scholarly journals Comprehensive family-based SNV association analysis shows new alleles associated to mealy traits in Prunus persica

2016 ◽  
Author(s):  
Paula Vizoso ◽  
Claudio Meneses ◽  
Reinaldo Campos ◽  
Ariel Orellana
Keyword(s):  
Prunus Persica ◽  
Chilling Injury ◽  
Genomic Region ◽  
Agricultural Industry ◽  
Surface Receptors ◽  
Peach Breeding ◽  
Synonymous Change ◽  
Polymorphism Rate ◽  
Family Based ◽  
Segregating Population

Identification of DNA markers associated with mealiness trait is an important tool to agricultural industry. Many peach breeding initiatives have as aim to improve early selection of varieties with better postharvest performance. We present a family-based approach to identify and develop an association panel to evaluate potential varieties susceptible to mealiness induced by chilling. We used whole-genome sequencing and SNV genotyping of parents and ten contrasting siblings (Juicy and mealy) obtained from segregating population of self-cross ‘Venus’. Results show that there are differences regarding SNVs and structural variants (SVs) that could be associated with mealy to be contrasted with individuals without such damage phenotype. Preliminary results showed a total of 30.564 SNVs and 2.297 SVs having a non-synonymous change in genes. Comparison of SNVs between segregants and parental revealed 1.963 SNVs associated genes presents in juicy segregants and 6.162 SNVs associated genes in segregants mealiness. We found 230 and 244 SVs with functional impact in genomes mealy and juicy. As proof of concept, all SNVs obtained were correlated with the information published in peach related to chilling injury (QTL genomic region, dbSNP, SDR chillpeach, upeach and RNA-seq available). Guided by preliminary analysis, we selected pools of alleles that display a frequency difference between mealy and juicy fruit and a selective sweep is observed around those alleles. Some of the SNVs have been previously correlated with chilling injury through transcriptome analysis. Additionally, we identify new genome regions associated with mealy susceptibility. Most of these genes were related to negative regulation of programmed cell death, cell surface receptors signaling pathways and cell wall remodeling. On the other hand, the genes affected by SV in the juicy segregating are classified according to the biological process in metabolism of sugars and fatty acid biosynthetic process. These results provide insights into genetics determinants related with susceptibility to mealiness. Analysis of the sequences revealed the existence of a high polymorphism rate in nectarines, and statistical analysis showed that the segments could be used as genetic barcodes that should be informative enough to allow reliable identification of cultivars. This study proposes a predictive panel of biomarkers to identify varieties at susceptible for mealiness and identifies new candidates genes linked to mealiness in peach.

scholarly journals Comprehensive family-based SNV association analysis shows new alleles associated to mealy traits in Prunus persica

2016 ◽  
Author(s):  
Paula Vizoso ◽  
Claudio Meneses ◽  
Reinaldo Campos ◽  
Ariel Orellana
Keyword(s):  
Prunus Persica ◽  
Chilling Injury ◽  
Genomic Region ◽  
Agricultural Industry ◽  
Surface Receptors ◽  
Peach Breeding ◽  
Synonymous Change ◽  
Polymorphism Rate ◽  
Family Based ◽  
Segregating Population

Identification of DNA markers associated with mealiness trait is an important tool to agricultural industry. Many peach breeding initiatives have as aim to improve early selection of varieties with better postharvest performance. We present a family-based approach to identify and develop an association panel to evaluate potential varieties susceptible to mealiness induced by chilling. We used whole-genome sequencing and SNV genotyping of parents and ten contrasting siblings (Juicy and mealy) obtained from segregating population of self-cross ‘Venus’. Results show that there are differences regarding SNVs and structural variants (SVs) that could be associated with mealy to be contrasted with individuals without such damage phenotype. Preliminary results showed a total of 30.564 SNVs and 2.297 SVs having a non-synonymous change in genes. Comparison of SNVs between segregants and parental revealed 1.963 SNVs associated genes presents in juicy segregants and 6.162 SNVs associated genes in segregants mealiness. We found 230 and 244 SVs with functional impact in genomes mealy and juicy. As proof of concept, all SNVs obtained were correlated with the information published in peach related to chilling injury (QTL genomic region, dbSNP, SDR chillpeach, upeach and RNA-seq available). Guided by preliminary analysis, we selected pools of alleles that display a frequency difference between mealy and juicy fruit and a selective sweep is observed around those alleles. Some of the SNVs have been previously correlated with chilling injury through transcriptome analysis. Additionally, we identify new genome regions associated with mealy susceptibility. Most of these genes were related to negative regulation of programmed cell death, cell surface receptors signaling pathways and cell wall remodeling. On the other hand, the genes affected by SV in the juicy segregating are classified according to the biological process in metabolism of sugars and fatty acid biosynthetic process. These results provide insights into genetics determinants related with susceptibility to mealiness. Analysis of the sequences revealed the existence of a high polymorphism rate in nectarines, and statistical analysis showed that the segments could be used as genetic barcodes that should be informative enough to allow reliable identification of cultivars. This study proposes a predictive panel of biomarkers to identify varieties at susceptible for mealiness and identifies new candidates genes linked to mealiness in peach.

Changes in ACC and conjugated ACC levels following controlled atmosphere storage of nectarine

2005 ◽  
Vol 45 (12) ◽  
pp. 1635 ◽  
Author(s):  
A. Uthairatanakij ◽  
P. Penchaiya ◽  
B. McGlasson ◽  
P. Holford
Keyword(s):  
Low Temperature ◽  
Cold Storage ◽  
Low Temperatures ◽  
Prunus Persica ◽  
Chilling Injury ◽  
Controlled Atmosphere ◽  
Controlled Atmosphere Storage ◽  
Gaseous Composition ◽  
Storage Atmosphere ◽  
Atmosphere Storage

Low temperature disorders of nectarines are thought to be expressions of chilling injury. Chilling injury is a form of stress usually associated with increased synthesis of ethylene and its immediate precursor, aminocyclopropane-1-carboxylic acid (ACC). However, other mechanisms for the development of chilling injury have been proposed. To help determine the nature of the processes leading to chilling injury in nectarines (Prunus persica) and how the gaseous composition of the storage atmosphere effects the development of low temperature disorders, levels of ACC and conjugated ACC were measured in fruit of the cv. Arctic Snow. These compounds were measured in fruit ripened at 20°C immediately after harvest, in fruit on removal from cold storage and in fruit ripened at 20°C following cold storage. During storage, fruit were kept at 0°C in the 4 following atmospheres: air; air + 15% CO2; air + 15 µL/L ethylene; and air + 15% CO2 + 15 µL/L ethylene. Concentrations of ACC remained low in all treatments and no significant changes in ACC levels due to added ethylene or CO2 were observed. Concentrations of conjugated ACC were about 10-times that of ACC and again were not influenced by the composition of the storage atmosphere. No significant changes in either ACC or conjugated ACC were observed until after flesh bleeding, the major symptoms of low temperature disorder expressed in these fruit, had begun to appear. It was concluded that disorders in nectarines stored at low temperatures are not a stress response involving a disruption of ethylene metabolism but may be associated with differential changes in the metabolism of enzymes associated with normal ripening.

scholarly journals Population Structure and Phylogeny of Some U.S. Peach Cultivars

2022 ◽  
Vol 147 (1) ◽  
pp. 1-6
Author(s):  
Chunxian Chen ◽  
William R. Okie
Keyword(s):  
Population Structure ◽  
Prunus Persica ◽  
Principal Component ◽  
Pairwise Distance ◽  
Limiting Factors ◽  
Genetic Admixture ◽  
Department Of Agriculture ◽  
Phylogenetic Relations ◽  
Cultivar Groups ◽  
Peach Breeding

Peach (Prunus persica) cultivars maintained at the U.S. Department of Agriculture program at Byron, GA, have never been characterized with any molecular markers. In this study, 20 microsatellite markers were used to genotype 112 cultivars and the data were analyzed to discern their population structure and phylogenetic relationships. STRUCTURE simulations revealed four K clusters and broad genetic admixture among the cultivars. Principal coordinate analysis (PCoA) showed the cultivar groups from western, northeastern, and southeastern U.S. states were adjacent to each other except cultivars from Michigan (close to most southeastern state groups) and Florida (most distant from the other groups). Principal component analysis (PCA) showed that these cultivars had no obvious PCA partitioning boundaries. The intertwined distribution in both PCoA and PCA partitions suggested many of them were genetically closely related to each other largely because most shared same ancestral parentages. Most pairwise distance means within and between the cultivar groups were relatively low, suggesting close phylogenetic relations among those cultivars, as were demonstrated in the phylogenetic tree. Limiting factors and perspectives relevant to peach breeding are discussed.

scholarly journals Identification of Metabolite and Lipid Profiles in a Segregating Peach Population Associated with Mealiness in Prunus persica (L.) Batsch

Metabolites ◽  
2020 ◽  
Vol 10 (4) ◽  
pp. 154 ◽  
Author(s):  
Victoria Lillo-Carmona ◽  
Alonso Espinoza ◽  
Karin Rothkegel ◽  
Miguel Rubilar ◽  
Ricardo Nilo-Poyanco ◽  
...  
Keyword(s):  
Cold Storage ◽  
Prunus Persica ◽  
Early Stage ◽  
Chilling Injury ◽  
Fruit Production ◽  
Lipid Profiles ◽  
Long Distance ◽  
Physiological Disorder ◽  
Export Markets ◽  
Long Time

The peach is the third most important temperate fruit crop considering fruit production and harvested area in the world. Exporting peaches represents a challenge due to the long-distance nature of export markets. This requires fruit to be placed in cold storage for a long time, which can induce a physiological disorder known as chilling injury (CI). The main symptom of CI is mealiness, which is perceived as non-juicy fruit by consumers. The purpose of this work was to identify and compare the metabolite and lipid profiles between two siblings from contrasting populations for juice content, at harvest and after 30 days at 0 °C. A total of 119 metabolites and 189 lipids were identified, which showed significant differences in abundance, mainly in amino acids, sugars and lipids. Metabolites displaying significant changes from the E1 to E3 stages corresponded to lipids such as phosphatidylglycerol (PG), monogalactosyldiacylglycerol (MGDG) and lysophosphatidylcholines (LPC), and sugars such as fructose 1 and 1-fructose-6 phosphate. These metabolites might be used as early stage biomarkers associated with mealiness at harvest and after cold storage.

Effect prediction of identified SNPs linked to fruit quality and chilling injury in peach [Prunus persica (L.) Batsch]

2012 ◽  
Vol 81 (1-2) ◽  
pp. 161-174 ◽  
Author(s):  
Pedro J. Martínez-García ◽  
Jonathan Fresnedo-Ramírez ◽  
Dan E. Parfitt ◽  
Thomas M. Gradziel ◽  
Carlos H. Crisosto
Keyword(s):  
Fruit Quality ◽  
Prunus Persica ◽  
Chilling Injury

1-Methylcyclopropene treatment modifies postharvest behavior of Fantasia nectarines

2008 ◽  
Vol 88 (4) ◽  
pp. 753-758 ◽  
Author(s):  
Jennifer R DeEll ◽  
Dennis P Murr ◽  
Behrouz Ehsani-Moghaddam
Keyword(s):  
Fruit Quality ◽  
Prunus Persica ◽  
Color Change ◽  
Chilling Injury ◽  
Soluble Solids ◽  
Solids Concentration ◽  
Ethylene Action ◽  
Volatile Production ◽  
Soluble Solids Concentration

The effects of 1-methylcyclopropene (1-MCP), an inhibitor of ethylene action, on the ripening and quality of Fantasia nectarines were examined. Fruit were harvested from two commercial orchards and subsequently exposed to 1 μL L-1 of 1-MCP for 24 h at 0°C. Following treatment, fruit were held at 0°C for 0, 2, or 4 wk, and then assessed for quality during a ripening period at 23°C. 1-MCP treatment improved postharvest firmness retention in nectarines after 0 and 2 wk at 0°C plus 4 days at 23°C. Soluble solids concentration (SSC) was lower in nectarines treated with 1 MCP and held for 0 or 4 wk at 0°C, compared with similar non-treated fruit. The peel ground color change from green to yellow was also delayed by 1-MCP. Nectarines treated with 1-MCP exhibited less CO2 and hydrophobic volatile production during 14 days at 23°C, compared with non-treated fruit. The overall inhibition of fruit ripening by 1-MCP appears transitory in Fantasia nectarines. Chilling injury was observed after 4 wk of storage at 0°C and 1-MCP-treated fruit had less visual chilling-related injury but greater chilling-induced flesh hardening. Further research is needed to determine the effects of 1-MCP on different chilling injury symptoms in nectarines. Key words: 1-MCP, fruit quality, ripening, storage, shelf-life, Prunus persica

scholarly journals Chilling Injury in Peaches: A Cytochemical and Ultrastructural Cell Wall Study

1992 ◽  
Vol 117 (1) ◽  
pp. 114-118 ◽  
Author(s):  
J.G. Luza ◽  
R. van Gorsel ◽  
V.S. Polito ◽  
A.A. Kader
Keyword(s):  
Cell Wall ◽  
Cell Walls ◽  
Prunus Persica ◽  
Periodic Acid ◽  
Chilling Injury ◽  
Middle Lamella ◽  
Wall Structure ◽  
Positive Staining ◽  
Intercellular Matrix ◽  
Parenchyma Cells

Fruits of mid- (`O'Henry'), late (`Airtime'), and extra-late-season (`Autumn Gem') peach [Prunus persica (L.) Batsch] cultivars were examined for changes in cell wall structure and cytochemistry that accompany the onset of mealiness and leatheriness of the mesocarp due to chilling injury. The peaches were stored at 10C for up to 18 days or at SC for up to 29 days. Plastic-embedded sections were stained by the Schiff's-periodic acid reaction, Calcofluor white MR2, and Coriphosphine to demonstrate total insoluble carbohydrates, ß-1,4 glucans, and pectins, respectively. Mealiness was characterized by separation of mesocarp parenchyma cells leading to increased intercellular spaces and accumulation of pectic substances in the intercellular matrix. Little structural change was apparent in the cellulosic component of the cell walls of these fruits. In leathery peaches, the mesocarp parenchyma cells collapsed, intercellular space continued to increase, and pectin-positive staining in the intercellular matrix increased greatly. In addition, the component of the cell walls that stained positively for ß-1,4 glucans became thickened relative to freshly harvested or mealy fruit. At the ultrastructural level, dissolution of the middle lamella, cell separation, irregular thickening of the primary wall, and plasmolysis of the mesocarp parenchyma cells were seen as internal breakdown progressed.

scholarly journals Estimated Implementation Costs of DNA-informed Breeding in a Peach Breeding Program

2020 ◽  
Vol 30 (3) ◽  
pp. 356-364 ◽  
Author(s):  
Seth D. Wannemuehler ◽  
Chengyan Yue ◽  
William W. Shane ◽  
R. Karina Gallardo ◽  
Vicki McCracken
Keyword(s):  
Cost Effectiveness ◽  
Prunus Persica ◽  
Early Stage ◽  
Cost Effective ◽  
Breeding Program ◽  
Breeding Cycle ◽  
Breeding Programs ◽  
Implementation Costs ◽  
Peach Breeding ◽  
Additional Costs

Marker-assisted selection (MAS) use in breeding programs allows for examination of seedlings at an early stage before accumulation of high field costs. However, introducing MAS into a breeding program implies additional costs and uncertainties about effective incorporation. Previous simulations in apple (Malus ×domestica) have shown cost-effective applications of MAS. To further evaluate MAS cost-effectiveness in perennial crops, we conducted a cost-effectiveness analysis examining MAS in an upper midwestern U.S. peach (Prunus persica) breeding program. Breeding program procedures and associated costs were collected and used as input into spreadsheet-based simulations of the breeding program. Simulations compared a conventional breeding program to MAS with varying cull rates of low, medium, and high at multiple stages in the breeding cycle. Cost-effective MAS implementation was identified at the end of seedling trials with a break-even cull rate of 4%. These results inform breeders of cost-effectiveness of MAS use in a peach breeding program.

scholarly journals A High Resolution Melting Analysis-Based Genotyping Toolkit for the Peach (Prunus persica) Chilling Requirement

2020 ◽  
Vol 21 (4) ◽  
pp. 1543
Author(s):  
Lin Chou ◽  
Shih-Jie Huang ◽  
Chen Hsieh ◽  
Ming-Te Lu ◽  
Chia-Wei Song ◽  
...  
Keyword(s):  
High Resolution ◽  
Prunus Persica ◽  
High Resolution Melting ◽  
Physical Map ◽  
Low Cost ◽  
Principal Component ◽  
Chilling Requirement ◽  
Nucleotide Polymorphisms ◽  
Genotyping Platform ◽  
Peach Breeding

The chilling requirement (CR) is the main factor controlling the peach floral bud break and subsequent reproductive growth. To date, several peach CR quantitative trait loci (QTLs) have been identified. To improve the accessibility and convenience of this genetic information for peach breeders, the aim of this study was to establish an easy-to-use genotype screening system using peach CR molecular markers as a toolkit for marker-assisted selection. Here, we integrated 22 CR-associated markers from three published QTLs and positioned them on the Prunus persica physical map. Then, we built a PCR-based genotyping platform by using high-resolution melting (HRM) analysis with specific primers and trained this platform with 27 peach cultivars. Due to ambiguous variant calls from a commercial HRM software, we developed an R-based pipeline using principal component analysis (PCA) to accurately differentiate genotypes. Based on the PCA results, this toolkit was able to determine the genotypes at the CR-related single nucleotide polymorphisms (SNPs) in all tested peach cultivars. In this study, we showed that this HRM-PCA pipeline served as a low-cost, high-throughput, and non-gel genotyping solution. This system has great potential to accelerate CR-focused peach breeding.

scholarly journals Is the Tolerance of Commercial Peach Cultivars to Brown Rot Caused by Monilinia laxa Modulated by its Antioxidant Content?

Plants ◽  
2020 ◽  
Vol 9 (5) ◽  
pp. 589
Author(s):  
Vitus I. Obi ◽  
Joaquín Montenegro ◽  
Juan J. Barriuso ◽  
Fayza Saidani ◽  
Christophe Aubert ◽  
...  
Keyword(s):  
Prunus Persica ◽  
Correlation Coefficients ◽  
Brown Rot ◽  
Total Phenolic ◽  
Fruit Traits ◽  
Total Polyphenols ◽  
Breeding Programs ◽  
Phenolic Contents ◽  
Artificial Fruit ◽  
Peach Breeding

Brown rot, caused by Monilinia spp., provokes pre- and post-harvest damage in peach (Prunus persica (L.) Batsch), which causes an economic impact in the industry. With a view to breeding for increased tolerance to this disease, a screening test based upon artificial fruit inoculation was validated on several parental lines of a peach breeding program during the two-period harvest. In addition, cultivars with different total phenolic contents were included in the two-year study. All physicochemical fruit traits recorded at harvest showed differences among all cultivars. The antioxidant compound content determined using spectrophotometry (to measure ascorbic acid and antioxidant capacity) and UPLC-MS (to measure and identify phenolic compounds) also revealed important differences among all genotypes. The rate of brown rot lesion following fruit inoculation varied widely among cultivars, and it was possible to discriminate between highly and less susceptible cultivars. Cultivars with minimal development of damage were identified as germplasm with the desirable allele combination to increase brown rot tolerance in peach breeding programs. Finally, Pearson’s correlation coefficients (r) between pairs of variables were calculated, searching for any biochemical candidate conferring tolerance. The correlation of phytopathological traits with the antioxidant composition, concerning contents of ascorbic, neochlorogenic, and chlorogenic acids and total polyphenols in fruit, is discussed.

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