Differential gene expression and alternative splicing between diploid and tetraploid watermelon lines

Authors: SAMINATHAN, T - West Virginia State University; NIMMAKAYALA, P - West Virginia State University; MANHUR, S - West Virginia State University; MALKARAM, S - West Virginia State University; ALMEIDA, A - West Virginia State University; CANTRELL, R - West Virginia State University; ABBURI, L - West Virginia State University; TOMASSON, Y - West Virginia State University; ABBURI, L - West Virginia State University; KUMAR, B - West Virginia State University; RAHMAN, M - West Virginia State University; Levi, Amnon; WEHNER, T - North Carolina State University; REDDY, U - West Virginia State University

Submitted to: New Phytologist
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 11/14/2014
Publication Date: N/A
Citation: N/A

Interpretive Summary: Watermelon is an important vegetable crop in the United States and throughout the world. Seedless watermelons have become highly popular and presently comprise over 90% of the U.S. watermelon market. However, the process of producing and growing seedless watermelon plants has been challenging for seed company breeders and for growers and there is no sufficient knowledge on the activity of genes in seedless watermelon plants compared with their activity in seeded watermelon plants. In this study, ARS scientists have collaborated with scientists and students at West Virginia State University on advanced genomic technologies to evaluate the activity of genes in seedless versus seeded watermelon plants. Using the advanced genomic technologies, the scientists identified several genes that are highly active in the seedless compared to seeded watermelon plants. These results indicate that the activity of certain genes could be entirely different in seeded versus seedless watermelon plants. The information obtained in this study should be useful for university scientists and students, and for seed company breeders interested in improving the quality of seedless watermelons and in improving their resistance to diseases and pests.

Technical Abstract: Synthetic tetraploid plants have been used for production of seedless triploid watermelon lines being pollinated with diploid plants. When compared to their diploid or triploid counterparts, the tetraploid exhibit wide phenotypic differences. Though many factors, including alternative splicing (AS), modulates gene expression affect plant growth and development. There is little knowledge on gene expression, resulting from AS in tetraploid versus, their diploid parental plants. In this study, tissues of leaf, stem, and fruit diploid and tetraploid sweet watermelon were used to determine differences in gene expression and occurrences of AS. RNA-seq analysis was performed along with RT-qPCR and RACE-PCR to prove changes in expression and splicing. All vegetative tetraploid tissues showed increased effect versus their diploid counterparts. We identified 5,362 and 1,288 gene sequences that uniquely up- and down regulated in tetraploid and diploids, respectively. Furthermore, 22 AS events were identified across tissues, indicating possibilities to generate different protein isoforms with altered functions of important transcription factors and transporters. The study showed biosynthesis of arginine, chlorophyllide, GDP-mannose, trehalose, and starch and sucrose degradation pathways are upregulated in autotetraploids. Phloem protein 2, chloroplastic PGR5-like protein, zinc finger protein, fructokinase-like 2, MYB transcription factor and nodulin MtN21 were primarily spliced in fruit tissues. A large set of genes were down regulated or spliced in fruit tissues when compared to high upregulation leaf and stem of tetraploid. This study elucidates gene expression may explain the phenotypic differences in tetraploid versus, their diploid parental watermelon plants.