No abstract

OPENRosaceae is the most important fruit-producing clade, and its key commercially relevant genera (Fragaria, Rosa, Rubus and Prunus) show broadly diverse growth habits, fruit types and compact diploid genomes. Peach, a diploid Prunus species, is one of the best genetically characterized deciduous trees. Here we describe the high-quality genome sequence of peach obtained from a completely homozygous genotype. We obtained a complete chromosome-scale assembly using Sanger whole-genome shotgun methods. We predicted 27,852 protein-coding genes, as well as noncoding RNAs. We investigated the path of peach domestication through whole-genome resequencing of 14 Prunus accessions. The analyses suggest major genetic bottlenecks that have substantially shaped peach genome diversity. Furthermore, comparative analyses showed that peach has not undergone recent whole-genome duplication, and even though the ancestral triplicated blocks in peach are fragmentary compared to those in grape, all seven paleosets of paralogs from the putative paleoancestor are detectable.

urum wheat (DW), Triticum turgidum L. ssp. durum (Desf.) Husn., genome BBAA, is a cereal grain mainly used for pasta production and evolved from domesticated emmer wheat (DEW), T. turgidum ssp. dicoccum (Schrank ex Schübl.) Thell. DEW itself derived from wild emmer wheat (WEW), T. turgidum ssp. dicoccoides (Körn. ex Asch. & Graebn.

Digital mammography may be more effective than screen-film mammography in contemporary screening practice in mobile units. The data indicate that digital mammography depicts more tumors than does screen-film mammography, especially lesions seen as microcalcifications. The potential association with improved outcome warrants further study.

The genomics revolution has spurred the undertaking of HapMap studies of numerous species, allowing for population genomics to increase the understanding of how selection has created genetic differences between subspecies populations. The objectives of this study were to (1) develop an approach to detect signatures of selection in subsets of phenotypically similar breeds of livestock by comparing single nucleotide polymorphism (SNP) diversity between the subset and a larger population, (2) verify this method in breeds selected for simply inherited traits, and (3) apply this method to the dairy breeds in the International Bovine HapMap (IBHM) study. The data consisted of genotypes for 32,689 SNPs of 497 animals from 19 breeds. For a given subset of breeds, the test statistic was the parametric composite log likelihood (CLL) of the differences in allelic frequencies between the subset and the IBHM for a sliding window of SNPs. The null distribution was obtained by calculating CLL for 50,000 random subsets (per chromosome) of individuals. The validity of this approach was confirmed by obtaining extremely large CLLs at the sites of causative variation for polled (BTA1) and black-coat-color (BTA18) phenotypes. Across the 30 bovine chromosomes, 699 putative selection signatures were detected. The largest CLL was on BTA6 and corresponded to KIT, which is responsible for the piebald phenotype present in four of the five dairy breeds. Potassium channel-related genes were at the site of the largest CLL on three chromosomes (BTA14, -16, and -25) whereas integrins (BTA18 and -19) and serine/arginine rich splicing factors (BTA20 and -23) each had the largest CLL on two chromosomes. On the basis of the results of this study, the application of population genomics to farm animals seems quite promising. Comparisons between breed groups have the potential to identify genomic regions influencing complex traits with no need for complex equipment and the collection of extensive phenotypic records and can contribute to the identification of candidate genes and to the understanding of the biological mechanisms controlling complex traits.

BackgroundSmall RNAs present in bovine ejaculate can be linked to sperm abnormalities and fertility disorders. At present, quality parameters routinely used in semen evaluation are not fully reliable to predict bull fertility. In order to provide additional quality measurements for cryopreserved semen used for breeding, a method based on deep sequencing of sperm microRNA (miRNA) and Piwi-interacting RNA (piRNA) from individual bulls was developed.To validate our method, two populations of spermatozoa isolated from high and low motile fractions separated by Percoll were sequenced, and their small RNAs content characterized.ResultsSperm cells from frozen thawed semen samples of 4 bulls were successfully separated in two fractions. We identified 83 miRNAs and 79 putative piRNAs clusters that were differentially expressed in both fractions. Gene pathways targeted by 40 known differentially expressed miRNAs were related to apoptosis. Dysregulation of miR-17-5p, miR-26a-5p, miR-486-5p, miR-122-5p, miR-184 and miR-20a-5p was found to target three pathways (PTEN, PI3K/AKT and STAT).ConclusionsSmall RNAs sequencing data obtained from single bulls are consistent with previous findings. Specific miRNAs are differentially represented in low versus high motile sperm, suggesting an alteration of cell functions and increased germ cell apoptosis in the low motile fraction.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-3394-7) contains supplementary material, which is available to authorized users.

A genome wide scan was performed on a total of 2093 Italian Holstein proven bulls genotyped with 50K single nucleotide polymorphisms (SNPs), with the objective of identifying loci associated with fertility related traits and to test their effects on milk production traits. The analysis was carried out using estimated breeding values for the aggregate fertility index and for each trait contributing to the index: angularity, calving interval, non-return rate at 56 days, days to first service, and 305 day first parity lactation. In addition, two production traits not included in the aggregate fertility index were analysed: fat yield and protein yield. Analyses were carried out using all SNPs treated separately, further the most significant marker on BTA14 associated to milk quality located in the DGAT1 region was treated as fixed effect. Genome wide association analysis identified 61 significant SNPs and 75 significant marker-trait associations. Eight additional SNP associations were detected when SNP located near DGAT1 was included as a fixed effect. As there were no obvious common SNPs between the traits analyzed independently in this study, a network analysis was carried out to identify unforeseen relationships that may link production and fertility traits.

P i e t r o Ciceri,a.l E l i s a b e t t a Gianazza,b B a r b a r a Lazzari,a G u i d o Lippoli,a A n n a m a r i a Genga,a Gisela Hoschek,c R o b e r t J. Schmidt,c a n d A n g e l o Viottiag2 a lstituto Biosintesi Vegetali, Consiglio Nazionale delle Ricerche, Via Bassini 15, 1-201 33 Milan, ltaly lstituto di Scienze Farmacologiche, Universita degli Studi di Milano, Via Balzaretti 9, 1-201 33 Milan, ltalyDepartment of Biology and Center for Molecular Genetics, University of California at San Diego, La Jolla, California 92093-01 16In the maize endosperm, the Opaque2 (02) basic leucine zipper transcriptional activator regulates the expression of a subset of the zein seed storage protein gene family. lmmunodetection of wild-type or mutant 0 2 polypeptides fractionated by SDS-PAGE resolved a closely spaced doublet migrating in the 68-t o 72-kD range, whereas by using isoelectric focusing, seven t o nine isoforms were detected for each allele. Phosphatase treatment simplified the protein patterns t o a single band corresponding t o the nonphosphorylated component. In vivo and in vitro labeling confirmed that 0 2 can be phosphorylated. In protein gel blots probed with DNA, only the nonphosphorylated and hypophosphorylated 0 2 polypeptides were able t o bind an oligonucleotide containing the 0 2 binding sequence. Upon in situ dephosphorylation of the focused isoforms by phosphatase treatment of the isoelectric focusing filter, the hyperphosphorylated forms acquired DNA binding activity. The ratio among the various isoforms remained constant throughout the developmental stages of endosperm growth but changed from daytime t o nighttime, with a significant increase of the hyperphosphorylated forms during the night period. These results indicate that 0 2 exists in vivo as a pool of differently phosphorylated polypeptides and demonstrate that 0 2 DNA binding activity is modulated by a phosphorylation/dephosphorylation mechanism that appears t o be influenced by environmental conditions. INTRODUCTIONProtein phosphorylation and dephosphorylation, catalyzed by protein kinases and phosphatases, respectively, are important control mechanisms for severa1 biological processes in yeast, plant, and animal cells. These processes include cell division, perception and transduction of externa1 stimuli, hormone sensitivity, and control of metabolic pathways (Ranjeva and Boudet, 1987;Ma, 1993). The control of gene expression at the transcriptional leve1 is determined by cisacting elements and trans-acting factors that modulate the expressivity of a gene in response to the above-mentioned biological processes. In particular, transcription factors themselves are often regulated or modulated in their capacity to transactivate a gene by post-translational modifications involving phosphorylation (reviewed in Hunter and Karin, 1992;Karin and Hunter, 1995).During cereal seed maturation, starch, proteins, and oil, which are the main storage products, accumulate during de-' Current address: Department of Biology and Center for Molecular Genetics,...