Effects of the application of a moderate alternate wetting and drying technique on the performance of different European varieties in Northern Italy rice system

Alternate wetting and drying (AWD) technique has been developed and evaluated on rice (Oryza sativa) systems in several countries worldwide for increasing water use efficiency and reducing negative effects of permanent flooding, like the increase in methane emissions and arsenic availability in soil. In this study, a paddy field experiment was carried out for two years to evaluate the application in Northern Italy rice area of a moderate AWD, i.e. only implemented during the vegetative phase of the crop and ponded water maintained thereafter, compared with Continuous Flooding (CF) system. The adaptability of 12 European commercial rice cultivars to AWD was investigated in terms of crop phenology, morphological traits, root production, nitrogen (N) uptake, yield, milled rice yield and microelement concentration in grains. Results showed substantial (40.7 %) water saving probably favoured by the presence of a shallow water table. In these pedoclimatic conditions, very limited effects of a mild AWD on crop status and final productivity were recorded and the commercial cultivars did not display significant different adaptabilities to the water stress. Moreover, AWD decreased arsenic (As) concentration in grain but increased grain Cadmium (Cd) being the degree of such a response dependent upon the variety, suggesting that the genotype plays an important role in this aspect of adaptation to AWD.info:eu-repo/semantics/acceptedVersio

Marker-Assisted Pyramiding of Blast-Resistance Genes in a <i>japonica</i> Elite Rice Cultivar through Forward and Background Selection

Rice blast, caused by Pyricularia oryzae, is one of the main rice diseases worldwide. The pyramiding of blast-resistance (Pi) genes, coupled to Marker-Assisted BackCrossing (MABC), provides broad-spectrum and potentially durable resistance while limiting the donor genome in the background of an elite cultivar. In this work, MABC coupled to foreground and background selections based on KASP marker assays has been applied to introgress four Pi genes (Piz, Pib, Pita, and Pik) in a renowned japonica Italian rice variety, highly susceptible to blast. Molecular analyses on the backcross (BC) lines highlighted the presence of an additional blast-resistance gene, the Pita-linked Pita2/Ptr gene, therefore increasing the number of blast-resistance introgressed genes to five. The recurrent genome was recovered up to 95.65%. Several lines carrying four (including Pita2) Pi genes with high recovery percentage levels were also obtained. Phenotypic evaluations confirmed the effectiveness of the pyramided lines against multivirulent strains, which also had broad patterns of resistance in comparison to those expected based on the pyramided Pi genes. The developed blast-resistant japonica lines represent useful donors of multiple blast-resistance genes for future rice-breeding programs related to the japonica group

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

Genome-Wide Analysis of japonica Rice Performance under Limited Water and Permanent Flooding Conditions

A rice GWAS panel of 281 accessions of japonica rice was phenotypically characterized for 26 traits related to phenology, plant and seed morphology, physiology and yield for 2 years in field conditions under permanent flooding (PF) and limited water (LW). A genome-wide analysis uncovered a total of 160 significant marker-trait associations (MTAs), of which 32 were LW-specific, 59 were PF-specific, and 69 were in common between the two water management systems. LW-specific associations were identified for several agronomic traits including days to maturation, days from flowering to maturation, leaf traits, plant height, panicle and seed traits, hundred grain weight, yield and tillering. Significant MTAs were detected across all the 12 rice chromosomes, while clusters of effects influencing different traits under LW or in both watering conditions were, respectively, observed on chromosomes 4, 8, and 12 and on chromosomes 1, 3, 4, 5, and 8. The analysis of genes annotated in the Nipponbare reference sequence and included in the regions associated to traits related to plant morphology, grain yield, and physiological parameters allowed the identification of genes that were demonstrated to affect the respective traits. Among these, three (OsOFP2, Dlf1, OsMADS56) and seven (SUI1, Sd1, OsCOL4, Nal1, OsphyB, GW5, Ehd1) candidate genes were, respectively, identified to co-localize with LW-specific associations and associations in common between the two water treatments. For several LW-specific MTAs, or in common among the two treatments, positional co-localizations with previously identified QTLs for rice adaptation to water shortages were observed, a result that further supports the role of the loci identified in this work in conferring adaptation to LW. The most robust associations identified here could represent suitable targets for genomic selection approaches to improve yield-related traits under LW

Genome-Wide Association Study for Traits Related to Plant and Grain Morphology, and Root Architecture in Temperate Rice Accessions

<div><p>Background</p><p>In this study we carried out a genome-wide association analysis for plant and grain morphology and root architecture in a unique panel of temperate rice accessions adapted to European pedo-climatic conditions. This is the first study to assess the association of selected phenotypic traits to specific genomic regions in the narrow genetic pool of temperate japonica. A set of 391 rice accessions were GBS-genotyped yielding—after data editing—57000 polymorphic and informative SNPS, among which 54% were in genic regions.</p><p>Results</p><p>In total, 42 significant genotype-phenotype associations were detected: 21 for plant morphology traits, 11 for grain quality traits, 10 for root architecture traits. The FDR of detected associations ranged from 3 · 10⁻⁷ to 0.92 (median: 0.25). In most cases, the significant detected associations co-localised with QTLs and candidate genes controlling the phenotypic variation of single or multiple traits. The most significant associations were those for flag leaf width on chromosome 4 (<i>FDR</i> = 3 · 10⁻⁷) and for plant height on chromosome 6 (<i>FDR</i> = 0.011).</p><p>Conclusions</p><p>We demonstrate the effectiveness and resolution of the developed platform for high-throughput phenotyping, genotyping and GWAS in detecting major QTLs for relevant traits in rice. We identified strong associations that may be used for selection in temperate irrigated rice breeding: e.g. associations for flag leaf width, plant height, root volume and length, grain length, grain width and their ratio. Our findings pave the way to successfully exploit the narrow genetic pool of European temperate rice and to pinpoint the most relevant genetic components contributing to the adaptability and high yield of this germplasm. The generated data could be of direct use in genomic-assisted breeding strategies.</p></div

Manhattan and Q-Q plots of GWAS results for shoot and root dry weight.

<p>Manhattan and Q-Q plots of GWAS results for shoot and root dry weight.</p

Phenotypic correlations among plant morphology, grain quality and root traits.

<p>Phenotypic correlations among plant morphology, grain quality and root traits.</p

Average LD as a function of inter-marker distance estimated in the panel of 391 accessions.

<p>Average LD as a function of inter-marker distance estimated in the panel of 391 accessions.</p

Stacked barplot for the ancestry of the available 391 rice accessions with K = 5.

<p>Stacked barplot for the ancestry of the available 391 rice accessions with K = 5.</p

Manhattan and Q-Q plots of GWAS results for root traits.

<p>Manhattan and Q-Q plots of GWAS results for root traits.</p