Evolutionary history of linked D4Z4 and Beta satellite clusters at the FSHD locus (4q35)

We performed a detailed genomic investigation of the chimpanzee locus syntenic to human chromosome 4q35.2, associated to the facioscapulohumeral dystrophy. Two contigs of approximately 150 kb and 200 kb were derived from PTR chromosomes 4q35 and 3p12, respectively: both regions showed a very similar sequence organization, including D4Z4 and Beta satellite linked clusters. Starting from these findings, we derived a hypothetical evolutionary history of human 4q35, 10q26 and 3p12 chromosome regions focusing on the D4Z4-Beta satellite linked organization. The D4Z4 unit showed an open reading frame (DUX4) at both PTR 4q35 and 3p12 regions; furthermore some subregions of the Beta satellite unit showed a high degree of conservation between chimpanzee and humans. In conclusion, this paper provides evidence that at the 4q subtelomere the linkage between D4Z4 and Beta satellite arrays is a feature that appeared late during evolution and is conserved between chimpanzee and humans

Inter-varietal structural variation in grapevine genomes

Grapevine (Vitis vinifera L.) is one of the world's most important crop plants, which is of large economic value for fruit and wine production. There is much interest in identifying genomic variations and their functional effects on inter-varietal, phenotypic differences. Using an approach developed for the analysis of human and mammalian genomes, which combines high-throughput sequencing, array comparative genomic hybridization, fluorescent in�situ hybridization and quantitative PCR, we created an inter-varietal atlas of structural variations and single nucleotide variants (SNVs) for the grapevine genome analyzing four economically and genetically relevant table grapevine varieties. We found 4.8 million SNVs and detected 8% of the grapevine genome to be affected by genomic variations. We identified more than 700 copy number variation (CNV) regions and more than 2000 genes subjected to CNV as potential candidates for phenotypic differences between varieties. � 2016 The Authors The Plant Journal � 2016 John Wiley & Sons Lt

SNP genotyping elucidates the genetic diversity of Magna Graecia grapevine germplasm and its historical origin and dissemination

BACKGROUND: Magna Graecia is the ancient name for the modern geopolitical region of South Italy extensively populated by Greek colonizers, shown by archeological and historical evidence to be the oldest wine growing region of Italy, crucial for the spread of specialized viticulture around Mediterranean shores. Here, the genetic diversity of Magna Graecia grape germplasm was assessed and its role in grapevine propagation around the Mediterranean basin was underlined. RESULTS: A large collection of grapevines from Magna Graecia was compared with germplasm from Georgia to the Iberian Peninsula using the 18\u2009K SNP array. A high level of genetic diversity of the analyzed germplasm was determined; clustering, structure analysis and DAPC (Discriminant Analysis of Principal Components) highlighted the genetic relationships among genotypes from South Italy and the Eastern Mediterranean (Greece). Gene flow from east (Georgia) to west (Iberian Peninsula) was identified throughout the large number of detected admixed samples. Pedigree analysis showed a complex and well-structured network of first degree relationships, where the cultivars from Magna Graecia were mainly involved. CONCLUSIONS: This study provided evidence that Magna Graecia germplasm was shaped by historical events that occurred in the area due to the robust link between South Italian and Greek genotypes, as well as, by the availability of different thermal resources for cultivars growing in such different winegrowing areas. The uniqueness of this ampelographic platform was mainly an outcome of complex natural or human-driven crosses involving elite cultivars

Copy number variation of individual cattle genomes using next-generation sequencing

Copy number variations (CNVs) affect a wide range of phenotypic traits; however, CNVs in or near segmental duplication regions are often intractable. Using a read depth approach based on next-generation sequencing, we examined genome - wide copy number differences among five taurine (three Angus, one Holstein, and one Hereford) and one indicine (Nelore) cattle. Within mapped chromosomal sequence, we identified 1265 CNV regions comprising ∼55.6-Mbp sequence-476 of which (~38%) have not previously been reported. We validated this sequence-based CNV call set with array comparative genomic hybridization (aCGH), quantitative PCR (qPCR), and fluorescent in situ hybridization (FISH), achieving a validation rate of 82% and a false positive rate of 8%. We further estimated absolute copy numbers for genomic segments and annotated genes in each individual. Surveys of the top 25 most variable genes revealed that the Nelore individual had the lowest copy numbers in 13 cases (∼52%, χ 2 test; P-value <0.05). In contrast, genes related to pathogen- and parasite-resistance, such as CATHL4 and ULBP17, were highly duplicated in the Nelore individual relative to the taurine cattle, while genes involved in lipid transport and metabolism, including APOL3 and FABP2, were highly duplicated in the beef breeds. These CNV regions also harbor genes like BPIFA2A (BSP30A) and WC1, suggesting that some CNVs may be associated with breed-specific differences in adaptation, health, and production traits. By providing the first individualized cattle CNV and segmental duplication maps and genome-wide gene copy number estimates, we enable future CNV studies into highly duplicated regions in the cattle genome. © 2012 by Cold Spring Harbor Laboratory Press

Analytical and sensory data correlation to understand consumers' grape preference

NIR spectroscopy is a rapid, economic and not destructive technique employed in food analysis. Concerning fresh table grape, the analysis is usually limited to juices, homogenates or skin extracts which usually give better NIR prediction models. Scanning of intact berries is challenging since each berry has specific features (berry shape, presence of superficial pigmentation, etc.) and, moreover, there are punctual variations even within the same berry. It would be of great interest to obtain information about maturity parameters and consumer's appreciation directly from intact berries, since it would save both time and money. In this article, near infrared (NIR) spectroscopy and chemometric methods have been employed to search for a correlation between sensory analysis and analytical data. The research findings show how it is possible to use a rapid, economic and not destructive emerging technology such as NIR spectroscopy to understand consumer's preference directly from intact berries

Phenotypic evaluation of segregant population derived by crossing table grape varieties

In the CREA-Viticoltura ed Enologia, Lab of Turi, during the last ten years, we started a breeding program for table grapes to obtain new seedless varieties, by using conventional breeding by crossings, and embryo rescue techniques. Other than seedlessness, additional targets for this breeding program are: the possibility of extending the harvesting period, the attitude to cold storage, transport and shelf-life, resistance to diseases both on the plant and in post-harvest conditions, the good productivity, the quality of the grapes, the easy cultivation management of the vineyard (reduced water, nutritional requirements, etc ...). More than 10.000 new genotypes have been obtained through the use of over 20 table grape varieties and more than 18 different crossing combinations. The following characteristics have been observed on these individuals for more than three years: berry color, length and weight cluster, average berry weight, sugars, pH, acidity, class of seedlessness, floral morphology, resistance to diseases. The results of these activities revealed that some combinations have better performance among all. In the near future, this activity will allow to focus on parental genotypes able to provide individuals with the best desired traits

Grapevine adaptation to drought: New candidate genes for the genotype-dependent response

Grapevine requires irrigation supply for its cultivation, especially in the arid and semiarid geographic areas. As consequence of the severe climatic changes, water consumption is becoming more and more important as environmental and cost factor that needs to be reduced. Water deficiency can affect berry and wine quality depending on the extent of plant perceived stress, which is a cultivar specific trait. In a four-year project, we tested the physiological and molecular responses to water deficiency of two different table grape cultivars, Italia and Autumn Royal, and we highlighted that they differently adapted to drought stress conditions. Physiological analyses on field-growth plants showed cultivar-specific variations in photosynthetic carbon assimilation and, stomatal conductance under water deficiency. We further combined “omic” analyses to identify candidate genes involved in drought stress response and adaptative traits. Microarray analyses revealed a broad response of cultivar Italia to drought stress conditions characterized by the modulation of 1037 genes involved in biological processes as cell wall organization, carbohydrate metabolism, ROS response, response to hormone and osmotic stress. On the contrary, Autumn Royal response was limited to the modulation of only 29 genes mainly involved in plant stress response, nitrogen metabolism and hormone signal transduction. Our data highlighted that ABA-perception and –signalling are key factors mediating the varietal-specific behavior of the early response to drought