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Kiwifruit (Actinidia chinensis var. deliciosa (A Chev) Liang et Ferguson) is a sub-tropical vine species from the Actinidiaceae family native to China. This species has an allohexaploid genome (from diploid and autotetraploid parents), contained in 174 chromosomes producing a climacteric and fleshy fruit called kiwifruit. Currently, only a small body of transcriptomic and proteomic data are available for A. chinensis var. deliciosa. In this low molecular knowledge context, the main goal of this study is to construct a tissue-specific de novo transcriptome assembly, generating differential expression analysis among these specific tissues, to obtain new useful transcriptomic information for a better knowledge of vegetative, floral and fruit growth in this species. In this study, we have analyzed different whole transcriptomes from shoot, leaf, flower bud, flower and fruit at four development stages (7, 50, 120 and 160 days after flowering; DAF) in kiwifruit obtained through RNA-seq sequencing. The first version of the developed A. chinensis var. deliciosa de novo transcriptome contained 142,025 contigs (
Juan Salazar; Cristian Vergara-Pulgar; Claudia Jorquera; Patricio Zapata; David Ruiz; Pedro Martínez-Gómez; Rodrigo Infante; Claudio Meneses. De Novo Transcriptome Sequencing in Kiwifruit (Actinidia chinensis var. deliciosa (A Chev) Liang et Ferguson) and Development of Tissue-Specific Transcriptomic Resources. Agronomy 2021, 11, 919 .
AMA StyleJuan Salazar, Cristian Vergara-Pulgar, Claudia Jorquera, Patricio Zapata, David Ruiz, Pedro Martínez-Gómez, Rodrigo Infante, Claudio Meneses. De Novo Transcriptome Sequencing in Kiwifruit (Actinidia chinensis var. deliciosa (A Chev) Liang et Ferguson) and Development of Tissue-Specific Transcriptomic Resources. Agronomy. 2021; 11 (5):919.
Chicago/Turabian StyleJuan Salazar; Cristian Vergara-Pulgar; Claudia Jorquera; Patricio Zapata; David Ruiz; Pedro Martínez-Gómez; Rodrigo Infante; Claudio Meneses. 2021. "De Novo Transcriptome Sequencing in Kiwifruit (Actinidia chinensis var. deliciosa (A Chev) Liang et Ferguson) and Development of Tissue-Specific Transcriptomic Resources." Agronomy 11, no. 5: 919.
Throughout history, new strategies and technologies have played a key role in promoting the development of agriculture. New strategies have led to substantial improvements in crop productivity and fruit quality. The cultivation of peach and apricot in controlled greenhouse conditions is one such strategy. The aim of the protected cultivation of these species in greenhouses is to grow fruit trees by modifying the natural environment of the tree, including the harvest duration, which can be extended. This protected cultivation should improve yield, thus increasing the benefit–cost ratio, especially in the case of organic production. Here we review the main factors involved in greenhouse fruit tree cultivation, including the planting systems and substrate, cultivar and rootstock selection, pollination management, orchard management, and environmental management. Greenhouse cultivation makes it possible to control environmental conditions like wind speed, moisture, temperature, mineral nutrients, light intensity, and the atmospheric composition, and thus gives us a better understanding of growth factor requirements, and the means to improve fruit productivity. A protected environment has been shown to be effective in maintaining a relatively high temperature and preventing leaf injury due to environmental factors, resulting in a longer period of photosynthetic activity, which increases the photosynthetic production, and is therefore a suitable alternative strategy for production in cold regions. The main benefits of apricot and peach cultivation in greenhouses are: (1) precocity; (2) high fruit quality, storage life, and market proximity; and (3) good plant health, suitable for organic cultivation. However, the main limiting factors for fruit tree production in greenhouse conditions to take into account are: (1) light scarcity at high latitudes; (2) a lack of cold for bud breaking, flowering, and fruit production; (3) potentially excessive temperatures in warm regions, which reduce the photosynthesis rate; and (4) a reduction of fruit quality, coloring, and aroma compounds in certain warm conditions with light day/night temperature variations.
Pedro Martínez-Gómez; Sama Rahimi Devin; Juan Salazar; Jesús López-Alcolea; Manuel Rubio; Pedro Martínez-García. Principles and Prospects of Prunus Cultivation in Greenhouse. Agronomy 2021, 11, 474 .
AMA StylePedro Martínez-Gómez, Sama Rahimi Devin, Juan Salazar, Jesús López-Alcolea, Manuel Rubio, Pedro Martínez-García. Principles and Prospects of Prunus Cultivation in Greenhouse. Agronomy. 2021; 11 (3):474.
Chicago/Turabian StylePedro Martínez-Gómez; Sama Rahimi Devin; Juan Salazar; Jesús López-Alcolea; Manuel Rubio; Pedro Martínez-García. 2021. "Principles and Prospects of Prunus Cultivation in Greenhouse." Agronomy 11, no. 3: 474.
Kiwifruit are climacteric fruit, so they must be harvested before they are fully ripe, allowing for the extension of their shelf-life via cold storage. Therefore, an adequate knowledge about how ethylene-induced fruit senescence is required to avoid significant economic losses. The main goal of the present study was to investigate the kiwifruit ripening process at the physiological and molecular levels by RNA-seq after 1-methylcyclopropene (1-MCP, ethylene inhibitor) and Ethrel® (ethylene stimulator) treatments. The results showed that Ethrel® (ethephon) treatment induced more accelerated fruit ripening, leading to rapid fruit senescence, meanwhile 1-MCP caused a slowing flesh softening, and thus a longer shelf-life period. The RNA-seq was carried out on the fruit after 4 and 13 days, considering day 4 as the most determinant in terms of differentially expressed genes (DEGs). The sequencing achieved 70.7% alignment with the ‘Hongyang’ genome, obtaining 18,036 DEGs. The protein-protein interaction (PPI) network shows the interaction between different pathways in two main clusters: (1) pentose and glucoronate interconversions, citrate cycle, glycolysis and gluconeogenesis or starch, and sucrose metabolism and (2) porphyrin and chlorophyll metabolism. The first cluster is mainly interconnected by G6PD1 (pentose pathway); E1 ALPHA and ACLB-2 (citrate cycle); Achn209711 (pentose and glucoronate); LOS2 (glycolysis); HKL1 and HXK1 (glycolysis—starch and sucrose); and PHS2 (starch and sucrose). In the second cluster, GUN5 through PORA is interacting with CRD1 and NYC1 which were overexpressed by 1-MCP in the porphyrin and chlorophyll metabolism. In addition, genes linked to PSBY and PSBP photosynthesis-linked proteins in photosystem 2 were overexpressed by 1-MCP which is undoubtedly related to chlorophyll degradation and fruit senescence. These results suggest that in kiwifruit, the main pathways that are regulated by ethylene-induced senescence comprise sugar catabolism and chlorophyll degradation.
Juan Salazar; Patricio Zapata; Claudia Silva; Makarena González; Igor Pacheco; Macarena Bastías; Claudio Meneses; Claudia Jorquera; Israel Moreno; Paulina Shinya; Rodrigo Infante. Transcriptome analysis and postharvest behavior of the kiwifruit ‘Actinidia deliciosa’ reveal the role of ethylene-related phytohormones during fruit ripening. Tree Genetics & Genomes 2021, 17, 1 -19.
AMA StyleJuan Salazar, Patricio Zapata, Claudia Silva, Makarena González, Igor Pacheco, Macarena Bastías, Claudio Meneses, Claudia Jorquera, Israel Moreno, Paulina Shinya, Rodrigo Infante. Transcriptome analysis and postharvest behavior of the kiwifruit ‘Actinidia deliciosa’ reveal the role of ethylene-related phytohormones during fruit ripening. Tree Genetics & Genomes. 2021; 17 (1):1-19.
Chicago/Turabian StyleJuan Salazar; Patricio Zapata; Claudia Silva; Makarena González; Igor Pacheco; Macarena Bastías; Claudio Meneses; Claudia Jorquera; Israel Moreno; Paulina Shinya; Rodrigo Infante. 2021. "Transcriptome analysis and postharvest behavior of the kiwifruit ‘Actinidia deliciosa’ reveal the role of ethylene-related phytohormones during fruit ripening." Tree Genetics & Genomes 17, no. 1: 1-19.
In plants, fruit ripening is a coordinated developmental process that requires the change in expression of hundreds to thousands of genes to modify many biochemical and physiological signal cascades such as carbohydrate and organic acid metabolism, cell wall restructuring, ethylene production, stress response, and organoleptic compound formation. In Prunus species (including peaches, apricots, plums, and cherries), fruit ripening leads to the breakdown of complex carbohydrates into sugars, fruit firmness reductions (softening by cell wall degradation and cuticle properties alteration), color changes (loss of green color by chlorophylls degradation and increase in non-photosynthetic pigments like anthocyanins and carotenoids), acidity decreases, and aroma increases (the production and release of organic volatile compounds). Actually, the level of information of molecular events at the transcriptional, biochemical, hormonal, and metabolite levels underlying ripening in Prunus fruits has increased considerably. However, we still poorly understand the molecular switch that occurs during the transition from unripe to ripe fruits. The objective of this review was to analyze of the molecular bases of fruit quality in Prunus species through an integrated metabolic, genomic, transcriptomic, and epigenetic approach to better understand the molecular switch involved in the ripening process with important consequences from a breeding point of view.
Beatriz E. García-Gómez; Juan A. Salazar; María Nicolás-Almansa; Mitra Razi; Manuel Rubio; David Ruiz; Pedro Martínez-Gómez. Molecular Bases of Fruit Quality in Prunus Species: An Integrated Genomic, Transcriptomic, and Metabolic Review with a Breeding Perspective. International Journal of Molecular Sciences 2020, 22, 333 .
AMA StyleBeatriz E. García-Gómez, Juan A. Salazar, María Nicolás-Almansa, Mitra Razi, Manuel Rubio, David Ruiz, Pedro Martínez-Gómez. Molecular Bases of Fruit Quality in Prunus Species: An Integrated Genomic, Transcriptomic, and Metabolic Review with a Breeding Perspective. International Journal of Molecular Sciences. 2020; 22 (1):333.
Chicago/Turabian StyleBeatriz E. García-Gómez; Juan A. Salazar; María Nicolás-Almansa; Mitra Razi; Manuel Rubio; David Ruiz; Pedro Martínez-Gómez. 2020. "Molecular Bases of Fruit Quality in Prunus Species: An Integrated Genomic, Transcriptomic, and Metabolic Review with a Breeding Perspective." International Journal of Molecular Sciences 22, no. 1: 333.
Japanese plums are popular fruits since they are exceptionally nutritious with high fiber and antioxidant content. This work has aimed to analyze the most critical phenology, fruit quality and postharvest parameters from a genomic point of view to identify molecular markers closely linked to the most significant Quantitative trait loci (QTLs). A genetic linkage map of an F1 population of 151 individuals from the cross '98–99’ × 'Angeleno' was constructed using previously reported Single Nucleotide polymorphism (SNP) data and 25 additional Simple Sequence Repeat (SSR) markers. Twenty-three phenotypic traits evaluated during three harvest seasons were assayed to estimate best linear unbiased predictors by using two genomic association QTL analysis approaches: General Linear Model-based single marker-trait associations (GLM) and Multiple QTL Model analyses (MQM). In addition, loss of weight and chlorophyll degradation between days 1 and 7 as well as fruit softening for days 1, 4, and 7 were monitored during two consecutive seasons. The most significant identified QTLs were linked to fruit development period and fruit weight in Linkage Groups (LG) 4 and 2, respectively. Regarding postharvest parameters, the identified QTLs related to chlorophyll degradation and loss of weight showed lower significance than phenology or fruit quality traits. In contrast, minor QTLs for fruit firmness evolution using destructive and non-destructive methods were confirmed in LG 4 and 5.
Juan Alfonso Salazar; Igor Pacheco; Patricio Zapata; Paulina Shinya; David Ruiz; Pedro Martínez-Gómez; R. Infante. Identification of loci controlling phenology, fruit quality and post-harvest quantitative parameters in Japanese plum (Prunus salicina Lindl.). Postharvest Biology and Technology 2020, 169, 111292 .
AMA StyleJuan Alfonso Salazar, Igor Pacheco, Patricio Zapata, Paulina Shinya, David Ruiz, Pedro Martínez-Gómez, R. Infante. Identification of loci controlling phenology, fruit quality and post-harvest quantitative parameters in Japanese plum (Prunus salicina Lindl.). Postharvest Biology and Technology. 2020; 169 ():111292.
Chicago/Turabian StyleJuan Alfonso Salazar; Igor Pacheco; Patricio Zapata; Paulina Shinya; David Ruiz; Pedro Martínez-Gómez; R. Infante. 2020. "Identification of loci controlling phenology, fruit quality and post-harvest quantitative parameters in Japanese plum (Prunus salicina Lindl.)." Postharvest Biology and Technology 169, no. : 111292.
The authors have withdrawn this preprint from Research Square
Juan Salazar; Cristian Vergara; Claudia Jorquera; Patricio Zapata; Pedro Martínez Gómez; Rodrigo Infante; Claudio Meneses. Tissue-specific de novo transcriptome analysis in kiwifruit [Actinidia deliciosa (A Chev) Liang et Ferguson]. 2019, 1 .
AMA StyleJuan Salazar, Cristian Vergara, Claudia Jorquera, Patricio Zapata, Pedro Martínez Gómez, Rodrigo Infante, Claudio Meneses. Tissue-specific de novo transcriptome analysis in kiwifruit [Actinidia deliciosa (A Chev) Liang et Ferguson]. . 2019; ():1.
Chicago/Turabian StyleJuan Salazar; Cristian Vergara; Claudia Jorquera; Patricio Zapata; Pedro Martínez Gómez; Rodrigo Infante; Claudio Meneses. 2019. "Tissue-specific de novo transcriptome analysis in kiwifruit [Actinidia deliciosa (A Chev) Liang et Ferguson]." , no. : 1.
Background Kiwifruit [Actinidia deliciosa (A Chev) Liang et Ferguson] is a sub-tropical vine from the Actinidiaceae family native from China. This specie has an allohexaploid genome (from a diploid and autotetraploid parents) contained in 174 chromosomes producing a climacteric and fleshy fruit called kiwifruit. Currently there's no too much genomic and transcriptomic information about this species. In this low molecular knowledge context, the main goal of this work is to construct a tissue-specific de novo transcriptome assembly generating a differential expression analysis among these specific tissues to obtain new useful database for a better knowledge of vegetative, floral and fruit growth in different phenological states of Actinidia deliciosa cv. ‘Hayward’. Results In the present study we have analyzed different whole transcriptomes from shoot, leaf, flower bud, flower and fruit at 4 development stages (7,50,120 and 160 days after flowering; DAF) in kiwifruit by using RNA-seq. We sequenced twenty-four libraries, obtaining 604,735,364 reads which were assembled using Trinity software. The first version of Actinidia deliciosa de novo transcriptome contained 142,025 contigs (x̅=1,044bp, N50=1,133bp). CEGMA and BUSCO were used for assembly quality assessment, obtaining close to 90.0% (35.1% partial) and over 85.0% (18.3% partial) of the ultra-conserved genes for eukaryote and plants, respectively. Annotation was performed with BLASTx against TAIR10 protein database and we found an annotation proportion of 35.6% (50,508), leaving 64.4% (91,517) of the contigs assembly without annotation. Conclusions These results represent a reference transcriptome for allohexaploid kiwifruit generating a database of Actinidia deliciosa genes related to leaf, flower and fruit development. Thus, the present study provides a high valuable information, identifying over 20,000 exclusive genes including all tissue comparisons, which are associated with the proteins involved in different biological processes and molecular functions. Transcriptome assembly and refining as well as the assembly metric assessment, has implied an enough quality to be a putative database of this specie and high number of ultra-conserved proteins were found. With respect to transcriptome close to 65% of contigs did not match with any protein. Therefore, future functional annotation will be required in order to obtain a better knowledge of the tissue-specific development.
Juan Salazar; Cristian Vergara; Claudia Jorquera; Patricio Zapata; Pedro Martínez Gómez; Rodrigo Infante; Claudio Meneses. Tissue-specific de novo transcriptome analysis in kiwifruit [Actinidia deliciosa (A Chev) Liang et Ferguson]. 2019, 1 .
AMA StyleJuan Salazar, Cristian Vergara, Claudia Jorquera, Patricio Zapata, Pedro Martínez Gómez, Rodrigo Infante, Claudio Meneses. Tissue-specific de novo transcriptome analysis in kiwifruit [Actinidia deliciosa (A Chev) Liang et Ferguson]. . 2019; ():1.
Chicago/Turabian StyleJuan Salazar; Cristian Vergara; Claudia Jorquera; Patricio Zapata; Pedro Martínez Gómez; Rodrigo Infante; Claudio Meneses. 2019. "Tissue-specific de novo transcriptome analysis in kiwifruit [Actinidia deliciosa (A Chev) Liang et Ferguson]." , no. : 1.
Genotyping by sequencing (GBS) provides a large quantity of useful data suitable for the identification of single nucleotide polymorphisms (SNPs), facilitating accurate genomic studies in plant species. In this study, GBS-based SNPs were used to characterise 11 Japanese plum cultivars and to explore their natural allelic diversity in relation to the most important phenology events (flowering date, ripening date and fruit development period) and fruit quality traits (weight, shape, skin and flesh colour, over colour, skin and flesh chlorophyll index, flesh firmness and soluble solids concentration). GBS-based SNPs were shown to be a powerful tool for genetic diversity and other genomic studies where SNP markers were related to several traits, particularly for flowering date, ripening date, fruit development period, skin chlorophyll degradation, flesh chlorophyll degradation and flesh colour. These results represent a preliminary approach using GBS as a possible breeding tool in current and new Japanese plum breeding programmes.
Juan Alfonso Salazar; Igor Pacheco; Claudia Silva; Patricio Zapata; Paulina Shinya; David Ruiz; Pedro Martínez-Gómez; Rodrigo Infante. Development and applicability of GBS approach for genomic studies in Japanese plum (Prunus salicina Lindl.). The Journal of Horticultural Science and Biotechnology 2018, 94, 284 -294.
AMA StyleJuan Alfonso Salazar, Igor Pacheco, Claudia Silva, Patricio Zapata, Paulina Shinya, David Ruiz, Pedro Martínez-Gómez, Rodrigo Infante. Development and applicability of GBS approach for genomic studies in Japanese plum (Prunus salicina Lindl.). The Journal of Horticultural Science and Biotechnology. 2018; 94 (3):284-294.
Chicago/Turabian StyleJuan Alfonso Salazar; Igor Pacheco; Claudia Silva; Patricio Zapata; Paulina Shinya; David Ruiz; Pedro Martínez-Gómez; Rodrigo Infante. 2018. "Development and applicability of GBS approach for genomic studies in Japanese plum (Prunus salicina Lindl.)." The Journal of Horticultural Science and Biotechnology 94, no. 3: 284-294.
Chile is the third largest exporter of kiwifruit in the world. Its varietal production has traditionally been focused on green-fleshed kiwifruit varieties, with ‘Hayward’ being the most exported variety. ‘Soreli’ is a new Italian kiwifruit variety, which is characterized by its early ripening, big size, sweet taste, as well as its yellow flesh. This gives ‘Soreli’ a good opportunity to promote the consumption of yellow-fleshed varieties, and a wider assortment of kiwifruit in the market. The aim of this work is to evaluate postharvest traits and consumer acceptance in kiwifruit var. ‘Soreli’, with a combination of storage temperatures of 0 °C and 20 °C and 1-methylcyclopropene (1-MCP) applications. Cold storage and 1-MCP treatments caused a positive response in kiwifruit var. 'Soreli'. In the case of fruits stored at 20 °C, 1-MCP treatment extended the postharvest life of the fruits at least 3 weeks while the fruits stored in cold at 0 °C treated with 1-MCP reached 8 weeks. In general, the respiration rate was higher in the control treatments with respect to the 1-MCP treatments, as well as the ethylene emission occurred earlier in the control. In addition, the kiwifruit sensory quality attributes were adequate in all cases, reaching a medium or high acceptability in the evaluation panel.
Juan Salazar; Claudia Jorquera; Reinaldo Campos-Vargas; Chad Jorgensen; Patricio Zapata; Rodrigo Infante. Effect of the application timing of 1-MCP on postharvest traits and sensory quality of a yellow-fleshed kiwifruit. Scientia Horticulturae 2018, 244, 82 -87.
AMA StyleJuan Salazar, Claudia Jorquera, Reinaldo Campos-Vargas, Chad Jorgensen, Patricio Zapata, Rodrigo Infante. Effect of the application timing of 1-MCP on postharvest traits and sensory quality of a yellow-fleshed kiwifruit. Scientia Horticulturae. 2018; 244 ():82-87.
Chicago/Turabian StyleJuan Salazar; Claudia Jorquera; Reinaldo Campos-Vargas; Chad Jorgensen; Patricio Zapata; Rodrigo Infante. 2018. "Effect of the application timing of 1-MCP on postharvest traits and sensory quality of a yellow-fleshed kiwifruit." Scientia Horticulturae 244, no. : 82-87.
The chilling requirements for dormancy release and heat requirements for flowering were studied for three successive years in eleven Prunus salicina L. cultivars that spanned the range of flowering times in this species. Different methods for estimating chilling requirements were evaluated and compared, and correlations between chilling requirements, heat requirements and flowering date were established. The cultivars examined showed a range of chilling requirements (chill units, CU), spanning from 334.3 CU (‘Pioneer’) to 987.5 CU (‘Songold’). The heat requirements for flowering ranged between 5990 and 9228 growing degree hours. The chilling requirements were significantly different among cultivars, whereas no cultivar effect was found for the heat requirement values. In addition, chill portions were the variable that correlated the most with flowering date in Japanese plum. The dissection of flowering date into chilling and heat requirements indicates that chilling requirements is the main variable driving the variation of flowering time within Japanese plum cultivars.
David Ruiz; José Egea; Juan Salazar; Jose Campoy. Chilling and heat requirements of Japanese plum cultivars for flowering. Scientia Horticulturae 2018, 242, 164 -169.
AMA StyleDavid Ruiz, José Egea, Juan Salazar, Jose Campoy. Chilling and heat requirements of Japanese plum cultivars for flowering. Scientia Horticulturae. 2018; 242 ():164-169.
Chicago/Turabian StyleDavid Ruiz; José Egea; Juan Salazar; Jose Campoy. 2018. "Chilling and heat requirements of Japanese plum cultivars for flowering." Scientia Horticulturae 242, no. : 164-169.
Simple sequence repeats (SSRs) are genome domains located in both coding and non-coding regions in eukaryotic genomes. Although SSRs are often characterized by low polymorphism, their DNA-flanking sequences could be a useful source of DNA markers, which could help in genetic studies and breeding because they are associated with genes that control traits of interest. In this study, 56 genotypes from different Prunus species were used, including peach, apricot, plum, and almond (already phenotyped for several agronomical traits, including self-compatibility, flowering and ripening time, fruit type, skin and flesh color, and shell hardness). These Prunus genotypes were molecularly characterized using 28 SSR markers developed in exons, introns, and intergenic regions. All these genes were located in specific regions where quantitative trait loci (QTLs) for certain fruit quality traits were also located, including flowering and ripening times and fruit flesh and skin color. A sum of 309 SSR alleles were identified in the whole panel of analyzed cultivars, with expected heterozygosity values of 0.61 (upstream SSRs), 0.17 (exonic SSRs), 0.65 (intronic SSRs), and 0.58 (downstream SSRs). These values prove the low level of polymorphism of the exonic (gene-coding regions) markers. Cluster and structural analysis based on SSR data clearly differentiated the genotypes according to either specie (for the four species) and pedigree (apricot) or geographic origin (Japanese plum). In addition, some SSR markers mainly developed in intergenic regions could be associated with genes that control traits of interest in breeding and could therefore help in marker-assisted breeding. These findings highlight the importance of using molecular markers able to discriminate between the functional roles of the gene allelic variants.
Beatriz Ester García-Gómez; Mitra Razi; Juan Salazar; Angela S. Prudencio; David Ruiz; Luca Dondini; Pedro Martínez-Gómez. Comparative Analysis of SSR Markers Developed in Exon, Intron, and Intergenic Regions and Distributed in Regions Controlling Fruit Quality Traits in Prunus Species: Genetic Diversity and Association Studies. Plant Molecular Biology Reporter 2017, 36, 23 -35.
AMA StyleBeatriz Ester García-Gómez, Mitra Razi, Juan Salazar, Angela S. Prudencio, David Ruiz, Luca Dondini, Pedro Martínez-Gómez. Comparative Analysis of SSR Markers Developed in Exon, Intron, and Intergenic Regions and Distributed in Regions Controlling Fruit Quality Traits in Prunus Species: Genetic Diversity and Association Studies. Plant Molecular Biology Reporter. 2017; 36 (1):23-35.
Chicago/Turabian StyleBeatriz Ester García-Gómez; Mitra Razi; Juan Salazar; Angela S. Prudencio; David Ruiz; Luca Dondini; Pedro Martínez-Gómez. 2017. "Comparative Analysis of SSR Markers Developed in Exon, Intron, and Intergenic Regions and Distributed in Regions Controlling Fruit Quality Traits in Prunus Species: Genetic Diversity and Association Studies." Plant Molecular Biology Reporter 36, no. 1: 23-35.
Marker-assisted selection (MAS) in stone fruit (Prunus species) breeding is currently difficult to achieve due to the polygenic nature of the most relevant agronomic traits linked to fruit quality. Genotyping by sequencing (GBS), however, provides a large quantity of useful data suitable for fine mapping using Single Nucleotide Polymorphisms (SNPs) from a reference genome. In this study, GBS was used to genotype 272 seedlings of three F1 Japanese plum (P. salicina Lindl) progenies derived from crossing ‘98-99’ (as a common female parent) with ‘Angeleno’, ‘September King’ and ‘September Queen’ as male parents. Raw sequences were aligned to the Peach genome v1, and 42,909 filtered SNPs were obtained after sequence alignment. In addition, 153 seedlings from the ‘98-99’ × ‘Angeleno’ cross were used to develop a genetic map for each parent. A total of 981 SNPs were mapped (479 for ’98-99’ and 502 for ‘Angeleno’), covering a genetic distance of 688.8 cM and 647.03 cM, respectively. Fifty five seedlings from this progeny were phenotyped for different fruit quality traits including ripening time, fruit weight, fruit shape, chlorophyll index, skin color, flesh color, over color, firmness and soluble solids content in the years 2015 and 2016. Linkage-based QTL analysis allowed the identification of genomic regions significantly associated with ripening time (LG4 of both parents and both phenotyping years), fruit skin color (LG3 and LG4 of both parents and both years), chlorophyll degradation index (LG3 of both parents in 2015) and fruit weight (LG7 of both parents in 2016). These results represent a promising situation for GBS in the identification of SNP variants associated to fruit quality traits, potentially applicable in breeding programs through MAS, in a highly heterozygous crop species such as Japanese plum.
Juan A. Salazar; Igor Pacheco; Paulina Shinya; Patricio Zapata; Claudia Silva; Mallikarjuna Aradhya; Dianne Velasco; David Ruiz; Pedro Martínez-Gómez; Rodrigo Infante. Genotyping by Sequencing for SNP-Based Linkage Analysis and Identification of QTLs Linked to Fruit Quality Traits in Japanese Plum (Prunus salicina Lindl.). Frontiers in Plant Science 2017, 8, 1 .
AMA StyleJuan A. Salazar, Igor Pacheco, Paulina Shinya, Patricio Zapata, Claudia Silva, Mallikarjuna Aradhya, Dianne Velasco, David Ruiz, Pedro Martínez-Gómez, Rodrigo Infante. Genotyping by Sequencing for SNP-Based Linkage Analysis and Identification of QTLs Linked to Fruit Quality Traits in Japanese Plum (Prunus salicina Lindl.). Frontiers in Plant Science. 2017; 8 ():1.
Chicago/Turabian StyleJuan A. Salazar; Igor Pacheco; Paulina Shinya; Patricio Zapata; Claudia Silva; Mallikarjuna Aradhya; Dianne Velasco; David Ruiz; Pedro Martínez-Gómez; Rodrigo Infante. 2017. "Genotyping by Sequencing for SNP-Based Linkage Analysis and Identification of QTLs Linked to Fruit Quality Traits in Japanese Plum (Prunus salicina Lindl.)." Frontiers in Plant Science 8, no. : 1.
Juan Alfonso Salazar; David Ruiz; José Antonio Campoy; Stefano Tartarini; Luca Dondini; Pedro Martínez-Gómez. Inheritance of reproductive phenology traits and related QTL identification in apricot. Tree Genetics & Genomes 2016, 12, 1 .
AMA StyleJuan Alfonso Salazar, David Ruiz, José Antonio Campoy, Stefano Tartarini, Luca Dondini, Pedro Martínez-Gómez. Inheritance of reproductive phenology traits and related QTL identification in apricot. Tree Genetics & Genomes. 2016; 12 (4):1.
Chicago/Turabian StyleJuan Alfonso Salazar; David Ruiz; José Antonio Campoy; Stefano Tartarini; Luca Dondini; Pedro Martínez-Gómez. 2016. "Inheritance of reproductive phenology traits and related QTL identification in apricot." Tree Genetics & Genomes 12, no. 4: 1.
Juan Alfonso Salazar; Mohamed-Amine Batnini; Neila Trifi-Farah; David Ruiz; Pedro Martínez-Gómez; Manuel Rubio. Quantitative trait loci (QTLs) identification and the transmission of resistance to powdery mildew in apricot. Euphytica 2016, 211, 245 -254.
AMA StyleJuan Alfonso Salazar, Mohamed-Amine Batnini, Neila Trifi-Farah, David Ruiz, Pedro Martínez-Gómez, Manuel Rubio. Quantitative trait loci (QTLs) identification and the transmission of resistance to powdery mildew in apricot. Euphytica. 2016; 211 (2):245-254.
Chicago/Turabian StyleJuan Alfonso Salazar; Mohamed-Amine Batnini; Neila Trifi-Farah; David Ruiz; Pedro Martínez-Gómez; Manuel Rubio. 2016. "Quantitative trait loci (QTLs) identification and the transmission of resistance to powdery mildew in apricot." Euphytica 211, no. 2: 245-254.
High-throughput DNA and RNA sequencing technologies have resulted in the successful identification of Single nucleotide polymorphisms (SNPs). In order to develop a large SNP set for wide application in apricot (Prunus armeniaca L.), we carried out RNA high-throughput sequencing (RNA-Seq) in two apricot genotypes, “Rojo Pasión” and “Z506-7.” After trimming and cleaning, 70 % of RNA-Seq reads were aligned to the reference peach genome. Sequences uniquely mapped on the peach genome allowed for the discovery of 300 k SNP/INDEL variations, with a density of one SNP per 850 bp. Some 95 SNPs of the 99 tested were analyzed in a set of 37 apricot accessions using SNPlex™ genotyping technology. The results provide accurate values for nucleotide diversity in coding sequences in apricot. The combination of a highly efficient RNA-Seq approach and SNPlex™ high-throughput genotyping technology thus provide a powerful tool for apricot genetic analysis. SNP markers produced a total of 267 allelic combinations in the 37 apricot accessions assayed with a mean of 2.8 combinations per locus, an observed heterozygosity per marker ranging from 0.06 to 0.65, and a power of discrimination ranging from 0.12 to 0.66. In addition, SNP markers confirmed parentage and also determined relationships between the accessions in a manner consistent with their pedigree relationships.
Juan Salazar; Manuel Rubio; David Ruiz; Stefano Tartarini; Pedro Martínez-Gómez; Luca Dondini. SNP development for genetic diversity analysis in apricot. Tree Genetics & Genomes 2015, 11, 1 -9.
AMA StyleJuan Salazar, Manuel Rubio, David Ruiz, Stefano Tartarini, Pedro Martínez-Gómez, Luca Dondini. SNP development for genetic diversity analysis in apricot. Tree Genetics & Genomes. 2015; 11 (1):1-9.
Chicago/Turabian StyleJuan Salazar; Manuel Rubio; David Ruiz; Stefano Tartarini; Pedro Martínez-Gómez; Luca Dondini. 2015. "SNP development for genetic diversity analysis in apricot." Tree Genetics & Genomes 11, no. 1: 1-9.
J.A. Salazar; M. Rasouli; P. Martinez-Gomez. RANDOM AMPLIFIED MICROSATELLITE POLYMORPHISM (RAMP) APPLICATION IN PRUNUS CHARACTERIZATION AND MAPPING. Acta Horticulturae 2014, 61 -64.
AMA StyleJ.A. Salazar, M. Rasouli, P. Martinez-Gomez. RANDOM AMPLIFIED MICROSATELLITE POLYMORPHISM (RAMP) APPLICATION IN PRUNUS CHARACTERIZATION AND MAPPING. Acta Horticulturae. 2014; (1028):61-64.
Chicago/Turabian StyleJ.A. Salazar; M. Rasouli; P. Martinez-Gomez. 2014. "RANDOM AMPLIFIED MICROSATELLITE POLYMORPHISM (RAMP) APPLICATION IN PRUNUS CHARACTERIZATION AND MAPPING." Acta Horticulturae , no. 1028: 61-64.
Evaluation of agronomic traits in Prunus breeding programs is a tedious process because of the long juvenile period of trees, the influence of juvenility and the existence of climatic factors affecting the expression of the trait. For these reasons, marker-assisted selection (MAS) strategies are particularly useful in these cases. The objective of this work is the analysis of alternative low- cost strategies for development of molecular markers linked to agronomic traits in Prunus including the application of modified Bulked segregant analysis (BSA) using Simple sequence repeat (SSRs) markers and the application of Random amplified polymorphism microsatellite (RAMP) markers. First BSA results showed that two SSR loci were found to be tightly linked to flowering time in almond. On the other hand, RAMP analysis has been demonstrated to be a potentially valuable molecular marker for the study of genetic relationships in Prunus. Results showed the dominant nature of these markers with a great abundance and transferability although with a reduced polymorphism. In addition, RAMP application in F1 progenies showed its suitability for molecular characterization and mapping, and later Quantitative trait loci (QTL) or BSA analysis.
Juan Salazar; Mousa Rasouli; Reza Fatahi Moghaddam; Zabihollah Zamani; Ali Imani; Pedro Martínez-Gómez. Low-Cost Strategies for Development of Molecular Markers Linked to Agronomic Traits in Prunus. Agricultural Sciences 2014, 05, 430 -439.
AMA StyleJuan Salazar, Mousa Rasouli, Reza Fatahi Moghaddam, Zabihollah Zamani, Ali Imani, Pedro Martínez-Gómez. Low-Cost Strategies for Development of Molecular Markers Linked to Agronomic Traits in Prunus. Agricultural Sciences. 2014; 05 (05):430-439.
Chicago/Turabian StyleJuan Salazar; Mousa Rasouli; Reza Fatahi Moghaddam; Zabihollah Zamani; Ali Imani; Pedro Martínez-Gómez. 2014. "Low-Cost Strategies for Development of Molecular Markers Linked to Agronomic Traits in Prunus." Agricultural Sciences 05, no. 05: 430-439.
Trait loci analysis, a classic procedure in quantitative (quantitative trait loci, QTL) and qualitative (Mendelian trait loci, MTL) genetics, continues to be the most important approach in studies of gene labeling in Prunus species from the Rosaceae family. Since 2011, the number of published Prunus QTLs and MTLs has doubled. With increased genomic resources, such as whole genome sequences and high-density genotyping platforms, trait loci analysis can be more readily converted to markers that can be directly utilized in marker-assisted breeding. To provide this important resource to the community and to integrate it with other genomic, genetic, and breeding data, a global review of the QTLs and MTLs linked to agronomic traits in Prunus has been performed and the data made available in the Genome Database for Rosaceae. We describe detailed information on 760 main QTLs and MTLs linked to a total of 110 agronomic traits related to tree development, pest and disease resistance, flowering, ripening, and fruit and seed quality. Access to these trait loci enables the application of this information in the post-genomic era, characterized by the availability of a high-quality peach reference genome and new high-throughput DNA and RNA analysis technologies.
Juan Alfonso Salazar; David Ruiz; José Antonio Campoy; Raquel Sánchez-Pérez; Carlos H. Crisosto; Pedro J. Martínez-García; Anna Blenda; Sook Jung; Rrie Main; Pedro Martínez-Gómez; Manuel Rubio. Quantitative Trait Loci (QTL) and Mendelian Trait Loci (MTL) Analysis in Prunus: a Breeding Perspective and Beyond. Plant Molecular Biology Reporter 2013, 32, 1 -18.
AMA StyleJuan Alfonso Salazar, David Ruiz, José Antonio Campoy, Raquel Sánchez-Pérez, Carlos H. Crisosto, Pedro J. Martínez-García, Anna Blenda, Sook Jung, Rrie Main, Pedro Martínez-Gómez, Manuel Rubio. Quantitative Trait Loci (QTL) and Mendelian Trait Loci (MTL) Analysis in Prunus: a Breeding Perspective and Beyond. Plant Molecular Biology Reporter. 2013; 32 (1):1-18.
Chicago/Turabian StyleJuan Alfonso Salazar; David Ruiz; José Antonio Campoy; Raquel Sánchez-Pérez; Carlos H. Crisosto; Pedro J. Martínez-García; Anna Blenda; Sook Jung; Rrie Main; Pedro Martínez-Gómez; Manuel Rubio. 2013. "Quantitative Trait Loci (QTL) and Mendelian Trait Loci (MTL) Analysis in Prunus: a Breeding Perspective and Beyond." Plant Molecular Biology Reporter 32, no. 1: 1-18.
Twelve important pomological traits related to fruit quality were studied during 3 years in an F1 apricot progeny of 160 seedlings derived from a cross between the Spanish selection ‘Z701-1’ and the South African cultivar ‘Palsteyn’. Results indicated quantitative transmission of most of the fruit quality traits studied. In addition, a clear influence of the genetic background of parents was observed. In some seedlings, values outside the range of the parent were observed due to the influence of this genetic background. No correlations were found among most agronomic traits in apricot during the 3 years of the study. However, high correlations between years were described for most of the evaluated traits, and the environment had limited influence on the expression of the trait. A genetic map was developed using 41 apricot and peach SSR markers. The map obtained showed eight linkage groups (corresponding to the eight chromosomes) covering a total distance of 369.3 cM and an average distance between markers of 9 cM. Fifty-four QTLs associated with different traits were identified, including: blooming date (linkage groups G1, G4 and G7); ripening time (G4 and G6); fruit development (G4 and G6); fruit weight (G1 and G4); stone weight (G1 and G7); flesh color (G1 and G6); pH (G1, G2 and G4); malic acid (G1, G2 and G4); and soluble solids content (G4 and G5). We have highlighted several QTLs in G4 that explain the variability in various traits related to fruit quality such as blooming date, ripening time, and soluble solids content. In addition, we have also highlighted an important QTL on G2 that explains much of the variation in levels of acidity.
Juan Alfonso Salazar; David Ruiz; Jose Egea; Pedro Martínez-Gómez. Transmission of Fruit Quality Traits in Apricot (Prunus armeniaca L.) and Analysis of Linked Quantitative Trait Loci (QTLs) Using Simple Sequence Repeat (SSR) Markers. Plant Molecular Biology Reporter 2013, 31, 1506 -1517.
AMA StyleJuan Alfonso Salazar, David Ruiz, Jose Egea, Pedro Martínez-Gómez. Transmission of Fruit Quality Traits in Apricot (Prunus armeniaca L.) and Analysis of Linked Quantitative Trait Loci (QTLs) Using Simple Sequence Repeat (SSR) Markers. Plant Molecular Biology Reporter. 2013; 31 (6):1506-1517.
Chicago/Turabian StyleJuan Alfonso Salazar; David Ruiz; Jose Egea; Pedro Martínez-Gómez. 2013. "Transmission of Fruit Quality Traits in Apricot (Prunus armeniaca L.) and Analysis of Linked Quantitative Trait Loci (QTLs) Using Simple Sequence Repeat (SSR) Markers." Plant Molecular Biology Reporter 31, no. 6: 1506-1517.