Development and bin mapping of a Rosaceae Conserved Ortholog Set (COS) of markers

12 pages, 5 tables, 6 figures, additional 3 files.Background: Detailed comparative genome analyses within the economically important Rosaceae family have not been conducted. This is largely due to the lack of conserved gene-based molecular markers that are transferable among the important crop genera within the family [e.g. Malus (apple), Fragaria (strawberry), and Prunus (peach, cherry, apricot and almond)]. The lack of molecular markers and comparative whole genome sequence analysis for this family severely hampers crop improvement efforts as well as QTL confirmation and validation studies. Results: We identified a set of 3,818 rosaceaous unigenes comprised of two or more ESTs that correspond to single copy Arabidopsis genes. From this Rosaceae Conserved Orthologous Set (RosCOS), 1039 were selected from which 857 were used for the development of intron-flanking primers and allele amplification. This led to successful amplification and subsequent mapping of 613 RosCOS onto the Prunus TxE reference map resulting in a genome-wide coverage of 0.67 to 1.06 gene-based markers per cM per linkage group. Furthermore, the RosCOS primers showed amplification success rates from 23 to 100% across the family indicating that a substantial part of the RosCOS primers can be directly employed in other less studied rosaceaous crops. Comparisons of the genetic map positions of the RosCOS with the physical locations of the orthologs in the Populus trichocarpa genome identified regions of colinearity between the genomes of Prunus-Rosaceae and Populus-Salicaceae. Conclusion: Conserved orthologous genes are extremely useful for the analysis of genome evolution among closely and distantly related species. The results presented in this study demonstrate the considerable potential of the mapped Prunus RosCOS for genome-wide marker employment and comparative whole genome studies within the Rosaceae family. Moreover, these markers will also function as useful anchor points for the genome sequencing efforts currently ongoing in this family as well as for comparative QTL analyses.This work is supported by USDA-NRI grants 2008-02259 and 2005-00743. AC was also supported by funds from the Department of Horticulture and Crop Science, The Ohio State University.Peer reviewe

Development and Evaluation of a 9K SNP Array for Peach by Internationally Coordinated SNP Detection and Validation in Breeding Germplasm

Correction 21 Jun 2012: Verde I, Bassil N, Scalabrin S, Gilmore B, Lawley CT, et al. (2012) Correction: Development and Evaluation of a 9K SNP Array for Peach by Internationally Coordinated SNP Detection and Validation in Breeding Germplasm. PLOS ONE 7(6): 10.1371/annotation/33f1ba92-c304-4757-91aa-555de64a0768.Although a large number of single nucleotide polymorphism (SNP) markers covering the entire genome are needed to enable molecular breeding efforts such as genome wide association studies, fine mapping, genomic selection and marker-assisted selection in peach [Prunus persica (L.) Batsch] and related Prunus species, only a limited number of genetic markers, including simple sequence repeats (SSRs), have been available to date. To address this need, an international consortium (The International Peach SNP Consortium; IPSC) has pursued a coordinated effort to perform genome-scale SNP discovery in peach using next generation sequencing platforms to develop and characterize a high-throughput Illumina Infinium® SNP genotyping array platform. We performed whole genome re-sequencing of 56 peach breeding accessions using the Illumina and Roche/454 sequencing technologies. Polymorphism detection algorithms identified a total of 1,022,354 SNPs. Validation with the Illumina GoldenGate® assay was performed on a subset of the predicted SNPs, verifying ~75% of genic (exonic and intronic) SNPs, whereas only about a third of intergenic SNPs were verified. Conservative filtering was applied to arrive at a set of 8,144 SNPs that were included on the IPSC peach SNP array v1, distributed over all eight peach chromosomes with an average spacing of 26.7 kb between SNPs. Use of this platform to screen a total of 709 accessions of peach in two separate evaluation panels identified a total of 6,869 (84.3%) polymorphic SNPs. The almost 7,000 SNPs verified as polymorphic through extensive empirical evaluation represent an excellent source of markers for future studies in genetic relatedness, genetic mapping, and dissecting the genetic architecture of complex agricultural traits. The IPSC peach SNP array v1 is commercially available and we expect that it will be used worldwide for genetic studies in peach and related stone fruit and nut species

Markers in fruit tree breeding: improvement of peach

International audiencePeach [Prunus persica (L.) Batsch] belongs to the Prunus genus, member of the Rosaceae family. The Prunus genus, within the subfamily Prunoideae, is characterized by species that produce drupes as fruit (also referred to as stone fruits), and contains a significant number of agriculturally important fruit tree species [i.e., almond (Prunus dulcis Mill.), apricot (Prunus armeniaca Linn.), sweet cherry (Prunus avium L.) and sour cherry (Prunus cerasus L.), and plum (Prunus japonica and Prunus domestica)]. Several other species like myrobalan plum (Prunus cerasifera Ehrh.) or Sainte Lucie cherry (Prunus mahaleb L.) are mainly used as Prunus rootstocks. Although Prunus is an economically and biologically important genus, little was known about the genome structure and organization until the breakthrough of DNA marker technologies. Peach has distinct advantages that make it suitable as a model species for comparative and functional genomics. It has a short juvenile phase (2–3 years) compared to many other tree species, and a small genome: 5.9×108 bp or 0.61 pg/diploid nucleus (Baird et al. 1994). This is only about twice the genome size of Arabidopsis thaliana (Arumuganathan and Earle 1991). All the Prunus species have a base chromosome number of x=8. Peach, almond, sweet cherry and myrobalan plum have a diploid genome (2n=2x=16), whereas sour cherry is tetraploid (2n=4x=32) and European plum hexaploid (2n=6x=48). Moreover, peach is genetically the bestcharacterized Prunus species with a fair number of genes controlling important traits and having a Mendelian behavior (Hesse 1975; Monet et al. 1996; Table 1). For all these reasons, peach was chosen as a model for Rosaceae and a physical map has been initiated

Diversity analysis

International audienc

The potential of Prunus davidiana for introgression into peach (Prunus persica (L.) Batsch) assessed by comparative mapping

International audienc

Synteny in the Rosaceae

International audienc

Synteny in the Rosaceae

International audienc

Sequences of the genomic DNAs encoding the S2, S9, S10, and S23 alleles from almond, Prunus dulcis

Partial genomic sequences of the S-alleles S2, S9, and S10, identified in genomic DNA selected from Prunus dulcis ´Cristomorto` (S1S2), ´Anxaneta` (S2S9), ´Primorskiy` (S5S9), and ´Gabaix` (S5S10), were found to contain introns of 562, 1,343, and ∼705 bp, and partial exons of 537, 486, and 495 bp respectively. In addition, another allele, characterized as S23, was identified in the two Australian cultivars Johnston`s Prolific and Pierce. This allele had an intron size of 662 bp and a partial exon size of 489 bp, and may have been introduced into Australia in the Spanish cultivar Ramillete (S6S23). The exoni/ntron splice junction sites of all alleles followed the GT/AG consensus sequence rule, and the sequences were found to be highly conserved.Chockpisit Channuntapipat, Margaret Sedgle, Ignasi Batlle, Pere Arús And Graham Collin

Development and bin mapping of a Rosaceae Conserved Ortholog Set (COS) of markers

Abstract Background Detailed comparative genome analyses within the economically important Rosaceae family have not been conducted. This is largely due to the lack of conserved gene-based molecular markers that are transferable among the important crop genera within the family [e.g. Malus (apple), Fragaria (strawberry), and Prunus (peach, cherry, apricot and almond)]. The lack of molecular markers and comparative whole genome sequence analysis for this family severely hampers crop improvement efforts as well as QTL confirmation and validation studies. Results We identified a set of 3,818 rosaceaous unigenes comprised of two or more ESTs that correspond to single copy Arabidopsis genes. From this Rosaceae Conserved Orthologous Set (RosCOS), 1039 were selected from which 857 were used for the development of intron-flanking primers and allele amplification. This led to successful amplification and subsequent mapping of 613 RosCOS onto the Prunus TxE reference map resulting in a genome-wide coverage of 0.67 to 1.06 gene-based markers per cM per linkage group. Furthermore, the RosCOS primers showed amplification success rates from 23 to 100% across the family indicating that a substantial part of the RosCOS primers can be directly employed in other less studied rosaceaous crops. Comparisons of the genetic map positions of the RosCOS with the physical locations of the orthologs in the Populus trichocarpa genome identified regions of colinearity between the genomes of Prunus-Rosaceae and Populus-Salicaceae. Conclusion Conserved orthologous genes are extremely useful for the analysis of genome evolution among closely and distantly related species. The results presented in this study demonstrate the considerable potential of the mapped Prunus RosCOS for genome-wide marker employment and comparative whole genome studies within the Rosaceae family. Moreover, these markers will also function as useful anchor points for the genome sequencing efforts currently ongoing in this family as well as for comparative QTL analyses.</p

Cell wall polysaccharide chemistry of peach genotypes with contrasted textures and other fruit traits

Publication Inra prise en compte dans l'analyse bibliométrique des publications scientifiques mondiales sur les Fruits, les Légumes et la Pomme de terre. Période 2000-2012. http://prodinra.inra.fr/record/256699International audienceCell wall composition, pectin, and hemicellulose fine structure variation were assessed in peach and related genotypes with contrasted texture and fruit shape. Cell walls were prepared from four commercial peaches, eight genotypes from the Jalousia x Fantasia peach cross, and six genotypes from the Earlygold peach x Texas almond cross. Sugar composition was determined chemically while fine structure of homogalacturonan pectin and xyloglucan hemicellulose were assessed by coupling pectin lyase and glucanase degradation, respectively, with MALDI-TOF MS analysis of the degradation products. The results indicate clear compositional and structural differences between the parents and their related genotypes on the basis of pectin versus cellulose/hemicellulose content and on the fine structure of homogalacturonan and xyloglucan. A relation between methyl- and acetyl-esterification of pectin with fruit shape is revealed in the Fantasia X Jalousia peach genotypes