The Peach v2.0 release: high-resolution linkage mapping and deep resequencing improve chromosome-scale assembly and contiguity

Verde, Ignazio; Jenkins, Jerry; Dondini, Luca; Micali, Simona; Pagliarani, Giulia; Vendramin, Elisa; Paris, Roberta; Aramini, Valeria; Gazza, Laura; Rossini, Laura; Bassi, D.; Troggio, Michela; Shu, Shengqiang; Grimwood, Jane; Tartarini, Stefano; Dettori, Maria Teresa; Schmutz, Jeremy

doi:10.1186/s12864-017-3606-9

Cited by 317 publications

(358 citation statements)

References 98 publications

(126 reference statements)

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“…For paired‐end sequencing data, both reads were filtered out if eight read of the paired‐end reads was adaptor‐polluted. Second, the paired‐end reads of all resequenced accessions described above were aligned against the peach reference genome v2.0 (Verde et al ., ) using the program Burrows–Wheeler Aligner (BWA) v0.7.12 (Li and Durbin, ). SAMtools v1.2 (Li et al ., ) was used to sort reads, and duplicate reads from PCR were removed using Picard Tools v1.13 (http://broadinstitute.github.io/picard/) MarkDuplicates.…”

Section: Methodsmentioning

confidence: 99%

“…After filtering the adapter from the sequencing reads, the data were aligned against the peach reference genome v2.0 (Verde et al, 2017) using TopHat v2.1.0 (Kim et al, 2013). Gene expression information was calculated as the FPKM using Cufflinks v2.1.1 (Trapnell et al, 2010) and RNA-Seq by Expectation Maximization (RSEM) v1.2.11 (Li and Dewey, 2011).…”

Section: Rna Sequencing and Analysis Of Expression Levelsmentioning

confidence: 99%

“…As the linkage disequilibrium decay in peach was approximately 20~50 kbp at the genome-wide level (Cao et al, 2014), candidate genes were identified within a 50-kb window spanning loci identified by GWAS, using the peach reference genome v2.0 (Verde et al, 2017). These potential candidates were evaluated using expression analysis (see above).…”

Section: Identification Of Potential Candidate Genesmentioning

confidence: 99%

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Comparative population genomics identified genomic regions and candidate genes associated with fruit domestication traits in peach

Cao

Deng

et al. 2019

Plant Biotechnology Journal

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Summary Crop evolution is a long‐term process involving selection by natural evolutionary forces and anthropogenic influences; however, the genetic mechanisms underlying the domestication and improvement of fruit crops have not been well studied to date. Here, we performed a population structure analysis in peach (Prunus persica) based on the genome‐wide resequencing of 418 accessions and confirmed the presence of an obvious domestication event during evolution. We identified 132 and 106 selective sweeps associated with domestication and improvement, respectively. Analysis of their tissue‐specific expression patterns indicated that the up‐regulation of selection genes during domestication occurred mostly in fruit and seeds as opposed to other organs. However, during the improvement stage, more up‐regulated selection genes were identified in leaves and seeds than in the other organs. Genome‐wide association studies (GWAS) using 4.24 million single nucleotide polymorphisms (SNPs) revealed 171 loci associated with 26 fruit domestication traits. Among these loci, three candidate genes were highly associated with fruit weight and the sorbitol and catechin content in fruit. We demonstrated that as the allele frequency of the SNPs associated with high polyphenol composition decreased during peach evolution, alleles associated with high sugar content increased significantly. This indicates that there is genetic potential for the breeding of more nutritious fruit with enhanced bioactive polyphenols without disturbing a harmonious sugar and acid balance by crossing with wild species. This study also describes the development of the genomic resources necessary for evolutionary research in peach and provides the large‐scale characterization of key agronomic traits in this crop species.

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Section: Methodsmentioning

confidence: 99%

Section: Rna Sequencing and Analysis Of Expression Levelsmentioning

confidence: 99%

Section: Identification Of Potential Candidate Genesmentioning

confidence: 99%

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Comparative population genomics identified genomic regions and candidate genes associated with fruit domestication traits in peach

Cao

Deng

et al. 2019

Plant Biotechnology Journal

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“…(Lesur et al 2015), and the quality and availability of P. persica genome annotation (Verde et al 2013(Verde et al , 2017.…”

Section: Polymorphisms Typology and Countsmentioning

confidence: 99%

The loops of the N-SH2 binding cleft do not serve as allosteric switch in SHP2 activation

Anselmi¹,

Hub

2018

Preprint

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In the post-genomics era, non-model species like most Fagaceae still lack operational diversity resources for population genomics studies. We completed the analyses of Sanger sequences produced from over 800 gene fragments covering ~530 kb across the genic partition of European oaks in a range-wide sampling of 25 individuals (11 Quercus petraea, 13 Q. robur, one Q. ilex as an outgroup). Regions targeted represented broad functional categories potentially involved in species ecological preferences, and a random set of genes.Using a high-quality dedicated pipeline, we provide a detailed characterization of over 14500 polymorphisms, including ~12500 SNPs -218 being triallelic-, over 1500 insertion-deletions, and ~200 novel di-and tri-nucleotide SSR loci. This catalog also includes various summary statistics within and among species, gene ontology information, and standard formats to assist loci choice for genotyping projects. The distribution of nucleotide diversity and differentiation across genic regions are also described for the first time in those species (mean  close to ~0.0049 in Q. petraea and to ~0.0045 in Q. robur across random regions, and mean F ST ~0.13 across SNPs). Robust patterns were observed which emphasize a slightly but significantly higher diversity in Q. petraea, across a random gene set and in the abiotic stress functional category, and a heterogeneous landscape of both diversity and differentiation. These patterns are discussed in the context of both species documented introgression history despite strong reproductive barriers. The quality, representativity in terms of species genomic diversity, and usefulness of the resources provided are discussed for possible applications in medium scale landscape ecology projects, and as a reference resource for validation purposes in larger-scale re-sequencing projects. These are preferentially recommended in oaks in contrast to SNP array development, given the large nucleotide variation and low levels of linkage disequilibrium revealed.

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“…in peach is complex, quantitative and multi-genic it would be of relevance to find candidate genes for resistance in peach. With the available version 2 of Prunus persica whole genome assembly and annotation [184] and new techniques such as GBS (Genome by Sequencing) we can search for new markers to fine mapping these quantitative regions or assay GWAs (Genome Wide Association).…”

Section: Host Resistance and Genetic Managementmentioning

confidence: 99%

Peach Brown Rot: Still in Search of an Ideal Management Option

2018

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Abstract:The peach is one of the most important global tree crops within the economically important Rosaceae family. The crop is threatened by numerous pests and diseases, especially fungal pathogens, in the field, in transit, and in the store. More than 50% of the global post-harvest loss has been ascribed to brown rot disease, especially in peach late-ripening varieties. In recent years, the disease has been so manifest in the orchards that some stone fruits were abandoned before harvest. In Spain, particularly, the disease has been associated with well over 60% of fruit loss after harvest. The most common management options available for the control of this disease involve agronomical, chemical, biological, and physical approaches. However, the effects of biochemical fungicides (biological and conventional fungicides), on the environment, human health, and strain fungicide resistance, tend to revise these control strategies. This review aims to comprehensively compile the information currently available on the species of the fungus Monilinia, which causes brown rot in peach, and the available options to control the disease. The breeding for brown rot-resistant varieties remains an ideal management option for brown rot disease control, considering the uniqueness of its sustainability in the chain of crop production.

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The Peach v2.0 release: high-resolution linkage mapping and deep resequencing improve chromosome-scale assembly and contiguity

Cited by 317 publications

References 98 publications

Comparative population genomics identified genomic regions and candidate genes associated with fruit domestication traits in peach

Comparative population genomics identified genomic regions and candidate genes associated with fruit domestication traits in peach

The loops of the N-SH2 binding cleft do not serve as allosteric switch in SHP2 activation

Peach Brown Rot: Still in Search of an Ideal Management Option

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