anthesis (Time point 2). Affymetrix transcriptomic analysis revealed 359 to 1077 probe sets with differential transcript abundance in the comparison of seedless versus (vs.) seedy fruits for each citrus genotypes and time point. The GDTA identified by 18 microarray probe sets were validated by quantitative polymerase chain reaction (qPCR). Hierarchical clustering analysis revealed a range of GDTA associated with development, hormone and protein metabolism, all of which may reflect genes associate with seedless fruit development. There were 14, 9 and 12 genes found exhibiting similar abundance ratios in all three seedless vs. seedy genotype comparisons at time point 1, 2 and 3, respectively. Among those genes were genes coding for an aspartic protease and a cysteine protease, which may play important roles in the seedlessness. New insight into seedless citrus fruit development may contribute to biotech approaches to create seedless cultivars.