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Ozkan H.,Cukurova University | Willcox G.,University of Lyon | Graner A.,Leibniz Institute of Plant Genetics and Crop Plant Research | Salamini F.,Fondazione Parco Tecnologico Padano | Kilian B.,Leibniz Institute of Plant Genetics and Crop Plant Research
Genetic Resources and Crop Evolution

The transition from hunting and gathering to agriculture had revolutionary consequences for the development of human societies. Crops such as wheat, barley, lentil, pea and chickpea played a crucial role in the establishment of complex civilizations in south west Asia. Wild emmer wheat (Triticum dicoccoides) was one of the first cereals to be domesticated in the Fertile Crescent between c. 12,000 and c. 10,000 years ago. This step provided the key for subsequent bread wheat evolution. Wild emmer is found today in the western Fertile Crescent in Jordan, Syria and Israel, the central part of southeastern Turkey and mountain areas in eastern Iraq and western Iran. In this review, we summarize issues concerning geography and domestication of wild emmer wheat based on published molecular and archaeobotanical data and on our recent findings. We suggest that modern domestic tetraploid wheats derived from wild emmer lines from southeast Turkey. However, our understanding of emmer domestication is not complete. The "dispersed-specific" domestication model proposed for einkorn might well be appropriate also for emmer. © 2010 Springer Science+Business Media B.V. Source

Chessa S.,CNR Institute of Agricultural Biology and Biotechnology | Nicolazzi E.L.,Fondazione Parco Tecnologico Padano | Nicoloso L.,University of Milan | Negrini R.,Catholic University of the Sacred Heart | And 5 more authors.
Livestock Science

A total of 113 DNA polymorphisms in 32 candidate genes were pre-screened to assess their variability in 32 Italian Simmental bulls. A total of 64 variants successfully genotyped and having a minor allele frequency (MAF) higher than 0.03 were then analyzed in 477 Italian Simmental bulls. Among these 37 had a MAF ≥0.05 and were investigated for association with milk production and functional traits. Daughter yield deviations (DYD) were available for milk, protein and fat yield (MY, PY and FY, respectively), somatic cell count (SCC), udder score (US), feet and legs score (FLS), while for protein percent (PP), calving ease direct effect (CED), fertility (FE) and milkability (MA) associations were computed using (EBVs).Twelve SNPs were significantly associated with at least one trait (P≤0.05). The strongest association (P=0.0009) was found between rs385640152 in the growth hormone receptor gene (GHR) and PP. Also marker rs42714483 in the thyroid hormone responsive gene (THRSP) was associated with PP (P=0.004). Pleiotropic effects were detected only for β-lactoglobulin (LGB or PAEP progestagen-associated endometrial protein) polymorphisms on. SNP rs29004488 in the leptin gene (LEP) and rs41974998 in milk fat globule-epidermal growth factor 8 protein gene (MFGE8) were associated with MY (P=0.043 and P=0.033, respectively). Suggestive associations with functional traits were also detected: rs43347906 in the leptin receptor gene (LEPR) with US (P=0.029), rs29004485 in LEP with FLS (P=0.049), rs41703837 in the v-src sarcoma (Schmidt-Ruppin A-2) viral oncogene homolog (SRC) with CED (P=0.021) and rs109019599 in the oxidized low density lipoprotein receptor 1 gene (OLR1) with MA (P=0.024). Our results both provide loci newly associated with functional traits and confirm associations already detected in Italian Holstein and Italian Brown breeds. © 2014 Elsevier B.V. Source

Scalabrin S.,Istituto di Genomica Applicata | Policriti A.,Istituto di Genomica Applicata | Nadalin F.,Istituto di Genomica Applicata | Pinosio S.,Istituto di Genomica Applicata | And 8 more authors.
Acta Horticulturae

Genome analysis based on next generation sequencing (NGS) technologies provides a novel approach for surveying molecular diversity among individuals, which in turn can generate tools for linkage and association mapping, gene cloning, molecular breeding, population genetics, germplasm management, and crop systematics and evolution. 'De novo' assembly of short reads is challenging in general and even more so as the size and complexity of genomes increase. A high quality and well annotated reference genome sequence can help solve most of the conflicts. Yet, the identification of several structural variants, such as the movement of transposable elements, large insertions/deletions, segmental duplications, inversions and other genomic features is still a challenge to algorithms and automatic procedures. We sequenced 14 Prunus accessions that include ten peach cultivars, two wild peach-related species, one almond and one apricot accession using the NGS Illumina platform. We produced 64 to 109 bp long single reads as well as paired ends from approx. 300-500 bp long fragments. The coverage varied from approximately 16 to 75 genome equivalents. Individual genomes were aligned using the reference sequence of the doubled haploid peach cultivar 'Lovell', recently released by the International Peach Genome Initiative (IPGI) (http://www.rosaceae. org/peach/genome). In this paper we present a repertoire of molecular variants that can be mined, namely SNPs (Single Nucleotide Polymorphisms), DIPs (Deletion/Insertion Polymorphisms), larger structural variations, which include movement of transposable elements, the so called copy-number variations, segmental duplications and others. Some of these variants, such as SNPs, are easily detectable and much commercial and open-access software can perform the search. Others variants, such as the large structural variations, still need analytical approaches to be implemented or improved. For several variants, theoretical and methodological approaches are presented and discussed and, when available, preliminary results are reported. Source

Agency: Cordis | Branch: FP7 | Program: BSG-SME | Phase: KBBE.2011.1.3-06 | Award Amount: 3.94M | Year: 2012

The Gene2Farm project will address the needs of the cattle industry, in particular of the SMEs and end users, for an accessible, adaptable and reliable system to apply the new genomic knowledge to underpin sustainability and profitability of European cattle farming. Gene2Farm will undertake a comprehensive programme of work from statistical theory development, through genome sequencing, to address new phenotyping approaches and the construction of tools, that will be validated in conjunction with SMEs and industry partners. Advanced statistical theory and applications will use the genomic and phenotypic information to optimise and customise genomic selection, breeding and population management and between breed predictions. The project will sequence key animals and exchange data with other international projects to create the most comprehensive bovine genome sequence database. Detailed analysis of these genome sequences will define genome structure, shared alleles, frequencies and historic haplotypes, within and between populations. This information will be used to optimise the informativeness of SNP panels and select SNPs to tag haplotypes, and hence ensure that genotype information can be used within and between breeds. The project will explore the opportunities for extended phenotypic collection, including the use of automated on farm systems and will develop standardisation protocols that, in consultation with ICAR, could be used by the industry for data collection and management. Developed tools will be tested and validated by demonstration in collaboration with dairy, dual purpose, beef and minority breed organisations. Finally a dissemination programme will ensure that training needs of the industry are served from an entry level training programme for farmers to advanced summer schools for the SMEs and expert user community.

Bomba L.,Istituto di Zootecnica | Nicolazzi E.L.,Fondazione Parco Tecnologico Padano | Milanesi M.,Istituto di Zootecnica | Negrini R.,Associazione Italiana Allevatori AIA | And 5 more authors.
Genetics Selection Evolution

Background: A number of methods are available to scan a genome for selection signatures by evaluating patterns of diversity within and between breeds. Among these, "extended haplotype homozygosity" (EHH) is a reliable approach to detect genome regions under recent selective pressure. The objective of this study was to use this approach to identify regions that are under recent positive selection and shared by the most representative Italian dairy and beef cattle breeds. Results: A total of 3220 animals from Italian Holstein (2179), Italian Brown (775), Simmental (493), Marchigiana (485) and Piedmontese (379) breeds were genotyped with the Illumina BovineSNP50 BeadChip v.1. After standard quality control procedures, genotypes were phased and core haplotypes were identified. The decay of linkage disequilibrium (LD) for each core haplotype was assessed by measuring the EHH. Since accurate estimates of local recombination rates were not available, relative EHH (rEHH) was calculated for each core haplotype. Genomic regions that carry frequent core haplotypes and with significant rEHH values were considered as candidates for recent positive selection. Candidate regions were aligned across to identify signals shared by dairy or beef cattle breeds. Overall, 82 and 87 common regions were detected among dairy and beef cattle breeds, respectively. Bioinformatic analysis identified 244 and 232 genes in these common genomic regions. Gene annotation and pathway analysis showed that these genes are involved in molecular functions that are biologically related to milk or meat production. Conclusions: Our results suggest that a multi-breed approach can lead to the identification of genomic signatures in breeds of cattle that are selected for the same production goal and thus to the localisation of genomic regions of interest in dairy and beef production. © 2015 Bomba et al.; licensee BioMed Central. Source

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