title: Deep sequencing transcriptional fingerprinting of rice kernels for dissecting grain quality traits.
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 of loci up or down-regulated in specific varieties, with respect to the others. Among them, we detected loci 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-related loci involved in starch biosynthesis (e.g. GBSSI, starch synthases and AGPase), genes encoding for transcription factors, additional seed storage proteins, allergens or belonging to additional nutraceutical compounds biosynthetic pathways and loci 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 of loci 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.
authors.affiliation: CREA- Council for Agricultural Research and Economics, Rice research unit, S. S. 11 to Torino Km 2,5, Vercelli, 13100, Italy. chiara.biselli@entecra.it.|CREA - Council for Agricultural Research and Economics, Genomics Research Centre, Via S. Protaso 302, Fiorenzuola d'Arda (PC), 29017, Italy. chiara.biselli@entecra.it.
authors.forename: Chiara
authors.initials: C
authors.lastname: Biselli
authors.affiliation: CREA - Council for Agricultural Research and Economics, Genomics Research Centre, Via S. Protaso 302, Fiorenzuola d'Arda (PC), 29017, Italy. paolo.bagnaresi@entecra.it.
authors.forename: Paolo
authors.initials: P
authors.lastname: Bagnaresi
authors.affiliation: CREA- Council for Agricultural Research and Economics, Rice research unit, S. S. 11 to Torino Km 2,5, Vercelli, 13100, Italy. ris@entecra.it.
authors.forename: Daniela
authors.initials: D
authors.lastname: Cavalluzzo
authors.affiliation: CREA - Council for Agricultural Research and Economics, Genomics Research Centre, Via S. Protaso 302, Fiorenzuola d'Arda (PC), 29017, Italy. simona.urso@libero.it.
authors.forename: Simona
authors.initials: S
authors.lastname: Urso
authors.affiliation: CREA - Council for Agricultural Research and Economics, Genomics Research Centre, Via S. Protaso 302, Fiorenzuola d'Arda (PC), 29017, Italy. francesca.desiderio@entecra.it.
authors.forename: Francesca
authors.initials: F
authors.lastname: Desiderio
authors.affiliation: CREA- Council for Agricultural Research and Economics, Rice research unit, S. S. 11 to Torino Km 2,5, Vercelli, 13100, Italy. gabriele.orasen@unimi.it.|DiSAA - Department of Agricultural and Environmental Sciences, Università degli Studi di Milano, Via G. Celoria 2, Milan, 20133, Italy. gabriele.orasen@unimi.it.
authors.forename: Gabriele
authors.initials: G
authors.lastname: Orasen
authors.affiliation: CREA - Council for Agricultural Research and Economics, Genomics Research Centre, Via S. Protaso 302, Fiorenzuola d'Arda (PC), 29017, Italy. alberto.gianinetti@entecra.it.
authors.forename: Alberto
authors.initials: A
authors.lastname: Gianinetti
authors.affiliation: DiSAA - Department of Agricultural and Environmental Sciences, Università degli Studi di Milano, Via G. Celoria 2, Milan, 20133, Italy. federico.righettini@unimi.it.
authors.forename: Federico
authors.initials: F
authors.lastname: Righettini
authors.affiliation: CREA- Council for Agricultural Research and Economics, Rice research unit, S. S. 11 to Torino Km 2,5, Vercelli, 13100, Italy. massimo.gennaro@entecra.it.
authors.forename: Massimo
authors.initials: M
authors.lastname: Gennaro
authors.affiliation: CREA- Council for Agricultural Research and Economics, Rice research unit, S. S. 11 to Torino Km 2,5, Vercelli, 13100, Italy. ris@entecra.it.
authors.forename: Rosaria
authors.initials: R
authors.lastname: Perrini
authors.affiliation: CREA- Council for Agricultural Research and Economics, Rice research unit, S. S. 11 to Torino Km 2,5, Vercelli, 13100, Italy. manel.benhassen@unimi.it.|DiSAA - Department of Agricultural and Environmental Sciences, Università degli Studi di Milano, Via G. Celoria 2, Milan, 20133, Italy. manel.benhassen@unimi.it.
authors.forename: Manel
authors.initials: M
authors.lastname: Ben Hassen
authors.affiliation: DiSAA - Department of Agricultural and Environmental Sciences, Università degli Studi di Milano, Via G. Celoria 2, Milan, 20133, Italy. gianattilio.sacchi@unimi.it.
authors.forename: Gian Attilio
authors.initials: GA
authors.lastname: Sacchi
authors.affiliation: CREA - Council for Agricultural Research and Economics, Genomics Research Centre, Via S. Protaso 302, Fiorenzuola d'Arda (PC), 29017, Italy. luigi.cattivelli@entecra.it.
authors.forename: Luigi
authors.initials: L
authors.lastname: Cattivelli
authors.affiliation: CREA- Council for Agricultural Research and Economics, Rice research unit, S. S. 11 to Torino Km 2,5, Vercelli, 13100, Italy. giampiero.vale@entecra.it.|CREA - Council for Agricultural Research and Economics, Genomics Research Centre, Via S. Protaso 302, Fiorenzuola d'Arda (PC), 29017, Italy. giampiero.vale@entecra.it.
authors.forename: Giampiero
authors.initials: G
authors.lastname: Valè
mesh_terms: D002874:Chromosome Mapping; D002523:Edible Grain / Q000235:genetics; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant; D005838:Genotype; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D012275:Oryza / Q000235:genetics* / Q000502:physiology; D010940:Plant Proteins / Q000235:genetics*; D020641:Polymorphism, Single Nucleotide; D040641:Quantitative Trait Loci; D017423:Sequence Analysis, RNA / Q000379:methods
chemical_list: D010940:Plant Proteins