BUSCADOR RECOLECTA

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., This research was funded by the Spanish Ministry Economy, Industry and Competitiveness (MINECO) grant numbers AGL2014-52063R and AGL2017-83358-R. This study has been supported by two research grants from MINECO co-financed with FEDER., Peer reviewed

2 .pdf Files ( extended abstract, 1 Pag.; 1 Poster copy from the original by Authors). Under Creative Commons License Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)., In order to investigate the responses of Prunus rootstocks to drought stress, an experiment was carried out as factorial completely randomized design, and the effects of three watering regimes were assayed under greenhouse conditions. Cuttings of four propagated rootstocks (Cadaman, Myrobolan 29C, GF677 and GN15) were grown in five liter pots containing soil and sand mixture during four months and under regular irrigation. Then, drought stress treatment (100%, 75% and 50% Field Capacity) was applied for 40 days. The morphological parameters such as height, leaf number and crown diameter were measured during the stress period., This work was partly funded by Spanish Ministry of Economy and Competitiveness
grant AGL2017-83358-R co-financed with FEDER funds and Government of
Aragón (Group A09_17R). ShN and MF were recipients of Iranian fellowships. NK
received a PhD fellowship awarded by the Government of Aragón., Peer reviewed

2 .pdf Files ( extended abstract, 1 Pag.; 1 Poster copy from the original by Authors). Under Creative Commons License Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)., In this experiment two micro-propagated Prunus rootstocks, GF 677 (Prunus amygdalus × P. persica), and Adesoto (P. insititia) were grown during 15 days then grafted with the peach cultivar ‘Catherina’. Plants were grown in 15 L containers with 1:1 sand-peat substrate for 10 days, divided randomly into four treatments and transferred to four temperate gradient greenhouses. Treatments were a combination of two CO2 levels, two temperature regimes and later submitted to deficit irrigation (daily watered with 80% of the evapotranspirated water). Dairy, soil water content was recorded by Watermark soil moisture sensors in control and water deficient plants. After 23 days, leaves and roots were separated, and fresh and dry weight, specific leaf area (SLA) and SPAD were measured in control and stressed plants. In both genotypes elevated CO2 and drought stress diminished shoot-to-root ratio and leaf DW diminished only under drought stress., This work was partly funded by Spanish Ministry of Economy and Competitiveness
grant AGL2017-83358-R co-financed with FEDER funds and Government of
Aragón (Group A09_17R). ShN and MF were recipients of Iranian fellowships. NK
received a PhD fellowship awarded by the Government of Aragón., Peer reviewed

18 Pags.- 6 Tabls.- 2 Figs. Copyright © 2020 Jiménez, Fattahi, Bedis, Nasrolahpour-moghadam, Irigoyen and
Gogorcena. This is an open-access article distributed under the terms of the Creative
Commons Attribution License (CC BY). The use, distribution or reproduction in other
forums is permitted, provided the original author(s) and the copyright owner(s) are
credited and that the original publication in this journal is cited, in accordance with
accepted academic practice. No use, distribution or reproduction is permitted which
does not comply with these terms., Environmental stress factors caused by climate change affect plant growth and crop production, and pose a growing threat to sustainable agriculture, especially for tree crops. In this context, we sought to investigate the responses to climate change of two Prunus rootstocks (GF677 and Adesoto) budded with Catherina peach cultivar. Plants were grown in 15 L pots in temperature gradient greenhouses for an 18 days acclimation period after which six treatments were applied: [CO2 levels (400 versus 700 µmol mol-1), temperature (ambient versus ambient + 4°C), and water availability (well irrigated versus drought)]. After 23 days, the effects of stress were evaluated as changes in physiological and biochemical traits, including expression of relevant genes. Stem water potential decreased under drought stress in plants grafted on GF677 and Adesoto rootstocks; however, elevated CO2 and temperature affected plant water content differently in both combinations. The photosynthetic rate of plants grafted on GF677 increased under high CO2, but decreased under high temperature and drought conditions. The photosynthetic rates of plants grafted onto Adesoto were only affected by drought treatment. Furthermore, in GF677–Catherina plants, elevated CO2 alleviated the effect of drought, whereas in those grafted onto Adesoto, the same condition produced acclimation in the rate. Stomatal conductance decreased under high CO2 and drought stress in both grafted rootstocks, and the combination of these conditions improved water-use efficiency. Changes in the sugar content in scion leaves and roots were significantly different under the stress conditions in both combinations. Meanwhile, the expression of most of the assessed genes was significantly affected by treatment. Regarding genotypes, GF677 rootstock showed more changes at the molecular and transcriptomic level than did Adesoto rootstock. A coordinated shift was found between the physiological status and the transcriptomic responses. This study revealed adaptive responses to climate change at the physiological, metabolic, and transcriptomic levels in two Prunus rootstocks budded with 'Catherina'. Overall, these results demonstrate the resilient capacity and plasticity of these contrasting genotypes, which can be further used to combat ongoing climate changes and support sustainable peach production., This work was partly funded by the Spanish Ministry of Economy and Competitiveness grants AGL2014-52063R, AGL2017-83358-R (MCIU/AEI/FEDER/UE); and the Government of Aragón with grants A44, A09_17R and La Caixa-GA-0007/2010 which were co-financed with FEDER funds. MF and SN-M were recipients of Iranian fellowships. SJ was supported by JAE-Doc-CSIC contract co-funded by ESF. KB received a Master's fellowship awarded by the CIHEAM-IAMZ., Peer reviewed

© 2020 by the authors., 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., This work was supported by the Spanish Ministry of Economy and Competitiveness grants AGL2014-52063R, AGL2017-83358-R (MCIU/AEI/FEDER/UE); and the Government of Aragón with grants A44, A09_17R co-financed with FEDER. FS was the recipient of a Master fellowship funded by the CIHEAM-IAMZ., Peer reviewed

The genetic diversity of many Spanish apple collections has been evaluated, but some areas from Central Spain have not been included. In the present work, a set of 41 accessions (33 diploids and 8 triploids) of 23 traditional apple cultivars collected in the region of Madrid and maintained at the IMIDRA collection was analysed with 13 simple sequence repeats (SSRs) to evaluate its diversity. Three reference cultivars (‘Fuji’, ‘Granny Smith’ and ‘Reineta Gris’) were included as reference to align the SSR profiles. The average number of alleles per locus was 7.66, which increased to 8.75 with triploids, and the number of rare alleles was 36. Moreover, the observed heterozygosity (Ho) was 0.74 and the expected heterozygosity (He) was 0.66, indicating disequilibrium. The probability to find two identical individuals was very low (PID = 3.60 × 10−12). After the cluster analysis, 29% of the accessions were found to have redundant profiles. Principal coordinate analysis, clustering and Bayesian model suggested the presence of four well-defined subgroups in the diploid of traditional apple. In clustering, diploid reference cultivars were nested with triploids independently from diploid traditional cultivars. Finally, after comparing profiles and names with other traditional Spanish cultivars, we conclude that the following studied collection shares the ubiquitous accessions from cultivar groups, such as «camuesas», «peros» and ‘Reineta’ but contains novel and uncharacterised cultivars with potential opportunities in breeding programmes and rural development: ‘Agridulce’, ‘Amarillo de El Paular’, ‘Hojancas’, ‘Maílla blanca’, ‘Pepita de melón’ and ‘Rabudas’. As these cultivars were collected in such a small area with environmental distinctiveness, they constitute a singular germplasm reservoir, which deserves to be preserved and more deeply studied., This work was supported by the IMIDRA (Madrid Institute for Research and Rural Development in Food and Agriculture), under the local project “Prospection, characterization, ethnobotanical documentation and conservation of traditional horticultural cultivars of the Community of Madrid” (ref. FP16-ETNOBOT) and a predoctoral contract funded by the INIA (National Institute for Agricultural and Food Research and Technology). Partial support was obtained from the Spanish State Research Agency (AEI) co-financed with the European Regional Development Fund (FEDER) (project AGL2017-83358-R to Y.G; AEI/FEDER, UE) and the Aragón Government (Group A09-20R)., Peer reviewed

17 Pags.- 3 Tabls.- 7 Figs. © Author(s) 2021. Published by Oxford University Press on behalf of American Society of Plant Biologists. This is an Open Access article distributed under the terms of the Creative Commons Attribution-NonCommercial-NoDerivs licence., The identification of functional elements encoded in plant genomes is necessary to understand gene regulation. Although much attention has been paid to model species like Arabidopsis (Arabidopsis thaliana), little is known about regulatory motifs in other plants. Here, we describe a bottom-up approach for de novo motif discovery using peach (Prunus persica) as an example. These predictions require pre-computed gene clusters grouped by their expression similarity. After optimizing the boundaries of proximal promoter regions, two motif discovery algorithms from RSAT::Plants (http://plants.rsat.eu) were tested (oligo and dyad analysis). Overall, 18 out of 45 co-expressed modules were enriched in motifs typical of well-known transcription factor (TF) families (bHLH, bZip, BZR, CAMTA, DOF, E2FE, AP2-ERF, Myb-like, NAC, TCP, and WRKY) and a few uncharacterized motifs. Our results indicate that small modules and promoter window of [–500 bp, +200 bp] relative to the transcription start site (TSS) maximize the number of motifs found and reduce low-complexity signals in peach. The distribution of discovered regulatory sites was unbalanced, as they accumulated around the TSS. This approach was benchmarked by testing two different expression-based clustering algorithms (network-based and hierarchical) and, as control, genes grouped for harboring ChIPseq peaks of the same Arabidopsis TF. The method was also verified on maize (Zea mays), a species with a large genome. In summary, this article presents a glimpse of the peach regulatory components at genome scale and provides a general protocol that can be applied to other species. A Docker software container is released to facilitate the reproduction of these analyses., This work was partly funded by the Spanish Ministry of
Economy and Competitiveness grants AGL2014-52063R,
AGL2017-83358-R (MCIU/AEI/FEDER/UE); and the
Government of Aragón with grants A44, A08_17R and
A09_17R, which were co-financed with FEDER funds. N.K. was funded by project AGL2014-52063R, two months of
Erasmus plus traineeship at Aix-Marseille University (AMU;
Lab.Technological Advances for Genomics and Clinics
(TAGC)) and at present a PhD contract awarded by the
Government of Aragón., Peer reviewed

52 Pags.- 10 Figs.- 11 Tabls. The definitive version is available at: https://www.sciencedirect.com/science/journal/00319422, Licorice (Glycyrrhiza glabra L.) is a medicinal plant species valued in many countries in Asia and Europe for its phytochemical characteristics. Licorice biodiversity is becoming threatened nowadays in Iran due to increasing demand and a drastic decline of its natural habitats. Therefore, licorice domestication would be necessary in the near future, and molecular breeding would help to introduce genotypes suitable for cultivation. The present study was carried out with 170 individual licorice plants sampled in the wild in 59 localizations in 21 provinces of Iran. The association of 436 polymorphic AFLP markers, produced by 15 primer combinations (EcoRI/MseI), with six phenotypic phytochemical traits was studied. The AMOVA analysis show gene diversity among and within localizations. The population structure analysis identified two main sub-populations with significant genetic variation. Significant associations were identified between three markers (E3/M40-4, E34/M4-12 and E12/M31-15) and glycyrrhizin concentration, and between four markers (E11/M34-12, E11/M34-15, E9/M7-29, and E9/M7-30) and phenolic compounds contents. Markers detected can be useful in the domestication of licorice as well as in breeding programs. Licorice sampled in four localizations (KBA1, KBA2, SKh2 and Fa1) were found to be superior in terms of glycyrrhizin and antioxidants content, and therefore they can be considered as elite genotypes which could be included in the domestication process., Authors acknowledge the support of the Agricultural Biotechnology Research Institute of Iran-Central Branch (ABRII-CB). This work was part of the research project on licorice 2-05-05-94109 in ABRII. Partial support was obtained from the Spanish State Research Agency (AEI) co-financed with the European Regional Development Fund (FEDER) (projects AGL2016-75226-R to J.A., and AGL2017-83358-R to Y.G; AEI/FEDER, EU), and the Aragón Government (Group A09-20R)., Peer reviewed

40 Pags.- 9 Tabls.- 8 Figs. The definitive version is available at: https://www.sciencedirect.com/science/journal/03044238, Environmentally-friendly management techniques such as arbuscular mycorrhizal fungi (AMF) strategies are urgently required to improve plant nutrition and overcome abiotic stress. In this study, we evaluated the influence of symbiotic AMF on four pistachio rootstocks subjected to drought (100 % as the control, and 80 %, 60 %, and 40 % of field capacity as the treatments) and salinity (0.91 as the control, and 7.57, 16.12, and 24.63 dS/m using NaCl as the treatments) stress for 60 days in two separate experiments. Under both drought and salinity stress conditions, the root and shoot dry weights of the pistachio rootstocks markedly increased in the AMF-inoculated plants (+M). The accumulation of minerals in the leaves and roots of (+M) plants was significantly higher than in the non-inoculated plants (-M). AMF improved the nutritional status (N, P, Mg2+, and Ca2+) of the genotypes under both stress conditions. Mycorrhizal association significantly decreased Na+ and Cl− concentrations in the leaves and roots of the pistachio rootstocks under salinity stress. In (+M) plants under drought stress, hydrogen peroxide (H2O2) and methylglyoxal (MG) concentrations in leaf and root tissues and malondialdehyde (MDA) in the roots, and under salinity stress, the H2O2 and MG concentrations in the leaves and MDA in both tissues were lower than those in the (-M) plants. The Sarakhs rootstock under salinity stress accumulated lower minerals (N, P, K+, and Ca2+) and more antioxidants than the other rootstocks, which could be due to its higher sensitivity to this stress. Both stresses reduced the chlorophyll concentration and increased the oxidant content and electrolyte leakage from the roots and leaves of the rootstocks. Sarakhs rootstock under drought stress and Badami-Riz–e-Zarand and UCB1 rootstocks under salinity stress behaved better in terms of mineral absorption. Thus, they were more tolerant of drought and salinity stress, respectively. Based on these findings, the association of mycorrhizal fungi and pistachio rootstocks is a sustainable strategy for increasing biomass, mineral, and Chl contents, and decreasing oxidant content, thereby enhancing the stress tolerance of plants., This work was funded by Iran National Science Foundation (INSF) and Shahrekord University, of Iran. Partial support was obtained from the Spanish State Research Agency (AEI) co-financed with the European Regional Development Fund (FEDER) (project AGL2017-83358-R to Y.G.; AEI/FEDER, UE), and the Aragón Government (Group A09-20R)., Peer reviewed

17 Pags.- 3 Figs.- 4 Tabls. © 2021 by the authors.
Licensee MDPI, Basel, Switzerland.
This article is an open access article
distributed under the terms and
conditions of the Creative Commons
Attribution (CC BY) license., The market demand together with the need for alternatives to withstand climate change led to the recovery of autochthonous grapevine varieties. Under climate change, the summer pruning of vineyards may lead to an increase of vegetative residuals of nutritional and medicinal interest. The objectives of our study were (1) to evaluate the nutritional properties of the leaves of three local Spanish grapevines (Tinto Velasco, TV, Pasera, PAS, and Ambrosina, AMB) when grown under climate change conditions, and (2) to test the potentiality of these grapevines as suitable candidates to be cultivated under climate change scenarios based on the quality of their must. Experimental assays were performed with fruit-bearing cuttings grown in temperature gradient greenhouses that simulate rising CO2 (700 μmol mol−1) and warming (ambient temperature +4 °C), either acting alone or in combination. TV and AMB were the most and the least affected by air temperature and CO2 concentration, respectively. The interaction of elevated CO2 with high temperature induced the accumulation of proteins and phenolic compounds in leaves of TV, thus enhancing their nutritional properties. In PAS, the negative effect of high temperature on protein contents was compensated for by elevated CO2. Warming was the most threatening scenario for maintaining the must quality in the three varieties, but elevated CO2 exerted a beneficial effect when acting alone and compensated for the negative effects of high temperatures. While TV may be a candidate to be cultivated in not very warm areas (higher altitudes or colder latitudes), PAS behaved as the most stable genotype under different environmental scenarios, making it the most versatile candidate for cultivation in areas affected by climate change., This research was funded by FUNDACIÓN UNIVERSITARIA DE NAVARRA (2018). Partial support was obtained from the SPANISH STATE RESEARCH AGENCY (AEI) cofinanced with the EUROPEAN REGIONAL DEVELOPMENT FUND (FEDER) (project AGL2017-83358-R to Y.G.; AEI/FEDER, UE), and the ARAGÓN GOVERNMENT (Group A09-20R)., Peer reviewed

17 pags.- 2 Figs.- 6 Tabls. © 2022 by the authors.
Licensee MDPI, Basel, Switzerland.
This article is an open access article
distributed under the terms and
conditions of the Creative Commons
Attribution (CC BY) license., One of the diseases that has the greatest negative effect on peach production is brown rot, produced by the fungus, Monilinia spp. The way to diminish this disease is the selection of genotypes with a high tolerance to Monilinia spp. while maintaining fruit quality. In this study, the tolerance to Monilinia laxa and agronomic and biochemical characteristics of forty-two hybrids derived from the ‘Andross’ × ‘Calante’ cross were studied under controlled conditions during two consecutive years, and compared with their parents. The assessment of tolerance to brown rot was estimated on inoculated fruit with M. laxa, recording the incidence of brown rot and colonization, lesion diameter and extent of colonization, to establish the severity of incidence and colonization. At harvest, physicochemical traits and antioxidant compounds (vitamin C, total phenolics, flavonoids and relative antioxidant capacity) were determined. We have found inverse relationships between fruit firmness, pH, titratable acidity and antioxidant contents with the disease symptoms in fruit. Our results confirm that the accumulation of antioxidants tends to reduce the lesion and colonization in inoculated fruit. Principal component analysis allowed the selection of two genotypes, AC-24 and AC-93, of ‘Calanda’-type peaches with a known standard quality, high antioxidant content and minimal susceptibility to brown rot., This research was supported by the Spanish Ministry of Economy and Competitiveness grants AGL2014-52063R, AGL2017-83358-R (MCIU/AEI/FEDER/UE) and the Government of Aragón with grants A44, A09_20R, co-financed with FEDER funds; and the CSIC grant 2020AEP119. J.M. was the recipient of a pre-doctoral contract awarded by the Government of Aragon (2020–2024)., Peer reviewed

7 Pags.- 2 Figs. © The Author(s) 2022. Published by Oxford University Press on behalf of Nucleic Acids Research.
This is an Open Access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/),, RSAT (Regulatory Sequence Analysis Tools) enables the detection and the analysis of cis-regulatory elements in genomic sequences. This software suite performs (i) de novo motif discovery (including from genome-wide datasets like ChIP-seq/ATAC-seq) (ii) genomic sequences scanning with known motifs, (iii) motif analysis (quality assessment, comparisons and clustering), (iv) analysis of regulatory variations and (v) comparative genomics. RSAT comprises 50 tools. Six public Web servers (including a teaching server) are offered to meet the needs of different biological communities. RSAT philosophy and originality are: (i) a multi-modal access depending on the user needs, through web forms, command-line for local installation and programmatic web services, (ii) a support for virtually any genome (animals, bacteria, plants, totalizing over 10 000 genomes directly accessible). Since the 2018 NAR Web Software Issue, we have developed a large REST API, extended the support for additional genomes and external motif collections, enhanced some tools and Web forms, and developed a novel tool that builds or refine gene regulatory networks using motif scanning (network-interactions). The RSAT website provides extensive documentation, tutorials and published protocols. RSAT code is under open-source license and now hosted in GitHub. RSAT is available at http://www.rsat.eu/., Institut Universitaire de France (to M.T.C., N.T.T.N.); ANR [ANR-14-CE11-0006-01 to M.T.C., N.T.T.N.]; ITMO Cancer [20CM114-00 to D.T., W.S.G.]; CONACYT [11311 to A.M.R., M.P.G.]; Universidad Nacional Autónoma de México PAPIIT (UNAM) [IA203021]; Spanish State Research Agency, EUROPEAN REGIONAL DEVELOPMENT FUND (FEDER) [AGL2017-83358-R to N.K.; AEI/FEDER, UE]; Gobierno de Aragón [A08_17R, A09_20R, Phd Contract to N.K.]; PRIMA [PCI2019-103526 to B.C.M.; Programación Conjunta Internacional, Programa Estatal de l+D+i Orientada a los Retos de la Sociedad]; Erasmus+ (to N.K.); Norwegian Research Council [288404 to J.A.C.M.]; Institut Français de Bioinformatique (IFB) [ANR-11-INBS-0013]; SEP-CONACYT-ECOS-ANUIES [291235 to A.M.R., M.T.C. and D.T.]. Funding for open access charge: Institut Universitaire de France., Peer reviewed

13 Pags.- 8 Figs.- 1 Tabl. Data Availability: Data will be made available on request. © 2023 The Authors. Published by Elsevier B.V. This is an open access article under the CC BY license., Iron (Fe) is an essential plant micronutrient, being a major limiting growth factor in calcareous soils. To increase Fe uptake, plants induce lateral roots growth, the expression of a Fe(III)-chelate reductase (FCR), a Fe(II)-transporter and a H+-ATPase and the secretion of flavins. Furthermore, auxin hormone family is involved in the Fe-deficiency responses but the action mechanism remains elusive. In this work, we evaluated the effect of the auxin-precursor indole-3-acetaldoxime (IAOx) on hydroponically grown Medicago truncatula plants under different Fe conditions.

Upon 4-days of Fe starvation, the pH of the nutrient solution decreased, while both the FCR activity and the presence of flavins increased. Exogenous IAOx increased lateral roots growth contributing to superroot phenotype, decreased chlorosis, and delayed up to 3-days the pH-decrease, the FCR-activity increase, and the presence of flavins, compared to Fe-deficient plants. Gene expression levels were in concordance with the physiological responses., This work was supported by the Spanish Research Agency [grant AGL2017-83358-R funded by MCIN/AEI/10.13039/501100011033 and by “ERDF A way of making Europe”] and the Government of Aragón [grant A09_23R], co-financed with FEDER funds; and the CSIC [grant 2020AEP119] to Y.G. This research was partially supported by [grants AGL2017-52396-P funded from MINECO (co-financed with FEDER funds) and PID-2020-1177 03GB-I00 from the Public University of Navarre] to J.F.M. J.M., M.U. and J.B. were the recipients of pre-doctoral contracts awarded by the Government of Aragon, Government of Navarre, and Public University of Navarre, Spain, respectively. A.R. was hired [grants AGL2017-83358-R and 2020AEP119]., Peer reviewed

8 Pags.- 2 Figs.- 2 Tabls. Article published from a contribution by the Authors to X International Peach Symposium (Naoussa, Grecia. 30 mayo-3 junio, 2022), Double digest RAD-seq (ddRAD-seq) is a flexible and cost-effective strategy that
has emerged as one of the most popular genotyping approaches in plants. It relies on
combining two restriction enzymes for library preparation followed by PCR
amplification of the template molecules. However, PCR introduces sequence duplicates
and may erroneously inflate the confidence of genotype calls at a particular site.
Although the process of variant calling is relatively straightforward, it is timeconsuming, involving multiple steps. Thus, removing any unneeded steps would reduce
the computation time and simplify the analysis. Hence, the primary aim of this study is
to evaluate the necessity of PCR duplicates and their effects on SNP and indel calling in
peach. On the other hand, the accuracy of genetic variant identification in plants is a
crucial step toward understanding phenotypical traits and monitoring breeding
programs. However, false positive calls are a common issue that could hamper the
detection of relevant variants. Thereby, a good combination of computational tools for
alignment and variant calling is crucial to tackle these artifacts. In response to this
challenge, three variant callers (BCFtools-mpileup, Freebayes and GATKHaplotypeCaller) were combined on top of the BWA-mem read mapper. Variants
derived from the intersection of these callers are selected as a high confidence set and
flagged for subsequent analysis. The pipeline is documented and available as a set of
Makefiles that can be adapted to any species. This work provides useful guidelines and
a reproducible workflow for variant detection using ddRAD-seq data., This work was funded by the Spanish Ministry of Economy and the Government of
Aragó n with grants AGL2014-52063-R, AGL2017-83358-R, 2020AEP119 y A09_20R which
were co-financed with FEDER funds. N.K. was funded with a pre-doctoral contract awarded
by the Government of Aragón., Peer reviewed

8 Pags.- 2 Figs.- 1 Tabl. Article published from a contribution by the Authors to X International Peach Symposium (Naoussa, Grecia. 30 mayo-3 junio, 2022), Unraveling the mechanisms that regulate gene expression is a complex challenge
in biology. A key step to decipher the regulatory machinery is to identify cis-regulatory
elements (CREs) buried in non-coding DNA sequences. CREs are short stretches of DNA
that serve as binding sites for transcription factors (TFs) and are frequently
summarized as sequence motifs or logos. Although much attention has been paid to
model species like Arabidopsis thaliana, little is known about regulatory motifs in other
ones. Here, we describe a bottom-up approach for de novo motif discovery using peach
as an example. These predictions require pre-computed gene clusters grouped by their
expression similarity. Proximal promoter regions were defined as four different
intervals: Up 1: [-1,500 bp, +200 bp], Up 2: [-500 bp, +200 bp], Up 3: [-500 bp, 0 bp] and
Up 4 [0 bp, +200 bp]. Two algorithms from RSAT::Plants (http://plants.rsat.eu) were
tested (oligo and dyad analysis). Overall, 18 out of 45 co-expressed modules were
enriched in motifs typical of well-known TF families (bHLH, bZip, BZR, CAMTA, DOF,
E2FE, AP2-ERF, Myb-like, NAC, TCP, and WRKY) and a few uncharacterized motifs. Our
results indicate that small module size and promoter window of [-500 bp, +200 bp]
relative to the transcription start site (TSS) maximize the number of motifs found and
reduce low-complexity signals in peach. This work yields a comprehensive collection of
Prunus persica motifs without prior knowledge and provides a pipeline that can be
applied to other species., This work was partly funded by the Spanish Ministry of Economy and Competitiveness
grants AGL2014-52063R, AGL2017-83358-R (MCIU/AEI/FEDER/UE); and the Government
of Aragón with grants A44, A08_17R and A09_17R, which were co-financed with FEDER funds.
N.K. was funded by project AGL2014-52063R, two months of Erasmus plus traineeship at AixMarseille University (AMU; Lab. Technological Advances for Genomics and Clinics (TAGC)) and
at present a PhD contract awarded by the Government of Aragón., Peer reviewed

8 Pags.- 2 Figs.- 1 Tabl. Article published from a contribution by the Authors to X International Peach Symposium (Naoussa, Grecia. 30 mayo-3 junio, 2022), The advance of next generation sequencing (NGS) technologies allows the
implementation of high-throughput genotyping at a reasonable cost. This open the
possibility to learn more about phylogenetic relationships, genetic variability, and the
development of new genetic markers for breeding purposes. In this work a previous
developed ddRAD-seq platform was applied for the genotyping of two peach collections
curated at the EEA San Pedro (237 genotypes) and the EE Aula Dei (89 genotypes). Here
we present a joint analysis of a total of 798×106 of paired-end (2×250 bp) reads
belonging to 326 genotypes (2,45M reads genotype-1). A total of 564,382 SNPs were
discovered and a reduced data set composed of 10,576 SNP (MAF >1% and missing data
<10%) was used in a combination of analyses (principal component analysis,
population structure and phylogeny). The results showed that the ancestral
germplasms differ largely from modern peach cultivars. In addition, genetic
relationships between American landraces (North American and Bolivian), American
ferals (Argentinian) and European landraces (Spanish and Italian) were revealed
suggesting a common origin which probably reflect the introduction of germplasm by
the Spaniards during the colonization period. These results with some outstanding
traits of ancestral genotypes (fruit quality, high yield/vigour, pathogen resistance,
thermal requirements, etc.) encourage the usage of this germplasm on breeding
programs for the development of new varieties with agricultural impact., This work was supported by National Agency of Scientific and Technological Promotion
(ANPCyT) from Argentina (grant PICT2014-0343) and National Institute for Agriculture
Technology (INTA) from Argentina (grant 2019-PE-E6-I114-001) and the Spanish State
Research Agency (grants AGL2014-52063-R, AGL2017-83358-R, AEI/FEDER, UE), Aragon
Government (Group A09-20R), co-found with European Regional Development Fund and CSIC
2020AEP119. Maximiliano Martı́n Aballay has an INTA-CONICET PhD fellowship. Najla Ksouri
has a predoctoral contract funded by Aragon Government (2017-2022)., Peer reviewed

69 Pags.- 15 Figs.- 11 Tabls. IAMZ-CIHEAM Thesis Master ("Master in Plant Breeding") realised at Laboratory of Genomics, Genetics and
Breeding of Fruit and Grapevine and the Laboratory of Computational & Structural Biology (EEAD - CSIC).

© The author. Under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International., [EN] The increase of genomic data in plants has become a revolution for plant biologists.
Nowadays, transcript expression can be investigated thanks to new sequencing
technologies, such as RNA-Seq. One of the objectives of these approaches is de novo
motif discovery in upstream sequences of co-expressed genes. However, a bottleneck of
these methods is to determine the appropriate length of the upstream region to be
sampled, something that has only been addressed so far in two plant species, rice and
Arabidopsis thaliana. Here, three computational approaches are presented with the aim
of delimiting proximal promoter regions at a genomic level, tested in three plant
species: Prunus persica, A. thaliana and Brachypodium distachyon. Two of the
approaches relied on nucleotide conservation, one aligning sequences of related species
(Prunus spp.), and the other by computing nucleotide polymorphism density. Finally,
the third approach was based on the frequency of detected putative regulatory
DNA-motifs. The comparative genomics approach suggested a limit of -576 nt or
-434 nt upstream of transcription start sites for Prunus persica, depending on the source
of the genome. The polymorphism density approach yielded proximal limits of -510 nt,
-520 nt and -450 nt for P. persica, A. thaliana and B. distachyon, respectively. Finally,
the frequency of predicted DNA-motifs provided alternative proximal promoter for the
three species, and the differences were discussed. A validation of these limits was
carried out by calculating the percentage of experimentally determined regulatory
motifs in plants inside the proposed ranges. We report that a -500 nt upstream window
contains approximately 80% of the motifs curated in TRANSFAC. Therefore, plant
proximal promoter regions were delimited with a length of -500 nt, with differences of -
50/-100 nt between species and/or methodologies. The availability of the developed
code will enable the scientific community to calculate the optimal length of proximal
promoter regions for any plant species., [ES] El aumento de datos genómicos en plantas se ha vuelto una revolución para los biólogos
de plantas. Actualmente, la expresión de tránscritos puede ser investigada gracias a las
nuevas tecnologías de secuenciación, como RNA-Seq. Uno de los objetivos principales
de estas aproximaciones es la identificación de novo de motivos de ADN en secuencias
aguas arriba de genes co-expresados. Sin embargo, un cuello de botella de estas
metodologías es determinar la longitud óptima de la región aguas arriba a ser estudiada,
cuestión que hasta ahora solo ha sido abordada en dos especies de plantas, arroz y
Arabidopsis thaliana. En esta tesis, tres aproximaciones computacionales son
presentadas con el objetivo de delimitar la región promotora proximal a nivel genómico,
probadas en tres especies de plantas: Prunus persica, A. thaliana y Brachypodium
distachyon. Dos de las aproximaciones se han basado en la conservación de nucleótidos,
una alineando secuencias de especies cercanas (Prunus spp.), y la otra calculando la
densidad de polimorfismos por nucleótido. Finalmente, la tercera aproximación se basó
en la frecuencia de motivos de ADN regulatorios putativos detectados. La aproximación
de genómica comparativa proporcionó un límite de -576 nt o -434 n aguas arribas del
sitio de inicio de transcripción t para Prunus persica, según el origen del genoma. La
aproximación de densidad de polimorfismo resultó en límites proximales de -510 nt,
-520 nt y -450 nt para P. persica, A. thaliana y B. distachyon, respectivamente.
Finalmente, la frecuencia de motivos de ADN predichos devolvió límites alternativos
del promotor proximal para las tres especies, y las diferencias fueron discutidas. Una
validación de estos límites fue llevada a cabo calculando el porcentaje de motivos
regulatorios de plantas identificados experimentalmente dentro de los rangos
propuestos. Reportamos que una ventana de -500 nt aguas arriba contiene
aproximadamente el 80% de los motivos depurados en TRANSFAC. Así, las regiones
promotoras proximales en plantas fueron delimitadas con una longitud de -500 nt, con
diferencias de -50/-100 nt entre especies y/o metodologías. La libre disposición del
código diseñado permitirá a la comunidad científica calcular la longitud óptima de la
región promotora proximal en cualquier especie de planta., [FR] L’augmentation des données génomiques des plantes s’est convertie en une révolution
pour les biologistes. Actuellement, la régulation transcriptionnelle est largement étudiée
grâce aux avancées des technologies à haut débit tel que le séquençage de l’ARN
(RNA-Seq). L´un des principaux objectifs de ces études est la découverte « de novo »
de motifs régulateurs en amont des gènes. Néanmoins, le goulet d’étranglement de ces
méthodes réside dans la longueur de la région en amont du gène, surtout que, seulement
deux espèces ont été étudiées en se concentrant sur la région proximale du promoteur, le
riz et Arabidopsis thaliana. Dans le présent travail, trois approches computationnelles
ont été dévoilées afin de délimiter une plage du promoteur proximal à un niveau
génomique et à partir de l’initiation du gène, testés chez trois espèces de plantes:
Prunus persica, Arabidopsis thaliana et Brachypodium distachyon. Deux parmi ces
trois approches reposent sur la conservation des nucléotides ; la première en alignant
des séquences d’espèces apparentées (appliquée sur Prunus persica) et l’autre basée sur
la densité du polymorphisme. La troisième est basée sur la fréquence des putatifs motifs
d’ADN détectés. La démarche de la génomique comparative a suggéré une limite de -
570 nt et -434 nt en amont du site d’initiation de la transcription pour Prunus persica,
selon l’origine du genome. L’approche de la densité de polymorphisme a proportionné
des limites proximales de -510 nt, -520 nt et -450 nt pour P. persica, A. thaliana et B.
distachyon, respectivement. Enfin, la fréquence des motifs d’ADN prédits a fourni un
promoteur proximal alternatif pour les trois espèces, et les différences discutées. Une
validation de ces limites a été donc effectuée en calculant le pourcentage de motifs
expérimentalement détectés dans ces intervalles de limites préalablement citées. On
mentionne qu’un intervalle approximatif de -500 nt contient environ 80% des motifs
sélectionnés en TRANSFAC. Par conséquent, les régions promotrices des plantes ont
été delimitées avec une longueur de -500 nt, avec des différences de -50 / -100 nt entre
les espèces et/ou les méthodologies. La disponibilité de notre code développé permettra
á la communités scientifique de calculer la longueur optimale des régions promotrices
proximales pour toute espèce de plante., Work supported by project AGL2017-83358-R., No

1 Pag. con resumen ampliado., El desarrollo de cultivares con rasgos superiores es la principal meta de los programas de mejora genética de melocotonero. El presente estudio se ha centrado en elucidar las bases genéticas de diversos caracteres agronómicos y otros relacionados con la calidad del fruto sobre un panel de 90 accesiones de Prunus persica genotipadas mediante ddRAD., El trabajo fue financiado por la Agencia Española de Investigación, Gobierno de Aragón y CSIC (MCIN/AEI/ 10.13039/501100011033, AGL2017-83358-R, A09_19R, A09_23R, A10_23R; 2020AEPI119) cofinanciado con FEDER. NK disfrutó de un contrato predoctoral del Gobierno de Aragón., Peer reviewed

The ornithine–urea cycle (urea cycle) makes a signifcant contribution to the metabolic responses of lower photosynthetic eukaryotes to episodes of high nitrogen availability. In this study, we compared the role of the plant urea
cycle and its relationships to polyamine metabolism in ammonium-fed and nitrate-fed Medicago truncatula plants.
High ammonium resulted in the accumulation of ammonium and pathway intermediates, particularly glutamine, arginine, ornithine, and putrescine. Arginine decarboxylase activity was decreased in roots, suggesting that the ornithine
decarboxylase-dependent production of putrescine was important in situations of ammonium stress. The activity
of copper amine oxidase, which releases ammonium from putrescine, was signifcantly decreased in both shoots
and roots. In addition, physiological concentrations of ammonium inhibited copper amine oxidase activity in in vitro
assays, supporting the conclusion that high ammonium accumulation favors putrescine synthesis. Moreover, early
supplementation of plants with putrescine avoided ammonium toxicity. The levels of transcripts encoding urea-cyclerelated proteins were increased and transcripts involved in polyamine catabolism were decreased under high ammonium concentrations. We conclude that the urea cycle and associated polyamine metabolism function as important
protective mechanisms limiting ammonium toxicity in M. truncatula. These fndings demonstrate the relevance of the
urea cycle to polyamine metabolism in higher plants., This work was supported by the grants from the Spanish Government
AGL2014-52396-P (MICINN) and AGL2017-86293-P (MINECO/
FEDER) to JFM, and the Basque Government, Spain, IT-1018-16
(UPV/EHU-GV) to RE. MU is a recipient of a pre-doctoral fellowship from the Government of Navarre, Spain. JB and PLG have received pre-doctoral fellowships from the Public University of Navarre,
Spain. PT has received funding from the Italian Ministry of Education,
University and Research (Grant to Department of Science, University
‘Roma Tre’-‘Dipartimenti di Eccellenza’, ARTICOLO 1, COMMI 314–
337. LEGGE 423 232/2016; PRIN 2017—CUP F84I19000730005).
Partial support was obtained from the Spanish State Research Agency
AGL2017-83358-R (AEI/FEDER) and the Government of Aragon,
Spain, Group A09-20R to YG. Open Access funding was provided by the
Public University of Navarra.

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.

A sustainable approach to control the incidence of brown rot in pre- and post-harvest management is to select genotypes with high contents of antioxidant compounds and tolerance to Monilinia laxa (Aderh. and Ruhland) Honey. In this study, 68 progenies of the ‘Babygold 9’ × ‘Crown Princess’ population from the EEAD-CSIC breeding program were screened under controlled conditions for a period of 3 years (2013–2015). Susceptibility to brown rot was evaluated after inoculating 20 healthy fruits per genotype with M. laxa. Brown rot incidence, lesion diameter, and colonization extent, as well as the severities of these issues, were calculated after 5 days of incubation. Physicochemical traits, such as fruit firmness and soluble solids content, were also recorded before and after storage. Titratable acidity, pH, and antioxidant composition were measured at harvest. Significant differences were found for pathogenic traits, as well as for contents of vitamin C, total phenolics, flavonoids, and anthocyanins, within genotypes in this population. Negative correlations were also found between the content of phytochemical compounds (such as anthocyanins and total phenolics), as well as disease incidence and severity. Differences in susceptibility to brown rot confirm the genetic variability available in these progeny. This allowed the selection of six genotypes highly resistant to brown rot of M. laxa, with high organoleptic properties and high phenol content, to be introduced in our peach breeding program.

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.

The "Pero de Cehegín"is an ancient local variety of apple grown in Murcia (Spain). In this study, microsatellites markers showed evidence of a unique profile that has never been reported before in other Spanish apple germplasm collections. Five "Pero de Cehegín"clones were evaluated and compared with two commercial apple varieties, "Fuji"and "Golden Delicious", to assess its marketing potential. For this, the physical (weight, height, and width of the fruit, moisture content, firmness, and color of the fruit, among others), and chemical (total soluble solids, total acidity, and maturity index) properties of the fruits were evaluated. In addition, the content of bioactive compounds such as total polyphenol content, total antioxidant activity using the ABTS+, DPPH, and FRAP methods, and the sugar profile were analyzed, and their sensory profile was also evaluated. Physico-chemical differences were found within the "Pero de Cehegín"clones and between the commercial varieties. "Pero de Cehegín"had a high firmness, high total soluble solids, very low total acidity, high FRAP antioxidant capacity, and more sucrose content in comparison with "Fuji"and "Golden Delicious". These distinctive characteristics and the good appearance of the fruit make this variety a marketable product that will increase the offering of traditional, local, but underutilized fruit varieties.

One of the diseases that has the greatest negative effect on peach production is brown rot, produced by the fungus, Monilinia spp. The way to diminish this disease is the selection of genotypes with a high tolerance to Monilinia spp. while maintaining fruit quality. In this study, the tolerance to Monilinia laxa and agronomic and biochemical characteristics of forty-two hybrids derived from the ‘Andross’ × ‘Calante’ cross were studied under controlled conditions during two consecutive years, and compared with their parents. The assessment of tolerance to brown rot was estimated on inoculated fruit with M. laxa, recording the incidence of brown rot and colonization, lesion diameter and extent of colonization, to establish the severity of incidence and colonization. At harvest, physicochemical traits and antioxidant compounds (vitamin C, total phenolics, flavonoids and relative antioxidant capacity) were determined. We have found inverse relationships between fruit firmness, pH, titratable acidity and antioxidant contents with the disease symptoms in fruit. Our results confirm that the accumulation of antioxidants tends to reduce the lesion and colonization in inoculated fruit. Principal component analysis allowed the selection of two genotypes, AC-24 and AC-93, of ‘Calanda’-type peaches with a known standard quality, high antioxidant content and minimal susceptibility to brown rot.