Huangwei Zhang1,2, Meng Li3, Min Kong1, Jim M Dunwell4, Yuyan Zhang5, Chao Yue6, Juyou Wu1, Shaoling Zhang7. 1. College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China. 2. College of Agro-Grassland Science, Nanjing Agricultural University, Nanjing, 210095, China. 3. College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China. mli@njau.edu.cn. 4. School of Agriculture, Policy and Development, University of Reading, Earley Gate, Reading, UK. 5. Institute of Pomology, Jiangsu Academy of Agricultural Sciences/Jiangsu Key Laboratory of Horticultural Crop Genetic Improvement, Nanjing, 210014, Jiangsu, China. 6. China Tobacco Jiangsu Industrial Co., Ltd, Nanjing, 210019, China. 7. College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China. slzhang@njau.edu.cn.
Abstract
BACKGROUND: Pears and apples are both perennial deciduous trees of the Rosaceae family, and both are important economic fruit trees worldwide. The emergence of many varieties in the market has been mostly domesticated from wild to cultivated and regulated by the differential expression of genes. However, the molecular process and pathways underlying this phenomenon remain unclear. Four typical wild and cultivar pear and apple trees at three developmental stages were used in our study to investigate the molecular process at the transcriptome level. RESULT: Physiological observations indicated the obvious differences of size, weight, sugar acid content and peel color in wild and cultivar fruit among each developmental stage. Using next-generation sequencing based RNA-seq expression profiling technology, we produced a transcriptome in procession of a large fraction of annotated pear and apple genes, and provided a molecular basis underlying the phenomenon of wild and cultivar fruit tree differences. 5921 and 5744 differential expression genes were identified in pear and apple at three developmental stages respectively. We performed temporal and spatial differential gene expression profiling in developing fruits. Several key pathways such as signal transduction, photosynthesis, translation and many metabolisms were identified as involved in the differentiation of wild and cultivar fruits. CONCLUSION: In this study, we reported on the next-generation sequencing study of the temporal and spatial mRNA expression profiling of pear and apple fruit trees. Also, we demonstrated that the integrated analysis of pear and apple transcriptome, which strongly revealed the consistent process of domestication in Rosaceae fruit trees. The results will be great influence to the improvement of cultivar species and the utilization of wild resources.
BACKGROUND:Pears and apples are both perennial deciduous trees of the Rosaceae family, and both are important economic fruit trees worldwide. The emergence of many varieties in the market has been mostly domesticated from wild to cultivated and regulated by the differential expression of genes. However, the molecular process and pathways underlying this phenomenon remain unclear. Four typical wild and cultivar pear and apple trees at three developmental stages were used in our study to investigate the molecular process at the transcriptome level. RESULT: Physiological observations indicated the obvious differences of size, weight, sugar acid content and peel color in wild and cultivar fruit among each developmental stage. Using next-generation sequencing based RNA-seq expression profiling technology, we produced a transcriptome in procession of a large fraction of annotated pear and apple genes, and provided a molecular basis underlying the phenomenon of wild and cultivar fruit tree differences. 5921 and 5744 differential expression genes were identified in pear and apple at three developmental stages respectively. We performed temporal and spatial differential gene expression profiling in developing fruits. Several key pathways such as signal transduction, photosynthesis, translation and many metabolisms were identified as involved in the differentiation of wild and cultivar fruits. CONCLUSION: In this study, we reported on the next-generation sequencing study of the temporal and spatial mRNA expression profiling of pear and apple fruit trees. Also, we demonstrated that the integrated analysis of pear and apple transcriptome, which strongly revealed the consistent process of domestication in Rosaceae fruit trees. The results will be great influence to the improvement of cultivar species and the utilization of wild resources.
Authors: Nicolas Daccord; Jean-Marc Celton; Gareth Linsmith; Claude Becker; Nathalie Choisne; Elio Schijlen; Henri van de Geest; Luca Bianco; Diego Micheletti; Riccardo Velasco; Erica Adele Di Pierro; Jérôme Gouzy; D Jasper G Rees; Philippe Guérif; Hélène Muranty; Charles-Eric Durel; François Laurens; Yves Lespinasse; Sylvain Gaillard; Sébastien Aubourg; Hadi Quesneville; Detlef Weigel; Eric van de Weg; Michela Troggio; Etienne Bucher Journal: Nat Genet Date: 2017-06-05 Impact factor: 38.330