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Castanera R, de Tomás C, Ruggieri V, Vicient C, Eduardo I, Aranzana MJ, Arús P, Casacuberta JM. A phased genome of the highly heterozygous 'Texas' almond uncovers patterns of allele-specific expression linked to heterozygous structural variants. HORTICULTURE RESEARCH 2024; 11:uhae106. [PMID: 38883330 PMCID: PMC11179849 DOI: 10.1093/hr/uhae106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Accepted: 04/01/2024] [Indexed: 06/18/2024]
Abstract
The vast majority of traditional almond varieties are self-incompatible, and the level of variability of the species is very high, resulting in a high-heterozygosity genome. Therefore, information on the different haplotypes is particularly relevant to understand the genetic basis of trait variability in this species. However, although reference genomes for several almond varieties exist, none of them is phased and has genome information at the haplotype level. Here, we present a phased assembly of genome of the almond cv. Texas. This new assembly has 13% more assembled sequence than the previous version of the Texas genome and has an increased contiguity, in particular in repetitive regions such as the centromeres. Our analysis shows that the 'Texas' genome has a high degree of heterozygosity, both at SNPs, short indels, and structural variants level. Many of the SVs are the result of heterozygous transposable element insertions, and in many cases, they also contain genic sequences. In addition to the direct consequences of this genic variability on the presence/absence of genes, our results show that variants located close to genes are often associated with allele-specific gene expression, which highlights the importance of heterozygous SVs in almond.
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Affiliation(s)
- Raúl Castanera
- Centre for Research in Agricultural Genomics, CRAG (CSIC-IRTA-UAB-UB), Campus UAB, 08193, Cerdanyola del Vallès, Barcelona, Spain
| | - Carlos de Tomás
- Centre for Research in Agricultural Genomics, CRAG (CSIC-IRTA-UAB-UB), Campus UAB, 08193, Cerdanyola del Vallès, Barcelona, Spain
| | | | - Carlos Vicient
- Centre for Research in Agricultural Genomics, CRAG (CSIC-IRTA-UAB-UB), Campus UAB, 08193, Cerdanyola del Vallès, Barcelona, Spain
| | - Iban Eduardo
- Centre for Research in Agricultural Genomics, CRAG (CSIC-IRTA-UAB-UB), Campus UAB, 08193, Cerdanyola del Vallès, Barcelona, Spain
- IRTA (Institut de Recerca i Tecnologia Agroalimentàries), 08140, Caldes de Montbui, Barcelona, Spain
| | - Maria José Aranzana
- Centre for Research in Agricultural Genomics, CRAG (CSIC-IRTA-UAB-UB), Campus UAB, 08193, Cerdanyola del Vallès, Barcelona, Spain
- IRTA (Institut de Recerca i Tecnologia Agroalimentàries), 08140, Caldes de Montbui, Barcelona, Spain
| | - Pere Arús
- Centre for Research in Agricultural Genomics, CRAG (CSIC-IRTA-UAB-UB), Campus UAB, 08193, Cerdanyola del Vallès, Barcelona, Spain
- IRTA (Institut de Recerca i Tecnologia Agroalimentàries), 08140, Caldes de Montbui, Barcelona, Spain
| | - Josep M Casacuberta
- Centre for Research in Agricultural Genomics, CRAG (CSIC-IRTA-UAB-UB), Campus UAB, 08193, Cerdanyola del Vallès, Barcelona, Spain
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Ppe.CR.1 DNA test for predicting chilling requirement in peach. Sci Rep 2023; 13:987. [PMID: 36653395 PMCID: PMC9849201 DOI: 10.1038/s41598-023-27475-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Accepted: 01/03/2023] [Indexed: 01/19/2023] Open
Abstract
Chilling requirement (CR) is an important agronomic trait controlling the floral bud break for proper flowering in peach. Even though it has been widely researched and several peach CR quantitative trait loci (QTLs) have been identified, no diagnostic DNA tests validated in the U.S. peach breeding germplasm are available for this trait. Breeders and growers need a simple DNA test to predict the CR of peach cultivars for their particular environment. Therefore, we developed a quick and reliable Kompetitive Allele Specific PCR (KASP) DNA test using haplotype information from 9K IPSC genotype data of the U.S. peach germplasm integrating four CR-associated SNP markers from the previously reported CR QTL region on linkage group 1. Four KASP assays (Ppe.CR.1-1 to -4) were developed and validated on 77 peach cultivars, and nine accessions from two F2 populations, with 96 and 74% accuracy in determining expected CR genotype (compared to SNP array) and predicting phenotype, respectively. Furthermore, the Ppe.CR.1 showed 80% accuracy in predicting the precise CR phenotype in the Clemson University peach breeding material. Only one Ppe.CR.1 KASP assay (Ppe.CR.1-1) is needed to distinguish between haplotypes with CR lower and higher than 800 chilling hours, and two Ppe.CR.1 assays (Pp.CR.1-1 and -4), are capable of distinguishing low, moderate, and high CR alleles. Coupled with the crude DNA extraction, the Ppe.CR.1 DNA test provides a low-cost option for breeders and growers to predict CR in peach material with more than 70% accuracy.
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Duval H, Coindre E, Ramos-Onsins SE, Alexiou KG, Rubio-Cabetas MJ, Martínez-García PJ, Wirthensohn M, Dhingra A, Samarina A, Arús P. Development and Evaluation of an Axiom TM 60K SNP Array for Almond ( Prunus dulcis). PLANTS (BASEL, SWITZERLAND) 2023; 12:242. [PMID: 36678957 PMCID: PMC9866729 DOI: 10.3390/plants12020242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Revised: 12/24/2022] [Accepted: 12/29/2022] [Indexed: 06/17/2023]
Abstract
A high-density single nucleotide polymorphism (SNP) array is essential to enable faster progress in plant breeding for new cultivar development. In this regard, we have developed an Axiom 60K almond SNP array by resequencing 81 almond accessions. For the validation of the array, a set of 210 accessions were genotyped and 82.8% of the SNPs were classified in the best recommended SNPs. The rate of missing data was between 0.4% and 2.7% for the almond accessions and less than 15.5% for the few peach and wild accessions, suggesting that this array can be used for peach and interspecific peach × almond genetic studies. The values of the two SNPs linked to the RMja (nematode resistance) and SK (bitterness) genes were consistent. We also genotyped 49 hybrids from an almond F2 progeny and could build a genetic map with a set of 1159 SNPs. Error rates, less than 1%, were evaluated by comparing replicates and by detection of departures from Mendelian inheritance in the F2 progeny. This almond array is commercially available and should be a cost-effective genotyping tool useful in the search for new genes and quantitative traits loci (QTL) involved in the control of agronomic traits.
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Affiliation(s)
- Henri Duval
- Unité de Génétique et Amélioration des Fruits et Légumes (GAFL), INRAE (French National Research Institute for Agriculture, Food and Environment), 84143 Montfavet, France
| | - Eva Coindre
- Unité de Génétique et Amélioration des Fruits et Légumes (GAFL), INRAE (French National Research Institute for Agriculture, Food and Environment), 84143 Montfavet, France
| | - Sebastian E. Ramos-Onsins
- Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Carrer de la Vall Moronta, Edifici CRAG, Campus UAB, Cerdanyola del Valles, 08193 Barcelona, Spain
| | - Konstantinos G. Alexiou
- Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Carrer de la Vall Moronta, Edifici CRAG, Campus UAB, Cerdanyola del Valles, 08193 Barcelona, Spain
- IRTA (Institute of Agrifood Research and Technology), Campus UAB, Edifici CRAG, Cerdanyola del Valles (Bellaterra), 08193 Barcelona, Spain
| | - Maria J. Rubio-Cabetas
- CITA (Agrifood Research and Technology Centre of Aragon), Department of Plant Science, Avda. Montañana 930, 50059 Zaragoza, Spain
| | - Pedro J. Martínez-García
- CEBAS (Centro de Edafología y Biología Aplicada del Segura), CSIC, Department of Plant Breeding, Campus Universitario de Espinardo, 30100 Espinardo, Spain
| | - Michelle Wirthensohn
- Waite Research Institute, University of Adelaide, PMB 1 Glen, Osmond, SA 5064, Australia
| | - Amit Dhingra
- Department of Horticulture, Washington State University, Pullman, WA 99164-6414, USA
| | - Anna Samarina
- Thermo Fisher Scientific, Frankfurter Str. 129B, 64293 Darmstadt, Germany
| | - Pere Arús
- Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Carrer de la Vall Moronta, Edifici CRAG, Campus UAB, Cerdanyola del Valles, 08193 Barcelona, Spain
- IRTA (Institute of Agrifood Research and Technology), Campus UAB, Edifici CRAG, Cerdanyola del Valles (Bellaterra), 08193 Barcelona, Spain
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Guajardo V, Martínez-García PJ, Solís S, Calleja-Satrustegui A, Saski C, Moreno MÁ. QTLs Identification for Iron Chlorosis in a Segregating Peach-Almond Progeny Through Double-Digest Sequence-Based Genotyping (SBG). FRONTIERS IN PLANT SCIENCE 2022; 13:872208. [PMID: 35712560 PMCID: PMC9194768 DOI: 10.3389/fpls.2022.872208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Accepted: 04/25/2022] [Indexed: 06/15/2023]
Abstract
Linkage maps are highly appreciated tools for cultivar and rootstock breeding programs because they are suitable for genetic and genomic studies. In this study, we report on using sequence-based genotyping (SBG) approach to simultaneously discover and genotype SNPs from two peach-based rootstocks ("Adafuel" and "Flordaguard") and their progeny (n = 118): from a initial mapping population composed of 131 seedlings. The plant material was developed at the EEAD-CSIC Prunus rootstocks breeding program, aiming to obtain a segregating progeny for a range of characters of agronomical interest to rootstock breeding (iron-chlorosis and root-asphyxia tolerance, nematode resistance, vigor traits, and other effects on scion cultivars). Sequence reads obtained from double-digest SBG were aligned to the P. persica reference genome (Peach v2.0). While eight linkage groups were constructed for "Adafuel," only four linkage groups were constructed for "Flordaguard," given the low heterozygosity of this last genotype. High synteny and co-linearity were observed between obtained maps and Peach v2.0. On the other hand, this work aimed to elucidate the genetic basis of leaf chlorosis tolerance using the phenotypic segregation of the progeny to iron-chlorosis tolerance, along with the QTLs responsible for leaf chlorosis. The F1 mapping population, composed initially of 131 seedlings, was growing in four field trials established on calcareous soils at the experimental field of the EEAD-CSIC in Zaragoza, Spain. From the initial mapping population, 131 individuals were selected for their phenotypical characterization with SPAD measurements of plants grown in the field, exhibiting a great variability. Significant QTLs associated with tolerance to iron chlorosis were found in LG1, LG5, LG7, and LG8. The significant QTLs detected in LG5 and LG7 have not been associated with this abiotic stress before in Prunus. Several candidate genes such as Prupe.1G541100, predicted as glutamyl-tRNA reductase 1, Prupe.1G468200, encoding a 2-oxoglutarate (2OG), and Fe(II)-dependent oxygenase superfamily protein or Prupe.1G577000 (ppa011050.m), a NIFU-like protein 2 (NIFU2) were detected. The exact biological function of some of these genes should be verified for the future development of marker-assisted selection for peach iron chlorosis tolerance.
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Affiliation(s)
| | - Pedro José Martínez-García
- Department of Plant Breeding, Centro de Edafología y Biología Aplicada del Segura - Consejo Superior de Investigaciones Científicas (CEBAS-CSIC), Murcia, Spain
| | - Simón Solís
- Centro de Estudios Avanzados en Fruticultura (CEAF), Rengo, Chile
| | - Aitziber Calleja-Satrustegui
- Department of Pomology, Estación Experimental de Aula Dei - Consejo Superior de Investigaciones Científicas (EEAD-CSIC), Zaragoza, Spain
- Department of Science, Institute for Multidisciplinary Research in Applied Biology-IMAB, Universidad Pública de Navarra, Pamplona, Spain
| | - Christopher Saski
- Department of Plant and Environmental Sciences, Clemson University, Clemson, SC, United States
| | - María Ángeles Moreno
- Department of Pomology, Estación Experimental de Aula Dei - Consejo Superior de Investigaciones Científicas (EEAD-CSIC), Zaragoza, Spain
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de Tomás C, Bardil A, Castanera R, Casacuberta JM, Vicient CM. Absence of major epigenetic and transcriptomic changes accompanying an interspecific cross between peach and almond. HORTICULTURE RESEARCH 2022; 9:uhac127. [PMID: 35928404 PMCID: PMC9343919 DOI: 10.1093/hr/uhac127] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Accepted: 05/24/2022] [Indexed: 06/15/2023]
Abstract
Hybridization has been widely used in breeding of cultivated species showing low genetic variability, such as peach (Prunus persica). The merging of two different genomes in a hybrid often triggers a so-called "genomic shock" with changes in DNA methylation and in the induction of transposable element expression and mobilization. Here, we analysed the DNA methylation and transcription levels of transposable elements and genes in leaves of Prunus persica and Prunus dulcis and in an F1 hybrid using high-throughput sequencing technologies. Contrary to the "genomic shock" expectations, we found that the overall levels of DNA methylation in the transposable elements in the hybrid are not significantly altered compared with those of the parental genomes. We also observed that the levels of transcription of the transposable elements in the hybrid are in most cases intermediate as compared with that of the parental species and we have not detected cases of higher transcription in the hybrid. We also found that the proportion of genes whose expression is altered in the hybrid compared with the parental species is low. The expression of genes potentially involved in the regulation of the activity of the transposable elements is not altered. We can conclude that the merging of the two parental genomes in this Prunus persica x Prunus dulcis hybrid does not result in a "genomic shock" with significant changes in the DNA methylation or in the transcription. The absence of major changes may facilitate using interspecific peach x almond crosses for peach improvement.
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Affiliation(s)
- Carlos de Tomás
- Centre for Research in Agricultural Genomics CSIC-IRTA-UAB-UB, Campus UAB, Edifici CRAG, Bellaterra, Barcelona 08193, Spain
| | - Amélie Bardil
- Institut écologie et environnement (INEE), CNRS, Montpelier, France
| | - Raúl Castanera
- Centre for Research in Agricultural Genomics CSIC-IRTA-UAB-UB, Campus UAB, Edifici CRAG, Bellaterra, Barcelona 08193, Spain
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Kalluri N, Serra O, Donoso JM, Picañol R, Howad W, Eduardo I, Arús P. Construction of a collection of introgression lines of "Texas" almond DNA fragments in the "Earlygold" peach genetic background. HORTICULTURE RESEARCH 2022; 9:uhac070. [PMID: 35669708 PMCID: PMC9157678 DOI: 10.1093/hr/uhac070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 03/09/2022] [Indexed: 06/15/2023]
Abstract
Peach [Prunus persica L. Batsch] is one of the major temperate fruit tree species, the commercial materials of which have a low level of genetic variability. Almond [P. dulcis (Mill) DA Webb], a close relative of peach cultivated for its kernels, has a much higher level of diversity. The species are inter-compatible and often produce fertile hybrids, almond being a possible source of new genes for peach that could provide biotic and abiotic stress tolerance traits. In this paper we describe the development of a collection of peach-almond introgression lines (ILs) having a single fragment of almond (cv. Texas) in the peach background (cv. Earlygold). Lines with few introgressions were selected with markers from successive generations from a "Texas" × "Earlygold" F1 hybrid, initially using a set of SSRs and later with the 18 k peach SNP chip, allowing for the final extraction of 67 lines, 39 with almond heterozygous introgressions covering 99% of the genome, and 28 with homozygous introgressions covering 83% of the genome. As a proof of concept, four major genes and four quantitative characters were examined in the selected ILs giving results generally consistent with previous information on the genetics of these characters. This collection is the first of its kind produced in a woody perennial species and promises to be a valuable tool for genetic analyses, including dissection of quantitative traits, positional cloning, epistasis and as prebreeding material to introgress almond genes of interest into the peach commercial gene pool.
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Affiliation(s)
- Naveen Kalluri
- Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Campus UAB, Edifici CRAG, Cerdanyola del Vallès (Bellaterra), 08193 Barcelona, Spain
| | - Octávio Serra
- Instituto Nacional de Investigação Agrária e Veterinária, I.P., Banco Português de Germoplasma Vegetal (BPGV), Braga, Portugal
| | - José Manuel Donoso
- Instituto de Investigaciones Agropecuarias (INIA), Centro Regional de Investigación Rayentué, Av. Salamanca s/n Sector Los Choapinos, Rengo 2940000, Chile
| | - Roger Picañol
- Rijk Zwaan Ibérica S.A. Finca La Marina-PJ Lo Contreras 30395, La Puebla|Cartagena (Murcia), Spain
| | - Werner Howad
- Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Campus UAB, Edifici CRAG, Cerdanyola del Vallès (Bellaterra), 08193 Barcelona, Spain
- IRTA, Campus UAB, Edifici CRAG, Cerdanyola del Vallès (Bellaterra), 08193 Barcelona, Spain
| | - Iban Eduardo
- Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Campus UAB, Edifici CRAG, Cerdanyola del Vallès (Bellaterra), 08193 Barcelona, Spain
- IRTA, Campus UAB, Edifici CRAG, Cerdanyola del Vallès (Bellaterra), 08193 Barcelona, Spain
| | - Pere Arús
- Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Campus UAB, Edifici CRAG, Cerdanyola del Vallès (Bellaterra), 08193 Barcelona, Spain
- IRTA, Campus UAB, Edifici CRAG, Cerdanyola del Vallès (Bellaterra), 08193 Barcelona, Spain
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Anisimova IN. Structural and Functional Organization of Genes That Induce and Suppress Cytoplasmic Male Sterility in Plants. RUSS J GENET+ 2020. [DOI: 10.1134/s1022795420110022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Eduardo I, Alegre S, Alexiou KG, Arús P. Resynthesis: Marker-Based Partial Reconstruction of Elite Genotypes in Clonally-Reproducing Plant Species. FRONTIERS IN PLANT SCIENCE 2020; 11:1205. [PMID: 32849747 PMCID: PMC7427350 DOI: 10.3389/fpls.2020.01205] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2020] [Accepted: 07/24/2020] [Indexed: 06/02/2023]
Abstract
We propose a method for marker-based selection of cultivars of clonally-reproducing plant species which keeps the basic genetic architecture of a top-performing cultivar (usually a partly heterozygous genotype), with the addition of some agronomically relevant differences (such as production time, product appearance or quality), providing added value to the product or cultivation process. The method is based on selecting a) two complementary nearly-inbred lines from successive selfing generations (ideally only F2 and F3) of large size, that may generate individuals with most of their genome identical to the original cultivar but being homozygous for either of the two component haplotypes in the rest, and b) individuals with such characteristics already occurring in the F2. Option a) allows for introgressing genes from other individuals in one or both of these nearly-inbred lines. Peach, a woody-perennial, clonally-reproduced species, was chosen as a model for a proof of concept of the Resynthesis process due to its biological characteristics: self-compatibility, compact and genetically well-known genome, low recombination rates and relatively short intergeneration time (3-4 years). From 416 F2 seedlings from cultivar Sweet Dream (SD), we obtained seven individuals with 76-94% identity with SD, and selected five pairs of complementary lines with average homozygosity of the two parents ≥0.70 such that crossing would produce some individuals highly similar to SD. The application of this scheme to other species with more complex genomes or biological features, including its generalization to F1 hybrids, is discussed.
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Affiliation(s)
- Iban Eduardo
- IRTA (Institut de Recerca i Tecnologia Agroalimentàries), Barcelona, Spain
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus UAB, Barcelona, Spain
| | - Simó Alegre
- IRTA (Institut de Recerca i Tecnologia Agroalimentàries), Barcelona, Spain
- Parc Científic i Tecnològic Agroalimentari de Lleida, Lleida, Spain
| | - Konstantinos G. Alexiou
- IRTA (Institut de Recerca i Tecnologia Agroalimentàries), Barcelona, Spain
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus UAB, Barcelona, Spain
| | - Pere Arús
- IRTA (Institut de Recerca i Tecnologia Agroalimentàries), Barcelona, Spain
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus UAB, Barcelona, Spain
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9
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What Does the Molecular Genetics of Different Types of Restorer-of-Fertility Genes Imply? PLANTS 2020; 9:plants9030361. [PMID: 32182978 PMCID: PMC7154926 DOI: 10.3390/plants9030361] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Revised: 03/11/2020] [Accepted: 03/11/2020] [Indexed: 12/13/2022]
Abstract
Cytoplasmic male sterility (CMS) is a widely used trait for hybrid seed production. Although male sterility is caused by S cytoplasm (male-sterility inducing mitochondria), the action of S cytoplasm is suppressed by restorer-of-fertility (Rf), a nuclear gene. Hence, the genetics of Rf has attained particular interest among plant breeders. The genetic model posits Rf diversity in which an Rf specifically suppresses the cognate S cytoplasm. Molecular analysis of Rf loci in plants has identified various genes; however, pentatricopeptide repeat (PPR) protein (a specific type of RNA-binding protein) is so prominent as the Rf-gene product that Rfs have been categorized into two classes, PPR and non-PPR. In contrast, several shared features between PPR- and some non-PPR Rfs are apparent, suggesting the possibility of another grouping. Our present focus is to group Rfs by molecular genetic classes other than the presence of PPRs. We propose three categories that define partially overlapping groups of Rfs: association with post-transcriptional regulation of mitochondrial gene expression, resistance gene-like copy number variation at the locus, and lack of a direct link to S-orf (a mitochondrial ORF associated with CMS). These groups appear to reflect their own evolutionary background and their mechanism of conferring S cytoplasm specificity.
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Alioto T, Alexiou KG, Bardil A, Barteri F, Castanera R, Cruz F, Dhingra A, Duval H, Fernández i Martí Á, Frias L, Galán B, García JL, Howad W, Gómez‐Garrido J, Gut M, Julca I, Morata J, Puigdomènech P, Ribeca P, Rubio Cabetas MJ, Vlasova A, Wirthensohn M, Garcia‐Mas J, Gabaldón T, Casacuberta JM, Arús P. Transposons played a major role in the diversification between the closely related almond and peach genomes: results from the almond genome sequence. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 101:455-472. [PMID: 31529539 PMCID: PMC7004133 DOI: 10.1111/tpj.14538] [Citation(s) in RCA: 60] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Revised: 08/29/2019] [Accepted: 09/02/2019] [Indexed: 05/19/2023]
Abstract
We sequenced the genome of the highly heterozygous almond Prunus dulcis cv. Texas combining short- and long-read sequencing. We obtained a genome assembly totaling 227.6 Mb of the estimated almond genome size of 238 Mb, of which 91% is anchored to eight pseudomolecules corresponding to its haploid chromosome complement, and annotated 27 969 protein-coding genes and 6747 non-coding transcripts. By phylogenomic comparison with the genomes of 16 additional close and distant species we estimated that almond and peach (Prunus persica) diverged around 5.88 million years ago. These two genomes are highly syntenic and show a high degree of sequence conservation (20 nucleotide substitutions per kb). However, they also exhibit a high number of presence/absence variants, many attributable to the movement of transposable elements (TEs). Transposable elements have generated an important number of presence/absence variants between almond and peach, and we show that the recent history of TE movement seems markedly different between them. Transposable elements may also be at the origin of important phenotypic differences between both species, and in particular for the sweet kernel phenotype, a key agronomic and domestication character for almond. Here we show that in sweet almond cultivars, highly methylated TE insertions surround a gene involved in the biosynthesis of amygdalin, whose reduced expression has been correlated with the sweet almond phenotype. Altogether, our results suggest a key role of TEs in the recent history and diversification of almond and its close relative peach.
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Affiliation(s)
- Tyler Alioto
- CNAG‐CRG, Centre for Genomic Regulation (CRG)Barcelona Institute of Science and Technology (BIST)Baldiri i Reixac 408028BarcelonaSpain
- Universitat Pompeu Fabra (UPF)08005BarcelonaSpain
| | - Konstantinos G. Alexiou
- IRTA, Campus UABEdifici CRAGCerdanyola del Vallès (Bellaterra)08193BarcelonaSpain
- Centre for Research in Agricultural Genomics (CRAG)CSIC‐IRTA‐UAB‐UB, Campus UABEdifici CRAGCerdanyola del Vallès (Bellaterra)08193BarcelonaSpain
| | - Amélie Bardil
- Centre for Research in Agricultural Genomics (CRAG)CSIC‐IRTA‐UAB‐UB, Campus UABEdifici CRAGCerdanyola del Vallès (Bellaterra)08193BarcelonaSpain
| | - Fabio Barteri
- Centre for Research in Agricultural Genomics (CRAG)CSIC‐IRTA‐UAB‐UB, Campus UABEdifici CRAGCerdanyola del Vallès (Bellaterra)08193BarcelonaSpain
| | - Raúl Castanera
- Centre for Research in Agricultural Genomics (CRAG)CSIC‐IRTA‐UAB‐UB, Campus UABEdifici CRAGCerdanyola del Vallès (Bellaterra)08193BarcelonaSpain
| | - Fernando Cruz
- CNAG‐CRG, Centre for Genomic Regulation (CRG)Barcelona Institute of Science and Technology (BIST)Baldiri i Reixac 408028BarcelonaSpain
- Universitat Pompeu Fabra (UPF)08005BarcelonaSpain
| | - Amit Dhingra
- Department of HorticultureWashington State University99164-6414PullmanWAUSA
| | - Henri Duval
- INRA, UR1052Unité de Génétique et Amélioration des Fruits et Légumes (GAFL)Domaine St. Maurice CS 6009484143Montfavet CedexFrance
| | - Ángel Fernández i Martí
- Department of Environmental Science Policy and ManagementUniversity of CaliforniaBerkeley94720CAUSA
- Innovative Genomics Institute (IGI)94720BerkeleyCAUSA
| | - Leonor Frias
- CNAG‐CRG, Centre for Genomic Regulation (CRG)Barcelona Institute of Science and Technology (BIST)Baldiri i Reixac 408028BarcelonaSpain
- Universitat Pompeu Fabra (UPF)08005BarcelonaSpain
| | - Beatriz Galán
- Department of Environmental BiologyCenter for Biological Research (CIB‐CSIC)Spanish National Research Council (CSIC)Ramiro de Maeztu 928040MadridSpain
| | - José L. García
- Department of Environmental BiologyCenter for Biological Research (CIB‐CSIC)Spanish National Research Council (CSIC)Ramiro de Maeztu 928040MadridSpain
| | - Werner Howad
- IRTA, Campus UABEdifici CRAGCerdanyola del Vallès (Bellaterra)08193BarcelonaSpain
- Centre for Research in Agricultural Genomics (CRAG)CSIC‐IRTA‐UAB‐UB, Campus UABEdifici CRAGCerdanyola del Vallès (Bellaterra)08193BarcelonaSpain
| | - Jèssica Gómez‐Garrido
- CNAG‐CRG, Centre for Genomic Regulation (CRG)Barcelona Institute of Science and Technology (BIST)Baldiri i Reixac 408028BarcelonaSpain
- Universitat Pompeu Fabra (UPF)08005BarcelonaSpain
| | - Marta Gut
- CNAG‐CRG, Centre for Genomic Regulation (CRG)Barcelona Institute of Science and Technology (BIST)Baldiri i Reixac 408028BarcelonaSpain
- Universitat Pompeu Fabra (UPF)08005BarcelonaSpain
| | - Irene Julca
- Universitat Pompeu Fabra (UPF)08005BarcelonaSpain
- Bioinformatics and Genomics ProgrammeCentre for Genomic Regulation (CRG)Dr Aiguader, 8808003BarcelonaSpain
| | - Jordi Morata
- Centre for Research in Agricultural Genomics (CRAG)CSIC‐IRTA‐UAB‐UB, Campus UABEdifici CRAGCerdanyola del Vallès (Bellaterra)08193BarcelonaSpain
| | - Pere Puigdomènech
- Centre for Research in Agricultural Genomics (CRAG)CSIC‐IRTA‐UAB‐UB, Campus UABEdifici CRAGCerdanyola del Vallès (Bellaterra)08193BarcelonaSpain
| | - Paolo Ribeca
- CNAG‐CRG, Centre for Genomic Regulation (CRG)Barcelona Institute of Science and Technology (BIST)Baldiri i Reixac 408028BarcelonaSpain
- Universitat Pompeu Fabra (UPF)08005BarcelonaSpain
- The Pirbright InstituteWokingSurreyGU24 0NFUK
| | - María J. Rubio Cabetas
- Centro de Investigación y Tecnología Agroalimentaria de Aragón (CITA)Unidad de HortofruticulturaGobierno de Aragón, Avda. Montañana 93050059ZaragozaSpain
- Instituto Agroalimentario de Aragón – IA2 (CITA‐Universidad de Zaragoza)Calle Miguel Servet 17750013ZaragozaSpain
| | - Anna Vlasova
- Bioinformatics and Genomics ProgrammeCentre for Genomic Regulation (CRG)Dr Aiguader, 8808003BarcelonaSpain
| | - Michelle Wirthensohn
- University of AdelaideWaite Research InstituteSchool of Agriculture, Food and WinePMB 1Glen OsmondSA5064Australia
| | - Jordi Garcia‐Mas
- IRTA, Campus UABEdifici CRAGCerdanyola del Vallès (Bellaterra)08193BarcelonaSpain
- Centre for Research in Agricultural Genomics (CRAG)CSIC‐IRTA‐UAB‐UB, Campus UABEdifici CRAGCerdanyola del Vallès (Bellaterra)08193BarcelonaSpain
| | - Toni Gabaldón
- Universitat Pompeu Fabra (UPF)08005BarcelonaSpain
- Bioinformatics and Genomics ProgrammeCentre for Genomic Regulation (CRG)Dr Aiguader, 8808003BarcelonaSpain
- Institució Catalana de Recerca i Estudis Avançats (ICREA)Pg Lluís Companys 2308010BarcelonaSpain
| | - Josep M. Casacuberta
- Centre for Research in Agricultural Genomics (CRAG)CSIC‐IRTA‐UAB‐UB, Campus UABEdifici CRAGCerdanyola del Vallès (Bellaterra)08193BarcelonaSpain
| | - Pere Arús
- IRTA, Campus UABEdifici CRAGCerdanyola del Vallès (Bellaterra)08193BarcelonaSpain
- Centre for Research in Agricultural Genomics (CRAG)CSIC‐IRTA‐UAB‐UB, Campus UABEdifici CRAGCerdanyola del Vallès (Bellaterra)08193BarcelonaSpain
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11
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Baró-Montel N, Eduardo I, Usall J, Casals C, Arús P, Teixidó N, Torres R. Exploring sources of resistance to brown rot in an interspecific almond × peach population. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2019; 99:4105-4113. [PMID: 30784078 DOI: 10.1002/jsfa.9640] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Revised: 01/29/2019] [Accepted: 02/11/2019] [Indexed: 05/28/2023]
Abstract
BACKGROUND Monilinia spp. are responsible for brown rot, one of the most significant stone fruit diseases. Planting resistant cultivars seems a promising alternative, although most commercial cultivars are susceptible to brown rot. The aim of this study was to explore resistance to Monilinia fructicola over two seasons in a backcross one interspecific population between almond 'Texas' and peach 'Earlygold' (named T1E). RESULTS 'Texas' almond was resistant to brown rot inoculation, whereas peach was highly susceptible. Phenotypic data from the T1E population indicated wide differences in response to M. fructicola. Additionally, several non-wounded individuals exhibited resistance to brown rot. Quantitative trait loci (QTLs) were identified in several linkage groups, but only two proximal QTLs in G4 were detected over both seasons and accounted for 11.3-16.2% of the phenotypic variation. CONCLUSION Analysis of the progeny allowed the identification of resistant genotypes that could serve as a source of resistance in peach breeding programs. The finding of loci associated with brown rot resistance would shed light on implementing a strategy based on marker-assisted selection (MAS) for introgression of this trait into elite peach materials. New peach cultivars resistant to brown rot may contribute to the implementation of more sustainable crop protection strategies. © 2019 Society of Chemical Industry.
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Affiliation(s)
- Núria Baró-Montel
- IRTA, XaRTA-Postharvest, Edifici Fruitcentre, Parc Científic i Tecnològic Agroalimentari de Lleida, Parc de Gardeny, Lleida, Spain
| | - Iban Eduardo
- IRTA, Centre de Recerca en Agrigenòmica CSIC-IRTA-UAB-UB, Edifici CRAG, Campus UAB, Cerdanyola del Vallès (Bellaterra), Barcelona, Spain
| | - Josep Usall
- IRTA, XaRTA-Postharvest, Edifici Fruitcentre, Parc Científic i Tecnològic Agroalimentari de Lleida, Parc de Gardeny, Lleida, Spain
| | - Carla Casals
- IRTA, XaRTA-Postharvest, Edifici Fruitcentre, Parc Científic i Tecnològic Agroalimentari de Lleida, Parc de Gardeny, Lleida, Spain
| | - Pere Arús
- IRTA, Centre de Recerca en Agrigenòmica CSIC-IRTA-UAB-UB, Edifici CRAG, Campus UAB, Cerdanyola del Vallès (Bellaterra), Barcelona, Spain
| | - Neus Teixidó
- IRTA, XaRTA-Postharvest, Edifici Fruitcentre, Parc Científic i Tecnològic Agroalimentari de Lleida, Parc de Gardeny, Lleida, Spain
| | - Rosario Torres
- IRTA, XaRTA-Postharvest, Edifici Fruitcentre, Parc Científic i Tecnològic Agroalimentari de Lleida, Parc de Gardeny, Lleida, Spain
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12
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da Silva Linge C, Antanaviciute L, Abdelghafar A, Arús P, Bassi D, Rossini L, Ficklin S, Gasic K. High-density multi-population consensus genetic linkage map for peach. PLoS One 2018; 13:e0207724. [PMID: 30462743 PMCID: PMC6248993 DOI: 10.1371/journal.pone.0207724] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2018] [Accepted: 11/04/2018] [Indexed: 11/19/2022] Open
Abstract
Highly saturated genetic linkage maps are extremely helpful to breeders and are an essential prerequisite for many biological applications such as the identification of marker-trait associations, mapping quantitative trait loci (QTL), candidate gene identification, development of molecular markers for marker-assisted selection (MAS) and comparative genetic studies. Several high-density genetic maps, constructed using the 9K SNP peach array, are available for peach. However, each of these maps is based on a single mapping population and has limited use for QTL discovery and comparative studies. A consensus genetic linkage map developed from multiple populations provides not only a higher marker density and a greater genome coverage when compared to the individual maps, but also serves as a valuable tool for estimating genetic positions of unmapped markers. In this study, a previously developed linkage map from the cross between two peach cultivars 'Zin Dai' and 'Crimson Lady' (ZC2) was improved by genotyping additional progenies. In addition, a peach consensus map was developed based on the combination of the improved ZC2 genetic linkage map with three existing high-density genetic maps of peach and a reference map of Prunus. A total of 1,476 SNPs representing 351 unique marker positions were mapped across eight linkage groups on the ZC2 genetic map. The ZC2 linkage map spans 483.3 cM with an average distance between markers of 1.38 cM/marker. The MergeMap and LPmerge tools were used for the construction of a consensus map based on markers shared across five genetic linkage maps. The consensus linkage map contains a total of 3,092 molecular markers, consisting of 2,975 SNPs, 116 SSRs and 1 morphological marker associated with slow ripening in peach (SR). The consensus map provides valuable information on marker order and genetic position for QTL identification in peach and other genetic studies within Prunus and Rosaceae.
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Affiliation(s)
- Cassia da Silva Linge
- Clemson University, Department of Plant and Environmental Sciences, Clemson, SC, United States of America
| | - Laima Antanaviciute
- Clemson University, Department of Plant and Environmental Sciences, Clemson, SC, United States of America
| | - Asma Abdelghafar
- Clemson University, Department of Plant and Environmental Sciences, Clemson, SC, United States of America
| | - Pere Arús
- Institut de Recerca i Tecnologia Agroalimentàries (IRTA), Centre de Recerca en Agrigenòmica Consejo Superior de Investigaciones Científicas (CSIC)-IRTA–Universitat Autònoma de Barcelona (UAB)–University of Barcelona (UB), Campus UAB, Bellaterra (Cerdanyola del Vallès), Barcelona, Spain
| | - Daniele Bassi
- Università degli Studi di Milano, Department of Agricultural and Environmental Sciences–Production, Landscape, Agroenergy, Milan, Italy
| | - Laura Rossini
- Università degli Studi di Milano, Department of Agricultural and Environmental Sciences–Production, Landscape, Agroenergy, Milan, Italy
| | - Stephen Ficklin
- Washington State University, Department of Horticulture, Pullman, WA, United States of America
| | - Ksenija Gasic
- Clemson University, Department of Plant and Environmental Sciences, Clemson, SC, United States of America
- * E-mail:
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13
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Cantín CM, Arús P, Eduardo I. Identification of a new allele of the Dw gene causing brachytic dwarfing in peach. BMC Res Notes 2018; 11:386. [PMID: 29898773 PMCID: PMC6000960 DOI: 10.1186/s13104-018-3490-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Accepted: 06/05/2018] [Indexed: 12/04/2022] Open
Abstract
Objective Peach brachytic dwarfism determined by Dwarf gene (Dw) is an undesired trait segregating in some peach breeding programs. Recently, a single nucleotide polymorphism (SNP) mutation in the gibberellin insensitive dwarf 1 (GID1) peach gene causing brachytic dwarfism was described. In this research we wanted to validate this marker in an F2 population of the ‘Nectavantop’ peach cultivar (Nv) to include it as a marker assisted selection tool for peach breeding programs. Results The observed segregation of the trait was in agreement with that of a recessive gene, the individuals homozygous for the recessive allele (dwdw) presenting the dwarf genotype. Dw was mapped to the distal part of linkage group 6 as previously described. The SNP marker based on the causal mutation previously described did not segregate in Nv F2 population. The sequence of the GID1c gene in Nv revealed a second SNP in its coding sequence which cosegregated with the dwarf phenotype. This SNP was predicted by the SNAP2 software to cause a major functional change and was validated in the dwarf peach cultivar ‘Small sunning’. These results suggest the existence of at least two independent mutations of the Dw gene causing the peach brachytic dwarf phenotype. Electronic supplementary material The online version of this article (10.1186/s13104-018-3490-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Celia M Cantín
- IRTA, FruitCentre, Parc Científic i Tecnològic Agroalimentari de Lleida (PCiTAL), Edifici Fruitcentre, Parc de Gardeny, 25003, Lleida, Spain
| | - Pere Arús
- IRTA, Centre de Recerca en Agrigenòmica CSIC-IRTA-UAB-UB, Campus UAB, Cerdanyola del Vallès (Bellaterra), 08193, Barcelona, Spain
| | - Iban Eduardo
- IRTA, Centre de Recerca en Agrigenòmica CSIC-IRTA-UAB-UB, Campus UAB, Cerdanyola del Vallès (Bellaterra), 08193, Barcelona, Spain.
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14
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Laurens F, Aranzana MJ, Arus P, Bassi D, Bink M, Bonany J, Caprera A, Corelli-Grappadelli L, Costes E, Durel CE, Mauroux JB, Muranty H, Nazzicari N, Pascal T, Patocchi A, Peil A, Quilot-Turion B, Rossini L, Stella A, Troggio M, Velasco R, van de Weg E. An integrated approach for increasing breeding efficiency in apple and peach in Europe. HORTICULTURE RESEARCH 2018; 5:11. [PMID: 29507735 PMCID: PMC5830435 DOI: 10.1038/s41438-018-0016-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Accepted: 12/23/2017] [Indexed: 05/02/2023]
Abstract
Despite the availability of whole genome sequences of apple and peach, there has been a considerable gap between genomics and breeding. To bridge the gap, the European Union funded the FruitBreedomics project (March 2011 to August 2015) involving 28 research institutes and private companies. Three complementary approaches were pursued: (i) tool and software development, (ii) deciphering genetic control of main horticultural traits taking into account allelic diversity and (iii) developing plant materials, tools and methodologies for breeders. Decisive breakthroughs were made including the making available of ready-to-go DNA diagnostic tests for Marker Assisted Breeding, development of new, dense SNP arrays in apple and peach, new phenotypic methods for some complex traits, software for gene/QTL discovery on breeding germplasm via Pedigree Based Analysis (PBA). This resulted in the discovery of highly predictive molecular markers for traits of horticultural interest via PBA and via Genome Wide Association Studies (GWAS) on several European genebank collections. FruitBreedomics also developed pre-breeding plant materials in which multiple sources of resistance were pyramided and software that can support breeders in their selection activities. Through FruitBreedomics, significant progresses were made in the field of apple and peach breeding, genetics, genomics and bioinformatics of which advantage will be made by breeders, germplasm curators and scientists. A major part of the data collected during the project has been stored in the FruitBreedomics database and has been made available to the public. This review covers the scientific discoveries made in this major endeavour, and perspective in the apple and peach breeding and genomics in Europe and beyond.
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Affiliation(s)
- Francois Laurens
- IRHS, INRA, Agrocampus-Ouest, Université d’Angers, SFR 4207 QuaSaV, Université Bretagne Loire, 42 rue Georges Morel, Beaucouzé, 49071 France
| | - Maria José Aranzana
- IRTA (Institut de Recerca i Tecnologia Agroalimentàries), Barcelona, Spain
- Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Campus UAB, Bellaterra, Barcelona Spain
| | - Pere Arus
- IRTA (Institut de Recerca i Tecnologia Agroalimentàries), Barcelona, Spain
- Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Campus UAB, Bellaterra, Barcelona Spain
| | - Daniele Bassi
- Università degli Studi di Milano - DiSAA, Via Celoria 2, Milan, 20133 Italy
| | - Marco Bink
- Biometris, Wageningen University and Research, Droevendaalsesteeg 1, Wageningen, 6708PB The Netherlands
- Present Address: Hendrix Genetics Research, Technology & Services, Boxmeer, 5830 AC The Netherlands
| | - Joan Bonany
- IRTA-Mas Badia, Mas Badia, La Tallada, 17134 Spain
| | - Andrea Caprera
- Parco Tecnologico Padano, Via Einstein, Loc. Cascina Codazza, Lodi, 26900 Italy
| | | | | | - Charles-Eric Durel
- IRHS, INRA, Agrocampus-Ouest, Université d’Angers, SFR 4207 QuaSaV, Université Bretagne Loire, 42 rue Georges Morel, Beaucouzé, 49071 France
| | | | - Hélène Muranty
- IRHS, INRA, Agrocampus-Ouest, Université d’Angers, SFR 4207 QuaSaV, Université Bretagne Loire, 42 rue Georges Morel, Beaucouzé, 49071 France
| | - Nelson Nazzicari
- Parco Tecnologico Padano, Via Einstein, Loc. Cascina Codazza, Lodi, 26900 Italy
| | | | - Andrea Patocchi
- Agroscope, Research Division Plant Breeding, Schloss 1, Wädenswil, 8820 Switzerland
| | - Andreas Peil
- Julius Kühn-Institute (JKI); Federal Research Centre for Cultivated Plants, Institute for Breeding Research on Fruit Crops, Pillnitzer Platz 3a, Dresden, 01326 Germany
| | | | - Laura Rossini
- Università degli Studi di Milano - DiSAA, Via Celoria 2, Milan, 20133 Italy
- Parco Tecnologico Padano, Via Einstein, Loc. Cascina Codazza, Lodi, 26900 Italy
| | - Alessandra Stella
- Parco Tecnologico Padano, Via Einstein, Loc. Cascina Codazza, Lodi, 26900 Italy
| | - Michela Troggio
- Research and Innovation Center, Fondazione Edmund Mach, San Michele all’Adige, Trento, Italy
| | - Riccardo Velasco
- Research and Innovation Center, Fondazione Edmund Mach, San Michele all’Adige, Trento, Italy
- CREA-VE, Center of Viticulture and Enology, via XXVIII Aprile 26, Conegliano (TV), 31015 Italy
| | - Eric van de Weg
- Plant Breeding, Wageningen University and Research, Droevendaalsesteeg 1, P.O.Box 386, Wageningen, 6700AJ The Netherlands
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15
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Hernández Mora JR, Micheletti D, Bink M, Van de Weg E, Cantín C, Nazzicari N, Caprera A, Dettori MT, Micali S, Banchi E, Campoy JA, Dirlewanger E, Lambert P, Pascal T, Troggio M, Bassi D, Rossini L, Verde I, Quilot-Turion B, Laurens F, Arús P, Aranzana MJ. Integrated QTL detection for key breeding traits in multiple peach progenies. BMC Genomics 2017; 18:404. [PMID: 28583082 PMCID: PMC5460339 DOI: 10.1186/s12864-017-3783-6] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2017] [Accepted: 05/10/2017] [Indexed: 01/23/2023] Open
Abstract
Background Peach (Prunus persica (L.) Batsch) is a major temperate fruit crop with an intense breeding activity. Breeding is facilitated by knowledge of the inheritance of the key traits that are often of a quantitative nature. QTLs have traditionally been studied using the phenotype of a single progeny (usually a full-sib progeny) and the correlation with a set of markers covering its genome. This approach has allowed the identification of various genes and QTLs but is limited by the small numbers of individuals used and by the narrow transect of the variability analyzed. In this article we propose the use of a multi-progeny mapping strategy that used pedigree information and Bayesian approaches that supports a more precise and complete survey of the available genetic variability. Results Seven key agronomic characters (data from 1 to 3 years) were analyzed in 18 progenies from crosses between occidental commercial genotypes and various exotic lines including accessions of other Prunus species. A total of 1467 plants from these progenies were genotyped with a 9 k SNP array. Forty-seven QTLs were identified, 22 coinciding with major genes and QTLs that have been consistently found in the same populations when studied individually and 25 were new. A substantial part of the QTLs observed (47%) would not have been detected in crosses between only commercial materials, showing the high value of exotic lines as a source of novel alleles for the commercial gene pool. Our strategy also provided estimations on the narrow sense heritability of each character, and the estimation of the QTL genotypes of each parent for the different QTLs and their breeding value. Conclusions The integrated strategy used provides a broader and more accurate picture of the variability available for peach breeding with the identification of many new QTLs, information on the sources of the alleles of interest and the breeding values of the potential donors of such valuable alleles. These results are first-hand information for breeders and a step forward towards the implementation of DNA-informed strategies to facilitate selection of new cultivars with improved productivity and quality. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3783-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- José R Hernández Mora
- IRTA, Centre de Recerca en Agrigenòmica CSIC-IRTA-UAB-UB; Campus UAB, Bellaterra (Cerdanyola del Vallès), 08193, Barcelona, Spain
| | - Diego Micheletti
- Research and Innovation Centre, Fondazione Edmund Mach (FEM), Via Mach 1, 38010, San Michele all'Adige, TN, Italy
| | - Marco Bink
- Hendrix Genetics Research, Technology & Services B.V., P.O. Box 114, 5830AC, Boxmeer, The Netherlands
| | - Eric Van de Weg
- Plant Breeding, Wageningen University and Research Droevendaalsesteeg 1, P.O. Box 386, 6700AJ, Wageningen, The Netherlands
| | - Celia Cantín
- IRTA, FruitCentreParc Cientific i Tecnològic Agroalimentari de Lleida (PCiTAL), Lleida, Spain
| | - Nelson Nazzicari
- PTP Science Park, Via Einstein, 26900, Lodi, Italy.,Council for Agricultural Research and Economics (CREA) Research Centre for Fodder Crops and Dairy Productions, Lodi, Italy
| | | | - Maria Teresa Dettori
- Consiglio per la Ricerca in Agricoltura e L'analisi Dell'economia Agraria (CREA) - Centro di Ricerca per la Frutticoltura, 00134, Roma, Italy
| | - Sabrina Micali
- Consiglio per la Ricerca in Agricoltura e L'analisi Dell'economia Agraria (CREA) - Centro di Ricerca per la Frutticoltura, 00134, Roma, Italy
| | - Elisa Banchi
- Research and Innovation Centre, Fondazione Edmund Mach (FEM), Via Mach 1, 38010, San Michele all'Adige, TN, Italy
| | | | | | | | | | - Michela Troggio
- Research and Innovation Centre, Fondazione Edmund Mach (FEM), Via Mach 1, 38010, San Michele all'Adige, TN, Italy
| | - Daniele Bassi
- Università degli Studi di Milano, DiSAA, Via Celoria 2, 20133, Milan, Italy
| | - Laura Rossini
- PTP Science Park, Via Einstein, 26900, Lodi, Italy.,Università degli Studi di Milano, DiSAA, Via Celoria 2, 20133, Milan, Italy
| | - Ignazio Verde
- Consiglio per la Ricerca in Agricoltura e L'analisi Dell'economia Agraria (CREA) - Centro di Ricerca per la Frutticoltura, 00134, Roma, Italy
| | | | | | - Pere Arús
- IRTA, Centre de Recerca en Agrigenòmica CSIC-IRTA-UAB-UB; Campus UAB, Bellaterra (Cerdanyola del Vallès), 08193, Barcelona, Spain
| | - Maria José Aranzana
- IRTA, Centre de Recerca en Agrigenòmica CSIC-IRTA-UAB-UB; Campus UAB, Bellaterra (Cerdanyola del Vallès), 08193, Barcelona, Spain.
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16
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Ashman TL, Tennessen JA, Dalton RM, Govindarajulu R, Koski MH, Liston A. Multilocus Sex Determination Revealed in Two Populations of Gynodioecious Wild Strawberry, Fragaria vesca subsp. bracteata. G3 (BETHESDA, MD.) 2015; 5:2759-73. [PMID: 26483011 PMCID: PMC4683647 DOI: 10.1534/g3.115.023358] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/31/2015] [Accepted: 10/09/2015] [Indexed: 11/18/2022]
Abstract
Gynodioecy, the coexistence of females and hermaphrodites, occurs in 20% of angiosperm families and often enables transitions between hermaphroditism and dioecy. Clarifying mechanisms of sex determination in gynodioecious species can thus illuminate sexual system evolution. Genetic determination of gynodioecy, however, can be complex and is not fully characterized in any wild species. We used targeted sequence capture to genetically map a novel nuclear contributor to male sterility in a self-pollinated hermaphrodite of Fragaria vesca subsp. bracteata from the southern portion of its range. To understand its interaction with another identified locus and possibly additional loci, we performed crosses within and between two populations separated by 2000 km, phenotyped the progeny and sequenced candidate markers at both sex-determining loci. The newly mapped locus contains a high density of pentatricopeptide repeat genes, a class commonly involved in restoration of fertility caused by cytoplasmic male sterility. Examination of all crosses revealed three unlinked epistatically interacting loci that determine sexual phenotype and vary in frequency between populations. Fragaria vesca subsp. bracteata represents the first wild gynodioecious species with genomic evidence of both cytoplasmic and nuclear genes in sex determination. We propose a model for the interactions between these loci and new hypotheses for the evolution of sex determining chromosomes in the subdioecious and dioecious Fragaria.
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Affiliation(s)
- Tia-Lynn Ashman
- Department of Biological Sciences, University of Pittsburgh, Pennsylvania 15260
| | - Jacob A Tennessen
- Department of Integrative Biology, Oregon State University, Corvallis, Oregon 97331
| | - Rebecca M Dalton
- Department of Biological Sciences, University of Pittsburgh, Pennsylvania 15260
| | | | - Matthew H Koski
- Department of Biological Sciences, University of Pittsburgh, Pennsylvania 15260
| | - Aaron Liston
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon 97331
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