Pseudo-chromosome-length genome assembly of a double haploid "Bartlett" pear (Pyrus communis L.)
Linsmith, Gareth ; Rombauts, Stephane ; Montanari, Sara ; Deng, Cecilia H. ; Celton, Jean Marc ; Guérif, Philippe ; Liu, Chang ; Lohaus, Rolf ; Zurn, Jason D. ; Cestaro, Alessandro ; Bassil, Nahla V. ; Bakker, Linda V. ; Schijlen, Elio ; Gardiner, Susan E. ; Lespinasse, Yves ; Durel, Charles Eric ; Velasco, Riccardo ; Neale, David B. ; Chagné, David ; Peer, Yves Van de; Troggio, Michela ; Bianco, Luca - \ 2019
GigaScience 8 (2019)12. - ISSN 2047-217X
chromosome-scale assembly - Hi-C - Pac-Bio sequencing - Pyrus communis L
BACKGROUND: We report an improved assembly and scaffolding of the European pear (Pyrus communis L.) genome (referred to as BartlettDHv2.0), obtained using a combination of Pacific Biosciences RSII long-read sequencing, Bionano optical mapping, chromatin interaction capture (Hi-C), and genetic mapping. The sample selected for sequencing is a double haploid derived from the same "Bartlett" reference pear that was previously sequenced. Sequencing of di-haploid plants makes assembly more tractable in highly heterozygous species such as P. communis. FINDINGS: A total of 496.9 Mb corresponding to 97% of the estimated genome size were assembled into 494 scaffolds. Hi-C data and a high-density genetic map allowed us to anchor and orient 87% of the sequence on the 17 pear chromosomes. Approximately 50% (247 Mb) of the genome consists of repetitive sequences. Gene annotation confirmed the presence of 37,445 protein-coding genes, which is 13% fewer than previously predicted. CONCLUSIONS: We showed that the use of a doubled-haploid plant is an effective solution to the problems presented by high levels of heterozygosity and duplication for the generation of high-quality genome assemblies. We present a high-quality chromosome-scale assembly of the European pear Pyrus communis and demostrate its high degree of synteny with the genomes of Malus x Domestica and Pyrus x bretschneideri.
Apple whole genome sequences : recent advances and new prospects
Peace, Cameron P. ; Bianco, Luca ; Troggio, Michela ; Weg, Eric van de; Howard, Nicholas P. ; Cornille, Amandine ; Durel, Charles Eric ; Myles, Sean ; Migicovsky, Zoë ; Schaffer, Robert J. ; Costes, Evelyne ; Fazio, Gennaro ; Yamane, Hisayo ; Nocker, Steve van; Gottschalk, Chris ; Costa, Fabrizio ; Chagné, David ; Zhang, Xinzhong ; Patocchi, Andrea ; Gardiner, Susan E. ; Hardner, Craig ; Kumar, Satish ; Laurens, Francois ; Bucher, Etienne ; Main, Dorrie ; Jung, Sook ; Vanderzande, Stijn - \ 2019
Horticulture Research 6 (2019)1. - ISSN 2052-7276
In 2010, a major scientific milestone was achieved for tree fruit crops: publication of the first draft whole genome sequence (WGS) for apple (Malus domestica). This WGS, v1.0, was valuable as the initial reference for sequence information, fine mapping, gene discovery, variant discovery, and tool development. A new, high quality apple WGS, GDDH13 v1.1, was released in 2017 and now serves as the reference genome for apple. Over the past decade, these apple WGSs have had an enormous impact on our understanding of apple biological functioning, trait physiology and inheritance, leading to practical applications for improving this highly valued crop. Causal gene identities for phenotypes of fundamental and practical interest can today be discovered much more rapidly. Genome-wide polymorphisms at high genetic resolution are screened efficiently over hundreds to thousands of individuals with new insights into genetic relationships and pedigrees. High-density genetic maps are constructed efficiently and quantitative trait loci for valuable traits are readily associated with positional candidate genes and/or converted into diagnostic tests for breeders. We understand the species, geographical, and genomic origins of domesticated apple more precisely, as well as its relationship to wild relatives. The WGS has turbo-charged application of these classical research steps to crop improvement and drives innovative methods to achieve more durable, environmentally sound, productive, and consumer-desirable apple production. This review includes examples of basic and practical breakthroughs and challenges in using the apple WGSs. Recommendations for “what’s next” focus on necessary upgrades to the genome sequence data pool, as well as for use of the data, to reach new frontiers in genomics-based scientific understanding of apple.
Priorities for protected area research
Dudley, Nigel ; Hockings, Marc ; Stolton, Sue ; Amend, Thora ; Badola, Ruchi ; Bianco, Mariasole ; Chettri, Nakul ; Cook, Carly ; Day, Jon C. ; Dearden, Phil ; Edwards, Mary ; Ferraro, Paul ; Foden, Wendy ; Gambino, Roberto ; Gaston, Kevin J. ; Hayward, Natalie ; Hickey, Valerie ; Irving, Jason ; Jeffries, Bruce ; Karapetyan, Areg ; Kettunen, Marianne ; Laestadius, Lars ; Laffoley, Dan ; Lham, Dechen ; Lichtenstein, Gabriela ; Makombo, John ; Marshall, Nina ; McGeoch, Melodie ; Nguyen, Dao ; Nogué, Sandra ; Paxton, Midori ; Rao, Madhu ; Reichelt, Russell ; Rivas, Jorge ; Roux, Dirk ; Rutte, Claudia ; Schreckenberg, Kate ; Sovinc, Andrej ; Sutyrina, Svetlana ; Utomo, Agus ; Vallauri, Daniel ; Vedeld, Pål Olav ; Verschuuren, Bas ; Waithaka, John ; Woodley, Stephen ; Wyborn, Carina ; Zhang, Yan - \ 2018
PARKS: the International of Protected Areas and Conservation 24 (2018)1. - ISSN 0960-233X - p. 35 - 50.
Managers - Protected areas - Research priorities - Researchers - Stakeholder assessment
A hundred research priorities of critical importance to protected area management were identified by a targeted survey of conservation professionals; half researchers and half practitioners. Respondents were selected to represent a range of disciplines, every continent except Antarctica and roughly equal numbers of men and women. The results analysed thematically and grouped as potential research topics as by both practitioners and researchers. Priority research gaps reveal a high interest to demonstrate the role of protected areas within a broader discussion about sustainable futures and if and how protected areas can address a range of conservation and socio-economic challenges effectively. The paper lists the hundred priorities structured under broad headings of management, ecology, governance and social (including political and economic issues) and helps contribute to setting future research agendas.
Genome-wide association mapping of flowering and ripening periods in apple
Urrestarazu, Jorge ; Muranty, Hélène ; Denancé, Caroline ; Leforestier, Diane ; Ravon, Elisa ; Guyader, Arnaud ; Guisnel, Rémi ; Feugey, Laurence ; Aubourg, Sébastien ; Celton, Jean Marc ; Daccord, Nicolas ; Dondini, Luca ; Gregori, Roberto ; Lateur, Marc ; Houben, Patrick ; Ordidge, Matthew ; Paprstein, Frantisek ; Sedlak, Jiri ; Nybom, Hilde ; Garkava-Gustavsson, Larisa ; Troggio, Michela ; Bianco, Luca ; Velasco, Riccardo ; Poncet, Charles ; Théron, Anthony ; Moriya, Shigeki ; Bink, Marco C.A.M. ; Laurens, François ; Tartarini, Stefano ; Durel, Charles Eric - \ 2017
Frontiers in Plant Science 8 (2017). - ISSN 1664-462X
Adaptive traits - Association genetics - Germplasm collection - GWAS - Malus × domestica Borkh - Microsynteny - Quantitative trait loci - SNP
Deciphering the genetic control of flowering and ripening periods in apple is essential for breeding cultivars adapted to their growing environments. We implemented a large Genome-Wide Association Study (GWAS) at the European level using an association panel of 1,168 different apple genotypes distributed over six locations and phenotyped for these phenological traits. The panel was genotyped at a high-density of SNPs using the Axiom®Apple 480 K SNP array. We ran GWAS with a multi-locus mixed model (MLMM), which handles the putatively confounding effect of significant SNPs elsewhere on the genome. Genomic regions were further investigated to reveal candidate genes responsible for the phenotypic variation. At the whole population level, GWAS retained two SNPs as cofactors on chromosome 9 for flowering period, and six for ripening period (four on chromosome 3, one on chromosome 10 and one on chromosome 16) which, together accounted for 8.9 and 17.2% of the phenotypic variance, respectively. For both traits, SNPs in weak linkage disequilibrium were detected nearby, thus suggesting the existence of allelic heterogeneity. The geographic origins and relationships of apple cultivars accounted for large parts of the phenotypic variation. Variation in genotypic frequency of the SNPs associated with the two traits was connected to the geographic origin of the genotypes (grouped as North+East, West and South Europe), and indicated differential selection in different growing environments. Genes encoding transcription factors containing either NAC or MADS domains were identified as major candidates within the small confidence intervals computed for the associated genomic regions. A strong microsynteny between apple and peach was revealed in all the four confidence interval regions. This study shows how association genetics can unravel the genetic control of important horticultural traits in apple, as well as reduce the confidence intervals of the associated regions identified by linkage mapping approaches. Our findings can be used for the improvement of apple through marker-assisted breeding strategies that take advantage of the accumulating additive effects of the identified SNPs.
Genome wide association study of two phenology traits (flowering time and maturity date) in apple
Muranty, Hélène ; Urrestarazu, J. ; Denancé, C. ; Leforestier, D. ; Ravon, E. ; Guyader, A. ; Guisnel, R. ; Feugey, L. ; Tartarini, S. ; Dondini, L. ; Gregori, R. ; Lateur, M. ; Houben, E.H.P. ; Sedlak, J. ; Paprstein, F. ; Ordidge, M. ; Nybom, H. ; Garkava-Gustavsson, L. ; Troggio, M. ; Bianco, L. ; Velasco, R. ; Poncet, C. ; Théron, Anthony ; Bink, M.C.A.M. ; Laurens, F. ; Durel, C.E. - \ 2017
In: 14th EUCARPIA Symposium on Fruit Breeding and Genetics International Society for Horticultural Science (Acta Horticulturae ) - ISBN 9789462611689 - p. 411 - 417.
Germplasm collections - Malus × domestica - Marker-assisted selection
The aim of Genome Wide Association Studies (GWAS) is to identify markers in tight linkage disequilibrium with loci controlling quantitative trait variation. These markers can then be used in marker-assisted selection (MAS) in fruit crops such as apple. The GWAS approach involves both phenotyping of a large population of mostly unrelated individuals for the traits of interest, and genotyping at high marker density. In the EU-FP7 project FruitBreedomics, almost 1,200 European diploid dessert apple accessions (old and/or local cultivars) from six germplasm collections were genotyped with the Affymetrix Axiom-Apple480K array (487,000 SNPs). Phenotypic data on a large number of traits have been gathered during the project. Here we focus on flowering period and harvesting date. Knowledge of the genetic control of these traits is necessary to develop cultivars that can face the challenges imposed by global climate change and to target cultivar development as a function of a prolonged vegetation period in the production regions. Different models were tested, including control for effects of population structure and relatedness between cultivars. The full model, controlling for both structure and relatedness, was shown to be the most appropriate to avoid spurious marker-trait associations. When analyzing data over all collections, one significant marker-trait association was obtained for each trait, on chromosomes 9 and 3, for flowering period and harvesting date, respectively. Thereby, genomic locations previously identified in bi-parental populations could now be confirmed for a genetically diverse germplasm.
Deciphering the genetic control of fruit texture in apple by multiple family-based analysis and genome-wide association
Guardo, Mario Di; Bink, Marco C.A.M. ; Guerra, Walter ; Letschka, Thomas ; Lozano, Lidia ; Busatto, Nicola ; Poles, Lara ; Tadiello, Alice ; Bianco, Luca ; Visser, Richard G.F. ; Weg, Eric van de; Costa, Fabrizio - \ 2017
Journal of Experimental Botany 68 (2017)7. - ISSN 0022-0957 - p. 1451 - 1466.
Apple - Bayesian statistics - Fruit texture - Genome-wide association study (GWAS) - High-resolution phenotyping - Pedigree-based analysis (PBA) - RT-qPCR - SNP
Fruit texture is a complex feature composed of mechanical and acoustic properties relying on the modifications occurring in the cell wall throughout fruit development and ripening. Apple is characterized by a large variation in fruit texture behavior that directly impacts both the consumer's appreciation and post-harvest performance. To decipher the genetic control of fruit texture comprehensively, two complementing quantitative trait locus (QTL) mapping approaches were employed. The first was represented by a pedigree-based analysis (PBA) carried out on six full-sib pedigreed families, while the second was a genome-wide association study (GWAS) performed on a collection of 233 apple accessions. Both plant materials were genotyped with a 20K single nucleotide polymorphism (SNP) array and phenotyped with a sophisticated high-resolution texture analyzer. The overall QTL results indicated the fundamental role of chromosome 10 in controlling the mechanical properties, while chromosomes 2 and 14 were more associated with the acoustic response. The latter QTL, moreover, showed a consistent relationship between the QTL-estimated genotypes and the acoustic performance assessed among seedlings. The in silico annotation of these intervals revealed interesting candidate genes potentially involved in fruit texture regulation, as suggested by the gene expression profile. The joint integration of these approaches sheds light on the specific control of fruit texture, enabling important genetic information to assist in the selection of valuable fruit quality apple varieties.
High-quality de novo assembly of the apple genome and methylome dynamics of early fruit development
Daccord, Nicolas ; Celton, Jean-Marc ; Linsmith, Gareth ; Becker, Claude ; Choisne, Nathalie ; Schijlen, Elio ; Geest, Henri van de; Bianco, Luca ; Micheletti, Diego ; Velasco, Riccardo ; Pierro, Erica Adele Di; Gouzy, Jérôme ; Rees, D.J.G. ; Guérif, Philippe ; Muranty, Hélène ; Durel, Charles Eric ; Laurens, François ; Lespinasse, Yves ; Gaillard, Sylvain ; Aubourg, Sébastien ; Quesneville, Hadi ; Weigel, Detlef ; Weg, Eric van de; Troggio, Michela ; Bucher, Etienne - \ 2017
Nature Genetics 49 (2017)7. - ISSN 1061-4036 - p. 1099 - 1106.
Using the latest sequencing and optical mapping technologies, we have produced a high-quality de novo assembly of the apple (Malus domestica Borkh.) genome. Repeat sequences, which represented over half of the assembly, provided an unprecedented opportunity to investigate the uncharacterized regions of a tree genome; we identified a new hyper-repetitive retrotransposon sequence that was over-represented in heterochromatic regions and estimated that a major burst of different transposable elements (TEs) occurred 21 million years ago. Notably, the timing of this TE burst coincided with the uplift of the Tian Shan mountains, which is thought to be the center of the location where the apple originated, suggesting that TEs and associated processes may have contributed to the diversification of the apple ancestor and possibly to its divergence from pear. Finally, genome-wide DNA methylation data suggest that epigenetic marks may contribute to agronomically relevant aspects, such as apple fruit development.
The developmental and environmental regulation of gravitropic setpoint angle in Arabidopsis and bean
Roychoudhry, Suruchi ; Kieffer, Martin ; Bianco, Marta Del; Liao, Che Yang ; Weijers, Dolf ; Kepinski, Stefan - \ 2017
Scientific Reports 7 (2017). - ISSN 2045-2322
Root and shoot branches are major determinants of plant form and critical for the effective capture of resources below and above ground. These branches are often maintained at specific angles with respect to gravity, known as gravitropic set point angles (GSAs). We have previously shown that the mechanism permitting the maintenance of non-vertical GSAs is highly auxin-dependent and here we investigate the developmental and environmental regulation of root and shoot branch GSA. We show that nitrogen and phosphorous deficiency have opposing, auxin signalling-dependent effects on lateral root GSA in Arabidopsis: while low nitrate induces less vertical lateral root GSA, phosphate deficiency results in a more vertical lateral root growth angle, a finding that contrasts with the previously reported growth angle response of bean adventitious roots. We find that this root-class-specific discrepancy in GSA response to low phosphorus is mirrored by similar differences in growth angle response to auxin treatment between these root types. Finally we show that both shaded, low red/far-red light conditions and high temperature induce more vertical growth in Arabidopsis shoot branches. We discuss the significance of these findings in the context of efforts to improve crop performance via the manipulation of root and shoot branch growth angle.
Frequency of a natural truncated allele of MdMLO19 in the germplasm of Malus domestica
Pessina, Stefano ; Palmieri, Luisa ; Bianco, Luca ; Gassmann, Jennifer ; De Weg, Eric Van; Visser, Richard G.F. ; Magnago, Pierluigi ; Schouten, Henk J. ; Bai, Yuling ; Riccardo Velasco, R. ; Malnoy, Mickael - \ 2017
Molecular Breeding 37 (2017)1. - ISSN 1380-3743
Podosphaera leucotricha is the causal agent of powdery mildew (PM) in apple. To reduce the amount of fungicides required to control this pathogen, the development of resistant apple cultivars should become a priority. Resistance to PM was achieved in various crops by knocking out specific members of the MLO gene family that are responsible for PM susceptibility (S-genes). In apple, the knockdown of MdMLO19 resulted in PM resistance. However, since gene silencing technologies such as RNAi are perceived unfavorably in Europe, a different approach that exploits this type of resistance is needed. This work evaluates the presence of non-functional naturally occurring alleles of MdMLO19 in apple germplasm. The screening of the re-sequencing data of 63 apple individuals led to the identification of 627 single nucleotide polymorphisms (SNPs) in five MLO genes (MdMLO5, MdMLO7, MdMLO11, MdMLO18, and MdMLO19), 127 of which were located in exons. The T-1201 insertion of a single nucleotide in MdMLO19 caused the formation of an early stop codon, resulting in a truncated protein lacking 185 amino acids, including the calmodulin-binding domain. The presence of the insertion was evaluated in 115 individuals. It was heterozygous in 64 and homozygous in 25. Twelve of the 25 individuals carrying the insertion in homozygosity were susceptible to PM. After barley, pea, cucumber, and tomato, apple would be the fifth species for which a natural non-functional mlo allele has been found
A high-density, multi-parental SNP genetic map on apple validates a new mapping approach for outcrossing species
Pierro, Erica A. Di; Gianfranceschi, Luca ; Guardo, Mario Di; Koehorst-Van Putten, Herma J.J. ; Kruisselbrink, Johannes W. ; Longhi, Sara ; Troggio, Michela ; Bianco, Luca ; Muranty, Hélène ; Pagliarani, Giulia ; Bink, Marco C.A.M. ; Voorrips, Roeland E. ; Weg, Eric van de - \ 2016
Horticulture Research 3 (2016). - ISSN 2052-7276
Quantitative trait loci (QTL) mapping approaches rely on the correct ordering of molecular markers along the chromosomes, which can be obtained from genetic linkage maps or a reference genome sequence. For apple (Malus domestica Borkh), the genome sequence v1 and v2 could not meet this need; therefore, a novel approach was devised to develop a dense genetic linkage map, providing the most reliable marker-loci order for the highest possible number of markers. The approach was based on four strategies: (i) the use of multiple full-sib families, (ii) the reduction of missing information through the use of HaploBlocks and alternative calling procedures for single-nucleotide polymorphism (SNP) markers, (iii) the construction of a single backcross-type data set including all families, and (iv) a two-step map generation procedure based on the sequential inclusion of markers. The map comprises 15 417 SNP markers, clustered in 3 K HaploBlock markers spanning 1 267 cM, with an average distance between adjacent markers of 0.37 cM and a maximum distance of 3.29 cM. Moreover, chromosome 5 was oriented according to its homoeologous chromosome 10. This map was useful to improve the apple genome sequence, design the Axiom Apple 480 K SNP array and perform multifamily-based QTL studies. Its collinearity with the genome sequences v1 and v3 are reported. To our knowledge, this is the shortest published SNP map in apple, while including the largest number of markers, families and individuals. This result validates our methodology, proving its value for the construction of integrated linkage maps for any outbreeding species.
Development and validation of the Axiom®Apple480K SNP genotyping array
Bianco, Luca ; Cestaro, Alessandro ; Linsmith, Gareth ; Muranty, Hélène ; Denancé, Caroline ; Théron, Anthony ; Poncet, Charles ; Micheletti, Diego ; Kerschbamer, Emanuela ; Pierro, Erica A. Di; Larger, Simone ; Pindo, Massimo ; De Weg, Eric Van; Davassi, Alessandro ; Laurens, François ; Velasco, Riccardo ; Durel, Charles Eric ; Troggio, Michela - \ 2016
The Plant Journal 86 (2016)1. - ISSN 0960-7412 - p. 62 - 74.
genome-wide association study - genotyping - linkage mapping - Malus × domestica Borkh. - SNP chip - validation
Cultivated apple (Malus × domestica Borkh.) is one of the most important fruit crops in temperate regions, and has great economic and cultural value. The apple genome is highly heterozygous and has undergone a recent duplication which, combined with a rapid linkage disequilibrium decay, makes it difficult to perform genome-wide association (GWA) studies. Single nucleotide polymorphism arrays offer highly multiplexed assays at a relatively low cost per data point and can be a valid tool for the identification of the markers associated with traits of interest. Here, we describe the development and validation of a 487K SNP Affymetrix Axiom® genotyping array for apple and discuss its potential applications. The array has been built from the high-depth resequencing of 63 different cultivars covering most of the genetic diversity in cultivated apple. The SNPs were chosen by applying a focal points approach to enrich genic regions, but also to reach a uniform coverage of non-genic regions. A total of 1324 apple accessions, including the 92 progenies of two mapping populations, have been genotyped with the Axiom®Apple480K to assess the effectiveness of the array. A large majority of SNPs (359 994 or 74%) fell in the stringent class of poly high resolution polymorphisms. We also devised a filtering procedure to identify a subset of 275K very robust markers that can be safely used for germplasm surveys in apple. The Axiom®Apple480K has now been commercially released both for public and proprietary use and will likely be a reference tool for GWA studies in apple.
Development and preliminary evaluation of a 90 K Axiom® SNP array for the allo-octoploid cultivated strawberry Fragaria × ananassa
Bassil, N.V. ; Davis, T.M. ; Zhang, Hailong ; Ficklin, Stephen ; Mittmann, Mike ; Webster, Teresa ; Mahoney, Lise ; Wood, David ; Alperin, E.S. ; Rosyara, U.R. ; Koehorst-vanc Putten, Herma ; Monfort, Amparo ; Sargent, D.J. ; Amaya, Iraida ; Denoyes, Beatrice ; Bianco, Luca ; Dijk, Thijs van; Pirani, Ali ; Iezzoni, Amy ; Main, Dorrie ; Peace, Cameron ; Yang, Yilong ; Whitaker, Vance ; Verma, Sujeet ; Bellon, Laurent ; Brew, Fiona ; Herrera, Raul ; Weg, Eric van de - \ 2015
BMC Genomics 16 (2015)1. - ISSN 1471-2164
Fragaria - Genotyping array - Plant breeding - Polyploidy - Reduced ploidy - Single nucleotide polymorphism - Strawberry
A high-throughput genotyping platform is needed to enable marker-assisted breeding in the allo-octoploid cultivated strawberry Fragaria × ananassa. Short-read sequences from one diploid and 19 octoploid accessions were aligned to the diploid Fragaria vesca 'Hawaii 4' reference genome to identify single nucleotide polymorphisms (SNPs) and indels for incorporation into a 90 K Affymetrix® Axiom® array. We report the development and preliminary evaluation of this array. Results: About 36 million sequence variants were identified in a 19 member, octoploid germplasm panel. Strategies and filtering pipelines were developed to identify and incorporate markers of several types: di-allelic SNPs (66.6%), multi-allelic SNPs (1.8%), indels (10.1%), and ploidy-reducing "haploSNPs" (11.7%). The remaining SNPs included those discovered in the diploid progenitor F. iinumae (3.9%), and speculative "codon-based" SNPs (5.9%). In genotyping 306 octoploid accessions, SNPs were assigned to six classes with Affymetrix's "SNPolisher" R package. The highest quality classes, PolyHigh Resolution (PHR), No Minor Homozygote (NMH), and Off-Target Variant (OTV) comprised 25%, 38%, and 1% of array markers, respectively. These markers were suitable for genetic studies as demonstrated in the full-sib family 'Holiday' × 'Korona' with the generation of a genetic linkage map consisting of 6,594 PHR SNPs evenly distributed across 28 chromosomes with an average density of approximately one marker per 0.5 cM, thus exceeding our goal of one marker per cM. Conclusions: The Affymetrix IStraw90 Axiom array is the first high-throughput genotyping platform for cultivated strawberry and is commercially available to the worldwide scientific community. The array's high success rate is likely driven by the presence of naturally occurring variation in ploidy level within the nominally octoploid genome, and by effectiveness of the employed array design and ploidy-reducing strategies. This array enables genetic analyses including generation of high-density linkage maps, identification of quantitative trait loci for economically important traits, and genome-wide association studies, thus providing a basis for marker-assisted breeding in this high value crop.
ASSIsT: An Automatic SNP ScorIng Tool for in- and outbreeding species
Guardo, M. Di; Micheletti, D. ; Bianco, L. ; Koehorst-van Putten, H.J.J. ; Longhi, S. ; Costa, F. ; Aranzana, M.J. ; Velasco, R. ; Arus, P. ; Troggio, M. ; Weg, W.E. van de - \ 2015
Bioinformatics 31 (2015)23. - ISSN 1367-4803 - p. 3873 - 3874.
ASSIsT (Automatic SNP ScorIng Tool) is a user-friendly customized pipeline for efficient calling and filtering of SNPs from Illumina Infinium arrays, specifically devised for custom genotyping arrays. Illumina has developed an integrated software for SNP data visualization and inspection called GenomeStudio® (GS).ASSIsT builds on GS derived data and identifies those markers that follow a bi-allelic genetic model and show reliable genotype calls. Moreover, ASSIsT re-edits SNP calls with null alleles or additional SNPs in the probe annealing site. ASSIsT can be employed in the analysis of different population types such as full-sib families and mating schemes used in the plant kingdom (backcross, F1, F2), and unrelated individuals. The final result can be directly exported in the format required by the most common software for genetic mapping and marker-trait association analysis. ASSIsT is developed in Python and runs in Windows and Linux.
Development and validation of a 20K Single Nucleotide Polymorphism (SNP) whole genome genotyping array for apple (Malus × domestica Borkh)
Bianco, L. ; Cestaro, A. ; Sargent, D.J. ; Guardo, M. Di; Jansen, J. ; Weg, W.E. van de - \ 2014
PLoS ONE 9 (2014)10. - ISSN 1932-6203 - 9 p.
linkage map - construction - cultivars - alignment - accurate - barley
High-density SNP arrays for genome-wide assessment of allelic variation have made high resolution genetic characterization of crop germplasm feasible. A medium density array for apple, the IRSC 8 K SNP array, has been successfully developed and used for screens of bi-parental populations. However, the number of robust and well-distributed markers contained on this array was not sufficient to perform genome-wide association analyses in wider germplasm sets, or Pedigree-Based Analysis at high precision, because of rapid decay of linkage disequilibrium. We describe the development of an Illumina Infinium array targeting 20 K SNPs. The SNPs were predicted from re-sequencing data derived from the genomes of 13 Malus × domestica apple cultivars and one accession belonging to a crab apple species (M. micromalus). A pipeline for SNP selection was devised that avoided the pitfalls associated with the inclusion of paralogous sequence variants, supported the construction of robust multi-allelic SNP haploblocks and selected up to 11 entries within narrow genomic regions of ±5 kb, termed focal points (FPs). Broad genome coverage was attained by placing FPs at 1 cM intervals on a consensus genetic map, complementing them with FPs to enrich the ends of each of the chromosomes, and by bridging physical intervals greater than 400 Kbps. The selection also included ~3.7 K validated SNPs from the IRSC 8 K array. The array has already been used in other studies where ~15.8 K SNP markers were mapped with an average of ~6.8 K SNPs per full-sib family. The newly developed array with its high density of polymorphic validated SNPs is expected to be of great utility for Pedigree-Based Analysis and Genomic Selection. It will also be a valuable tool to help dissect the genetic mechanisms controlling important fruit quality traits, and to aid the identification of marker-trait associations suitable for the application of Marker Assisted Selection in apple breeding programs.
In male rats with concurrent iron and (n-3) fatty acid deficiency, provision of either iron or (n-3) fatty acids alone alters monoamine metabolism and exacerbates the cognitive deficits associated with combined deficiency
Baumgartner, J. ; Smuts, C.M. ; Malan, L. ; Arnold, M. ; Yee, B.K. ; Bianco, L.E. ; Boekschoten, M.V. ; Muller, M.R. ; Langhans, W. ; Hurrell, R.F. ; Zimmermann, M.B. - \ 2012
The Journal of Nutrition 142 (2012)8. - ISSN 0022-3166 - p. 1472 - 1478.
brain iron - phospholipid supplementation - dopamine metabolism - working-memory - behavior - mice - performance - myelination - nutrition - repletion
Concurrent deficiencies of iron (Fe) (ID) and (n-3) fatty acids [(n-3)FAD)] in rats can alter brain monoamine pathways and impair learning and memory. We examined whether repletion with Fe and DHA/EPA, alone and in combination, corrects the deficits in brain monoamine activity (by measuring monoamines and related gene expression) and spatial working and reference memory [by Morris water maze (MWM) testing] associated with deficiency. Using a 2 × 2 design, male rats with concurrent ID and (n-3)FAD [ID+(n-3)FAD] were fed an Fe+DHA/EPA, Fe+(n-3)FAD, ID+DHA/EPA, or ID+(n-3)FAD diet for 5 wk [postnatal d 56–91]. Biochemical measures and MWM performance after repletion were compared to age-matched control rats. The provision of Fe in combination with DHA/EPA synergistically increased Fe concentrations in the olfactory bulb (OB) (Fe x DHA/EPA interaction). Similarly, provision of DHA/EPA in combination with Fe resulted in higher brain DHA concentrations than provision of DHA alone in the frontal cortex (FC) and OB (P <0.05). Dopamine (DA) receptor D1 was upregulated in the hippocampus of Fe+DHA/EPA rats (fold-change = 1.25; P <0.05) and there were significant Fe x DHA/EPA interactions on serotonin (5-HT) in the OB and on the DA metabolite dihydroxyphenylacetic acid in the FC and striatum. Working memory performance was impaired in ID+DHA/EPA rats compared with controls (P <0.05). In the reference memory task, Fe+DHA/EPA improved learning behavior, but Fe or DHA/EPA alone did not. These findings suggest that feeding either Fe or DHA/EPA alone to adult rats with both ID and (n-3)FAD affects the DA and 5-HT pathways differently than combined repletion and exacerbates the cognitive deficits associated with combined deficiency.
Combined deficiency of iron and (n-3) fatty acids in male rates disrupts brain monoamine metabolism and produces greater memory deficits than iron deficiency or (n-3) fatty acid deficiency alone
Baumgartner, J. ; Smuts, C.M. ; Malan, L. ; Arnold, M. ; Yee, B.K. ; Bianco, L.E. ; Boekschoten, M.V. ; Muller, M.R. ; Langhans, W. ; Hurrell, R.F. ; Zimmermann, M.B. - \ 2012
The Journal of Nutrition 142 (2012)8. - ISSN 0022-3166 - p. 1463 - 1471.
serotoninergic neurotransmission - working-memory - early-life - dopamine - oligodendrocytes - supplementation - myelination - impairment - expression - nutrition
Deficiencies of iron (Fe) (ID) and (n-3) fatty acids (FA) [(n-3)FAD] may impair brain development and function through shared mechanisms. However, little is known about the potential interactions between these 2 common deficiencies. We studied the effects of ID and (n-3)FAD, alone and in combination, on brain monoamine pathways (by measuring monoamines and related gene expression) and spatial working and reference memory (by Morris water maze testing). Using a 2 × 2 design, male rats were fed an ID, (n-3)FAD, ID+(n-3)FAD, or control diet for 5 wk postweaning (postnatal d 21–56) after (n-3)FAD had been induced over 2 generations. The (n-3)FAD and ID diets decreased brain (n-3) FA by 70–76% and Fe by 20–32%, respectively. ID and (n-3)FAD significantly increased dopamine (DA) concentrations in the olfactory bulb (OB) and striatum, with an additive 1- to 2-fold increase in ID+(n-3)FAD rats compared with controls (P <0.05). ID decreased serotonin (5-HT) levels in OB, with a significant decrease in ID+(n-3)FAD rats. Furthermore, norepinephrine concentrations were increased 2-fold in the frontal cortex (FC) of (n-3)FAD rats (P <0.05). Dopa decarboxylase was downregulated in the hippocampus of ID and ID+(n-3)FAD rats (fold-change = -1.33; P <0.05). ID and (n-3)FAD significantly impaired working memory performance and the impairment positively correlated with DA concentrations in FC (r = 0.39; P = 0.026). Reference memory was impaired in the ID+(n-3)FAD rats (P <0.05) and was negatively associated with 5-HT in FC (r = -0.42; P = 0.018). These results suggest that the combined deficiencies of Fe and (n-3) FA disrupt brain monoamine metabolism and produce greater deficits in reference memory than ID or (n-3)FAD alone.
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Groen, A.F. - \ 2000
Bianco Nero 2000 (2000)April. - p. 51 - 53.