The DSpace digital repository system captures, stores, indexes, preserves, and distributes digital research material. http://http://dspace.unitus.it:80 2013-06-20T04:52:25Z 2013-06-20T04:52:25Z Ibrahim Basha, Amer Padulosi, Stefano Chabane, Kamel Hadj-Hassan, Adnan Dulloo, Ehsan Pagnotta, Mario Augusto Porceddu, Enrico http://hdl.handle.net/2067/1650 2011-06-30T09:14:24Z 2006-12-31T23:00:00Z

Title: Genetic diversity of Syrian pistachio varieties evaluated by AFLP markers Authors: Ibrahim Basha, Amer; Padulosi, Stefano; Chabane, Kamel; Hadj-Hassan, Adnan; Dulloo, Ehsan; Pagnotta, Mario Augusto; Porceddu, Enrico Abstract: Pistachio (Pistacia vera L.) is a strategic nut tree species in the Middle East which holds comparative advantage over other fruit trees in view of its hardiness, income generation opportunities and benefits for the ecosystem. Yet pistachio cultivation depends on a very narrow genetic base, in spite of the existence of many varieties still marginally exploited. Syria is an important center of diversity for pistachio. A country wide ecogeographic survey in this country was carried out to determine the extent of pistachio genetic diversity and its use. As a whole, 114 accessions were collected from 37 farms to assess diversity at morphological and molecular level. Molecular evaluation was carried out using Amplified Fragment Length Polymorphism (AFLP) technique and performed using seven primer pair combinations. Results from the studies allowed the identification of 25 pistachio female varieties in Syria, some of which unique and described for the first time. Three groups of pistachio diversity were identified by cluster analysis which provides useful information about the distribution of genetic diversity in Syria for enhanced use and sustainable conservation. Description: L'articolo è disponibile sul sito dell'editore: http://www.springerlink.com

2006-12-31T23:00:00Z Paolacci, Anna Rita Miraldi, Cristiano Tanzarella, Oronzo A. Badiani, Maurizio Porceddu, Enrico Nali, Cristina Lorenzini, Giacomo Ciaffi, Mario http://hdl.handle.net/2067/1613 2011-06-29T17:26:05Z 2006-12-31T23:00:00Z

Title: Gene expression induced by chronic ozone in the Mediterranean shrub Phillyrea latifolia: analylis cDNA-AFLP. Authors: Paolacci, Anna Rita; Miraldi, Cristiano; Tanzarella, Oronzo A.; Badiani, Maurizio; Porceddu, Enrico; Nali, Cristina; Lorenzini, Giacomo; Ciaffi, Mario Abstract: Seedlings of Phillyrea latifolia L., a Mediterranean shrub, were exposed for 90 days to 110 nl l –1 ozone (O3). Comparison of the cDNA-amplified fragment length polymorphism (cDNA-AFLP) patterns for treated and control plants allowed the identification and cloning of 88 differential sequences induced by O3. The differential expression of 67 cloned sequenceswas further confirmed byRT-PCR. The functions of 36 cloned sequences, corresponding to seven of the twelve gene functional classes of Arabidopsis, were presumed on the basis of their homology with characterized gene sequences. Ozone induction of genes homologous to 24 of the clones has been reported in other plant species, whereas the induction of the 12 remaining sequences has not been observed before. Ozone activation of these newly identified genes could be a result of the chronic exposure to low O3 concentration, because in most previous studies, acute treatments, involving high O3 dosages, were applied. Possible roles of the cloned sequences in the response of P. latifolia to O3 and other causes of oxidative stress are discussed.

2006-12-31T23:00:00Z d'Aloisio, Elisa Tanzarella, Oronzo A. Dhanapal, Arun Prabhu Porceddu, Enrico Ciaffi, Mario http://hdl.handle.net/2067/1619 2011-06-30T16:41:34Z 2007-12-31T23:00:00Z

Title: The PDI (Protein Disulfide Isomerase) gene family in wheat. Authors: d'Aloisio, Elisa; Tanzarella, Oronzo A.; Dhanapal, Arun Prabhu; Porceddu, Enrico; Ciaffi, Mario Abstract: The PDI (Protein Disulfide Isomerase) gene family includes several members whose products are responsible for diversified metabolic functions. PDI and PDI-like proteins differ for number and position of thioredoxin-like (TRX-like) active (a type) and inactive (b type) domains, for presence/absence of other domains and of the KDEL signal of retention in the endoplasmic reticulum (ER). The phylogenetic analysis of typical PDI and PDI-like protein sequences resolved them into 10 groups (1), 5 of them (I-V) had 2 TRX-like active domains, whereas the remaining ones owned only a single TRX-like active domain (VI-VIII, QSOX and APRL). In particular, QRX and APRL were not included in this study due to their putative non-isomerase enzymatic activities encoded by an additional domain. The aim of the present research was the study of the complexity and diversity of the PDI gene family in wheat, with particular focus on the genes encoding PDIlike proteins structurally similar to TaPDIL1-1 (group I), the first identified and best characterized member of the PDI family, also named typical PDI. The most important function of typical PDI is the formation and isomerization of disulfide bonds during protein folding, which are accomplished by its two active TRX-like sites sharing the characteristic tetrapeptide –CGHC-. Several studies of molecular characterization, expression analysis and cell localisation in rice and maize have suggested the involvement of typical PDI in the assembly and deposition of storage proteins in these species (2, 3, 4). The characterization and chromosome location of the three homoeologous gene sequences encoding typical PDI and of their promoter sequences have been reported previously (5).

2007-12-31T23:00:00Z d'Aloisio, Elisa Paolacci, Anna Rita Dhanapal, Arun Prabhu Tanzarella, Oronzo A. Porceddu, Enrico Ciaffi, Mario http://hdl.handle.net/2067/1609 2011-07-22T09:34:29Z 2009-12-31T23:00:00Z

Title: The Protein Disulfide Isomerase gene family in bread wheat (T. aestivum L.) Authors: d'Aloisio, Elisa; Paolacci, Anna Rita; Dhanapal, Arun Prabhu; Tanzarella, Oronzo A.; Porceddu, Enrico; Ciaffi, Mario Abstract: Background: The Protein Disulfide Isomerase (PDI) gene family encodes several PDI and PDI-like proteins containing thioredoxin domains and controlling diversified metabolic functions, including disulfide bond formation and isomerisation during protein folding. Genomic, cDNA and promoter sequences of the three homoeologous wheat genes encoding the "typical" PDI had been cloned and characterized in a previous work. The purpose of present research was the cloning and characterization of the complete set of genes encoding PDI and PDI like proteins in bread wheat (Triticum aestivum cv Chinese Spring) and the comparison of their sequence, structure and expression with homologous genes from other plant species. Results: Eight new non-homoeologous wheat genes were cloned and characterized. The nine PDI and PDI-like sequences of wheat were located in chromosome regions syntenic to those in rice and assigned to eight plant phylogenetic groups. The nine wheat genes differed in their sequences, genomic organization as well as in the domain composition and architecture of their deduced proteins; conversely each of them showed high structural conservation with genes from other plant species in the same phylogenetic group. The extensive quantitative RT-PCR analysis of the nine genes in a set of 23 wheat samples, including tissues and developmental stages, showed their constitutive, even though highly variable expression. Conclusions: The nine wheat genes showed high diversity, while the members of each phylogenetic group were highly conserved even between taxonomically distant plant species like the moss Physcomitrella patens. Although constitutively expressed the nine wheat genes were characterized by different expression profiles reflecting their different genomic organization, protein domain architecture and probably promoter sequences; the high conservation among species indicated the ancient origin and diversification of the still evolving gene family. The comprehensive structural and expression characterization of the complete set of PDI and PDI-like wheat genes represents a basis for the functional characterization of this gene family in the hexaploid context of bread wheat. Description: L'articolo é disponibile sul sito dell'editore: http://www.biomedcentral.com

2009-12-31T23:00:00Z Paolacci, Anna Rita Tanzarella, Oronzo A. Porceddu, Enrico Ciaffi, Mario http://hdl.handle.net/2067/1610 2011-07-22T09:10:22Z 2008-12-31T23:00:00Z

Title: Identification and validation of reference genes for quantitative RT-PCR normalization in wheat Authors: Paolacci, Anna Rita; Tanzarella, Oronzo A.; Porceddu, Enrico; Ciaffi, Mario Abstract: Background: Usually the reference genes used in gene expression analysis have been chosen for their known or suspected housekeeping roles, however the variation observed in most of them hinders their effective use. The assessed lack of validated reference genes emphasizes the importance of a systematic study for their identification. For selecting candidate reference genes we have developed a simple in silico method based on the data publicly available in the wheat databases Unigene and TIGR. Results: The expression stability of 32 genes was assessed by qRT-PCR using a set of cDNAs from 24 different plant samples, which included different tissues, developmental stages and temperature stresses. The selected sequences included 12 well-known HKGs representing different functional classes and 20 genes novel with reference to the normalization issue. The expression stability of the 32 candidate genes was tested by the computer programs geNorm and NormFinder using five different data-sets. Some discrepancies were detected in the ranking of the candidate reference genes, but there was substantial agreement between the groups of genes with the most and least stable expression. Three new identified reference genes appear more effective than the well-known and frequently used HKGs to normalize gene expression in wheat. Finally, the expression study of a gene encoding a PDI-like protein showed that its correct evaluation relies on the adoption of suitable normalization genes and can be negatively affected by the use of traditional HKGs with unstable expression, such as actin and α-tubulin. Conclusion: The present research represents the first wide screening aimed to the identification of reference genes and of the corresponding primer pairs specifically designed for gene expression studies in wheat, in particular for qRT-PCR analyses. Several of the new identified reference genes outperformed the traditional HKGs in terms of expression stability under all the tested conditions. The new reference genes will enable more accurate normalization and quantification of gene expression in wheat and will be helpful for designing primer pairs targeting orthologous genes in other plant species. Description: L'articolo è disponibile sul sito dell'editore: http://www.biomedcentral.com

2008-12-31T23:00:00Z Paolacci, Anna Rita Tanzarella, Oronzo A. Porceddu, Enrico Ciaffi, Mario http://hdl.handle.net/2067/1617 2011-06-30T13:06:23Z 2007-12-31T23:00:00Z

Title: MIKC type genes of the MADS-box family in wheat: molecular and phylogenetic analysis. Authors: Paolacci, Anna Rita; Tanzarella, Oronzo A.; Porceddu, Enrico; Ciaffi, Mario Abstract: The MADS-box family of transcription factors play key roles in the control of development and signal transduction in eukaryotes (1). The MADS family contains a DNA-binding domain (MADS box) and includes two main lineages, type I and type II, both of which are present in plants, animals and fungi (2). Type II MADS-box proteins of plants,also named as MIKCtype proteins, possess three more domains than Type I MADS-box proteins: intervening (I) domain, keratinlike (K) domain and C-terminal (C) domain. In plants MIKC-type genes are involved in several important developmental processes, such as flower morphogenesis, ovule development, vegetative growth, embryogenesis and fruit formation, and through phylogenetic analysis based on sequence comparison, they have been classified into 13 subfamilies (3). The MIKC transcription factors controlling floral organ identity are the best characterized. Analysis of homeotic floral mutants of Arabidopsis resulted in the formulation of the ABCDE genetic model, which explains how the combined functions and organ-specific expression of five gene classes (A, B, C, D and E) specify the identity of the floral organs (sepals, petals, stamens and carpels), forming the four concentric whorls, and ovules (4,5). The most comprehensive cloning and characterization of MIKC genes of grasses have been carried out in maize and rice (6,7). In this study we extend a detailed characterization of the diversity and complexity of MIKC-type genes to hexaploid wheat.

2007-12-31T23:00:00Z Paolacci, Anna Rita Tanzarella, Oronzo A. Porceddu, Enrico Varotto, Serena Ciaffi, Mario http://hdl.handle.net/2067/1612 2011-06-30T13:09:06Z 2006-12-31T23:00:00Z

Title: Molecular and phylogenetic analysis of MADS-box genes of MIKC type and chromosome location of SEP-lke genes in n wheat (Triticum aestivum L.). Authors: Paolacci, Anna Rita; Tanzarella, Oronzo A.; Porceddu, Enrico; Varotto, Serena; Ciaffi, Mario Abstract: Transcription factors encoded by MIKC-type MADS-box genes control many important functions in plants, including Xower development and morphogenesis. The cloning and characterization of 45 MIKC-type MADSbox full-length cDNA sequences of common wheat is reported in the present paper. Wheat EST databases were searched by known sequences of MIKC-type genes and primers were designed for cDNA cloning by RT-PCR. Full-length cDNAs were obtained by 5 and 3 RACE extension. Southern analysis showed that three copies of the MIKC sequences, corresponding to the three homoeologous genes, were present. This genome organization was further conWrmed by aneuploid analysis of six SEP-like genes, each showing three copies located in diVerent homoeologous chromosomes. Phylogenetic analysis included the wheat MIKC cDNAs into 11 of the 13 MIKC subclasses identiWed in plants and corresponding to most genes controlling the Xoral homeotic functions. The expression patterns of the cDNAs corresponding to diVerent homeotic classes was analysed in 18 wheat tissues and Xoral organs by RT-PCR, real time RT-PCR and northern hybridisation. Description: L'articolo è disponibile sul sito dell'editore: http://www.springerlink.com

2006-12-31T23:00:00Z Ciaffi, Mario Paolacci, Anna Rita d'Aloisio, Elisa Dhanapal, Arun Prabhu Tanzarella, Oronzo A. Porceddu, Enrico http://hdl.handle.net/2067/1621 2011-07-22T09:40:36Z 2009-12-31T23:00:00Z

Title: Protein disulfide isomerase gene family in wheat: genomic structure, phylogenetic and expression analyses. Authors: Ciaffi, Mario; Paolacci, Anna Rita; d'Aloisio, Elisa; Dhanapal, Arun Prabhu; Tanzarella, Oronzo A.; Porceddu, Enrico Abstract: PDI and PDI-like proteins are responsible for multiple metabolic functions, including secretory protein folding, chaperone activity and redox signalling. Most studies on their diversified metabolic roles have been carried out in mammalians, whereas in plants the knowledge on the structural and functional features of these proteins and of their encoding genes is much less extensive. The purpose of the present research was the cloning and characterization of the genes encoding PDI and PDI like proteins in bread wheat and the comparison of their structure and expression with those of homologous genes isolated in other plant species. Former studies in wheat and other cereal species had been restricted to the genes encoding the typical PDI, which may accomplish an important role in the folding and deposition of seed storage proteins. Since wheat flour quality is strongly affected by composition and structure of seed storage proteins, the potential involvement of the PDI and of some PDI-like proteins of wheat in the seed storage protein folding and in the formation of intra- and inter-molecular disulfide bonds makes their study particularly interesting. Fourteen wheat cDNA sequences of PDI-like genes were amplified and cloned; eight of them were relative to distinct PDI-like genes, whereas six corresponded to homoeologous sequences. Also the genomic sequences of the eight non-homoeologous genes were amplified and cloned. Phylogenetic analyses, which included the eight PDI-like genes cloned in this research and the typical PDI gene, assign at least one of them to each of the eight major clades identified in the phylogenetic tree of the PDI gene family of plants. Although not probable, the presence of additional wheat genes of the PDI family can not be ruled out. The genes of the wheat PDI family were located in chromosome regions syntenic with the chromosome locations of their rice homologs, confirming their close syntenic relationships. Within the same phylogenetic group a high level of conservation, in terms of sequence homology, genomic structure and domain organization, was detected between the wheat sequences and those of the compared plant species. The wheat proteins of five groups (I-V) have two thioredoxin-like active domains and show structural similarities to the corresponding proteins of higher eukaryotes, whereas those of the remaining three groups (VI-VIII) contain a single thioredoxin-like active domain. Phylogenetic analysis showed that the complete set of PDI and PDI-like genes was already present in P. patens and that extended phenomena of duplication events have characterized the evolution of this gene family in different plant taxa. The comparison of the exon/intron structure showed a very similar genomic organization across the analysed species, including P. patens, whereas the alga C. reinhardtii showed a different intron/exon structure. The high conservation level of sequence and genomic organization within the PDI gene family, even between distant plant species, might be ascribed to the key metabolic roles of their protein products. The expression analysis of the nine non-homoeologous wheat genes, which was carried out by quantitative real time RT-PCR (qRT-PCR) in a set of 29 samples including tissues, developmental stages and temperature stresses, showed their constitutive, even though highly variable transcription rate. The comprehensive structural and expression characterization of the complete set of PDI and PDI-like genes of wheat performed in this study represents a basis for future functional characterization of this gene family in the hexaploid context of bread wheat.

2009-12-31T23:00:00Z Mondini, Linda Farina, Anna Porceddu, Enrico Pagnotta, Mario Augusto http://hdl.handle.net/2067/1564 2011-06-28T13:28:23Z 2009-12-31T23:00:00Z

Title: Analysis of durum wheat germplasm adapted to different climatic conditions Authors: Mondini, Linda; Farina, Anna; Porceddu, Enrico; Pagnotta, Mario Augusto Abstract: A study of the extent and patterns of microsatellite diversity in 234 genotypes from Ethiopian durum wheat (Triticum turgidum) landraces was conducted to identify areas of diversity that could be used as a source of new germplasm for developing high yielding and stable varieties. Landraces belonging to nine populations, from three Ethiopian regions [Tigray (T), Gonder (G) and Shewa (S)] with different climates, were analysed by using 28 simple sequence repeat (SSR) markers. The level of polymorphism was high and quite consistent among populations underlining the great diversity existing. The highest level of diversity was found within populations, about 75.9%, while about 5.3% was attributed to differences between regions. The level of expected heterozygosity was on an average, rather high, ranging from 39% to 56%, whereas the observed heterozygosity was, on an average, limited to 14%. An average of about five alleles per locus was detected in each population. Nevertheless, alleles were not equally present in populations as confirmed by the high level of expected heterozygosity. The polymorphism information content (PIC) for the markers assessed showed a wide range of values from 0.14 to 0.92. The likelihood relationships among the nine Ethiopian populations indicated that thematerial collected in the Gonder region (a wet climate) was genetically more diverse than the materials from Shewa and Tigray (dryer climates). The high number of loci in linkage disequilibrium (LD), up to 23, has demonstrated that the loci were associated irrespective of their physical location. This holds true even if the loci are located on different chromosome arms. Genetic diversity values between populations was very different and was used to produce a dendrogram showing population relationships. Description: L'articolo è disponibile sul sito dell'editore:http://www.onlinelibrary.wiley.com

2009-12-31T23:00:00Z Nachit, Miloudi M. Elouafi, Ismahane Pagnotta, Mario Augusto El Saleh, A. Iacono, E. Labhilili, Mustapha Asbati, A. Azrak, M. Hazzam, Hani Benscher, David Khairallah, Mirelle M. Ribaut, Jean Marcel Tanzarella, Oronzo A. Porceddu, Enrico Sorrells, Mark Earl http://hdl.handle.net/2067/1644 2011-07-18T09:48:27Z 2000-12-31T23:00:00Z

Title: Molecular linkage map for an intraspecific recombinant inbred population of durum wheat (Triticum turgidum L. var. durum). Authors: Nachit, Miloudi M.; Elouafi, Ismahane; Pagnotta, Mario Augusto; El Saleh, A.; Iacono, E.; Labhilili, Mustapha; Asbati, A.; Azrak, M.; Hazzam, Hani; Benscher, David; Khairallah, Mirelle M.; Ribaut, Jean Marcel; Tanzarella, Oronzo A.; Porceddu, Enrico; Sorrells, Mark Earl Abstract: Durum wheat (Triticum turgidum L. var. durum) is an economically and nutritionally important cereal crop in the Mediterranean region. To further our understanding of durum genome organization we constructed a durum linkage map using restriction fragment length polymorphisms (RFLPs), simple sequence repeats (SSRs) known as Gatersleben wheat microsatellites (GWMs), amplified fragment length polymorphisms (AFLPs), and seed storage proteins (SSPs: gliadins and glutenins). A population of 110 F9 recombinant inbred lines (RILs) was derived from an intraspecific cross between two durum cultivars, Jennah Khetifa and Cham 1. The two parents exhibit contrasting traits for resistance to biotic and abiotic stresses and for grain quality. In total, 306 markers have been placed on the linkage map – 138 RFLPs, 26 SSRs, 134 AFLPs, five SSPs, and three known genes (one pyruvate decarboxylase and two lipoxygenases). The map is 3598 cM long, with an average distance between markers of 11.8 cM, and 12.1% of the markers deviated significantly from the expected Mendelian ratio 1:1. The molecular markers were evenly distributed between the A and B genomes. The chromosome with the most markers is 1B (41 markers), followed by 3B and 7B, with 25 markers each. The chromosomes with the fewest markers are 2A (11 markers), 5A (12 markers), and 4B (15 markers). In general, there is a good agreement between the map obtained and the Triticeae linkage consensus maps. This intraspecific map provides a useful tool for marker-assisted selection and map-based breeding for resistance to biotic and abiotic stresses and for improvement of grain quality. Description: L'articolo è disponibile sul sito dell'editore: http://www.springerlink.com

2000-12-31T23:00:00Z Mondini, Linda Nachit, Miloudi Porceddu, Enrico Pagnotta, Mario Augusto http://hdl.handle.net/2067/2184 2011-08-04T23:05:12Z 2010-12-31T23:00:00Z

Title: HRM technology for the identification and characterization of INDEL and SNPs mutations in genes involved in drought and salt tolerance of durum wheat Authors: Mondini, Linda; Nachit, Miloudi; Porceddu, Enrico; Pagnotta, Mario Augusto Abstract: WRKY transcription factors are one of the largest families of transcriptional regulators and form an integral part of signalling webs which modulate many plant processes, such as abiotic stress tolerance. In the present paper, an innovative method has been applied to identify novel WRKY-1 alleles involved in the responses to salt and drought stresses in Triticum durum. This technique involves scanning for sequencing variations in cDNA-derived PCR amplicons, using high-resolution melting (HRM) followed by direct Sanger sequencing of only those amplicons which were predicted to carry nucleotide changes. HRM represents a novel advance in detection of single-nucleotide polymorphisms (SNPs) by measuring temperature-induced strand separation of short PCR amplicons. The use of this approach is still limited in the field of plant biology. Here, HRM analysis has been applied to the discovery and genotyping of durum wheat SNPs. Specific primers have been designed, starting at multi-alignment of WRKY-1-conserved portions. The PCR amplicons, containing single SNPs, produce distinctive HRM profiles, and by sequencing the PCR products identified, SNPs have been characterized and validated. The results showed that all the revealed SNPs are located on salt-tolerant varieties, confirming their value in breeding activities. Description: L'articolo è disponibile sul sito dell'editore http://www.cambridge.org

2010-12-31T23:00:00Z