1 research outputs found
Deep sequencing transcriptional fingerprinting of rice kernels for dissecting grain quality traits
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