GENOME-WIDE ANALYSIS OF JAPONICA RICE PERFORMANCES UNDER ALTERNATE WETTING AND DRYING AND PERMANENT FLOODING CONDITIONS.

A rice GWAS panel of 281 accessions of japonica rice was phenotypically characterized for traits related to phenology, plant and seed morphology, physiology, yield and grain ionome for two years in field conditions under permanent flooding (PF) or AWD. A genome-wide analysis approach uncovered a total of 360 significant marker-trait associations (MTAs), of which 105 were AWD-specific, 178 were PF-specific and 77 were in common between the two water management systems. AWD-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, tillering, mineral nutrient and toxic trace elements level in grains. Significant MTAs were detected across all the 12 rice chromosomes. The analysis of genes annotated in the Nipponbare reference sequence and included in the regions associated to the analyzed traits allowed the identification of several loci known to affect the respective traits. The high number of MTAs identified open new perspectives for the development of functional genomic and breeding strategies

A possible role of the trehalose/trehalose-6-phosphate/SnRK1 system in rice response to salt stress

Among the abiotic stresses exacerbated by climate change, soil salinity is one of the most harmful for crops. Rice (Oryza sativa L.) is a very salt-sensitive cereal, with particular regard to the cultivars belonging to the subspecies japonica. In order to identify genomic traits conferring salt tolerance, a collection of 277 rice accessions (ssp. japonica) has been phenotypized under mild-salinity considering germination kinetic parameters and seedling emergence rate. Genotyping By Sequencing (GBS) followed by a Genome Wide Association Study (GWASs) were carried out. A total of 31.421 SNPs were used for the analysis. Significant genotypic-phenotypic associations were observed and a few Marker-Trait Associations (MTAs) were identified. By alignment with the rice reference genome (Os-Nipponbare-Reference-IRGSP-1.0), some of the genes putatively involved in salt stress were highlighted. Among them, our interest has been focused on OsTPP7 (chromosome 9) and OsTPP10 (chromosome 7), genes that belong to the OsTPP gene family encoding for Trehalose-6-Phosphate Phosphatase (TPP) enzymes catalyzing the dephosphorylation of Trehalose-6-Phosphate (T6P) to Trehalose (Tre). The level of T6P plays a central role in abiotic stress tolerance, acting as a signal in the cascade of events regulating sugar metabolism (sucrose) during seed germination and seedling growth. This activity is mediated by Snf1-Related protein Kinase-1 (SnRK1), a metabolic sensor fundamental in maintaining carbon homeostasis under stress condition. Biochemical and molecular analyses were performed on two rice accessions showing opposite behavior under salt stress (Olcenengo, tolerant, and SR113, sensitive). Results concerning T6P, Tre and sucrose levels in growing embryos, the evaluation of the time course of \u3b1-amylase enzyme (target of the SnRK1 system) activity and of OsTPP10-OsTPP7 gene expression appear to allow us to define a picture coherent with the different effects of salt stress in Olcenengo and SR113. Functional characterization of OsTPP10 gene and its allele mining analysis within the 277 rice accessions are in progress

The Trehalose-6-phosphate/SnRK1 system in the response to saline conditions during germination of two rice (O. sativa L., ssp. japonica) cultivars with different salt sensitivity

Soil salinity is extremely harmful for crops, and, among cereals, for rice (Oryza sativa L.), with particular regard to the ssp. japonica. Seed germination and seedling emergence are among the phenological stages particularly sensitive to this stress condition. A Genome Wide Association Study (GWAS) with a total of 31.421 SNPs was conducted on a collection of 277 japonica rice accessions phenotyped under mid-salinity considering germination kinetic parameters and seedling emergence rate. A few Marker-Trait Associations were identified on the basis of significant genotype-phenotype association analysis. Among the genes putatively involved in the salt response, two were particularly interesting: OsTPP7 (chromosome 9) and OsTPP10 (chromosome 7), both belonging to the family encoding Trehalose-6-Phosphate Phosphatase (TPP) catalyzing the dephosphorylation of Trehalose-6-Phosphate (T6P) to Trehalose. Salt stress affects carbohydrate production and the mobilization/use of C storage compounds altering the sink-source relationships, sugar allocation and energy metabolism. In this framework, the ratios T6P/Tre, regulated by TPP activity, acts as a signal in the cascade of events that regulate, through sugar metabolism, plant development with particular regard to seed germination and seedling growth. In turn, T6P regulates the activity of Snf1-Related protein Kinase-1 (SnRK1), a metabolic sensor able to regulate \u3b1-amylase and fundamental in maintaining C homeostasis under stress. Aim of the work was to establish the role of the SnRK1/Tre6P/Tre/Sucrose system and in particular of the OsTPP7 and OsTPP10 genes in the tolerance of japonica rice to salt stress during seed germination and early seedling development. In two model rice accessions (Olcenengo, tolerant, and SR113, sensitive) with opposite behavior in salt stress, biochemical and molecular analyses were conducted. In particular, have been considered: in the growing embryos, T6P, Tre, and sucrose levels, and OsTPP7-OsTPP10 gene expression; in the endosperm, the time-course of \u3b1-amylase activity. Te results define a picture coherent with the different effects of salt stress in Olcenengo and SR113. Functional characterization of the OsTPP10 gene and its allele mining analysis within the 277 rice accessions are in progress

Transmembrane transporters and salt tolerance in temperate japonica rice

Several investigations aimed at identifying molecular tools useful for the selection and/or the constitution of high-yield salt tolerant rice have been successfully carried out, concerning in particular indica and/ or tropical rice genotypes. Te global warming process is nowadays determining the intrusion of saline wedge into coastal fresh-water streams, and the soil salt concentration of many European rice areas, where temperate rice cultivars are mainly grown, is more and more increasing. In order to identify molecular markers and/or new loci related to salt tolerance, a Genome Wide Association Study (GWAS) has been carried out using a panel of 277 japonica rice accessions. Te panel has been subjected to Genotyping By Sequencing and phenotyping concerning tolerance to a mild-salt stress soil condition (5 dS m-1) expressed at the 4th-5th leaf developmental stage using the Standard Evaluation Score (SES) proposed by IRRI. On the basis of GWAS, a QTL including a few genes that in the indica rice genome are localized within the major salinity tolerance-related QTL \u2018SalTol\u2019 have been identified. Among them, the Os01g0337500 gene encoding the vacuolar H+-pyrophosphatase 6 (OsOVP6) is present. Since the role of the OsOVP6 activity is considered central in regulating the cellular Na+ homeostasis in both roots and leaves, investigations comparing some elements of the complex mechanisms involved in this process have been carried out. A physiological approach evaluating this possibility has been conducted in two japonica rice varieties (Galileo and Virgo) that resulted salt-tolerant, in one japonica rice variety (PL12) known to be quite salt-susceptible, and in the salt-tolerant indica inbred genotype FL478 (containing the \u2018SalTol\u2019 QTL) as reference genotype. Te root and shoot Na+/K+ ratio, Na+ influx and K+ efflux, H+ extrusion activity, cytosolic and vacuolar pH by in vivo 31P-NMR techniques were evaluated in roots of the four rice genotypes. Te results obtained, together with the electrophysiological evaluation of the whole root Na+ conductance, allow to define a picture that may explain the different salt tolerance observed among the rice genotypes analyzed. As a whole, these results confirm the interest towards a deep allele mining analysis, concerning OsOVP6, within the most significant members of the japonica rice accession panel under investigation

Continuous Flooding or Alternate Wetting and Drying Differently Affect the Accumulation of Health-Promoting Phytochemicals and Minerals in Rice Brown Grain

Climate changes impose adoption of water-saving techniques to improve the sustainability of irrigated rice systems. This study was aimed, by a two-years side-by-side comparison, at verifying the hypothesis whether \u201cAlternate Wetting and Drying\u201d (AWD) affects the concentrations of health-related compounds and minerals in brown grains of three japonica rice (Oryza sativa L.) cvs (\u2018Baldo\u2019, \u2018Gladio\u2019, and \u2018Loto\u2019) usually grown in temperate areas in continuous flooding (CF). Due to the rotational turns in water distribution imposed by local authorities and to the weather behavior, different AWD timing and severity occurred in the two years of the study. AWD induced in both seasons yield losses in \u2018Baldo\u2019 and \u2018Gladio\u2019 but not in \u2018Loto\u2019. In the brown grains of \u2018Loto\u2019, AWD increased the concentrations of total tocols, \u3b3-oryzanol, flavonoids, and the antioxidant activity. AWD affected the concentrations of minerals, particularly increasing copper, cadmium and nickel, and decreasing manganese, arsenic and zinc. In the sensitive cultivars, \u2018Baldo\u2019 and \u2018Gladio\u2019, AWD seems to affect plant yield, rather than for severity of the dry period, for prolonged absence of ponded water that exposes plants to cooler temperatures. The selection of suitable cultivars, like \u2018Loto\u2019, tolerant to AWD-related stresses, could combine environmental, yield-related, and nutritional benefits improving the product quality

Marker-Assisted Pyramiding of Blast-Resistance Genes in a japonica 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

Rice diversity panel provides accurate genomic predictions for complex traits in the progenies of biparental crosses involving members of the panel

So far, most potential applications of genomic prediction in plant improvement have been explored using cross validation approaches. This is the first empirical study to evaluate the accuracy of genomic prediction of the performances of progenies in a typical rice breeding program. Using a cross validation approach, we first analyzed the effects of marker selection and statistical methods on the accuracy of prediction of three different heritability traits in a reference population (RP) of 284 inbred accessions. Next, we investigated the size and the degree of relatedness with the progeny population (PP) of sub-sets of the RP that maximize the accuracy of prediction of phenotype across generations, i.e., for 97 F5–F7 lines derived from biparental crosses between 31 accessions of the RP. The extent of linkage disequilibrium was high (r2 = 0.2 at 0.80 Mb in RP and at 1.1 Mb in PP). Consequently, average marker density above one per 22 kb did not improve the accuracy of predictions in the RP. The accuracy of progeny prediction varied greatly depending on the composition of the training set, the trait, LD and minor allele frequency. The highest accuracy achieved for each trait exceeded 0.50 and was only slightly below the accuracy achieved by cross validation in the RP. Our results thus show that relatively high accuracy (0.41–0.54) can be achieved using only a rather small share of the RP, most related to the PP, as the training set. The practical implications of these results for rice breeding programs are discussed. (Résumé d'auteur

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