Alberto Gianinetti

Improvement of marker-based predictability of Apparent Amylose Content in japonica rice through GBSSI allele mining

BackgroundApparent Amylose Content (AAC), regulated by the Waxy gene, represents the key determinant of rice cooking properties. In occidental countries high AAC rice represents the most requested market class but the availability of molecular markers allowing specific selection of high AAC varieties is limited.ResultsIn this study, the effectiveness of available molecular markers in predicting AAC was evaluated in a collection of 127 rice accessions (125 japonica ssp. and 2 indica ssp.) characterized by AAC values from glutinous to 26%. The analyses highlighted the presence of several different allelic patterns identifiable by a few molecular markers, and two of them, i.e., the SNPs at intron1 and exon 6, were able to explain a maximum of 79.5% of AAC variation. However, the available molecular markers haplotypes did not provide tools for predicting accessions with AAC higher than 24.5%. To identify additional polymorphisms, the re-sequencing of the Waxy gene and 1kbp of the putative upstream regulatory region was performed in 21 genotypes representing all the AAC classes identified. Several previously un-characterized SNPs were identified and four of them were used to develop dCAPS markers.ConclusionsThe addition of the SNPs newly identified slightly increased the AAC explained variation and allowed the identification of a haplotype almost unequivocally associated to AAC higher than 24.5%. Haplotypes at the waxy locus were also associated to grain length and length/width (L/W) ratio. In particular, the SNP at the first intron, which identifies the Wxa and Wxb alleles, was associated with differences in the width of the grain, the L/W ratio and the length of the kernel, most likely as a result of human selection.

TOCOLS IN HULL-LESS AND HULLED BARLEY GENOTYPES GROWN IN CONTRASTING ENVIRONMENTS

Abstract The content of tocols is a parameter of increasing interest in evaluating the quality of plant-based food. Cereal grains are amongst the most widely occurring plant food components and their potential for enriching the content of vitamin E and/or hypocholesterolemic active compounds in food is therefore of interest. We investigated the presence of tocol homologues in hulled and hull-less barley, as influenced by genotype and location. Both factors significantly influenced the amount of tocols in the barley kernel, with genotype having the greater effect for most homologues. Significant genotype×location interaction was observed for six out of eight homologues, but not for total tocotrienols and total tocols; however, the coefficient of determination for genotype was high for most homologues, so that selection for this traits should be possible. The hull-less trait negatively affected the content of total tocols, influencing both tocopherols (positively) and tocotrienols (negatively). Statistical analysis suggests this is due to a different sub-set of homologues, which is preferentially accumulated in hull-less vs. hulled barleys. As hulled barley had a greater accumulation of more bioactive homologues, the selection of hull-less barleys for this trait should be considered for enhancing food quality.

Effects of barley β-glucan-enriched flour fractions on the glycaemic index of bread

The aim of this research was to evaluate β-glucan-enriched flours, obtained from barleys with either normal or waxy starch, for their effects on the glycaemic index (GI) and the quality of bread. Rheological results confirmed that when barley flour was included in the dough the overall quality of bread slightly worsened. However, positive consequences on glycaemia were obtained with the normal starch barley: the GI of all-wheat bread (82.8 ± 7.2) was significantly reduced (57.2 ± 7.9) when 40% of wheat flour was substituted with β-glucan-enriched barley flour (6.0% ± 0.1 β-glucan in the final flour blend). In contrast, this positive effect was significantly reduced (GI: 70.1 ± 9.1) when 40% of wheat flour was substituted with the β-glucan-enriched flour of a waxy barley (CDC Alamo; 6.6 ± 0.2 β-glucan in the final flour blend), suggesting that the ability of β-glucans to lower the GI was affected by the barley starch-type.

Constitutive differences between steely and mealy barley samples associated with endosperm modification

BACKGROUND Structurally different areas may occur in the endosperm of the barley grain, and they can be visually classified as either mealy or steely. Barleys with a high proportion of grains that are mostly steely often show uneven physical-chemical modification of the endosperm during malting. To study the relationship between steeliness and endosperm modification, two samples of barley cv. Scarlett with contrasting malting quality were analysed. RESULTS The proportions of steely grains were 77% and 46% in the two samples, which were then defined as steely sample and mealy sample, respectively. The steely sample showed slower modification during malting (in terms of beta-glucan degradation, friability increase, and Calcofluor staining), lower hot water extract (HWE) and acrospire growth, and higher extract viscosity. Endosperm permeation to large molecules (tested with the fluorescein isothiocyanate-dextran conjugate, FITC-D) closely followed cell wall modification in the steely sample, but this was not so in the mealy sample. CONCLUSIONS Higher steeliness was associated with higher levels of C hordeins in the grain of barley cv. Scarlett. It is proposed that such hordeins can increase the permeability to large molecules (FITC-D) but slow modification. Like steeliness and the level of C hordeins, permeability to FITC-D appears to be more linked to environmental rather than genetic effects. Although a more general association of C hordeins with steeliness of malting barley still has to be ascertained, the negative role of C hordeins in malting quality has been confirmed.

Seed dormancy in red rice. XIII: Interaction of dry-afterripening and hydration temperature

Department of Plant Pathology and Crop Physiology, Louisiana State University Agricultural Center,302 Life Sciences Building, Baton Rouge, LA 70803, USAAbstractWhile red rice (Oryza sativa L.) can remain dormantand viable for many years when fully imbibed, theenvironmental factors that stimulate germination orinducesecondarydormancyinthefieldhavenotbeencharacterized. In this study, the interactions betweenthe extent of dry-afterripening and germinationtemperature have been evaluated as possible factors.Red rice dispersal units (florets) were afterripenedfor 0–10 weeks at 308C and incubated in water at 1, 5,15, 20, 25, 30 and 358C for 2 weeks; then, all theungerminated florets were transferred to 308C for twoadditional weeks. Germination at the end of each ofthe two sequential treatments was compared to defineboth the effect of differing temperatures on germina-tion (first treatment), and the effect of these tempera-tures on subsequent germination at the optimumtemperature(308C,secondtreatment).Inafterripeningred rice, the opening of the temperature window forgermination begins at 25–358C. Fully dormant floretsacquired the ability to germinate

A criticism of the value of midparent in polyploidization

90% at 308C after4 weeks of dry-afterripening. However, imbibingflorets for 2 weeks at 158C followed by 2 weeks at308C, yielded suboptimal germination and induced adegree of secondary dormancy, dependent upon theextent of previous dry-afterripening. Cold stratification(18C) had a consistent promotive effect on thesubsequent germination, particularly when precededby 1–2 weeks of dry-afterripening at 308C. To monitorthe effects of germination temperature, median after-ripening time was utilized as a relative dormancyindex, and changes in this index have been inter-preted as an overlapping of germination and thetemperature-inducedchangesinthedormancystatus.Field weather data suggested that low-temperaturestratification may be a germination trigger in the field,even in southern Louisiana, and this merits furtherinvestigation in studies of soil-buried seeds.Keywords: cold stratification, dry-afterripening, Oryzasativa, seed dormancy, temperatureIntroductionRed rice, a noxious weed when present in crop fields,is widespread in the USA, Latin America and Europe.Redriceisconsideredtobethesamespeciesas cultivated rice (Oryza sativa L.), but possessesunfavourable agronomic characters such as shatter-ing, red pericarp and seed dormancy (Noldin et al.,1999). The shattered dispersal units remain in the soiland perpetuate the weed in subsequent years (Gossand Brown, 1939). Environmental factors triggeringits field germination are not known, but inductionof secondary dormancy and dormancy cycling havebeen reported (Teekachunhatean, 1985), and themagnitude of the red rice soil seed bank suggeststhat such mechanisms should be important forfield survival. A better comprehension of seedbank ecology and dormancy cycling may be a keyto improved forecast modelling for red rice weedmanagement, as has been demonstrated for otherweeds (Forcella et al., 1997; Forcella, 1998).In Polygonum persicaria, temperature exerts a dualroleinregulatinggermination,firstcontrollingchangesin dormancy status, and thereafter modulatinggermination of the non-dormant seeds (Bouwmeesterand Karssen, 1992). In rice cv. Kasalath, completelyafterripened florets were induced into secondarydormancy after imbibition and incubation at tempera-tures between 8 and 198C (particularly at 10 and 158C)when subsequently tested for germination at 258C(Miura and Araki, 1996). With imbibition at 58C, nodormancy developed, and florets germinated 99%when transferred to 258C. However, secondary

QTLs for Woolly Poplar Aphid (Phloeomyzus passerinii L.) Resistance Detected in an Inter-Specific Populus deltoides x P. nigra Mapping Population

The hypothesis of genetic additivity states that the effects of different alleles, or different genes, add up to produce the phenotype. When considering the F1 progeny of a cross, the hypothesis of additivity of the genetic dosages provided by the parents is tested against the mid-parent value (MPV), which is the average of parental phenotypes and represents the reference value for genetic additivity. Non-additive effects (genetic interactions) are typically measured as deviations from MPV. Recently, however, the use of MPV has been directly transposed to the study of genetic additivity in newly synthesized plant polyploids, assuming that they should as well display mid-parent expression patterns for additive traits. It is shown here that this direct transposition is incorrect. It is suggested that, in neo-polyploids, mid-parent expression has to be reconsidered in terms of reduced genetic additivity. Homeostatic mechanisms are deemed to be the obvious ones responsible for this effect. Genomes are therefore ruled by negative epistasis, and heterosis in allopolyploids is due to a decreased interaction of the parental repressive systems. It is contended that focalizing on the right perspective has relevant theoretical consequences and makes the studies of neo-polyploids very important for our understanding of how genomes work.

Barley: An Overview of a Versatile Cereal Grain with Many Food and Feed Uses

The genus Populus represents one of the most economically important groups of forest trees. It is composed by approximately 30 species used for wood and non-wood products, phytoremediation and biomass. Poplar is subjected to several biological and environmental threats although, compared to annual crops, we know far less about the genetic bases of biotic stress resistance. Woolly poplar aphid (Phloeomyzus passerinii) is considered a main pest of cultivated poplars in European and American countries. In this work we present two high density linkage maps in poplar obtained by a genotyping by sequencing (GBS) approach and the identification of QTLs involved in Ph. passerinii resistance. A total of 5,667 polymorphic markers (5,606 SNPs and 61 SSRs) identified on expressed sequences have been used to genotype 131 plants of an F1 population P ×canadensis obtained by an interspecific mate between Populus deltoides (resistant to woolly poplar aphid) and Populus nigra (susceptible to woolly poplar aphid). The two linkage maps, obtained following the two-way pseudo-testcross mapping strategy, have been used to investigate the genetic bases of woolly poplar aphid resistance. One major QTL and two QTLs with minor effects (mapped on LGV, LGXVI and LG XIX) explaining the 65.8% of the genetic variance observed in the progeny in response to Ph. passerinii attack were found. The high density coverage of functional markers allowed the identification of three genes belonging to disease resistance pathway as putative candidates for P. deltoides resistance to woolly poplar aphid. This work is the first report on genetic of woolly poplar aphid genetic resistance and the resistant loci associated markers identified represent a valuable tool in resistance poplar breeding programs.

Seed Dormancy Involves a Transcriptional Program That Supports Early Plastid Functionality during Imbibition

The history of barley as a crop begins in the Fertile Crescent at the beginning of the Neolithic Era. During the process of domestication, barley has gradually accumulated traits that facilitated agricultural production. Several morphological forms have evolved, including winter, spring, two-row, six-row, awned, awnless, hooded, naked and covered, malting, feed (grain and forage), and food type. The grain is used for feed, food, malt for beer and whisky, and the development of functional food.

The Caryopsis of Red-Grained Rice Has Enhanced Resistance to Fungal Attack

Red rice fully dormant seeds do not germinate even under favorable germination conditions. In several species, including rice, seed dormancy can be removed by dry-afterripening (warm storage); thus, dormant and non-dormant seeds can be compared for the same genotype. A weedy (red) rice genotype with strong dormancy was used for mRNA expression profiling, by RNA-Seq, of dormant and non-dormant dehulled caryopses (here addressed as seeds) at two temperatures (30 °C and 10 °C) and two durations of incubation in water (8 h and 8 days). Aim of the study was to highlight the differences in the transcriptome of dormant and non-dormant imbibed seeds. Transcript data suggested important differences between these seeds (at least, as inferred by expression-based metabolism reconstruction): dry-afterripening seems to impose a respiratory impairment onto non-dormant seeds, thus glycolysis is deduced to be preferentially directed to alcoholic fermentation in non-dormant seeds but to alanine production in dormant ones; phosphoenolpyruvate carboxykinase, pyruvate phosphate dikinase and alanine aminotransferase pathways appear to have an important gluconeogenetic role associated with the restoration of plastid functions in the dormant seed following imbibition; correspondingly, co-expression analysis pointed out a commitment to guarantee plastid functionality in dormant seeds. At 8 h of imbibition, as inferred by gene expression, dormant seeds appear to preferentially use carbon and nitrogen resources for biosynthetic processes in the plastid, including starch and proanthocyanidins accumulation. Chromatin modification appears to be a possible mechanism involved in the transition from dormancy to germination. Non-dormant seeds show higher expression of genes related to cell wall modification, suggesting they prepare for acrospire/radicle elongation.