15 years of GDR: New data and functionality in the Genome Database for Rosaceae

Nucleic Acids Research, Journal Year: 2018, Volume and Issue: 47(D1), P. D1137 - D1145

Published: Oct. 9, 2018

The Genome Database for Rosaceae (GDR, https://www.rosaceae.org) is an integrated web-based community database resource providing access to publicly available genomics, genetics and breeding data data-mining tools facilitate basic, translational applied research in Rosaceae. volume of GDR has increased greatly over the last 5 years. now houses multiple versions whole genome assembly annotation from 14 species, made by recent advances sequencing technology. Annotated searchable reference transcriptomes, RefTrans, combining peer-reviewed published RNA-Seq as well EST datasets, are newly major crop species. Significantly more quantitative trait loci, genetic maps markers MapViewer, a new visualization tool that better integrates with other pages GDR. Pathways can be accessed through Cyc databases, synteny among newest assemblies eight species viewed browser, SynView. Collated single-nucleotide polymorphism diversity phenotypic datasets relevant data. Also, Breeding Information Management System allows breeders upload, manage analyze their private within secure server option release publicly.

Language: Английский

---

Resistance to Sharka in Apricot: Comparison of Phase-Reconstructed Resistant and Susceptible Haplotypes of ‘Lito’ Chromosome 1 and Analysis of Candidate Genes

Frontiers in Plant Science, Journal Year: 2019, Volume and Issue: 10

Published: Dec. 4, 2019

Sharka, a common disease among most stone fruit crops, is caused by the Plum Pox Virus (PPV). Resistant genotypes have been found in apricot (Prunus armeniaca L.), one of which-the cultivar 'Lito' heterozygous for resistance-has used to map major quantitative trait locus (QTL) on linkage group 1, following pseudo-test-cross mating design with 231 individuals. In addition, 19 SNP markers were selected from hundreds previously developed, which allowed region be limited 236 kb chromosome 1. A bacterial artificial (BAC) library was produced, screened region, and positive BAC clones sequenced. (R) susceptible (S) haplotypes assembled independently. To refine assembly, whole genome sequenced high coverage (98×) using PacBio technology, enabling development detailed assembly that able predict annotate genes QTL region. The not only discriminate structural variants between two haplotypic regions but also distinguish specific allele expression, contributing towards mining PPVres locus. light these findings, indicated (i.e., MATHd genes) possible role PPV resistance further analyzed, new candidates discussed. Although results are conclusive, accurate independent R S valuable resource test alternative transcription regulation mechanisms underpinning resistance.

Language: Английский

---

A manually annotated Actinidia chinensis var. chinensis (kiwifruit) genome highlights the challenges associated with draft genomes and gene prediction in plants

BMC Genomics, Journal Year: 2018, Volume and Issue: 19(1)

Published: April 16, 2018

Most published genome sequences are drafts, and most dominated by computational gene prediction. Draft genomes typically incorporate considerable sequence data that not assigned to chromosomes, predicted genes without quality confidence measures. The current Actinidia chinensis (kiwifruit) 'Hongyang' draft has 164 Mb of unassigned pseudo-chromosomes, omissions have been identified in the models.A second an A. (genotype Red5) was fully sequenced. This new resulted a 554.0 assembly with all but 6 pseudo-chromosomes. Pseudo-chromosomal comparisons showed number translocation events occurred following whole duplication (WGD) event some consistent centromeric Robertsonian-like translocations. RNA sequencing from 12 tissues ab initio analysis informed genome-wide manual annotation, using WebApollo tool. In total, 33,044 loci represented 33,123 isoforms were identified, named tagged for evidential support. Of these 3114 (9.4%) identical protein within Kiwifruit Information Resource (KIR v2). Some proportion differences will be varietal polymorphisms. However, as computationally Red5 models required re-annotation this is expected small. tested 550 cloned 'Hort16A' cDNAs comparing both original revised annotation KIR v2. Only 48.9% 63.5% had match 90% identity or better respectively, compared 90.9% models.Our study highlights need take cautious approach genes. Our use tool facilitated checking correction enabling improvement utility especially relevant certain types families such EXPANSIN like Finally, high set supply kiwifruit general plant community genomics other comparative analysis.

Language: Английский

---

Near-gapless and haplotype-resolved apple genomes provide insights into the genetic basis of rootstock-induced dwarfing

Nature Genetics, Journal Year: 2024, Volume and Issue: 56(3), P. 505 - 516

Published: Feb. 12, 2024

Language: Английский

---

Prunus genetics and applications after de novo genome sequencing: achievements and prospects

Horticulture Research, Journal Year: 2019, Volume and Issue: 6(1)

Published: April 5, 2019

Prior to the availability of whole-genome sequences, our understanding structural and functional aspects Prunus tree genomes was limited mostly molecular genetic mapping important traits development EST resources. With public release peach genome others that followed, significant advances in knowledge underpinnings ensued. In this review, we highlight key achievements genetics breeding driven by these sequences. Within evolutionary contexts, summarize: (1) current status sequences; (2) preliminary ongoing work on sequence structure diversity genomes; (3) analyses evolution natural man-made selection; (4) provide insight into haploblocking as a means define genome-scale patterns can be leveraged for trait selection pedigree-based programs worldwide. Functionally, summarize recent leverages sequences identify characterize genes controlling 22 agronomically traits. These include phenology, fruit quality, allergens, disease resistance, architecture, self-incompatibility. Translationally, explore application sequence-based marker-assisted technologies other sequence-guided biotechnological approaches crop improvement. Finally, present publically available genomics data housed mainly Genome Database Rosaceae (GDR) its updated functionalities future bioinformatics-based inquiry.

Language: Английский

---

Transposons played a major role in the diversification between the closely related almond and peach genomes: results from the almond genome sequence

The Plant Journal, Journal Year: 2019, Volume and Issue: 101(2), P. 455 - 472

Published: Sept. 17, 2019

Summary We sequenced the genome of highly heterozygous almond Prunus dulcis cv. Texas combining short‐ and long‐read sequencing. obtained a assembly totaling 227.6 Mb estimated size 238 Mb, which 91% is anchored to eight pseudomolecules corresponding its haploid chromosome complement, annotated 27 969 protein‐coding genes 6747 non‐coding transcripts. By phylogenomic comparison with genomes 16 additional close distant species we that peach ( persica ) diverged around 5.88 million years ago. These two are syntenic show high degree sequence conservation (20 nucleotide substitutions per kb). However, they also exhibit number presence/absence variants, many attributable movement transposable elements (TEs). Transposable have generated an important variants between peach, recent history TE seems markedly different them. may be at origin phenotypic differences both species, in particular for sweet kernel phenotype, key agronomic domestication character almond. Here cultivars, methylated insertions surround gene involved biosynthesis amygdalin, whose reduced expression has been correlated phenotype. Altogether, our results suggest role TEs diversification relative peach.

Language: Английский

---

The architecture of intra-organism mutation rate variation in plants

PLoS Biology, Journal Year: 2019, Volume and Issue: 17(4), P. e3000191 - e3000191

Published: April 9, 2019

Given the disposability of somatic tissue, selection can favor a higher mutation rate in early segregating soma than germline, as seen some animals. Although plants intra-organismic heterogeneity is poorly resolved, same selectionist logic predict lower shoot root and longer-lived terminal tissues (e.g., leaves) ontogenetically similar short-lived ones petals), that should be deterministic with no significant differences between biological replicates. To address these expectations, we sequenced 754 genomes from various eight plant species. Consistent model, accumulation per unit time apical meristem perennials, which high proportion mutations shoots are themselves transmissible, but not annuals, tend to transmissible. Similarly, number accumulated leaves commonly within petal plant, there more rates replicate branches expected by chance. High runners strawberry is, argue, exception proves rule, transmission patterns indicate runner has restricted germline. However, also find vitro callus tissue (per time) wild-grown comparator, suggesting nonadaptive mutational "fragility". As fragility does obviously explain why shoot-root difference varies longevity, conclude variation consistent theory mechanistic null considered.

Language: Английский

---

An integrated peach genome structural variation map uncovers genes associated with fruit traits

Genome biology, Journal Year: 2020, Volume and Issue: 21(1)

Published: Oct. 6, 2020

Abstract Background Genome structural variations (SVs) have been associated with key traits in a wide range of agronomically important species; however, SV profiles peach and their functional impacts remain largely unexplored. Results Here, we present an integrated map 202,273 SVs from 336 genomes. A substantial number selected during domestication improvement, which together affect 2268 genes. Genome-wide association studies 26 agronomic using these identify candidate causal variants. 9-bp insertion Prupe.4G186800 , encodes NAC transcription factor, is shown to be early fruit maturity, 487-bp deletion the promoter PpMYB10.1 flesh color around stone. In addition, 1.67 Mb inversion highly shape, gene adjacent breakpoint, PpOFP1 regulates flat shape formation. Conclusions The identified genes variants represent valuable resources for future genomic research breeding peach.

Language: Английский

---

Genome-Wide Association Mapping of Flowering and Ripening Periods in Apple

Frontiers in Plant Science, Journal Year: 2017, Volume and Issue: 8

Published: Nov. 10, 2017

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 European level using an association panel 1,168 different genotypes distributed over six locations phenotyped these phenological traits. The was genotyped high-density SNPs Axiom®Apple 480 K SNP array. ran GWAS with multi-locus mixed model (MLMM), which handles putatively confounding effect significant elsewhere on genome. Genomic regions were further investigated reveal candidate genes responsible phenotypic variation. At whole population level, retained two as cofactors chromosome 9 period, period (four 3, one 10 16) which, together accounted 8.9% 17.2% variance, respectively. For both traits, weak linkage disequilibrium detected nearby, thus suggesting existence allelic heterogeneity. geographic origins relationships parts Variation genotypic frequency associated traits connected origin (grouped North+East, West South Europe), indicated differential selection Genes encoding transcription factors containing either NAC or MADS domains identified major candidates within small confidence intervals computed genomic regions. A strong microsynteny between peach revealed all four interval This study shows how genetics can unravel important horticultural apple, well reduce by mapping approaches. Our findings be used improvement through marker-assisted strategies that take advantage accumulating additive effects

Language: Английский

---

Apple whole genome sequences: recent advances and new prospects

Horticulture Research, Journal Year: 2019, Volume and Issue: 6(1)

Published: April 5, 2019

In 2010, a major scientific milestone was achieved for tree fruit crops: publication of the first draft whole genome sequence (WGS) apple (Malus domestica). This WGS, v1.0, valuable as initial reference information, fine mapping, gene discovery, variant and tool development. A new, high quality GDDH13 v1.1, released in 2017 now serves apple. Over past decade, these WGSs have had an enormous impact on our understanding biological functioning, trait physiology inheritance, leading to practical applications improving this highly valued crop. Causal identities phenotypes fundamental interest can today be discovered much more rapidly. Genome-wide polymorphisms at genetic resolution are screened efficiently over hundreds thousands individuals with new insights into relationships pedigrees. High-density maps constructed quantitative loci traits readily associated positional candidate genes and/or converted diagnostic tests breeders. We understand species, geographical, genomic origins domesticated precisely, well its relationship wild relatives. The WGS has turbo-charged application classical research steps crop improvement drives innovative methods achieve durable, environmentally sound, productive, consumer-desirable production. review includes examples basic breakthroughs challenges using WGSs. Recommendations "what's next" focus necessary upgrades data pool, use data, reach frontiers genomics-based

Language: Английский

---