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Rey-Serra P, Mnejja M, Monfort A. Shape, firmness and fruit quality QTLs shared in two non-related strawberry populations. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2021; 311:111010. [PMID: 34482914 DOI: 10.1016/j.plantsci.2021.111010] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 07/22/2021] [Accepted: 07/26/2021] [Indexed: 05/24/2023]
Abstract
The cultivated strawberry (Fragaria x ananassa) is an octoploid species (2n = 8x = 56), appreciated widely for its fruit. There have been very few studies on fruit quality traits, which are known to be mostly polygenic and environmentally dependent. To identify higher genetic variability, two non-related populations were genotyped: an F1 population cross between 'FC50' and 'FD54' and an F2 population cross between 'Camarosa' and 'Dover', hybridizing both with IStraw35k and IStraw90k SNP arrays, respectively. The F1 genetic map was constructed with 14595 SNPs and the F2 map with 7977 SNPs. High collinearity was observed when comparing one genetic map with the other and on comparing both with the octoploid genome. To assess fruit variability, both populations were phenotyped for shape, firmness, taste and other fruit traits over the 2016-2019 period. With QTL analyses, 33 stable QTLs were mapped in the 'FC50xFD54' population, and three hotspot regions were found for shape traits in LG3A, LG4D and LG6D. In the '21AF' population, only eight stable QTLs were detected. Despite that, two major and stable QTLs were mapped in the same interval of confidence for both populations. A shared fruit shape ratio QTL which explained around 25 % of trait variance was mapped in LG3A, and a shared firmness QTL explaining 26.9 % of trait variance in LG7C. For the first time, two QTLs were discovered in LG3A and LG4A for a phenotype neck without achenes. When analysing two different mapping populations, in addition to finding specific QTL regions for the studied traits, a narrowing down of the interval of confidence for the shared QTLs is achieved. As a result of this study, a new set of SNPs for fruit firmness and shape is now available for use in MAS in strawberry breeding programs.
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Affiliation(s)
- Pol Rey-Serra
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Bellaterra, Barcelona, Spain; Institut de Recerca i Tecnologia Agroalimentàries (IRTA), Barcelona, Spain
| | - Mourad Mnejja
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Bellaterra, Barcelona, Spain; Institut de Recerca i Tecnologia Agroalimentàries (IRTA), Barcelona, Spain
| | - Amparo Monfort
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Bellaterra, Barcelona, Spain; Institut de Recerca i Tecnologia Agroalimentàries (IRTA), Barcelona, Spain.
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Yamamoto E, Kataoka S, Shirasawa K, Noguchi Y, Isobe S. Genomic Selection for F 1 Hybrid Breeding in Strawberry ( Fragaria × ananassa). FRONTIERS IN PLANT SCIENCE 2021; 12:645111. [PMID: 33747025 PMCID: PMC7969887 DOI: 10.3389/fpls.2021.645111] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Accepted: 02/09/2021] [Indexed: 05/27/2023]
Abstract
Cultivated strawberry is the most widely consumed fruit crop in the world, and therefore, many breeding programs are underway to improve its agronomic traits such as fruit quality. Strawberry cultivars were vegetatively propagated through runners and carried a high risk of infection with viruses and insects. To solve this problem, the development of F1 hybrid seeds has been proposed as an alternative breeding strategy in strawberry. In this study, we conducted a potential assessment of genomic selection (GS) in strawberry F1 hybrid breeding. A total of 105 inbred lines were developed as candidate parents of strawberry F1 hybrids. In addition, 275 parental combinations were randomly selected from the 105 inbred lines and crossed to develop test F1 hybrids for GS model training. These populations were phenotyped for petiole length, leaf area, Brix, fruit hardness, and pericarp color. Whole-genome shotgun sequencing of the 105 inbred lines detected 20,811 single nucleotide polymorphism sites that were provided for subsequent GS analyses. In a GS model construction, inclusion of dominant effects showed a slight advantage in GS accuracy. In the across population prediction analysis, GS models using the inbred lines showed predictability for the test F1 hybrids and vice versa, except for Brix. Finally, the GS models were used for phenotype prediction of 5,460 possible F1 hybrids from 105 inbred lines to select F1 hybrids with high fruit hardness or high pericarp color. These F1 hybrids were developed and phenotyped to evaluate the efficacy of the GS. As expected, F1 hybrids that were predicted to have high fruit hardness or high pericarp color expressed higher observed phenotypic values than the F1 hybrids that were selected for other objectives. Through the analyses in this study, we demonstrated that GS can be applied for strawberry F1 hybrid breeding.
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Affiliation(s)
- Eiji Yamamoto
- Graduate School of Agriculture, Meiji University, Kawasaki, Japan
| | - Sono Kataoka
- Institute of Vegetable and Floriculture Science, National Agriculture and Food Research Organization, Tsu, Japan
| | - Kenta Shirasawa
- Department of Frontier Research and Development, Kazusa DNA Research Institute, Kisarazu, Japan
| | - Yuji Noguchi
- Institute of Vegetable and Floriculture Science, National Agriculture and Food Research Organization, Tsu, Japan
| | - Sachiko Isobe
- Department of Frontier Research and Development, Kazusa DNA Research Institute, Kisarazu, Japan
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Comparative transcriptome and metabolome analyses of two strawberry cultivars with different storability. PLoS One 2020; 15:e0242556. [PMID: 33264316 PMCID: PMC7710044 DOI: 10.1371/journal.pone.0242556] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Accepted: 11/04/2020] [Indexed: 12/04/2022] Open
Abstract
Postharvest storability is an important trait for breeding strawberry (Fragaria × ananassa Duch.). We evaluated the postharvest fruit quality of five strawberry cultivars (‘Durihyang’, ‘Kingsberry’, ‘Maehyang’, ‘Seolhyang’, and ‘Sunnyberry’) and identified differences in their fruit ripening during the transition from the big-green to fully-red stage between two cultivars with the highest (‘Sunnyberry’) and lowest (‘Kingsberry’) storability, using comparative transcriptome and -metabolome analysis. The differentially expressed genes revealed transcriptome changes related to anthocyanin biosynthesis and cell walls. Consistently, the metabolites of both cultivars showed general changes during ripening along with cultivar-specific characteristics in sugar and amino acid profiles. To identify the genes responsible for storability differences, we surveyed the expression of transcription factors, and found that the expression levels of WRKY31, WRKY70, and NAC83 correlated with delayed senescence and increased storability. Among them, the expression levels of NAC83, and its downstream target genes, in the five cultivars suggested that NAC83 expression can be used to predict postharvest strawberry fruit storability.
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Torello Marinoni D, Nishio S, Valentini N, Shirasawa K, Acquadro A, Portis E, Alma A, Akkak A, Pavese V, Cavalet-Giorsa E, Botta R. Development of High-Density Genetic Linkage Maps and Identification of Loci for Chestnut Gall Wasp Resistance in Castanea spp. PLANTS 2020; 9:plants9081048. [PMID: 32824716 PMCID: PMC7465717 DOI: 10.3390/plants9081048] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Revised: 08/12/2020] [Accepted: 08/13/2020] [Indexed: 11/29/2022]
Abstract
Castanea sativa is an important multipurpose species in Europe for nut and timber production as well as for its role in the landscape and in the forest ecosystem. This species has low tolerance to chestnut gall wasp (Dryocosmus kuriphilus Yasumatsu), which is a pest that was accidentally introduced into Europe in early 2000 and devastated forest and orchard trees. Resistance to the gall wasp was found in the hybrid cultivar ‘Bouche de Bétizac’ (C. sativa × C. crenata) and studied by developing genetic linkage maps using a population derived from a cross between ‘Bouche de Bétizac’ and the susceptible cultivar ‘Madonna’ (C. sativa). The high-density genetic maps were constructed using double-digest restriction site-associated DNA-seq and simple sequence repeat markers. The map of ‘Bouche de Bétizac’ consisted of 1459 loci and spanned 809.6 cM; the map of ‘Madonna’ consisted of 1089 loci and spanned 753.3 cM. In both maps, 12 linkage groups were identified. A single major QTL was recognized on the ‘Bouche de Bétizac’ map, explaining up to 67–69% of the phenotypic variance of the resistance trait (Rdk1). The Rdk1 quantitative trait loci (QTL) region included 11 scaffolds and two candidate genes putatively involved in the resistance response were identified. This study will contribute to C. sativa breeding programs and to the study of Rdk1 genes.
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Affiliation(s)
- Daniela Torello Marinoni
- Dipartimento di Scienze Agrarie, Forestali e Alimentari—DISAFA, Università degli Studi di Torino, Largo Paolo Braccini 2, Grugliasco, 10095 Torino, Italy; (N.V.); (A.A.); (E.P.); (A.A.); (V.P.); (E.C.-G.); (R.B.)
- Correspondence:
| | - Sogo Nishio
- Institute of Fruit Tree and Tea Science, NARO, 2-1 Fujimoto, Tsukuba, Ibaraki 305-8605, Japan;
| | - Nadia Valentini
- Dipartimento di Scienze Agrarie, Forestali e Alimentari—DISAFA, Università degli Studi di Torino, Largo Paolo Braccini 2, Grugliasco, 10095 Torino, Italy; (N.V.); (A.A.); (E.P.); (A.A.); (V.P.); (E.C.-G.); (R.B.)
| | - Kenta Shirasawa
- Kazusa DNA Research Institute, 2-6-7 Kazusa-Kamatari, Kisarazu, Chiba 292-0818, Japan;
| | - Alberto Acquadro
- Dipartimento di Scienze Agrarie, Forestali e Alimentari—DISAFA, Università degli Studi di Torino, Largo Paolo Braccini 2, Grugliasco, 10095 Torino, Italy; (N.V.); (A.A.); (E.P.); (A.A.); (V.P.); (E.C.-G.); (R.B.)
| | - Ezio Portis
- Dipartimento di Scienze Agrarie, Forestali e Alimentari—DISAFA, Università degli Studi di Torino, Largo Paolo Braccini 2, Grugliasco, 10095 Torino, Italy; (N.V.); (A.A.); (E.P.); (A.A.); (V.P.); (E.C.-G.); (R.B.)
| | - Alberto Alma
- Dipartimento di Scienze Agrarie, Forestali e Alimentari—DISAFA, Università degli Studi di Torino, Largo Paolo Braccini 2, Grugliasco, 10095 Torino, Italy; (N.V.); (A.A.); (E.P.); (A.A.); (V.P.); (E.C.-G.); (R.B.)
| | - Aziz Akkak
- Dipartimento di Scienze Agrarie, degli Alimenti e dell’Ambiente, Università degli Studi di Foggia, Via Napoli 25, 71121 Foggia, Italy;
| | - Vera Pavese
- Dipartimento di Scienze Agrarie, Forestali e Alimentari—DISAFA, Università degli Studi di Torino, Largo Paolo Braccini 2, Grugliasco, 10095 Torino, Italy; (N.V.); (A.A.); (E.P.); (A.A.); (V.P.); (E.C.-G.); (R.B.)
| | - Emile Cavalet-Giorsa
- Dipartimento di Scienze Agrarie, Forestali e Alimentari—DISAFA, Università degli Studi di Torino, Largo Paolo Braccini 2, Grugliasco, 10095 Torino, Italy; (N.V.); (A.A.); (E.P.); (A.A.); (V.P.); (E.C.-G.); (R.B.)
| | - Roberto Botta
- Dipartimento di Scienze Agrarie, Forestali e Alimentari—DISAFA, Università degli Studi di Torino, Largo Paolo Braccini 2, Grugliasco, 10095 Torino, Italy; (N.V.); (A.A.); (E.P.); (A.A.); (V.P.); (E.C.-G.); (R.B.)
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Letelier L, Gaete-Eastman C, Peñailillo P, Moya-León MA, Herrera R. Southern Species From the Biodiversity Hotspot of Central Chile: A Source of Color, Aroma, and Metabolites for Global Agriculture and Food Industry in a Scenario of Climate Change. FRONTIERS IN PLANT SCIENCE 2020; 11:1002. [PMID: 32719706 PMCID: PMC7348657 DOI: 10.3389/fpls.2020.01002] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Accepted: 06/19/2020] [Indexed: 05/09/2023]
Abstract
Two interesting plants within the Chilean flora (wild and crop species) can be found with a history related to modern fruticulture: Fragaria chiloensis subsp. chiloensis (Rosaceae) and Vasconcellea pubescens (Caricaceae). Both species have a wide natural distribution, which goes from the Andes mountains to the sea (East-West), and from the Atacama desert to the South of Chile (North-South). The growing locations are included within the Chilean Winter Rainfall-Valdivian Forest hotspot. Global warming is of great concern as it increases the risk of losing wild plant species, but at the same time, gives a chance for usually longer term genetic improvement using naturally adapted material and the source for generating healthy foods. Modern agriculture intensifies the attractiveness of native undomesticated species as a way to provide compounds like antioxidants or tolerant plants for climate change scenario. F. chiloensis subsp. chiloensis as the mother of commercial strawberry (Fragaria × ananassa) is an interesting genetic source for the improvement of fruit flavor and stress tolerance. On the other hand, V. pubescens produces fruit with high level of antioxidants and proteolytic enzymes of interest to the food industry. The current review compiles the botanical, physiological and phytochemical description of F. chiloensis subsp. chiloensis and V. pubescens, highlighting their potential as functional foods and as source of compounds with several applications in the pharmaceutical, biotechnological, and food science. The impact of global warming scenario on the distribution of the species is also discussed.
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Affiliation(s)
- Luis Letelier
- Laboratorio de Fisiología Vegetal y Genética Molecular, Instituto de Ciencias Biológicas, Universidad de Talca, Talca, Chile
- Núcleo Científico Multidisciplinario, Dirección de Investigación, Universidad de Talca, Talca, Chile
| | - Carlos Gaete-Eastman
- Laboratorio de Fisiología Vegetal y Genética Molecular, Instituto de Ciencias Biológicas, Universidad de Talca, Talca, Chile
| | - Patricio Peñailillo
- Laboratorio de Fisiología Vegetal y Genética Molecular, Instituto de Ciencias Biológicas, Universidad de Talca, Talca, Chile
| | - María A. Moya-León
- Laboratorio de Fisiología Vegetal y Genética Molecular, Instituto de Ciencias Biológicas, Universidad de Talca, Talca, Chile
| | - Raúl Herrera
- Laboratorio de Fisiología Vegetal y Genética Molecular, Instituto de Ciencias Biológicas, Universidad de Talca, Talca, Chile
- *Correspondence: Raúl Herrera,
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Vining KJ, Salinas N, Tennessen JA, Zurn JD, Sargent DJ, Hancock J, Bassil NV. Genotyping-by-sequencing enables linkage mapping in three octoploid cultivated strawberry families. PeerJ 2017; 5:e3731. [PMID: 28875078 PMCID: PMC5581533 DOI: 10.7717/peerj.3731] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2017] [Accepted: 08/03/2017] [Indexed: 12/30/2022] Open
Abstract
Genotyping-by-sequencing (GBS) was used to survey genome-wide single-nucleotide polymorphisms (SNPs) in three biparental strawberry (Fragaria × ananassa) populations with the goal of evaluating this technique in a species with a complex octoploid genome. GBS sequence data were aligned to the F. vesca ‘Fvb’ reference genome in order to call SNPs. Numbers of polymorphic SNPs per population ranged from 1,163 to 3,190. Linkage maps consisting of 30–65 linkage groups were produced from the SNP sets derived from each parent. The linkage groups covered 99% of the Fvb reference genome, with three to seven linkage groups from a given parent aligned to any particular chromosome. A phylogenetic analysis performed using the POLiMAPS pipeline revealed linkage groups that were most similar to ancestral species F. vesca for each chromosome. Linkage groups that were most similar to a second ancestral species, F. iinumae, were only resolved for Fvb 4. The quantity of missing data and heterogeneity in genome coverage inherent in GBS complicated the analysis, but POLiMAPS resolved F. × ananassa chromosomal regions derived from diploid ancestor F. vesca.
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Affiliation(s)
- Kelly J Vining
- Department of Horticulture, Oregon State University, Corvallis, OR, United States of America
| | - Natalia Salinas
- Department of Horticulture, University of Florida, Wimauma, FL, United States of America
| | - Jacob A Tennessen
- Department of Integrative Biology, Oregon State University, Corvallis, OR, United States of America
| | - Jason D Zurn
- National Clonal Germplasm Repository, United States Department of Agriculture, Agricultural Research Service, Corvallis, OR, United States of America
| | - Daniel James Sargent
- Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, Italy.,East Malling Enterprise Centre, Driscoll's Genetics Limited, East Malling, United Kingdom
| | - James Hancock
- Department of Horticulture, Michigan State University, East Lansing, MI, United States of America
| | - Nahla V Bassil
- Department of Horticulture, Oregon State University, Corvallis, OR, United States of America.,National Clonal Germplasm Repository, United States Department of Agriculture, Agricultural Research Service, Corvallis, OR, United States of America
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