Publications by authors named "Anna M Mastrangelo"

25 Publications

  • Page 1 of 1

Importance of Landraces in Cereal Breeding for Stress Tolerance.

Plants (Basel) 2021 Jun 22;10(7). Epub 2021 Jun 22.

Council for Agricultural Research and Economics, Research Centre for Cereal and Industrial Crops, S.S. 673, Km 25,200, 71122 Foggia, Italy.

The renewed focus on cereal landraces is a response to some negative consequences of modern agriculture and conventional breeding which led to a reduction of genetic diversity. Cereal landraces are still cultivated on marginal lands due to their adaptability to unfavourable conditions, constituting an important source of genetic diversity usable in modern plant breeding to improve the adaptation to abiotic or biotic stresses, yield performance and quality traits in limiting environments. Traditional agricultural production systems have played an important role in the evolution and conservation of wide variability in gene pools within species. Today, on-farm and ex situ conservation in gene bank collections, together with data sharing among researchers and breeders, will greatly benefit cereal improvement. Many efforts are usually made to collect, organize and phenotypically and genotypically analyse cereal landrace collections, which also utilize genomic approaches. Their use in breeding programs based on genomic selection, and the discovery of beneficial untapped QTL/genes/alleles which could be introgressed into modern varieties by MAS, pyramiding or biotechnological tools, increase the potential for their better deployment and exploitation in breeding for a more sustainable agricultural production, particularly enhancing adaptation and productivity in stress-prone environments to cope with current climate changes.
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http://dx.doi.org/10.3390/plants10071267DOI Listing
June 2021

What Makes Bread and Durum Wheat Different?

Trends Plant Sci 2021 07;26(7):677-684

CREA Research Centre for Genomics and Bioinformatics, Fiorenzuola d'Arda, 29017, Italy. Electronic address:

Durum wheat (tetraploid) and bread wheat (hexaploid) are two closely related species with potentially different adaptation capacities and only a few distinct technological properties that make durum semolina and wheat flour more suitable for pasta, or bread and bakery products, respectively. Interspecific crosses and new breeding technologies now allow researchers to develop wheat lines with durum or bread quality features in either a tetraploid or hexaploid genetic background; such lines combine any technological properties of wheat with the different adaptation capacity expressed by tetraploid and hexaploid wheat genomes. Here, we discuss what makes bread and durum wheat different, consider their environmental adaptation capacity and the major quality-related genes that explain the different end-uses of semolina and bread flour and that could be targets for future wheat breeding programs.
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http://dx.doi.org/10.1016/j.tplants.2021.01.004DOI Listing
July 2021

The Global Durum Wheat Panel (GDP): An International Platform to Identify and Exchange Beneficial Alleles.

Front Plant Sci 2020 21;11:569905. Epub 2020 Dec 21.

Department of Agricultural and Food Sciences, University of Bologna, Bologna, Italy.

Representative, broad and diverse collections are a primary resource to dissect genetic diversity and meet pre-breeding and breeding goals through the identification of beneficial alleles for target traits. From 2,500 tetraploid wheat accessions obtained through an international collaborative effort, a Global Durum wheat Panel (GDP) of 1,011 genotypes was assembled that captured 94-97% of the original diversity. The GDP consists of a wide representation of ssp. modern germplasm and landraces, along with a selection of emmer and primitive tetraploid wheats to maximize diversity. GDP accessions were genotyped using the wheat iSelect 90K SNP array. Among modern durum accessions, breeding programs from Italy, France and Central Asia provided the highest level of genetic diversity, with only a moderate decrease in genetic diversity observed across nearly 50 years of breeding (1970-2018). Further, the breeding programs from Europe had the largest sets of unique alleles. LD was lower in the landraces (0.4 Mbp) than in modern germplasm (1.8 Mbp) at = 0.5. analysis of modern germplasm defined a minimum of 13 distinct genetic clusters (), which could be traced to the breeding program of origin. Chromosome regions putatively subjected to strong selection pressure were identified from fixation index ( ) and diversity reduction index () metrics in pairwise comparisons among decades of release and breeding programs. Clusters of putative selection sweeps (PSW) were identified as co-localized with major loci controlling phenology ( and ), plant height () and quality (gliadins and glutenins), underlining the role of the corresponding genes as driving elements in modern breeding. Public seed availability and deep genetic characterization of the GDP make this collection a unique and ideal resource to identify and map useful genetic diversity at loci of interest to any breeding program.
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http://dx.doi.org/10.3389/fpls.2020.569905DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7779600PMC
December 2020

Durum wheat genome highlights past domestication signatures and future improvement targets.

Nat Genet 2019 05 8;51(5):885-895. Epub 2019 Apr 8.

CREA-Research Centre for Genomics and Bioinformatics, Fiorenzuola d'Arda, Italy.

The domestication of wild emmer wheat led to the selection of modern durum wheat, grown mainly for pasta production. We describe the 10.45 gigabase (Gb) assembly of the genome of durum wheat cultivar Svevo. The assembly enabled genome-wide genetic diversity analyses revealing the changes imposed by thousands of years of empirical selection and breeding. Regions exhibiting strong signatures of genetic divergence associated with domestication and breeding were widespread in the genome with several major diversity losses in the pericentromeric regions. A locus on chromosome 5B carries a gene encoding a metal transporter (TdHMA3-B1) with a non-functional variant causing high accumulation of cadmium in grain. The high-cadmium allele, widespread among durum cultivars but undetected in wild emmer accessions, increased in frequency from domesticated emmer to modern durum wheat. The rapid cloning of TdHMA3-B1 rescues a wild beneficial allele and demonstrates the practical use of the Svevo genome for wheat improvement.
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http://dx.doi.org/10.1038/s41588-019-0381-3DOI Listing
May 2019

Genetic markers associated to arbuscular mycorrhizal colonization in durum wheat.

Sci Rep 2018 Jul 13;8(1):10612. Epub 2018 Jul 13.

Dipartimento di Scienze Agrarie, Alimentari e Agro-Ambientali, Università di Pisa, Via del Borghetto 80, 56124, Pisa, Italy.

In this work we investigated the variability and the genetic basis of susceptibility to arbuscular mycorrhizal (AM) colonization of wheat roots. The mycorrhizal status of wild, domesticated and cultivated tetraploid wheat accessions, inoculated with the AM species Funneliformis mosseae, was evaluated. In addition, to detect genetic markers in linkage with chromosome regions involved in AM root colonization, a genome wide association analysis was carried out on 108 durum wheat varieties and two AM fungal species (F. mosseae and Rhizoglomus irregulare). Our findings showed that a century of breeding on durum wheat and the introgression of Reduced height (Rht) genes associated with increased grain yields did not select against AM symbiosis in durum wheat. Seven putative Quantitative Trait Loci (QTLs) linked with durum wheat mycorrhizal susceptibility in both experiments, located on chromosomes 1A, 2B, 5A, 6A, 7A and 7B, were detected. The individual QTL effects (r) ranged from 7 to 16%, suggesting a genetic basis for this trait. Marker functional analysis identified predicted proteins with potential roles in host-parasite interactions, degradation of cellular proteins, homeostasis regulation, plant growth and disease/defence. The results of this work emphasize the potential for further enhancement of root colonization exploiting the genetic variability present in wheat.
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http://dx.doi.org/10.1038/s41598-018-29020-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6045686PMC
July 2018

Regulation and Evolution of NLR Genes: A Close Interconnection for Plant Immunity.

Int J Mol Sci 2018 Jun 4;19(6). Epub 2018 Jun 4.

Council for Agricultural Research and Economics-Research Centre for Cereal and Industrial Crops, via Stezzano 24, 24126 Bergamo, Italy.

NLR (NOD-like receptor) genes belong to one of the largest gene families in plants. Their role in plants' resistance to pathogens has been clearly described for many members of this gene family, and dysregulation or overexpression of some of these genes has been shown to induce an autoimmunity state that strongly affects plant growth and yield. For this reason, these genes have to be tightly regulated in their expression and activity, and several regulatory mechanisms are described here that tune their gene expression and protein levels. This gene family is subjected to rapid evolution, and to maintain diversity at NLRs, a plethora of genetic mechanisms have been identified as sources of variation. Interestingly, regulation of gene expression and evolution of this gene family are two strictly interconnected aspects. Indeed, some examples have been reported in which mechanisms of gene expression regulation have roles in promotion of the evolution of this gene family. Moreover, co-evolution of the gene family and other gene families devoted to their control has been recently demonstrated, as in the case of miRNAs.
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http://dx.doi.org/10.3390/ijms19061662DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6032283PMC
June 2018

Environmental and Genetic Variation for Yield-Related Traits of Durum Wheat as Affected by Development.

Front Plant Sci 2018 18;9. Epub 2018 Jan 18.

Sez. Agronomia, Coltivazioni erbacee e Genetica, Dipartimento di Agraria, University of Sassari, Sassari, Italy.

Phenology has a profound effect on adaptation and productivity of crops. The impact of phenology on tillering and fertility traits of durum wheat ( L. subsp. Desf.) was evaluated with the aim of specifying which group of flowering genes (, or ) was involved in their control. A recombinant inbred line population was grown under four contrasting conditions of vernalization and daylength. Phenotyping was carried out according to robust phenological models dissecting both phenological and yield related traits. Whole-genome profiling was performed using the DArT-Seq technology. The genetic variability for tillering was mainly related to the genetic variability for vernalization sensitivity, as shown by the many quantitative trait loci (QTLs) identified in non-vernalized plants associated to both tillering and phenological traits. No effects of photoperiod sensitivity on spikelet number were detected in short-day-grown plants, apparently because of limited genetic variability in photoperiod sensitivity of the population. Earliness was involved in control of spikelet number via final leaf number, with these traits genetically correlated and sharing some QTLs. Chaff weight and number of kernels per g chaff were negatively associated and related to anthesis date under most conditions. QTL mapping uncovered novel loci involved in phenological control of tillering and fertility traits, and confirmed the presence of several well-established loci. Phenotyping of both phenology and kernel number according to a robust physiological model amplified the possibility of identifying genetic factors underlying their variations. Also, isolating known flowering gene cues by manipulation of environmental conditions provided the opportunity for each group of genes to be expressed without confounding effects of the others. This information helps to predict the consequences of either genetic manipulation of flowering genes and changes in environmental conditions on the potential yield of durum wheat.
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http://dx.doi.org/10.3389/fpls.2018.00008DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5778143PMC
January 2018

Genetic dissection of the relationships between grain yield components by genome-wide association mapping in a collection of tetraploid wheats.

PLoS One 2018 11;13(1):e0190162. Epub 2018 Jan 11.

Department of Soil, Plant & Food Sciences, Genetics and Plant Breeding Section, University Aldo Moro, Bari, Italy.

Increasing grain yield potential in wheat has been a major target of most breeding programs. Genetic advance has been frequently hindered by negative correlations among yield components that have been often observed in segregant populations and germplasm collections. A tetraploid wheat collection was evaluated in seven environments and genotyped with a 90K SNP assay to identify major and stable quantitative trait loci (QTL) for grain yield per spike (GYS), kernel number per spike (KNS) and thousand-kernel weight (TKW), and to analyse the genetic relationships between the yield components at QTL level. The genome-wide association analysis detected eight, eleven and ten QTL for KNS, TKW and GYS, respectively, significant in at least three environments or two environments and the mean across environments. Most of the QTL for TKW and KNS were found located in different marker intervals, indicating that they are genetically controlled independently by each other. Out of eight KNS QTL, three were associated to significant increases of GYS, while the increased grain number of five additional QTL was completely or partially compensated by decreases in grain weight, thus producing no or reduced effects on GYS. Similarly, four consistent and five suggestive TKW QTL resulted in visible increase of GYS, while seven additional QTL were associated to reduced effects in grain number and no effects on GYS. Our results showed that QTL analysis for detecting TKW or KNS alleles useful for improving grain yield potential should consider the pleiotropic effects of the QTL or the association to other QTLs.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0190162PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5764242PMC
January 2018

Identification of New Resistance Loci to African Stem Rust Race TTKSK in Tetraploid Wheats Based on Linkage and Genome-Wide Association Mapping.

Front Plant Sci 2015 9;6:1033. Epub 2015 Dec 9.

Cereal Research Centre, Council for Agricultural Research and Economics Foggia, Italy.

Stem rust, caused by Puccinia graminis Pers. f. sp. tritici Eriks. and E. Henn. (Pgt), is one of the most destructive diseases of wheat. Races of the pathogen in the "Ug99 lineage" are of international concern due to their virulence for widely used stem rust resistance genes and their spread throughout Africa. Disease resistant cultivars provide one of the best means for controlling stem rust. To identify quantitative trait loci (QTL) conferring resistance to African stem rust race TTKSK at the seedling stage, we evaluated an association mapping (AM) panel consisting of 230 tetraploid wheat accessions under greenhouse conditions. A high level of phenotypic variation was observed in response to race TTKSK in the AM panel, allowing for genome-wide association mapping of resistance QTL in wild, landrace, and cultivated tetraploid wheats. Thirty-five resistance QTL were identified on all chromosomes, and seventeen are of particular interest as identified by multiple associations. Many of the identified resistance loci were coincident with previously identified rust resistance genes; however, nine on chromosomes 1AL, 2AL, 4AL, 5BL, and 7BS may be novel. To validate AM results, a biparental population of 146 recombinant inbred lines was also considered, which derived from a cross between the resistant cultivar "Cirillo" and susceptible "Neodur." The stem rust resistance of Cirillo was conferred by a single gene on the distal region of chromosome arm 6AL in an interval map coincident with the resistance gene Sr13, and confirmed one of the resistance loci identified by AM. A search for candidate resistance genes was carried out in the regions where QTL were identified, and many of them corresponded to NBS-LRR genes and protein kinases with LRR domains. The results obtained in the present study are of great interest as a high level of genetic variability for resistance to race TTKSK was described in a germplasm panel comprising most of the tetraploid wheat sub-species.
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http://dx.doi.org/10.3389/fpls.2015.01033DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4673868PMC
December 2015

Conservation of AtTZF1, AtTZF2, and AtTZF3 homolog gene regulation by salt stress in evolutionarily distant plant species.

Front Plant Sci 2015 16;6:394. Epub 2015 Jun 16.

Cereal Research Centre, Council for Agricultural Research and Economics Foggia, Italy.

Arginine-rich tandem zinc-finger proteins (RR-TZF) participate in a wide range of plant developmental processes and adaptive responses to abiotic stress, such as cold, salt, and drought. This study investigates the conservation of the genes AtTZF1-5 at the level of their sequences and expression across plant species. The genomic sequences of the two RR-TZF genes TdTZF1-A and TdTZF1-B were isolated in durum wheat and assigned to chromosomes 3A and 3B, respectively. Sequence comparisons revealed that they encode proteins that are highly homologous to AtTZF1, AtTZF2, and AtTZF3. The expression profiles of these RR-TZF durum wheat and Arabidopsis proteins support a common function in the regulation of seed germination and responses to abiotic stress. In particular, analysis of plants with attenuated and overexpressed AtTZF3 indicate that AtTZF3 is a negative regulator of seed germination under conditions of salt stress. Finally, comparative sequence analyses establish that the RR-TZF genes are encoded by lower plants, including the bryophyte Physcomitrella patens and the alga Chlamydomonas reinhardtii. The regulation of the Physcomitrella AtTZF1-2-3-like genes by salt stress strongly suggests that a subgroup of the RR-TZF proteins has a function that has been conserved throughout evolution.
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http://dx.doi.org/10.3389/fpls.2015.00394DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4468379PMC
July 2015

Post-transcriptional and post-translational regulations of drought and heat response in plants: a spider's web of mechanisms.

Front Plant Sci 2015 11;6:57. Epub 2015 Feb 11.

Genomics Research Centre, Consiglio per la Ricerca e la Sperimentazione in Agricoltura, Fiorenzuola d'Arda , Piacenza, Italy.

Drought and heat tolerance are complex quantitative traits. Moreover, the adaptive significance of some stress-related traits is more related to plant survival than to agronomic performance. A web of regulatory mechanisms fine-tunes the expression of stress-related traits and integrates both environmental and developmental signals. Both post-transcriptional and post-translational modifications contribute substantially to this network with a pivotal regulatory function of the transcriptional changes related to cellular and plant stress response. Alternative splicing and RNA-mediated silencing control the amount of specific transcripts, while ubiquitin and SUMO modify activity, sub-cellular localization and half-life of proteins. Interactions across these modification mechanisms ensure temporally and spatially appropriate patterns of downstream-gene expression. For key molecular components of these regulatory mechanisms, natural genetic diversity exists among genotypes with different behavior in terms of stress tolerance, with effects upon the expression of adaptive morphological and/or physiological target traits.
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http://dx.doi.org/10.3389/fpls.2015.00057DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4324062PMC
February 2015

Linkage disequilibrium and genome-wide association mapping in tetraploid wheat (Triticum turgidum L.).

PLoS One 2014 23;9(4):e95211. Epub 2014 Apr 23.

Consiglio per la Ricerca e la sperimentazione in Agricoltura, Cereal Research Centre, Foggia, Italy.

Association mapping is a powerful tool for the identification of quantitative trait loci through the exploitation of the differential decay of linkage disequilibrium (LD) between marker loci and genes of interest in natural and domesticated populations. Using a sample of 230 tetraploid wheat lines (Triticum turgidum ssp), which included naked and hulled accessions, we analysed the pattern of LD considering 26 simple sequence repeats and 970 mostly mapped diversity array technology loci. In addition, to validate the potential for association mapping in durum wheat, we evaluated the same genotypes for plant height, heading date, protein content, and thousand-kernel weight. Molecular and phenotypic data were used to: (i) investigate the genetic and phenotypic diversity; (ii) study the dynamics of LD across the durum wheat genome, by investigating the patterns of LD decay; and (iii) test the potential of our panel to identify marker-trait associations through the analysis of four quantitative traits of major agronomic importance. Moreover, we compared and validated the association mapping results with outlier detection analysis based on population divergence. Overall, in tetraploid wheat, the pattern of LD is extremely population dependent and is related to the domestication and breeding history of durum wheat. Comparing our data with several other studies in wheat, we confirm the position of many major genes and quantitative trait loci for the traits considered. Finally, the analysis of the selection signature represents a very useful complement to validate marker-trait associations.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0095211PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3997356PMC
January 2015

Characterization of polyploid wheat genomic diversity using a high-density 90,000 single nucleotide polymorphism array.

Plant Biotechnol J 2014 Aug 20;12(6):787-96. Epub 2014 Mar 20.

Department of Plant Pathology, Kansas State University, Manhattan, KS, USA.

High-density single nucleotide polymorphism (SNP) genotyping arrays are a powerful tool for studying genomic patterns of diversity, inferring ancestral relationships between individuals in populations and studying marker-trait associations in mapping experiments. We developed a genotyping array including about 90,000 gene-associated SNPs and used it to characterize genetic variation in allohexaploid and allotetraploid wheat populations. The array includes a significant fraction of common genome-wide distributed SNPs that are represented in populations of diverse geographical origin. We used density-based spatial clustering algorithms to enable high-throughput genotype calling in complex data sets obtained for polyploid wheat. We show that these model-free clustering algorithms provide accurate genotype calling in the presence of multiple clusters including clusters with low signal intensity resulting from significant sequence divergence at the target SNP site or gene deletions. Assays that detect low-intensity clusters can provide insight into the distribution of presence-absence variation (PAV) in wheat populations. A total of 46 977 SNPs from the wheat 90K array were genetically mapped using a combination of eight mapping populations. The developed array and cluster identification algorithms provide an opportunity to infer detailed haplotype structure in polyploid wheat and will serve as an invaluable resource for diversity studies and investigating the genetic basis of trait variation in wheat.
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http://dx.doi.org/10.1111/pbi.12183DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4265271PMC
August 2014

Aerosol-assisted atmospheric cold plasma deposition and characterization of superhydrophobic organic-inorganic nanocomposite thin films.

Langmuir 2014 Jan 10;30(3):857-65. Epub 2014 Jan 10.

Institute of Inorganic Methodologies and Plasmas, National Research Council (IMIP-CNR), c/o Department of Chemistry, University of Bari Aldo Moro , via Orabona 4, 70126 Bari, Italy.

A facile atmospheric pressure cold plasma process is presented to deposit a novel organic-inorganic hydrocarbon polymer/ZnO nanoparticles nanocomposite coating. Specifically, this method involves the utilization of an atmospheric pressure dielectric barrier discharge (DBD) fed with helium and the aerosol of a dispersion of oleate-capped ZnO nanoparticles (NPs) in n-octane. As assessed by X-ray photoelectron spectroscopy (XPS) and attenuated total reflectance-Fourier transform infrared (ATR-FTIR) spectroscopy, the deposited nanocomposite coating combines the chemical features of both the oleate-capped ZnO NPs and the polyethylene-like organic component originated from the plasma polymerization of n-octane. Additionally, scanning electron microscopy (SEM) and transmission scanning electron microscopy (TSEM) confirm the synthesis of hierarchical micro/nanostructured coatings containing quasi-spherical NPs agglomerates. The polyethylene-like polymer covers the NPs agglomerates to different extents and contributes to their immobilization in the three-dimensional network of the coating. The increase of both the deposition time (1-10 min) and the NPs concentration in the dispersion (0.5-5 wt %) has a significant effect on the chemical and morphological structure of the thin films and, in fact, results in the increase the ZnO NPs content, which ultimately leads to superhydrophobic surfaces (advancing and receding water contact angles higher than 160°) with low hysteresis due to the hierarchical multiscale roughness of the coating.
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http://dx.doi.org/10.1021/la404755nDOI Listing
January 2014

Different stress responsive strategies to drought and heat in two durum wheat cultivars with contrasting water use efficiency.

BMC Genomics 2013 Nov 22;14:821. Epub 2013 Nov 22.

Department of Biological and Environmental Sciences and Technologies, University of Salento, Prov,le Lecce Monteroni, I-73100 Lecce, Italy.

Background: Durum wheat often faces water scarcity and high temperatures, two events that usually occur simultaneously in the fields. Here we report on the stress responsive strategy of two durum wheat cultivars, characterized by different water use efficiency, subjected to drought, heat and a combination of both stresses.

Results: The cv Ofanto (lower water use efficiency) activated a large set of well-known drought-related genes after drought treatment, while Cappelli (higher water use efficiency) showed the constitutive expression of several genes induced by drought in Ofanto and a modulation of a limited number of genes in response to stress. At molecular level the two cvs differed for the activation of molecular messengers, genes involved in the regulation of chromatin condensation, nuclear speckles and stomatal closure. Noteworthy, the heat response in Cappelli involved also the up-regulation of genes belonging to fatty acid β-oxidation pathway, glyoxylate cycle and senescence, suggesting an early activation of senescence in this cv. A gene of unknown function having the greatest expression difference between the two cultivars was selected and used for expression QTL analysis, the corresponding QTL was mapped on chromosome 6B.

Conclusion: Ofanto and Cappelli are characterized by two opposite stress-responsive strategies. In Ofanto the combination of drought and heat stress led to an increased number of modulated genes, exceeding the simple cumulative effects of the two single stresses, whereas in Cappelli the same treatment triggered a number of differentially expressed genes lower than those altered in response to heat stress alone. This work provides clear evidences that the genetic system based on Cappelli and Ofanto represents an ideal tool for the genetic dissection of the molecular response to drought and other abiotic stresses.
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http://dx.doi.org/10.1186/1471-2164-14-821DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4046701PMC
November 2013

Genetic basis of qualitative and quantitative resistance to powdery mildew in wheat: from consensus regions to candidate genes.

BMC Genomics 2013 Aug 19;14:562. Epub 2013 Aug 19.

Background: Powdery mildew (Blumeria graminis f. sp. tritici) is one of the most damaging diseases of wheat. The objective of this study was to identify the wheat genomic regions that are involved in the control of powdery mildew resistance through a quantitative trait loci (QTL) meta-analysis approach. This meta-analysis allows the use of collected QTL data from different published studies to obtain consensus QTL across different genetic backgrounds, thus providing a better definition of the regions responsible for the trait, and the possibility to obtain molecular markers that will be suitable for marker-assisted selection.

Results: Five QTL for resistance to powdery mildew were identified under field conditions in the durum-wheat segregating population Creso × Pedroso. An integrated map was developed for the projection of resistance genes/ alleles and the QTL from the present study and the literature, and to investigate their distribution in the wheat genome. Molecular markers that correspond to candidate genes for plant responses to pathogens were also projected onto the map, particularly considering NBS-LRR and receptor-like protein kinases. More than 80 independent QTL and 51 resistance genes from 62 different mapping populations were projected onto the consensus map using the Biomercator statistical software. Twenty-four MQTL that comprised 2-6 initial QTL that had widely varying confidence intervals were found on 15 chromosomes. The co-location of the resistance QTL and genes was investigated. Moreover, from analysis of the sequences of DArT markers, 28 DArT clones mapped on wheat chromosomes have been shown to be associated with the NBS-LRR genes and positioned in the same regions as the MQTL for powdery mildew resistance.

Conclusions: The results from the present study provide a detailed analysis of the genetic basis of resistance to powdery mildew in wheat. The study of the Creso × Pedroso durum-wheat population has revealed some QTL that had not been previously identified. Furthermore, the analysis of the co-localization of resistance loci and functional markers provides a large list of candidate genes and opens up a new perspective for the fine mapping and isolation of resistance genes, and for the marker-assisted improvement of resistance in wheat.
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http://dx.doi.org/10.1186/1471-2164-14-562DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3765315PMC
August 2013

Genetic Diversity and Population Structure of Tetraploid Wheats (Triticum turgidum L.) Estimated by SSR, DArT and Pedigree Data.

PLoS One 2013 27;8(6):e67280. Epub 2013 Jun 27.

Consiglio per la Ricerca e la sperimentazione in Agricoltura, Cereal Research Centre, Foggia, Italy.

Levels of genetic diversity and population genetic structure of a collection of 230 accessions of seven tetraploid Triticum turgidum L. subspecies were investigated using six morphological, nine seed storage protein loci, 26 SSRs and 970 DArT markers. The genetic diversity of the morphological traits and seed storage proteins was always lower in the durum wheat compared to the wild and domesticated emmer. Using Bayesian clustering (K = 2), both of the sets of molecular markers distinguished the durum wheat cultivars from the other tetraploid subspecies, and two distinct subgroups were detected within the durum wheat subspecies, which is in agreement with their origin and year of release. The genetic diversity of morphological traits and seed storage proteins was always lower in the improved durum cultivars registered after 1990, than in the intermediate and older ones. This marked effect on diversity was not observed for molecular markers, where there was only a weak reduction. At K >2, the SSR markers showed a greater degree of resolution than for DArT, with their identification of a greater number of groups within each subspecies. Analysis of DArT marker differentiation between the wheat subspecies indicated outlier loci that are potentially linked to genes controlling some important agronomic traits. Among the 211 loci identified under selection, 109 markers were recently mapped, and some of these markers were clustered into specific regions on chromosome arms 2BL, 3BS and 4AL, where several genes/quantitative trait loci (QTLs) are involved in the domestication of tetraploid wheats, such as the tenacious glumes (Tg) and brittle rachis (Br) characteristics. On the basis of these results, it can be assumed that the population structure of the tetraploid wheat collection partially reflects the evolutionary history of Triticum turgidum L. subspecies and the genetic potential of landraces and wild accessions for the detection of unexplored alleles.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0067280PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3694930PMC
October 2017

Plant nucleotide binding site-leucine-rich repeat (NBS-LRR) genes: active guardians in host defense responses.

Int J Mol Sci 2013 Apr 2;14(4):7302-26. Epub 2013 Apr 2.

Consiglio per la Ricerca e la Sperimentazione in Agricoltura, Agricultural Research Council-Cereal Research Centre (CRA-CER), SS 16 km 675, 71122 Foggia, Italy.

The most represented group of resistance genes are those of the nucleotide binding site-leucine-rich repeat (NBS-LRR) class. These genes are very numerous in the plant genome, and they often occur in clusters at specific loci following gene duplication and amplification events. To date, hundreds of resistance genes and relatively few quantitative trait loci for plant resistance to pathogens have been mapped in different species, with some also cloned. When these NBS-LRR genes have been physically or genetically mapped, many cases have shown co-localization between resistance loci and NBS-LRR genes. This has allowed the identification of candidate genes for resistance, and the development of molecular markers linked to R genes. This review is focused on recent genomics studies that have described the abundance, distribution and evolution of NBS-LRR genes in plant genomes. Furthermore, in terms of their expression, NBS-LRR genes are under fine regulation by cis- and trans-acting elements. Recent findings have provided insights into the roles of alternative splicing, the ubiquitin/ proteasome system, and miRNAs and secondary siRNAs in the regulation of NBS-LRR gene expression at the post-transcriptional, post-translational and epigenetic levels. The possibility to use this knowledge for genetic improvement of plant resistance to pathogens is discussed.
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http://dx.doi.org/10.3390/ijms14047302DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3645687PMC
April 2013

Characterization of wheat DArT markers: genetic and functional features.

Mol Genet Genomics 2012 Sep 8;287(9):741-53. Epub 2012 Aug 8.

CRA, Cereal Research Centre, SS16 km 675, 71122 Foggia, Italy.

Diversity array technology (DArT) markers are largely used for mapping, genetic diversity, and association mapping studies. For years, they have been used as anonymous genomic markers, as their sequences were not known. As the sequences of 2,000 wheat DArT clones are now available, this study was designed to analyze these sequences with bioinformatic approaches, and to study the genetic features of a subset of 291 markers positioned on the A and B genomes in three durum wheat genetic maps. A set of 1,757 non-redundant sequences was identified, and used as queries for similarity searches. Analysis of the genetic positions of markers corresponding to nearly identical sequences indicates that redundancy of sequences is one of the factors that explains the clustering of these markers in specific genomic regions. Of a total of 1,124 DArT clones (64 %) that represent putatively expressed sequences, putative functions are proposed for more than 700 of them. Of note, many clones correspond to genes that are related to disease resistance, as characterized by leucine-rich repeat domains, and 40 of these clones are positioned in the three genetic maps presented in this study. Finally, DArT markers have been used to find syntenic regions in the Brachypodium and rice genomes. In conclusion, the analyses herein presented contribute to explain the main features of DArT markers observed in genetic maps, as clustering in short chromosome regions. Moreover, the attribution of putative gene functions for more than 700 sequences makes these markers an optimal tool for collinearity studies or for the identification of candidate genes.
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http://dx.doi.org/10.1007/s00438-012-0714-8DOI Listing
September 2012

A high-density consensus map of A and B wheat genomes.

Theor Appl Genet 2012 Dec 8;125(8):1619-38. Epub 2012 Aug 8.

CRA-Cereal Research Centre, SS16 km 675, 71122 Foggia, Italy.

A durum wheat consensus linkage map was developed by combining segregation data from six mapping populations. All of the crosses were derived from durum wheat cultivars, except for one accession of T. ssp. dicoccoides. The consensus map was composed of 1,898 loci arranged into 27 linkage groups covering all 14 chromosomes. The length of the integrated map and the average marker distance were 3,058.6 and 1.6 cM, respectively. The order of the loci was generally in agreement with respect to the individual maps and with previously published maps. When the consensus map was aligned to the deletion bin map, 493 markers were assigned to specific bins. Segregation distortion was found across many durum wheat chromosomes, with a higher frequency for the B genome. This high-density consensus map allowed the scanning of the genome for chromosomal rearrangements occurring during the wheat evolution. Translocations and inversions that were already known in literature were confirmed, and new putative rearrangements are proposed. The consensus map herein described provides a more complete coverage of the durum wheat genome compared with previously developed maps. It also represents a step forward in durum wheat genomics and an essential tool for further research and studies on evolution of the wheat genome.
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http://dx.doi.org/10.1007/s00122-012-1939-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3493672PMC
December 2012

Alternative splicing: enhancing ability to cope with stress via transcriptome plasticity.

Plant Sci 2012 Apr 28;185-186:40-9. Epub 2011 Sep 28.

CRA - Cereal Research Centre - SS 16 km675, 71122 Foggia, Italy.

Alternative splicing is a mechanism for the regulation of gene expression that is widespread in higher eukaryotes. Genome-wide approaches, based on comparison of expressed and genomic sequences, on tiling arrays, and on next-generation sequencing, have provided growing knowledge of the extent, distribution and association of alternative splicing with stress-related genes in plants. The functional meaning of alternative splicing in response to stress has been defined for many genes, and in particular for those involved in the regulation of the stress responses, such as protein kinases, transcription factors, splicing regulators and pathogen-resistance genes. The production of proteins with diverse domain rearrangements from the same gene is the main alternative splicing mechanism for pathogen-resistance genes. The plant response to abiotic stress is also characterized by a second mechanism, which consists of the expression of alternative transcripts that are targeted to nonsense-mediated decay. These quantitatively regulate stress-related gene expression. Many alternative splicing events are well conserved among plant species, and also across kingdoms, especially those observed in response to stress, for genes encoding splicing regulators, and other classes of RNA-binding proteins. Nevertheless, non-conserved events indicate that alternative splicing represents an evolutionary strategy that rapidly increases genome plasticity and develops new gene functions, along with other mechanisms such as gene duplication. Finally, the study of the naturally occurring variability of alternative splicing and the identification of genomic regions involved in the regulation of alternative splicing in crops are proposed as strategies for selecting genotypes with superior performance under adverse environmental conditions.
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http://dx.doi.org/10.1016/j.plantsci.2011.09.006DOI Listing
April 2012

Insight into durum wheat Lpx-B1: a small gene family coding for the lipoxygenase responsible for carotenoid bleaching in mature grains.

BMC Plant Biol 2010 Nov 26;10:263. Epub 2010 Nov 26.

CRA-Cereal Research Centre, S.S. 16, Km 675 - 71122 Foggia, Italy.

Background: The yellow colour of pasta products is one of the main criteria used by consumers to assess pasta quality. This character is due to the presence of carotenoid pigments in semolina. During pasta processing, oxidative degradation of carotenoid pigments occurs mainly due to lipoxygenase (LOX). In durum wheat (Triticum durum Desf.), two Lpx-1 genes have been identified on chromosome 4B, Lpx-B1.1 and Lpx-B1.2, and evidences have been reported that the deletion of Lpx-B1.1 is associated with a strong reduction in LOX activity in semolina. In the present study, we characterised the Lpx-B1 gene family identified in a durum wheat germplasm collection and related the distribution and expression of the Lpx-B1 genes and alleles to variations in LOX activity in the mature grains.

Results: In addition to the already known Lpx-B1.1 and Lpx-B1.2 genes, a new gene was identified, Lpx-B1.3, along with three different Lpx-B1.1 alleles, Lpx-B1.1a, Lpx-B1.1b and the partially deleted Lpx-B1.1c. Screening of the germplasm collection showed that all of the genotypes have one of the three Lpx-B1.1 alleles, associated with either Lpx-B1.2 or Lpx-B1.3, thus showing that in this collection the two genes are alternatives. Therefore, based on Lpx-B1 distribution, three different haplotypes were distinguished: haplotype I, carrying Lpx-B1.3 and the Lpx-B1.1b allele; haplotype II carrying Lpx-B1.2 and the Lpx-B1.1a allele; and haplotype III carrying Lpx-B1.2 and the Lpx-B1.1c allele. Determination of Lpx-B1 transcript abundance and total LOX activity in mature grains revealed differences among these three haplotypes: haplotypes I, II and III showed high, intermediate and low levels, respectively, of functional Lpx-B1 transcripts and enzymatic activity.

Conclusions: In this germplasm collection, the Lpx-B1 gene family accounts for most of the total LOX activity in the mature grains. Information on these Lpx-B1 haplotypes provides significant improvement for prediction of LOX-1 activity levels in mature grains, and will therefore help in breeding programmes aimed at selection of new durum wheat genotypes with higher carotenoid contents in their end products.
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http://dx.doi.org/10.1186/1471-2229-10-263DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3017847PMC
November 2010

Transcriptional profiling in response to terminal drought stress reveals differential responses along the wheat genome.

BMC Genomics 2009 Jun 24;10:279. Epub 2009 Jun 24.

CRA-Genomic Research Centre, Fiorenzuola d'Arda, Piacenza, Italy.

Background: Water stress during grain filling has a marked effect on grain yield, leading to a reduced endosperm cell number and thus sink capacity to accumulate dry matter. The bread wheat cultivar Chinese Spring (CS), a Chinese Spring terminal deletion line (CS_5AL-10) and the durum wheat cultivar Creso were subjected to transcriptional profiling after exposure to mild and severe drought stress at the grain filling stage to find evidences of differential stress responses associated to different wheat genome regions.

Results: The transcriptome analysis of Creso, CS and its deletion line revealed 8,552 non redundant probe sets with different expression levels, mainly due to the comparisons between the two species. The drought treatments modified the expression of 3,056 probe sets. Besides a set of genes showing a similar drought response in Creso and CS, cluster analysis revealed several drought response features that can be associated to the different genomic structure of Creso, CS and CS_5AL-10. Some drought-related genes were expressed at lower level (or not expressed) in Creso (which lacks the D genome) or in the CS_5AL-10 deletion line compared to CS. The chromosome location of a set of these genes was confirmed by PCR-based mapping on the D genome (or the 5AL-10 region). Many clusters were characterized by different level of expression in Creso, CS and CS_AL-10, suggesting that the different genome organization of the three genotypes may affect plant adaptation to stress. Clusters with similar expression trend were grouped and functional classified to mine the biological mean of their activation or repression. Genes involved in ABA, proline, glycine-betaine and sorbitol pathways were found up-regulated by drought stress. Furthermore, the enhanced expression of a set of transposons and retrotransposons was detected in CS_5AL-10.

Conclusion: Bread and durum wheat genotypes were characterized by a different physiological reaction to water stress and by a substantially different molecular response. The genome organization accounted for differences in the expression level of hundreds of genes located on the D genome or controlled by regulators located on the D genome. When a genomic stress (deletion of a chromosomal region) was combined with low water availability, a molecular response based on the activation of transposons and retrotransposons was observed.
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http://dx.doi.org/10.1186/1471-2164-10-279DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2713995PMC
June 2009

The transcript levels of two plant mitochondrial uncoupling protein (pUCP)-related genes are not affected by hyperosmotic stress in durum wheat seedlings showing an increased level of pUCP activity.

Biosci Rep 2006 Jun;26(3):251-61

Istituto Sperimentale per la Cerealicoltura-CRA, S.S. 16 Km 675, 71100, Foggia, Italy.

Etiolated early seedlings of durum wheat submitted to moderate and severe salt (NaCl) and osmotic (mannitol) stress showed no relevant increase of both transcript levels of two plant uncoupling protein (pUCP)-related genes and maximal pUCP activity in purified mitochondria (which estimates protein level); contrarily, pUCP functioning due to endogenous free fatty acids strongly increased. These results show that pUCP activation under hyperosmotic stress may be due to modulation of pUCP reaction rather than to an increased protein synthesis. Finally, a properly developed method, based on a single membrane potential measurement, to evaluate both pUCP maximal activity and functioning, is reported.
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http://dx.doi.org/10.1007/s10540-006-9020-1DOI Listing
June 2006

Chromosome regions and stress-related sequences involved in resistance to abiotic stress in Triticeae.

Plant Mol Biol 2002 Mar-Apr;48(5-6):649-65

Istituto Sperimentale per la Cerealicoltura, Fiorenzuola d'Arda, PC, Italy.

Drought, low temperature and salinity are the most important abiotic stress factors limiting crop productivity. A genomic map of major loci and QTLs affecting stress tolerance in Triticeae identified the crucial role of the group 5 chromosomes, where the highest concentration of QTLs and major loci controlling plant's adaptation to the environment (heading date, frost and salt tolerance) has been found. In addition, a conserved region with a major role in drought tolerance has been localized to the group 7 chromosomes. Extensive molecular biological studies have led to the cloning of many stress-related genes and responsive elements. The expression of some stress-related genes was shown to be linked to stress-tolerant QTLs, suggesting that these genes may represent the molecular basis of stress tolerance. The development of suitable genetic tools will allow the role of stress-related sequences and their relationship with stress-tolerant loci to be established in the near future.
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http://dx.doi.org/10.1023/a:1014824404623DOI Listing
June 2002