Deep sequencing transcriptional fingerprinting of rice kernels for dissecting grain quality traits. (December 2015)

• Record Type: Journal Article
• Authors: Biselli, Chiara; Bagnaresi, Paolo; Cavalluzzo, Daniela; Urso, Simona; Desiderio, Francesca; Orasen, Gabriele; Gianinetti, Alberto; Righettini, Federico; Gennaro, Massimo; Perrini, Rosaria; Ben Hassen, Manel; Sacchi, Gian; Cattivelli, Luigi; Valè, Giampiero
• Is Part Of: BMC genomics. Volume 16:Number 1(2015)
• Page Start: 1
• Page End: 28
• Publication Date: 2015-12
• Subjects: Rice -- Caryopsis -- Grain quality -- RNA-Seq -- Co-regulation -- SNP; Genomes -- Periodicals; Gene mapping -- Periodicals; Genomics -- Periodicals; Base Sequence -- Periodicals; Chromosome Mapping -- Periodicals; Genetic Techniques -- Periodicals; Sequence Analysis, DNA -- Periodicals; 572.8605
• DOI: 10.1186/s12864-015-2321-7
• Languages: English
• ISSNs: 1471-2164

Abstract

Abstract Background Rice represents one the most important foods all over the world. In Europe, Italy is the first rice producer and Italian production is driven by tradition and quality. All main rice grain quality traits, like cooking properties, texture, gelatinization temperature, chalkiness and yield, are related to the content and composition of starch and seed-storage proteins in the endosperm and to grain shape. In addition, a number of nutraceutical compounds and allergens are known to have a significant effect on grain quality determination. To investigate the genetic bases underlying the qualitative differences that characterize traditional Italian rice cultivars, a comparative RNA-Seq-based transcriptomic analysis of developing caryopsis was conducted at 14 days after flowering on six popular Italian varieties (Carnaroli, Arborio, Balilla, Vialone Nano, Gigante Vercelli and Volano) phenotypically differing for qualitative grain-related traits. Results Co-regulation analyses of differentially expressed genes showing the same expression patterns in the six genotypes highlighted clusters ofloci up or down-regulated in specific varieties, with respect to the others. Among them, we detectedloci involved in cell wall biosynthesis, protein metabolism and redox homeostasis, classes of genes affecting in chalkiness determination. Moreover, loci encoding for seed-storage proteins, allergens or involved in the biosynthesis of specific nutraceutical compounds were also present and specifically regulated in the different clusters. A wider investigation of all the DEGs detected in pair-wise comparisons revealed transcriptional variation, among the six genotypes, for quality-relatedloci involved in starch biosynthesis (e.g.GBSSI, starch synthases andAGPase ), genes encoding for transcription factors, additional seed storage proteins, allergens or belonging to additional nutraceutical compounds biosynthetic pathways andloci affecting grain size. Putative functional SNPs associated to amylose content in starch, gelatinization temperature and grain size were also identified. Conclusions The present work represents a more extended phenotypic characterization of a set of rice accessions that present a wider genetic variability than described nowadays in literature. The results provide the first transcriptional picture for several of the grain quality differences observed among the Italian rice varieties analyzed and reveal that each variety is characterized by the over-expression of a peculiar set ofloci affecting grain appearance and quality. A list of candidates and SNPs affecting specific grain properties has been identified offering a starting point for further works aimed to characterize genes and molecular markers for breeding programs.