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Ren J, Li W, Guo Z, Ma Z, Wan D, Lu S, Guo L, Gou H, Chen B, Mao J. Whole-genome resequencing and transcriptome analyses of four generation mutants to reveal spur-type and skin-color related genes in apple (Malus domestica Borkh. Cv. Red delicious). BMC PLANT BIOLOGY 2023; 23:607. [PMID: 38030998 PMCID: PMC10688089 DOI: 10.1186/s12870-023-04631-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Accepted: 11/24/2023] [Indexed: 12/01/2023]
Abstract
BACKGROUND Bud sport is a kind of somatic mutation that usually occurred in apple. 'Red Delicious' is considered to be a special plant material of bud sport, whereas the genetic basis of plant mutants is still unknown. In this study, we used whole-genome resequencing and transcriptome sequencing to identify genes related to spur-type and skin-color in the 'Red Delicious' (G0) and its four generation mutants including 'Starking Red' (G1), 'Starkrimson' (G2), 'Campbell Redchief' (G3) and 'Vallee Spur' (G4). RESULTS The number of single nucleotide polymorphisms (SNPs), insertions and deletions (InDels) and structural variations (SVs) were decreased in four generation mutants compared to G0, and the number of unique SNPs and InDels were over 9-fold and 4-fold higher in G1 versus (vs.) G2 and G2 vs. G3, respectively. Chromosomes 2, 5, 11 and 15 carried the most SNPs, InDels and SVs, while chromosomes 1 and 6 carried the least. Meanwhile, we identified 4,356 variation genes by whole-genome resequencing and transcriptome, and obtained 13 and 16 differentially expressed genes (DEGs) related to spur-type and skin-color by gene expression levels. Among them, DELLA and 4CL7 were the potential genes that regulate the difference of spur-type and skin-color characters, respectively. CONCLUSIONS Our study identified potential genes associated with spur-type and skin-color differences in 'Red Delicious' and its four generation mutants, which provides a theoretical foundation for the mechanism of the apple bud sport.
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Affiliation(s)
- Jiaxuan Ren
- College of Horticulture, Gansu Agricultural University, Lanzhou, 730070, PR China
| | - Wenfang Li
- College of Horticulture, Gansu Agricultural University, Lanzhou, 730070, PR China
| | - Zhigang Guo
- Tianshui Normal University, Tianshui, 741001, PR China
| | - Zonghuan Ma
- College of Horticulture, Gansu Agricultural University, Lanzhou, 730070, PR China
| | - Dongshi Wan
- College of Ecology, Lanzhou University, Lanzhou, 730000, PR China
| | - Shixiong Lu
- College of Horticulture, Gansu Agricultural University, Lanzhou, 730070, PR China
| | - Lili Guo
- College of Horticulture, Gansu Agricultural University, Lanzhou, 730070, PR China
| | - Huimin Gou
- College of Horticulture, Gansu Agricultural University, Lanzhou, 730070, PR China
| | - Baihong Chen
- College of Horticulture, Gansu Agricultural University, Lanzhou, 730070, PR China.
| | - Juan Mao
- College of Horticulture, Gansu Agricultural University, Lanzhou, 730070, PR China.
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Donkpegan ASL, Bernard A, Barreneche T, Quero-García J, Bonnet H, Fouché M, Le Dantec L, Wenden B, Dirlewanger E. Genome-wide association mapping in a sweet cherry germplasm collection ( Prunus avium L.) reveals candidate genes for fruit quality traits. HORTICULTURE RESEARCH 2023; 10:uhad191. [PMID: 38239559 PMCID: PMC10794993 DOI: 10.1093/hr/uhad191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Accepted: 09/12/2023] [Indexed: 01/22/2024]
Abstract
In sweet cherry (Prunus avium L.), large variability exists for various traits related to fruit quality. There is a need to discover the genetic architecture of these traits in order to enhance the efficiency of breeding strategies for consumer and producer demands. With this objective, a germplasm collection consisting of 116 sweet cherry accessions was evaluated for 23 agronomic fruit quality traits over 2-6 years, and characterized using a genotyping-by-sequencing approach. The SNP coverage collected was used to conduct a genome-wide association study using two multilocus models and three reference genomes. We identified numerous SNP-trait associations for global fruit size (weight, width, and thickness), fruit cracking, fruit firmness, and stone size, and we pinpointed several candidate genes involved in phytohormone, calcium, and cell wall metabolisms. Finally, we conducted a precise literature review focusing on the genetic architecture of fruit quality traits in sweet cherry to compare our results with potential colocalizations of marker-trait associations. This study brings new knowledge of the genetic control of important agronomic traits related to fruit quality, and to the development of marker-assisted selection strategies targeted towards the facilitation of breeding efforts.
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Affiliation(s)
- Armel S L Donkpegan
- UMR BFP, INRAE, University of Bordeaux, 71 Avenue Edouard
Bourlaux, F-33882 Villenave d’Ornon, France
- UMR BOA, SYSAAF, Centre INRAE Val de Loire, 37380
Nouzilly, France
| | - Anthony Bernard
- UMR BFP, INRAE, University of Bordeaux, 71 Avenue Edouard
Bourlaux, F-33882 Villenave d’Ornon, France
| | - Teresa Barreneche
- UMR BFP, INRAE, University of Bordeaux, 71 Avenue Edouard
Bourlaux, F-33882 Villenave d’Ornon, France
| | - José Quero-García
- UMR BFP, INRAE, University of Bordeaux, 71 Avenue Edouard
Bourlaux, F-33882 Villenave d’Ornon, France
| | - Hélène Bonnet
- UMR BFP, INRAE, University of Bordeaux, 71 Avenue Edouard
Bourlaux, F-33882 Villenave d’Ornon, France
| | - Mathieu Fouché
- UMR BFP, INRAE, University of Bordeaux, 71 Avenue Edouard
Bourlaux, F-33882 Villenave d’Ornon, France
| | - Loïck Le Dantec
- UMR BFP, INRAE, University of Bordeaux, 71 Avenue Edouard
Bourlaux, F-33882 Villenave d’Ornon, France
| | - Bénédicte Wenden
- UMR BFP, INRAE, University of Bordeaux, 71 Avenue Edouard
Bourlaux, F-33882 Villenave d’Ornon, France
| | - Elisabeth Dirlewanger
- UMR BFP, INRAE, University of Bordeaux, 71 Avenue Edouard
Bourlaux, F-33882 Villenave d’Ornon, France
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Kaya HB, Dilli Y, Oncu-Oner T, Ünal A. Exploring genetic diversity and population structure of a large grapevine ( Vitis vinifera L.) germplasm collection in Türkiye. FRONTIERS IN PLANT SCIENCE 2023; 14:1121811. [PMID: 37235025 PMCID: PMC10208073 DOI: 10.3389/fpls.2023.1121811] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 04/06/2023] [Indexed: 05/28/2023]
Abstract
Grapevine (Vitis Vinifera L.) has been one of the significant perennial crops in widespread temperate climate regions since its domestication around 6000 years ago. Grapevine and its products, particularly wine, table grapes, and raisins, have significant economic importance not only in grapevine-growing countries but also worldwide. Grapevine cultivation in Türkiye dates back to ancient times, and Anatolia is considered one of the main grapevine migration routes around the Mediterranean basin. Turkish germplasm collection, conserved at the Turkish Viticulture Research Institutes, includes cultivars and wild relatives mainly collected in Türkiye, breeding lines, rootstock varieties, and mutants, but also cultivars of international origin. Genotyping with high-throughput markers enables the investigation of genetic diversity, population structure, and linkage disequilibrium, which are crucial for applying genomic-assisted breeding. Here, we present the results of a high-throughput genotyping-by-sequencing (GBS) study of 341 genotypes from grapevine germplasm collection at Manisa Viticulture Research Institute. A total of 272,962 high-quality single nucleotide polymorphisms (SNP) markers on the nineteen chromosomes were identified using genotyping-by-sequencing (GBS) technology. The high-density coverage of SNPs resulted in an average of 14,366 markers per chromosome, an average polymorphism information content (PIC) value of 0.23 and an expected heterozygosity (He) value of 0.28 indicating the genetic diversity within 341 genotypes. LD decayed very fast when r2 was between 0.45 and 0.2 and became flat when r2 was 0.05. The average LD decay for the entire genome was 30 kb when r2 = 0.2. The PCA and structure analysis did not distinguish the grapevine genotypes based on different origins, highlighting the occurrence of gene flow and a high amount of admixture. Analysis of molecular variance (AMOVA) results indicated a high level of genetic differentiation within populations, while variation among populations was extremely low. This study provides comprehensive information on the genetic diversity and population structure of Turkish grapevine genotypes.
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Affiliation(s)
- Hilal Betul Kaya
- Department of Bioengineering, Manisa Celal Bayar University, Manisa, Türkiye
| | - Yıldız Dilli
- Republic of Türkiye Ministry of Agriculture and Forestry, Viticulture Research Institute, Manisa, Türkiye
| | - Tulay Oncu-Oner
- Department of Bioengineering, Manisa Celal Bayar University, Manisa, Türkiye
| | - Akay Ünal
- Republic of Türkiye Ministry of Agriculture and Forestry, Viticulture Research Institute, Manisa, Türkiye
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Bhattarai K, Sharma S, Verma S, Peres NA, Xiao S, Clark DG, Deng Z. Construction of a genome-wide genetic linkage map and identification of quantitative trait loci for powdery mildew resistance in Gerbera daisy. FRONTIERS IN PLANT SCIENCE 2023; 13:1072717. [PMID: 36684731 PMCID: PMC9853552 DOI: 10.3389/fpls.2022.1072717] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Accepted: 12/09/2022] [Indexed: 06/17/2023]
Abstract
Powdery mildew (PM) is a common fungal disease in many important crops. The PM caused by Podosphaera xanthii has been the most challenging problem in commercial Gerbera (Gerbera hybrida) production globally, often leading to severe losses of crop yield and quality. A small number of PM-resistant breeding lines and cultivars have been reported in Gerbera, but the underlying genetics for PM resistance in Gerbera is largely unknown. Scarcity of genomic resources such as genetic linkage maps and molecular markers has severely hindered the effort to understand the genetic basis and locate loci controlling PM resistance in Gerbera. This study aimed to construct a genome-wide genetic linkage map, identify quantitative trait loci (QTL), and molecular markers for PM resistance in Gerbera. A segregating mapping population was developed by crossing PM-resistant and -susceptible Gerbera breeding lines, genotyped by sequencing, and phenotyped for PM resistance. A genome-wide genetic linkage map constructed with 791 single polymorphic site (SNP) markers spans 1912.30 cM across 27 linkage groups (LG) and reaches a density of 1 marker per 2.42 cM. One major consistent QTL was discovered in LG16, explaining more than 16.6% of the phenotypic variance for PM resistance. The QTL was tagged with two flanking SNP markers. The availability of this genetic linkage map will be very useful for locating and tagging QTLs for other important traits in Gerbera, and the newly discovered QTL and SNP markers will enable development of molecular markers for improving Gerbera for resistance to PM.
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Affiliation(s)
- Krishna Bhattarai
- Department of Environmental Horticulture, Gulf Coast Research and Education Center, University of Florida, Institute of Food and Agricultural Sciences (IFAS), Wimauma, FL, United States
| | - Sadikshya Sharma
- Department of Horticultural Science, Gulf Coast Research and Education Center, University of Florida, Wimauma, FL, United States
| | - Sujeet Verma
- Department of Horticultural Science, Gulf Coast Research and Education Center, University of Florida, Wimauma, FL, United States
| | - Natalia A. Peres
- Department of Plant Pathology, Gulf Coast Research and Education Center, University of Florida, IFAS, Wimauma, FL, United States
| | - Shunyuan Xiao
- University of Maryland, Institute for Bioscience and Biotechnology Research, University of Maryland College Park, Rockville, MD, United States
| | - David G. Clark
- Department of Environmental Horticulture, University of Florida, IFAS, Gainesville, FL, United States
| | - Zhanao Deng
- Department of Environmental Horticulture, Gulf Coast Research and Education Center, University of Florida, Institute of Food and Agricultural Sciences (IFAS), Wimauma, FL, United States
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Palasciano M, Zuluaga DL, Cerbino D, Blanco E, Aufiero G, D’Agostino N, Sonnante G. Sweet Cherry Diversity and Relationships in Modern and Local Varieties Based on SNP Markers. PLANTS (BASEL, SWITZERLAND) 2022; 12:136. [PMID: 36616264 PMCID: PMC9824393 DOI: 10.3390/plants12010136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 12/20/2022] [Accepted: 12/22/2022] [Indexed: 06/17/2023]
Abstract
The sweet cherry is an important fruit species that is widespread globally. In addition to the well-known traditional and modern varieties, a myriad of landraces is present in Europe, as well as in southern Italy. This study aims to evaluate the population structure, genetic relationships, and cases of duplicate samples in a collection of 143 accessions using GBS-derived SNP markers. The genetic material under investigation includes modern commercial varieties, ancient European and American varieties, landraces, and individuals retrieved from small orchards. Some of the known varieties were genetically analyzed here for the first time. In addition, several genotypes were collected from the Basilicata region (southern Italy), an area largely unexplored for sweet cherry genetic resources. The relationships among genotypes were assessed using four different methods: allele frequency and ancestry estimation, principal component analysis, Neighbor-Joining tree, and identity-by-state estimation. The analyses returned quite congruent results and highlighted the presence of four main genetic groups, namely: (i) American varieties, (ii) the 'Germersdorfer-Ferrovia' cluster, (iii) the 'Burlat' group, and (iv) the group of Italian landraces. The main drivers of clustering were ancestry, geographical distribution, and some important traits such as self-compatibility. The sweet cherries from Basilicata, herewith examined for the first time, were mostly distributed within the group of Italian landraces, being particularly linked to the autochthonous varieties of the Campania region. However, some genotypes were outside this group, thus suggesting the introduction of genetic material from other Italian regions or from European countries. The considerable amount of American and European modern varieties analyzed are genetically very closely related, suggesting a reduced genetic basis. In addition, we highlighted the discriminating ability of SNP markers to distinguish between an original variety and its mutant. Overall, our results may be useful in defining conservation strategies for sweet cherry germplasm and developing future breeding programs to enlarge the genetic basis of commercial varieties.
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Affiliation(s)
- Marino Palasciano
- Department of Soil, Plant and Food Sciences, University of Bari “Aldo Moro”, Via G. Amendola 165/A, 70126 Bari, Italy
| | - Diana L. Zuluaga
- Institute of Biosciences and Bioresources, National Research Council, Via Amendola 165/A, 70126 Bari, Italy
| | - Domenico Cerbino
- Agenzia Lucana di Sviluppo e di Innovazione in Agricoltura (ALSIA) Pollino, C.da Piano Incoronata, 85048 Rotonda, Italy
| | - Emanuela Blanco
- Institute of Biosciences and Bioresources, National Research Council, Via Amendola 165/A, 70126 Bari, Italy
| | - Gaetano Aufiero
- Department of Agricultural Sciences, University of Naples Federico II, Via Università 100, 80055 Portici, Italy
| | - Nunzio D’Agostino
- Department of Agricultural Sciences, University of Naples Federico II, Via Università 100, 80055 Portici, Italy
| | - Gabriella Sonnante
- Institute of Biosciences and Bioresources, National Research Council, Via Amendola 165/A, 70126 Bari, Italy
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Vignati E, Lipska M, Dunwell JM, Caccamo M, Simkin AJ. Fruit Development in Sweet Cherry. PLANTS (BASEL, SWITZERLAND) 2022; 11:plants11121531. [PMID: 35736682 PMCID: PMC9227597 DOI: 10.3390/plants11121531] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 06/02/2022] [Accepted: 06/04/2022] [Indexed: 05/19/2023]
Abstract
Fruits are an important source of vitamins, minerals and nutrients in the human diet. They also contain several compounds of nutraceutical importance that have significant antioxidant and anti-inflammatory roles, which can protect the consumer from diseases, such as cancer, and cardiovascular disease as well as having roles in reducing the build-up of LDL-cholesterol in blood plasma and generally reduce the risks of disease and age-related decline in health. Cherries contain high concentrations of bioactive compounds and minerals, including calcium, phosphorous, potassium and magnesium, and it is, therefore, unsurprising that cherry consumption has a positive impact on health. This review highlights the development of sweet cherry fruit, the health benefits of cherry consumption, and the options for increasing consumer acceptance and consumption.
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Affiliation(s)
- Edoardo Vignati
- NIAB, New Road, East Malling ME19 6BJ, UK; (E.V.); (M.L.)
- School of Agriculture, Policy and Development, University of Reading, Whiteknights, Reading RG6 6EU, UK;
| | - Marzena Lipska
- NIAB, New Road, East Malling ME19 6BJ, UK; (E.V.); (M.L.)
| | - Jim M. Dunwell
- School of Agriculture, Policy and Development, University of Reading, Whiteknights, Reading RG6 6EU, UK;
| | - Mario Caccamo
- NIAB, Cambridge Crop Research, Lawrence Weaver Road, Cambridge CB3 0LE, UK;
| | - Andrew J. Simkin
- NIAB, New Road, East Malling ME19 6BJ, UK; (E.V.); (M.L.)
- School of Biosciences, University of Kent, Canterbury CT2 7NJ, UK
- Correspondence:
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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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Quezada M, Amadeu RR, Vignale B, Cabrera D, Pritsch C, Garcia AAF. Construction of a High-Density Genetic Map of Acca sellowiana (Berg.) Burret, an Outcrossing Species, Based on Two Connected Mapping Populations. FRONTIERS IN PLANT SCIENCE 2021; 12:626811. [PMID: 33708232 PMCID: PMC7940835 DOI: 10.3389/fpls.2021.626811] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Accepted: 01/12/2021] [Indexed: 06/12/2023]
Abstract
Acca sellowiana, known as feijoa or pineapple guava, is a diploid, (2n = 2x = 22) outcrossing fruit tree species native to Uruguay and Brazil. The species stands out for its highly aromatic fruits, with nutraceutical and therapeutic value. Despite its promising agronomical value, genetic studies on this species are limited. Linkage genetic maps are valuable tools for genetic and genomic studies, and constitute essential tools in breeding programs to support the development of molecular breeding strategies. A high-density composite genetic linkage map of A. sellowiana was constructed using two genetically connected populations: H5 (TCO × BR, N = 160) and H6 (TCO × DP, N = 184). Genotyping by sequencing (GBS) approach was successfully applied for developing single nucleotide polymorphism (SNP) markers. A total of 4,921 SNP markers were identified using the reference genome of the closely related species Eucalyptus grandis, whereas other 4,656 SNPs were discovered using a de novo pipeline. The individual H5 and H6 maps comprised 1,236 and 1,302 markers distributed over the expected 11 linkage groups, respectively. These two maps spanned a map length of 1,593 and 1,572 cM, with an average inter-marker distance of 1.29 and 1.21 cM, respectively. A large proportion of markers were common to both maps and showed a high degree of collinearity. The composite map consisted of 1,897 SNPs markers with a total map length of 1,314 cM and an average inter-marker distance of 0.69. A novel approach for the construction of composite maps where the meiosis information of individuals of two connected populations is captured in a single estimator is described. A high-density, accurate composite map based on a consensus ordering of markers provides a valuable contribution for future genetic research and breeding efforts in A. sellowiana. A novel mapping approach based on an estimation of multipopulation recombination fraction described here may be applied in the construction of dense composite genetic maps for any other outcrossing diploid species.
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Affiliation(s)
- Marianella Quezada
- Laboratorio de Biotecnología, Departamento de Biología Vegetal, Facultad de Agronomía, Universidad de la República, Montevideo, Uruguay
| | - Rodrigo Rampazo Amadeu
- Laboratório de Genética Estatística, Departamento de Genética, Escola Superior de Agricultura “Luiz de Queiroz”, Universidade de São Paulo, Piracicaba, Brazil
| | - Beatriz Vignale
- Mejoramiento Genético, Departamento de Producción Vegetal, Estación Experimental de la Facultad de Agronomía, Universidad de la República, Salto, Uruguay
| | - Danilo Cabrera
- Programa de Investigación en Producción Fruticola, Instituto Nacional de Investigación Agropecuaria (INIA), Estación Experimental “Wilson Ferreira Aldunate”, Canelones, Uruguay
| | - Clara Pritsch
- Laboratorio de Biotecnología, Departamento de Biología Vegetal, Facultad de Agronomía, Universidad de la República, Montevideo, Uruguay
| | - Antonio Augusto Franco Garcia
- Laboratório de Genética Estatística, Departamento de Genética, Escola Superior de Agricultura “Luiz de Queiroz”, Universidade de São Paulo, Piracicaba, Brazil
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Pina A, Irisarri P, Errea P, Zhebentyayeva T. Mapping Quantitative Trait Loci Associated With Graft (In)Compatibility in Apricot ( Prunus armeniaca L.). FRONTIERS IN PLANT SCIENCE 2021; 12:622906. [PMID: 33679836 PMCID: PMC7933020 DOI: 10.3389/fpls.2021.622906] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Accepted: 01/08/2021] [Indexed: 05/29/2023]
Abstract
Graft incompatibility (GI) between the most popular Prunus rootstocks and apricot cultivars is one of the major problems for rootstock usage and improvement. Failure in producing long-leaving healthy grafts greatly affects the range of available Prunus rootstocks for apricot cultivation. Despite recent advances related to the molecular mechanisms of a graft-union formation between rootstock and scion, information on genetic control of this trait in woody plants is essentially missing because of a lack of hybrid crosses, segregating for the trait. In this study, we have employed the next-generation sequencing technology to generate the single-nucleotide polymorphism (SNP) markers and construct parental linkage maps for an apricot F1 population "Moniqui (Mo)" × "Paviot (Pa)" segregating for ability to form successful grafts with universal Prunus rootstock "Marianna 2624". To localize genomic regions associated with this trait, we genotyped 138 individuals from the "Mo × Pa" cross and constructed medium-saturated genetic maps. The female "Mo" and male "Pa" maps were composed of 557 and 501 SNPs and organized in eight linkage groups that covered 780.2 and 690.4 cM of genetic distance, respectively. Parental maps were aligned to the Prunus persica v2.0 genome and revealed a high colinearity with the Prunus reference map. Two-year phenotypic data for characters associated with unsuccessful grafting such as necrotic line (NL), bark and wood discontinuities (BD and WD), and an overall estimate of graft (in)compatibility (GI) were collected for mapping quantitative trait loci (QTLs) on both parental maps. On the map of the graft-compatible parent "Pa", two genomic regions on LG5 (44.9-60.8 cM) and LG8 (33.2-39.2 cM) were associated with graft (in)compatibility characters at different significance level, depending on phenotypic dataset. Of these, the LG8 QTL interval was most consistent between the years and supported by two significant and two putative QTLs. To our best knowledge, this is the first report on QTLs for graft (in)compatibility in woody plants. Results of this work will provide a valuable genomic resource for apricot breeding programs and facilitate future efforts focused on candidate genes discovery for graft (in)compatibility in apricot and other Prunus species.
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Affiliation(s)
- Ana Pina
- Unidad de Hortofruticultura, Centro de Investigación y Tecnología Agroalimentaria de Aragón (CITA), Zaragoza, Spain
- Instituto Agroalimentario de Aragón – IA2 (CITA-Universidad de Zaragoza), Zaragoza, Spain
| | - Patricia Irisarri
- Unidad de Hortofruticultura, Centro de Investigación y Tecnología Agroalimentaria de Aragón (CITA), Zaragoza, Spain
- Instituto Agroalimentario de Aragón – IA2 (CITA-Universidad de Zaragoza), Zaragoza, Spain
| | - Pilar Errea
- Unidad de Hortofruticultura, Centro de Investigación y Tecnología Agroalimentaria de Aragón (CITA), Zaragoza, Spain
- Instituto Agroalimentario de Aragón – IA2 (CITA-Universidad de Zaragoza), Zaragoza, Spain
| | - Tetyana Zhebentyayeva
- The Schatz Center for Tree Molecular Genetics, Department of Ecosystem Science and Management, The Pennsylvania State University, University Park, PA, United States
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Genomic Resource Development for Hydrangea (Hydrangea macrophylla (Thunb.) Ser.)—A Transcriptome Assembly and a High-Density Genetic Linkage Map. HORTICULTURAE 2021. [DOI: 10.3390/horticulturae7020025] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Hydrangea (Hydrangea macrophylla) is an important ornamental crop that has been cultivated for more than 300 years. Despite the economic importance, genetic studies for hydrangea have been limited by the lack of genetic resources. Genetic linkage maps and subsequent trait mapping are essential tools to identify and make markers available for marker-assisted breeding. A transcriptomic study was performed on two important cultivars, Veitchii and Endless Summer, to discover simple sequence repeat (SSR) markers and an F1 population based on the cross ‘Veitchii’ × ‘Endless Summer’ was established for genetic linkage map construction. Genotyping by sequencing (GBS) was performed on the mapping population along with SSR genotyping. From an analysis of 42,682 putative transcripts, 8780 SSRs were identified and 1535 were validated in the mapping parents. A total of 267 polymorphic SSRs were selected for linkage map construction. The GBS yielded 3923 high quality single nucleotide polymorphisms (SNPs) in the mapping population, resulting in a total of 4190 markers that were used to generate maps for each parent and a consensus map. The consensus linkage map contained 1767 positioned markers (146 SSRs and 1621 SNPs), spanned 1383.4 centiMorgans (cM), and was comprised of 18 linkage groups, with an average mapping interval of 0.8 cM. The transcriptome information and large-scale marker development in this study greatly expanded the genetic resources that are available for hydrangea. The high-density genetic linkage maps presented here will serve as an important foundation for quantitative trait loci mapping, map-based gene cloning, and marker-assisted selection of H. macrophylla.
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11
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Pinosio S, Marroni F, Zuccolo A, Vitulo N, Mariette S, Sonnante G, Aravanopoulos FA, Ganopoulos I, Palasciano M, Vidotto M, Magris G, Iezzoni A, Vendramin GG, Morgante M. A draft genome of sweet cherry (Prunus avium L.) reveals genome-wide and local effects of domestication. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 103:1420-1432. [PMID: 32391598 DOI: 10.1111/tpj.14809] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Revised: 04/24/2020] [Accepted: 05/01/2020] [Indexed: 05/26/2023]
Abstract
Sweet cherry (Prunus avium L.) trees are both economically important fruit crops but also important components of natural forest ecosystems in Europe, Asia and Africa. Wild and domesticated trees currently coexist in the same geographic areas with important questions arising on their historical relationships. Little is known about the effects of the domestication process on the evolution of the sweet cherry genome. We assembled and annotated the genome of the cultivated variety "Big Star*" and assessed the genetic diversity among 97 sweet cherry accessions representing three different stages in the domestication and breeding process (wild trees, landraces and modern varieties). The genetic diversity analysis revealed significant genome-wide losses of variation among the three stages and supports a clear distinction between wild and domesticated trees, with only limited gene flow being detected between wild trees and domesticated landraces. We identified 11 domestication sweeps and five breeding sweeps covering, respectively, 11.0 and 2.4 Mb of the P. avium genome. A considerable fraction of the domestication sweeps overlaps with those detected in the related species, Prunus persica (peach), indicating that artificial selection during domestication may have acted independently on the same regions and genes in the two species. We detected 104 candidate genes in sweep regions involved in different processes, such as the determination of fruit texture, the regulation of flowering and fruit ripening and the resistance to pathogens. The signatures of selection identified will enable future evolutionary studies and provide a valuable resource for genetic improvement and conservation programs in sweet cherry.
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Affiliation(s)
- Sara Pinosio
- Institute of Biosciences and Bioresources (IBBR), National Research Council, Via Madonna del Piano 10, Sesto Fiorentino, 50019, Italy
- Istituto di Genomica Applicata (IGA), Via Jacopo Linussio 51, Udine, 33100, Italy
| | - Fabio Marroni
- Istituto di Genomica Applicata (IGA), Via Jacopo Linussio 51, Udine, 33100, Italy
- Dipartimento di Scienze Agro-alimentari Ambientali e Animali (DI4A), Università di Udine, via delle Scienze 206, Udine, 33100, Italy
| | - Andrea Zuccolo
- Institute of Life Sciences, Scuola Superiore Sant'Anna, Pisa, 56124, Italy
| | - Nicola Vitulo
- Dipartimento di Biotecnologie, Università degli Studi di Verona, Strada Le Grazie 15, Verona, 37134, Italy
| | - Stephanie Mariette
- BIOGECO, INRA, University of Bordeaux, route d'Arcachon 69, Cestas, 33612, France
| | - Gabriella Sonnante
- Institute of Biosciences and Bioresources (IBBR), National Research Council, via Amendola 165/A, Bari, 70126, Italy
| | - Filippos A Aravanopoulos
- Faculty of Forestry and Natural Environment, Laboratory of Forest Genetics and Tree Breeding, Aristotle University of Thessaloniki, Thessaloníki, 54124, Greece
| | - Ioannis Ganopoulos
- Institute of Plant Breeding and Genetic Resources, Hellenic Agricultural Organization-DEMETER, Thermi, 57001, Greece
| | - Marino Palasciano
- Dipartimento di Scienze del Suolo, Università degli Studi di Bari Aldo Moro, della Pianta e degli Alimenti, Piazza Umberto I, Bari, 70121, Italy
| | - Michele Vidotto
- Istituto di Genomica Applicata (IGA), Via Jacopo Linussio 51, Udine, 33100, Italy
| | - Gabriele Magris
- Istituto di Genomica Applicata (IGA), Via Jacopo Linussio 51, Udine, 33100, Italy
- Dipartimento di Scienze Agro-alimentari Ambientali e Animali (DI4A), Università di Udine, via delle Scienze 206, Udine, 33100, Italy
| | - Amy Iezzoni
- Department of Horticulture, Michigan State University, 1066 Bogue Street, East Lansing, MI, 48824-1325, USA
| | - Giovanni G Vendramin
- Institute of Biosciences and Bioresources (IBBR), National Research Council, Via Madonna del Piano 10, Sesto Fiorentino, 50019, Italy
| | - Michele Morgante
- Istituto di Genomica Applicata (IGA), Via Jacopo Linussio 51, Udine, 33100, Italy
- Dipartimento di Scienze Agro-alimentari Ambientali e Animali (DI4A), Università di Udine, via delle Scienze 206, Udine, 33100, Italy
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12
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Zhang B, Jia L, He X, Chen C, Liu H, Liu K, Zhao N, Bao B. Large scale SNP unearthing and genetic architecture analysis in sea-captured and cultured populations of Cynoglossus semilaevis. Genomics 2020; 112:3238-3246. [PMID: 32531446 DOI: 10.1016/j.ygeno.2020.06.013] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2020] [Revised: 05/09/2020] [Accepted: 06/06/2020] [Indexed: 01/07/2023]
Abstract
Knowledge on population structure and genetic diversity is a focal point for association mapping studies and genomic selection. Genotyping by sequencing (GBS) represents an innovative method for large scale SNP detection and genotyping of genetic resources. Here we used the GBS approach for the genome-wide identification of SNPs in a collection of Cynoglossus semilaevis and for the assessment of the level of genetic diversity in C. semilaevis genotypes. GBS analysis generated a total of 55.12 Gb high-quality sequence data, with an average of 0.63 Gb per sample. The total number of SNP markers was 563, 109. In order to explore the genetic diversity of C. semilaevis and to select a minimal core set representing most of the total genetic variation with minimum redundancy, C. semilaevis sequences were analyzed using high quality SNPs. Based on hierarchical clustering, it was possible to divide the collection into 2 clusters. The marine fishing populations were clustered and clearly separated from the cultured populations, and the cultured populations from Hebei was also distinct from the other two local populations. These analyses showed that genotypes were clustered based on species-related features. Differential significant SNPs were also captured and validated by GBS and SNaPshot, with linkage disequilibrium and haplotype analysis, seven SNPs have been confirmed to have obvious differentiation in two populations, which may be used as the characteristic evaluation sites of sea-captured and cultured Cynoglossus semilaevis populations. And SNP markers and information on population structure developed in this study will undoubtedly support genome-wide association mapping studies and marker-assisted selection programs. These differential SNPs could be also employed as the characteristic evaluation sites of sea-captured and cultured Cynoglossus semilaevis populations in future.
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Affiliation(s)
- Bo Zhang
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources (Shanghai Ocean University), Ministry of Education, Shanghai 201306, China;International Research Center for Marine Biosciences at Shanghai Ocean University, Ministry of Science and Technology, Shanghai 201306, China; National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai 201306, China; Tianjin Sea Fisheries Research Institute, Tianjin, China
| | - Lei Jia
- Tianjin Sea Fisheries Research Institute, Tianjin, China
| | - Xiaoxu He
- Tianjin Sea Fisheries Research Institute, Tianjin, China
| | - Chunxiu Chen
- Tianjin Sea Fisheries Research Institute, Tianjin, China
| | - Hao Liu
- Tianjin Sea Fisheries Research Institute, Tianjin, China
| | - Kefeng Liu
- Tianjin Sea Fisheries Research Institute, Tianjin, China
| | - Na Zhao
- Tianjin Haolinsaiao Biotechnology Co, Ltd, Tianjin, China.
| | - Baolong Bao
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources (Shanghai Ocean University), Ministry of Education, Shanghai 201306, China;International Research Center for Marine Biosciences at Shanghai Ocean University, Ministry of Science and Technology, Shanghai 201306, China; National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai 201306, China.
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13
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Wang J, Liu W, Zhu D, Zhou X, Hong P, Zhao H, Tan Y, Chen X, Zong X, Xu L, Zhang L, Wei H, Liu Q. A de novo assembly of the sweet cherry ( Prunus avium cv. Tieton) genome using linked-read sequencing technology. PeerJ 2020; 8:e9114. [PMID: 32547856 PMCID: PMC7278891 DOI: 10.7717/peerj.9114] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Accepted: 04/10/2020] [Indexed: 11/20/2022] Open
Abstract
The sweet cherry (Prunus avium) is one of the most economically important fruit species in the world. However, there is a limited amount of genetic information available for this species, which hinders breeding efforts at a molecular level. We were able to describe a high-quality reference genome assembly and annotation of the diploid sweet cherry (2n = 2x = 16) cv. Tieton using linked-read sequencing technology. We generated over 750 million clean reads, representing 112.63 GB of raw sequencing data. The Supernova assembler produced a more highly-ordered and continuous genome sequence than the current P. avium draft genome, with a contig N50 of 63.65 KB and a scaffold N50 of 2.48 MB. The final scaffold assembly was 280.33 MB in length, representing 82.12% of the estimated Tieton genome. Eight chromosome-scale pseudomolecules were constructed, completing a 214 MB sequence of the final scaffold assembly. De novo, homology-based, and RNA-seq methods were used together to predict 30,975 protein-coding loci. 98.39% of core eukaryotic genes and 97.43% of single copy orthologues were identified in the embryo plant, indicating the completeness of the assembly. Linked-read sequencing technology was effective in constructing a high-quality reference genome of the sweet cherry, which will benefit the molecular breeding and cultivar identification in this species.
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Affiliation(s)
- Jiawei Wang
- Scientific Observation and Experiment Station of Fruits in Huang-huai Area, Ministry of Agriculture, Shandong Institute of Pomology, Taian, Shandong, China
| | - Weizhen Liu
- School of Computer Science and Technology, Wuhan University of Technology, Wuhan, Hubei, China
| | - Dongzi Zhu
- Scientific Observation and Experiment Station of Fruits in Huang-huai Area, Ministry of Agriculture, Shandong Institute of Pomology, Taian, Shandong, China
| | - Xiang Zhou
- Key Laboratory of Agricultural Animal Genetics, Breeding, and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Po Hong
- Scientific Observation and Experiment Station of Fruits in Huang-huai Area, Ministry of Agriculture, Shandong Institute of Pomology, Taian, Shandong, China
| | - Hongjun Zhao
- Scientific Observation and Experiment Station of Fruits in Huang-huai Area, Ministry of Agriculture, Shandong Institute of Pomology, Taian, Shandong, China
| | - Yue Tan
- Scientific Observation and Experiment Station of Fruits in Huang-huai Area, Ministry of Agriculture, Shandong Institute of Pomology, Taian, Shandong, China
| | - Xin Chen
- Scientific Observation and Experiment Station of Fruits in Huang-huai Area, Ministry of Agriculture, Shandong Institute of Pomology, Taian, Shandong, China
| | - Xiaojuan Zong
- Scientific Observation and Experiment Station of Fruits in Huang-huai Area, Ministry of Agriculture, Shandong Institute of Pomology, Taian, Shandong, China
| | - Li Xu
- Scientific Observation and Experiment Station of Fruits in Huang-huai Area, Ministry of Agriculture, Shandong Institute of Pomology, Taian, Shandong, China
| | - Lisi Zhang
- Scientific Observation and Experiment Station of Fruits in Huang-huai Area, Ministry of Agriculture, Shandong Institute of Pomology, Taian, Shandong, China
| | - Hairong Wei
- Scientific Observation and Experiment Station of Fruits in Huang-huai Area, Ministry of Agriculture, Shandong Institute of Pomology, Taian, Shandong, China
| | - Qingzhong Liu
- Scientific Observation and Experiment Station of Fruits in Huang-huai Area, Ministry of Agriculture, Shandong Institute of Pomology, Taian, Shandong, China
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14
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Vanderzande S, Zheng P, Cai L, Barac G, Gasic K, Main D, Iezzoni A, Peace C. The cherry 6+9K SNP array: a cost-effective improvement to the cherry 6K SNP array for genetic studies. Sci Rep 2020; 10:7613. [PMID: 32376836 PMCID: PMC7203174 DOI: 10.1038/s41598-020-64438-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2019] [Accepted: 04/14/2020] [Indexed: 11/09/2022] Open
Abstract
Cherry breeding and genetic studies can benefit from genome-wide genetic marker assays. Currently, a 6K SNP array enables genome scans in cherry; however, only a third of these SNPs are informative, with low coverage in many genomic regions. Adding previously detected SNPs to this array could provide a cost-efficient upgrade with increased genomic coverage across the 670 cM/352.9 Mb cherry whole genome sequence. For sweet cherry, new SNPs were chosen following a focal point strategy, grouping six to eight SNPs within 10-kb windows with an average of 0.6 cM (627 kb) between focal points. Additional SNPs were chosen to represent important regions. Sweet cherry, the fruticosa subgenome of sour cherry, and cherry organellar genomes were targeted with 6942, 2020, and 38 new SNPs, respectively. The +9K add-on provided 2128, 1091, and 70 new reliable, polymorphic SNPs for sweet cherry and the avium and the fruticosa subgenomes of sour cherry, respectively. For sweet cherry, 1241 reliable polymorphic SNPs formed 237 informative focal points, with another 2504 SNPs in-between. The +9K SNPs increased genetic resolution and genome coverage of the original cherry SNP array and will help increase understanding of the genetic control of key traits and relationships among individuals in cherry.
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Affiliation(s)
- Stijn Vanderzande
- Department of Horticulture, Washington State University, Pullman, WA, USA.
| | - Ping Zheng
- Department of Horticulture, Washington State University, Pullman, WA, USA
| | - Lichun Cai
- Department of Horticulture, Michigan State University, East Lansing, MI, USA
| | - Goran Barac
- Department of Fruit Growing, Viticulture, Horticulture and Landscape Architecture, University of Novi Sad, Novi Sad, Serbia
| | - Ksenija Gasic
- Department of Plant and Environmental Sciences, Clemson University, Clemson, SC, USA
| | - Dorrie Main
- Department of Horticulture, Washington State University, Pullman, WA, USA
| | - Amy Iezzoni
- Department of Horticulture, Michigan State University, East Lansing, MI, USA
| | - Cameron Peace
- Department of Horticulture, Washington State University, Pullman, WA, USA
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15
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Guajardo V, Solís S, Almada R, Saski C, Gasic K, Moreno MÁ. Genome-wide SNP identification in Prunus rootstocks germplasm collections using Genotyping-by-Sequencing: phylogenetic analysis, distribution of SNPs and prediction of their effect on gene function. Sci Rep 2020; 10:1467. [PMID: 32001784 PMCID: PMC6992769 DOI: 10.1038/s41598-020-58271-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Accepted: 12/15/2019] [Indexed: 01/09/2023] Open
Abstract
Genotyping-by-Sequencing (GBS) was applied in a set of 53 diploid Prunus rootstocks and five scion cultivars from three subgenera (Amygdalus, Prunus and Cerasus) for genome-wide SNP identification and to assess genetic diversity of both Chilean and Spanish germplasm collections. A group of 45,382 high quality SNPs (MAF >0.05; missing data <5%) were selected for analysis of this group of 58 accessions. These SNPs were distributed in genic and intergenic regions in the eight pseudomolecules of the peach genome (Peach v2.0), with an average of 53% located in exonic regions. The genetic diversity detected among the studied accessions divided them in three groups, which are in agreement with their current taxonomic classification. SNPs were classified based on their putative effect on annotated genes and KOG analysis was carried out to provide a deeper understanding of the function of 119 genes affected by high-impact SNPs. Results demonstrate the high utility for Prunus rootstocks identification and studies of diversity in Prunus species. Also, given the high number of SNPs identified in exonic regions, this strategy represents an important tool for finding candidate genes underlying traits of interest and potential functional markers for use in marker-assisted selection.
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Affiliation(s)
| | - Simón Solís
- Centro de Estudios Avanzados en Fruticultura (CEAF), Rengo, Chile
| | - Rubén Almada
- Centro de Estudios Avanzados en Fruticultura (CEAF), Rengo, Chile
| | - Christopher Saski
- Department of Plant and Environmental Sciences, Clemson University, Clemson, SC, 29634, USA
| | - Ksenija Gasic
- Department of Plant and Environmental Sciences, Clemson University, Clemson, SC, 29634, USA
| | - María Ángeles Moreno
- Department of Pomology, Estación Experimental de Aula Dei-CSIC, 50059, Zaragoza, Spain.
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16
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Kaya HB, Akdemir D, Lozano R, Cetin O, Sozer Kaya H, Sahin M, Smith JL, Tanyolac B, Jannink JL. Genome wide association study of 5 agronomic traits in olive (Olea europaea L.). Sci Rep 2019; 9:18764. [PMID: 31822760 PMCID: PMC6904458 DOI: 10.1038/s41598-019-55338-w] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2019] [Accepted: 11/05/2019] [Indexed: 01/08/2023] Open
Abstract
Olive (Olea europaea L.) is one of the most economically and historically important fruit crops worldwide. Genetic progress for valuable agronomic traits has been slow in olive despite its importance and benefits. Advances in next generation sequencing technologies provide inexpensive and highly reproducible genotyping approaches such as Genotyping by Sequencing, enabling genome wide association study (GWAS). Here we present the first comprehensive GWAS study on olive using GBS. A total of 183 accessions (FULL panel) were genotyped using GBS, 94 from the Turkish Olive GenBank Resource (TOGR panel) and 89 from the USDA-ARS National Clonal Germplasm Repository (NCGR panel) in the USA. After filtering low quality and redundant markers, GWAS was conducted using 24,977 SNPs in FULL, TOGR and NCGR panels. In total, 52 significant associations were detected for leaf length, fruit weight, stone weight and fruit flesh to pit ratio using the MLM_K. Significant GWAS hits were mapped to their positions and 19 candidate genes were identified within a 10-kb distance of the most significant SNP. Our findings provide a framework for the development of markers and identification of candidate genes that could be used in olive breeding programs.
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Affiliation(s)
- Hilal Betul Kaya
- Department of Bioengineering, Faculty of Engineering, Manisa Celal Bayar University, Manisa, Turkey.
- School of Integrative Plant Science, Plant Breeding and Genetics Section, Cornell University, Ithaca, NY, USA.
| | - Deniz Akdemir
- Cornell Statistical Consulting Unit, Cornell University, Ithaca, NY, USA
| | - Roberto Lozano
- School of Integrative Plant Science, Plant Breeding and Genetics Section, Cornell University, Ithaca, NY, USA
| | | | | | | | - Jenny L Smith
- National Clonal Germplasm Repository, USDA-ARS, One Shields Avenue, Davis, CA, USA
| | - Bahattin Tanyolac
- Department of Bioengineering, Faculty of Engineering, Ege University, Bornova, Izmir, Turkey
| | - Jean-Luc Jannink
- School of Integrative Plant Science, Plant Breeding and Genetics Section, Cornell University, Ithaca, NY, USA
- USDA ARS, Robert W. Holley Center for Agriculture & Health, Ithaca, NY, USA
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17
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Wang Z, Zhang Z, Tang H, Zhang Q, Zhou G, Li X. High-Density Genetic Map Construction and QTL Mapping of Leaf and Needling Traits in Ziziphus jujuba Mill. FRONTIERS IN PLANT SCIENCE 2019; 10:1424. [PMID: 31824522 PMCID: PMC6882864 DOI: 10.3389/fpls.2019.01424] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Accepted: 10/14/2019] [Indexed: 05/23/2023]
Abstract
The Chinese jujube (Ziziphus jujuba Mill., 2n = 2x = 24), one of the most popular fruit trees in Asia, is widely cultivated and utilized in China, where it is traditionally consumed as both a fresh and dried food resource. A high-density genetic map can provide the necessary framework for quantitative trait loci (QTL) analyses and map-based gene cloning and molecular breeding. In this study, we constructed a new high-density genetic linkage map via a genotyping-by-sequencing approach. For the consensus linkage map, a total of 3,792 markers spanning 2,167.5 cM were mapped onto 12 linkage groups, with an average marker interval distance of 0.358 cM. The genetic map anchored 301 Mb (85.7%) of scaffolds from the sequenced Z. jujuba "Junzao" genome. Based on this genetic map, 30 potential QTLs were detected, including 27 QTLs for leaf traits and 3 QTLs for needling length. This high-density genetic map and the identified QTLs for relevant agronomic traits lay the groundwork for functional genetic mapping, map-based cloning, and marker-assisted selection in jujube.
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Affiliation(s)
- Zhongtang Wang
- College of Forestry, Northwest A&F University, Yangling, China
- Country Shandong Institute of Pomology, Taian, China
| | - Zhong Zhang
- College of Forestry, Northwest A&F University, Yangling, China
- Research Centre for Jujube Engineering and Technology of State Forestry and Grassland Administration, Northwest A&F University, Yangling, China
| | - Haixia Tang
- Country Shandong Institute of Pomology, Taian, China
| | - Qiong Zhang
- Country Shandong Institute of Pomology, Taian, China
| | | | - Xingang Li
- College of Forestry, Northwest A&F University, Yangling, China
- Research Centre for Jujube Engineering and Technology of State Forestry and Grassland Administration, Northwest A&F University, Yangling, China
- Key Comprehensive Laboratory of Forestry of Shaanxi Province, Northwest A&F University, Yangling, China
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18
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Nantawan U, Kanchana-udomkan C, Bar I, Ford R. Linkage mapping and quantitative trait loci analysis of sweetness and other fruit quality traits in papaya. BMC PLANT BIOLOGY 2019; 19:449. [PMID: 31655544 PMCID: PMC6815024 DOI: 10.1186/s12870-019-2043-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Accepted: 09/20/2019] [Indexed: 05/09/2023]
Abstract
BACKGROUND The identification and characterisation of quantitative trait loci (QTL) is an important step towards identifying functional sequences underpinning important crop traits and for developing accurate markers for selective breeding strategies. In this study, a genotyping-by-sequencing (GBS) approach detected QTL conditioning desirable fruit quality traits in papaya. RESULTS For this, a linkage map was constructed comprising 219 single nucleotide polymorphism (SNP) loci across 10 linkage groups and covering 509 centiMorgan (cM). In total, 21 QTLs were identified for seven key fruit quality traits, including flesh sweetness, fruit weight, fruit length, fruit width skin freckle, flesh thickness and fruit firmness. Several QTL for flesh sweetness, fruit weight, length, width and firmness were stable across harvest years and individually explained up to 19.8% of the phenotypic variance of a particular trait. Where possible, candidate genes were proposed and explored further for their application to marker-assisted breeding. CONCLUSIONS This study has extended knowledge on the inheritance and genetic control for key papaya physiological and fruit quality traits. Candidate genes together with associated SNP markers represent a valuable resource for the future of strategic selective breeding of elite Australian papaya cultivars.
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Affiliation(s)
- Usana Nantawan
- Environmental Futures Research Institute, School of Environment and Sciences, Griffith University, 170 Kessels Road Nathan, Nathan, QLD 4111 Australia
| | - Chutchamas Kanchana-udomkan
- Environmental Futures Research Institute, School of Environment and Sciences, Griffith University, 170 Kessels Road Nathan, Nathan, QLD 4111 Australia
| | - Ido Bar
- Environmental Futures Research Institute, School of Environment and Sciences, Griffith University, 170 Kessels Road Nathan, Nathan, QLD 4111 Australia
| | - Rebecca Ford
- Environmental Futures Research Institute, School of Environment and Sciences, Griffith University, 170 Kessels Road Nathan, Nathan, QLD 4111 Australia
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19
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Yu A, Li F, Xu W, Wang Z, Sun C, Han B, Wang Y, Wang B, Cheng X, Liu A. Application of a high-resolution genetic map for chromosome-scale genome assembly and fine QTLs mapping of seed size and weight traits in castor bean. Sci Rep 2019; 9:11950. [PMID: 31420567 PMCID: PMC6697702 DOI: 10.1038/s41598-019-48492-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Accepted: 06/07/2019] [Indexed: 01/27/2023] Open
Abstract
Castor bean (Ricinus communis L., Euphorbiaceae) is a critical biodiesel crop and its seed derivatives have important industrial applications. Due to lack of a high-density genetic map, the breeding and genetic improvement of castor bean has been largely restricted. In this study, based on a recombinant inbred line (RIL) population consisting of 200 individuals, we generated 8,896 high-quality genomic SNP markers and constructed a high-resolution genetic map with 10 linkage groups (LGs), spanning 1,852.33 centiMorgan (cM). Based on the genetic map, 996 scaffolds from the draft reference genome were anchored onto 10 pseudo-chromosomes, covering 84.43% of the castor bean genome. Furthermore, the quality of the pseudo-chromosome scale assembly genome was confirmed via genome collinearity analysis within the castor bean genome as well as between castor bean and cassava. Our results provide new evidence that the phylogenetic position of castor bean is relatively solitary from other taxa in the Euphorbiaceae family. Based on the genetic map, we identified 16 QTLs that control seed size and weight (covering 851 candidate genes). The findings will be helpful for further research into potential new mechanisms controlling seed size and weight in castor bean. The genetic map and improved pseudo-chromosome scale genome provide crucial foundations for marker-assisted selection (MAS) of QTL governing important agronomic traits, as well as the accelerated molecular breeding of castor bean in a cost-effective pattern.
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Affiliation(s)
- Anmin Yu
- Key Laboratory of Economic Plants and Biotechnology, Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China.,University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Fei Li
- Key Laboratory of Economic Plants and Biotechnology, Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | - Wei Xu
- Key Laboratory of Economic Plants and Biotechnology, Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | - Zaiqing Wang
- Key Laboratory of Economic Plants and Biotechnology, Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China.,University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Chao Sun
- Key Laboratory of Economic Plants and Biotechnology, Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | - Bing Han
- Key Laboratory of Economic Plants and Biotechnology, Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China.,University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Yue Wang
- Key Laboratory of Economic Plants and Biotechnology, Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | - Bo Wang
- Wuhan Genoseq Technology Co., Ltd, Wuhan, 430070, China
| | - Xiaomao Cheng
- Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, Southwest Forestry University, Kunming, 650224, China
| | - Aizhong Liu
- Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, Southwest Forestry University, Kunming, 650224, China.
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20
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Hardner CM, Hayes BJ, Kumar S, Vanderzande S, Cai L, Piaskowski J, Quero-Garcia J, Campoy JA, Barreneche T, Giovannini D, Liverani A, Charlot G, Villamil-Castro M, Oraguzie N, Peace CP. Prediction of genetic value for sweet cherry fruit maturity among environments using a 6K SNP array. HORTICULTURE RESEARCH 2019; 6:6. [PMID: 30603092 PMCID: PMC6312542 DOI: 10.1038/s41438-018-0081-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Revised: 06/08/2018] [Accepted: 07/15/2018] [Indexed: 05/21/2023]
Abstract
The timing of fruit maturity is an important trait in sweet cherry production and breeding. Phenotypic variation for phenology of fruit maturity in sweet cherry appears to be under strong genetic control, but that control might be complicated by phenotypic instability across environments. Although such genotype-by-environment interaction (G × E) is a common phenomenon in crop plants, knowledge about it is lacking for fruit maturity timing and other sweet cherry traits. In this study, 1673 genome-wide SNP markers were used to estimate genomic relationships among 597 weakly pedigree-connected individuals evaluated over two seasons at three locations in Europe and one location in the USA, thus sampling eight 'environments'. The combined dataset enabled a single meta-analysis to investigate the environmental stability of genomic predictions. Linkage disequilibrium among marker loci declined rapidly with physical distance, and ordination of the relationship matrix suggested no strong structure among germplasm. The most parsimonious G × E model allowed heterogeneous genetic variance and pairwise covariances among environments. Narrow-sense genomic heritability was very high (0.60-0.83), as was accuracy of predicted breeding values (>0.62). Average correlation of additive effects among environments was high (0.96) and breeding values were highly correlated across locations. Results indicated that genomic models can be used in cherry to accurately predict date of fruit maturity for untested individuals in new environments. Limited G × E for this trait indicated that phenotypes of individuals will be stable across similar environments. Equivalent analyses for other sweet cherry traits, for which multiple years of data are commonly available among breeders and cultivar testers, would be informative for predicting performance of elite selections and cultivars in new environments.
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Affiliation(s)
- Craig M. Hardner
- University of Queensland, Queensland Alliance for Agriculture and Food Innovation, Brisbane, QLD 4072 Australia
| | - Ben J. Hayes
- University of Queensland, Queensland Alliance for Agriculture and Food Innovation, Brisbane, QLD 4072 Australia
| | - Satish Kumar
- The New Zealand Institute for Plant and Food Research Limited, Hawke’s Bay Research Centre, Hastings, 4130 New Zealand
| | - Stijn Vanderzande
- Department of Horticulture, Washington State University, Pullman, WA 99164 USA
| | - Lichun Cai
- Department of Horticulture, Michigan State University, East Lansing, MI 48824 USA
| | - Julia Piaskowski
- Department of Horticulture, Washington State University, Pullman, WA 99164 USA
| | - José Quero-Garcia
- UMR 1332 BFP, INRA, University of Bordeaux, 33140 Nouvelle-Aquitaine, France
| | - José Antonio Campoy
- UMR 1332 BFP, INRA, University of Bordeaux, 33140 Nouvelle-Aquitaine, France
| | - Teresa Barreneche
- UMR 1332 BFP, INRA, University of Bordeaux, 33140 Nouvelle-Aquitaine, France
| | - Daniela Giovannini
- Council for Agricultural Research and Economics (CREA), Fruit Unit of Forlì, Via la Canapona, 1 bis, 47121 Emilia-Romagna, Italy
| | - Alessandro Liverani
- Council for Agricultural Research and Economics (CREA), Fruit Unit of Forlì, Via la Canapona, 1 bis, 47121 Emilia-Romagna, Italy
| | - Gérard Charlot
- Centre Technique Interprofessionnel des Fruits et Légumes (CTIFL), 751 Chemin de Balandran, 30127 Bellegarde, France
| | - Miguel Villamil-Castro
- University of Queensland, Queensland Alliance for Agriculture and Food Innovation, Brisbane, QLD 4072 Australia
| | - Nnadozie Oraguzie
- Department of Horticulture, Washington State University, Irrigated Agriculture Research and Extension Center, 24106N Bunn Road, Prosser, WA 99350 USA
| | - Cameron P. Peace
- Department of Horticulture, Washington State University, Pullman, WA 99164 USA
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21
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Carrasco B, González M, Gebauer M, García-González R, Maldonado J, Silva H. Construction of a highly saturated linkage map in Japanese plum (Prunus salicina L.) using GBS for SNP marker calling. PLoS One 2018; 13:e0208032. [PMID: 30507961 PMCID: PMC6277071 DOI: 10.1371/journal.pone.0208032] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Accepted: 11/09/2018] [Indexed: 11/19/2022] Open
Abstract
This study reports the construction of high density linkage maps of Japanese plum (Prunus salicina Lindl.) using single nucleotide polymorphism markers (SNPs), obtained with a GBS strategy. The mapping population (An x Au) was obtained by crossing cv. "Angeleno" (An) as maternal line and cv. "Aurora" (Au) as the pollen donor. A total of 49,826 SNPs were identified using the peach genome V2.1 as a reference. Then a stringent filtering was carried out, which revealed 1,441 high quality SNPs in 137 An x Au offspring, which were mapped in eight linkage groups. Finally, the consensus map was built using 732 SNPs which spanned 617 cM with an average of 0.96 cM between adjacent markers. The majority of the SNPs were distributed in the intragenic region in all the linkage groups. Considering all linkage groups together, 85.6% of the SNPs were located in intragenic regions and only 14.4% were located in intergenic regions. The genetic linkage analysis was able to co-localize two to three SNPs over 37 putative orthologous genes in eight linkage groups in the Japanese plum map. These results indicate a high level of synteny and collinearity between Japanese plum and peach genomes.
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Affiliation(s)
- Basilio Carrasco
- Pontificia Universidad Católica de Chile, Facultad de Agronomía e Ingeniería Forestal, Departamento de Ciencias Vegetales, Macul, Santiago, Chile
| | - Máximo González
- Pontificia Universidad Católica de Chile, Facultad de Agronomía e Ingeniería Forestal, Departamento de Ciencias Vegetales, Macul, Santiago, Chile
| | - Marlene Gebauer
- Pontificia Universidad Católica de Chile, Facultad de Agronomía e Ingeniería Forestal, Departamento de Ciencias Vegetales, Macul, Santiago, Chile
| | - Rolando García-González
- Sociedad BioTECNOS Ltda, R&D Department Camino a Pangal Km 2 1/2, San Javier, Región del Maule, Chile
- Facultad de Ciencias Agrarias y Forestales, Centro de Biotecnología de los Recursos Naturales (CENBio), Universidad Católica del Maule, Talca, Chile
| | - Jonathan Maldonado
- Universidad de Chile, Facultad de Ciencias Agronómicas, Departamento de Producción Agrícola, Laboratorio de Genómica Funcional & Bioinformática, La Pintana, Santiago, Chile
| | - Herman Silva
- Universidad de Chile, Facultad de Ciencias Agronómicas, Departamento de Producción Agrícola, Laboratorio de Genómica Funcional & Bioinformática, La Pintana, Santiago, Chile
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22
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Yang Q, Yang Z, Tang H, Yu Y, Chen Z, Wei S, Sun Q, Peng Z. High-density genetic map construction and mapping of the homologous transformation sterility gene (hts) in wheat using GBS markers. BMC PLANT BIOLOGY 2018; 18:301. [PMID: 30477426 PMCID: PMC6258151 DOI: 10.1186/s12870-018-1532-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Accepted: 11/16/2018] [Indexed: 05/07/2023]
Abstract
BACKGROUND Homologous transformation sterility-1 (HTS-1) is a novel wheat mutant that exhibits pistillody, the transformation of stamens into pistils or pistil-like structures. More extreme phenotypes of this mutation can have six pistils or pistil-like structures without any stamens in a floret. Thus, HTS-1 is highly valuable for studies of wheat hybrid breeding and flower development. Previous studies have shown that two major genes (Pis1 and hts) control pistillody in HTS-1. The Pis1 gene controls the three-pistil trait in the three-pistil wheat mutant and has been mapped on chromosome 2D, but the hts gene has not been mapped or identified. To do so, we crossed HTS-1 with CM28TP (three-pistil mutant) and constructed a high-density linkage map with the F2 population (200 individuals). RESULTS The map covered 2779.96 cM, and the genetic distance per chromosome ranged from 37.59 cM to 318.95 cM. The average distance between markers was 1.04 cM. We then mapped hts between GBS-SNP markers 4A_109 and 4A_119, separated by 2.0 cM and 5.2 Mb. To find the candidate genes, the hts region was enlarged to 7.2 Mb, encompassing 752 protein-coding genes. We identified TaWin1 as a possible candidate gene after comparing the 752 genes with 206 common differentially expressed genes between pistillody stamens (PS) versus normal stamens (S) and pistils (P) versus S. Real-time PCR indicated that TaWin1 was highly expressed in HTS-1 during the pistil-and-stamen-differentiating stage, at levels approximately 120 times greater than those in CM28TP. Further analysis indicated that TaWin1 was mainly expressed in HTS-1 PS, supporting its status as a candidate gene of hts. Thus, TaWin1 overexpression probably leads to the transformation of stamens into pistils in wheat. CONCLUSIONS The results of this study provide a foundation for further research on stamen and pistil development, with implications for wheat-hybrid breeding programs.
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Affiliation(s)
- Qian Yang
- Key Laboratory of Southwest China Wildlife Resources Conservation (ministry of education), College of Life Science, China West Normal University, Nanchong, 637009 Sichuan China
| | - Zaijun Yang
- Key Laboratory of Southwest China Wildlife Resources Conservation (ministry of education), College of Life Science, China West Normal University, Nanchong, 637009 Sichuan China
| | - Haifeng Tang
- Key Laboratory of Southwest China Wildlife Resources Conservation (ministry of education), College of Life Science, China West Normal University, Nanchong, 637009 Sichuan China
| | - Yan Yu
- Key Laboratory of Southwest China Wildlife Resources Conservation (ministry of education), College of Life Science, China West Normal University, Nanchong, 637009 Sichuan China
| | - Zhenyong Chen
- Key Laboratory of Southwest China Wildlife Resources Conservation (ministry of education), College of Life Science, China West Normal University, Nanchong, 637009 Sichuan China
| | - Shuhong Wei
- Key Laboratory of Southwest China Wildlife Resources Conservation (ministry of education), College of Life Science, China West Normal University, Nanchong, 637009 Sichuan China
| | - Qinxu Sun
- Key Laboratory of Southwest China Wildlife Resources Conservation (ministry of education), College of Life Science, China West Normal University, Nanchong, 637009 Sichuan China
| | - Zhengsong Peng
- School of Agricultural Science, Xichang University, Xichang, 615000 Sichuan China
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23
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Yao X, Wu K, Yao Y, Bai Y, Ye J, Chi D. Construction of a high-density genetic map: genotyping by sequencing (GBS) to map purple seed coat color ( Psc) in hulless barley. Hereditas 2018; 155:37. [PMID: 30473656 PMCID: PMC6240233 DOI: 10.1186/s41065-018-0072-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Accepted: 10/18/2018] [Indexed: 01/24/2023] Open
Abstract
Background Colored hulless barley are more suitable in food processing compared to normal (yellow) varieties because it is rich in bioactive compounds and produces higher extraction pearling fractions. Therefore, seed coat color is an important agronomic trait for the breeding and study of hulless barley. Results Genotyping-by-sequencing single-nucleotide polymorphism (GBS-SNP) analysis of a doubled haploid (DH) mapping population (Nierumuzha × Kunlun10) was conducted to map the purple seed coat color genes (Psc). A high-density genetic map of hulless barley was constructed, which contains 3662 efficient SNP markers with 1129 bin markers. Seven linkage groups were resolved, which had a total length of 645.56 cM. Chromosome length ranged from 60.21 cM to 127.21 cM, with average marker density of 0.57 cM. A total of five loci accounting for 3.79% to 23.86% of the observed phenotypic variation for Psc were detected using this high-density map. Five structural candidate genes (F3’M, HID, UF3GT, UFGT and 5MAT) and one regulatory factor (Ant1) related to flavonoid or anthocyanin biosynthesis were identified.. Conclusions Five structural candidate genes and one regulatory factor related to flavonoid or anthocyanin biosynthesis have been identified using a high-density genetic map of hulless barley. This study lays the foundation for map-based cloning of Psc but provides a valuable tool for studying marker-trait associations and its application to marker-assisted breeding of hulless barley. Electronic supplementary material The online version of this article (10.1186/s41065-018-0072-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Xiaohua Yao
- 1State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, 810016 China.,2Academy of Agricultural and Forestry Sciences, Qinghai University, Xining, 810016 China.,Qinghai Key Laboratory of Hulless Barley Genetics and Breeding, Xining, 810016 China.,Qinghai Subcenter of National Hulless Barley Improvement, Xining, 810016 China
| | - Kunlun Wu
- 1State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, 810016 China.,2Academy of Agricultural and Forestry Sciences, Qinghai University, Xining, 810016 China.,Qinghai Key Laboratory of Hulless Barley Genetics and Breeding, Xining, 810016 China.,Qinghai Subcenter of National Hulless Barley Improvement, Xining, 810016 China
| | - Youhua Yao
- 1State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, 810016 China.,2Academy of Agricultural and Forestry Sciences, Qinghai University, Xining, 810016 China.,Qinghai Key Laboratory of Hulless Barley Genetics and Breeding, Xining, 810016 China.,Qinghai Subcenter of National Hulless Barley Improvement, Xining, 810016 China
| | - Yixiong Bai
- 1State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, 810016 China.,2Academy of Agricultural and Forestry Sciences, Qinghai University, Xining, 810016 China.,Qinghai Key Laboratory of Hulless Barley Genetics and Breeding, Xining, 810016 China.,Qinghai Subcenter of National Hulless Barley Improvement, Xining, 810016 China
| | - Jingxiu Ye
- 1State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, 810016 China.,2Academy of Agricultural and Forestry Sciences, Qinghai University, Xining, 810016 China
| | - Dezhao Chi
- 1State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, 810016 China.,2Academy of Agricultural and Forestry Sciences, Qinghai University, Xining, 810016 China.,Qinghai Key Laboratory of Hulless Barley Genetics and Breeding, Xining, 810016 China.,Qinghai Subcenter of National Hulless Barley Improvement, Xining, 810016 China
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24
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Conson ARO, Taniguti CH, Amadeu RR, Andreotti IAA, de Souza LM, dos Santos LHB, Rosa JRBF, Mantello CC, da Silva CC, José Scaloppi Junior E, Ribeiro RV, Le Guen V, Garcia AAF, Gonçalves PDS, de Souza AP. High-Resolution Genetic Map and QTL Analysis of Growth-Related Traits of Hevea brasiliensis Cultivated Under Suboptimal Temperature and Humidity Conditions. FRONTIERS IN PLANT SCIENCE 2018; 9:1255. [PMID: 30197655 PMCID: PMC6117502 DOI: 10.3389/fpls.2018.01255] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Accepted: 08/08/2018] [Indexed: 06/02/2023]
Abstract
Rubber tree (Hevea brasiliensis) cultivation is the main source of natural rubber worldwide and has been extended to areas with suboptimal climates and lengthy drought periods; this transition affects growth and latex production. High-density genetic maps with reliable markers support precise mapping of quantitative trait loci (QTL), which can help reveal the complex genome of the species, provide tools to enhance molecular breeding, and shorten the breeding cycle. In this study, QTL mapping of the stem diameter, tree height, and number of whorls was performed for a full-sibling population derived from a GT1 and RRIM701 cross. A total of 225 simple sequence repeats (SSRs) and 186 single-nucleotide polymorphism (SNP) markers were used to construct a base map with 18 linkage groups and to anchor 671 SNPs from genotyping by sequencing (GBS) to produce a very dense linkage map with small intervals between loci. The final map was composed of 1,079 markers, spanned 3,779.7 cM with an average marker density of 3.5 cM, and showed collinearity between markers from previous studies. Significant variation in phenotypic characteristics was found over a 59-month evaluation period with a total of 38 QTLs being identified through a composite interval mapping method. Linkage group 4 showed the greatest number of QTLs (7), with phenotypic explained values varying from 7.67 to 14.07%. Additionally, we estimated segregation patterns, dominance, and additive effects for each QTL. A total of 53 significant effects for stem diameter were observed, and these effects were mostly related to additivity in the GT1 clone. Associating accurate genome assemblies and genetic maps represents a promising strategy for identifying the genetic basis of phenotypic traits in rubber trees. Then, further research can benefit from the QTLs identified herein, providing a better understanding of the key determinant genes associated with growth of Hevea brasiliensis under limiting water conditions.
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Affiliation(s)
- André R. O. Conson
- Molecular Biology and Genetic Engineering Center, University of Campinas, Campinas, Brazil
| | - Cristiane H. Taniguti
- Department of Genetics, Luiz de Queiroz College of Agriculture, University of São Paulo, Piracicaba, Brazil
| | - Rodrigo R. Amadeu
- Department of Genetics, Luiz de Queiroz College of Agriculture, University of São Paulo, Piracicaba, Brazil
| | | | - Livia M. de Souza
- Molecular Biology and Genetic Engineering Center, University of Campinas, Campinas, Brazil
| | | | - João R. B. F. Rosa
- Department of Genetics, Luiz de Queiroz College of Agriculture, University of São Paulo, Piracicaba, Brazil
- FTS Sementes S.A., Research and Development Center, Ponta Grossa, Brazil
| | - Camila C. Mantello
- Molecular Biology and Genetic Engineering Center, University of Campinas, Campinas, Brazil
- National Institute of Agricultural Botany (NIAB), Cambridge, United Kingdom
| | - Carla C. da Silva
- Molecular Biology and Genetic Engineering Center, University of Campinas, Campinas, Brazil
| | | | - Rafael V. Ribeiro
- Department of Plant Biology, Institute of Biology, University of Campinas, Campinas, Brazil
| | - Vincent Le Guen
- French Agricultural Research Centre for International Development (CIRAD), UMR AGAP, Montpellier, France
| | - Antonio A. F. Garcia
- Department of Genetics, Luiz de Queiroz College of Agriculture, University of São Paulo, Piracicaba, Brazil
| | | | - Anete P. de Souza
- Molecular Biology and Genetic Engineering Center, University of Campinas, Campinas, Brazil
- Department of Plant Biology, Institute of Biology, University of Campinas, Campinas, Brazil
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25
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Ji F, Wei W, Liu Y, Wang G, Zhang Q, Xing Y, Zhang S, Liu Z, Cao Q, Qin L. Construction of a SNP-Based High-Density Genetic Map Using Genotyping by Sequencing (GBS) and QTL Analysis of Nut Traits in Chinese Chestnut ( Castanea mollissima Blume). FRONTIERS IN PLANT SCIENCE 2018; 9:816. [PMID: 29963069 PMCID: PMC6011034 DOI: 10.3389/fpls.2018.00816] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Accepted: 05/28/2018] [Indexed: 05/09/2023]
Abstract
Chinese chestnut is a wildly distributed nut species with importantly economic value. The nut size and ripening period are mainly desired breeding objectives in Chinese chestnut. However, high-density linkage maps and quantitative trait loci (QTL) analyses related to nut traits are less than satisfactory, which hinders progress in the breeding of Chinese chestnut. Here, a single nucleotide polymorphism (SNP)-based high-density linkage map was constructed through genotyping-by-sequencing (GBS) of an F1 cross between the two widely grown Chinese chestnut cultivars 'Yanshanzaofeng' and 'Guanting No. 10'. The genetic linkage map consists of 2,620 SNP markers with a total length of 1078.06 cM in 12 linkage groups (LGs) and an average marker distance of 0.41 cM. 17 QTLs were identified for five nut traits, specifically single-nut weight (SNW), nut width (NW), nut thickness (NT), nut height (NH), and ripening period (RP), based on phenotypic data from two successive years. Of the 17 QTLs, two major QTLs, i.e., qNT-I-1 and qRP-B-1 related to the NT and RP traits, respectively, were exploited. Moreover, the data revealed one pleiotropic QTL at 23.97 cM on LG I, which might simultaneously control SNW, NT, and NW. This study provides useful benchmark information concerning high-density genetic mapping and QTLs identification related to nut size and ripening period, and will accelerate genetic improvements for nuts in the marker-assisted selection (MAS) breeding of Chinese chestnut.
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Affiliation(s)
- Feiyang Ji
- Department of Plant Science and Technology, Beijing Key Laboratory of Agricultural Application and New Technique, Beijing University of Agriculture, Beijing, China
| | - Wei Wei
- Department of Plant Science and Technology, Beijing Key Laboratory of Agricultural Application and New Technique, Beijing University of Agriculture, Beijing, China
| | - Yang Liu
- Department of Plant Science and Technology, Beijing Key Laboratory of Agricultural Application and New Technique, Beijing University of Agriculture, Beijing, China
| | - Guangpeng Wang
- Changli Institute of Pomology, Hebei Academy of Agriculture and Forestry Sciences, Changli, China
| | - Qing Zhang
- Department of Plant Science and Technology, Beijing Key Laboratory of Agricultural Application and New Technique, Beijing University of Agriculture, Beijing, China
| | - Yu Xing
- Department of Plant Science and Technology, Beijing Key Laboratory of Agricultural Application and New Technique, Beijing University of Agriculture, Beijing, China
- Beijing Collaborative Innovation Center for Eco-Environmental Improvement with Forestry and Fruit Trees, Beijing, China
| | - Shuhang Zhang
- Changli Institute of Pomology, Hebei Academy of Agriculture and Forestry Sciences, Changli, China
| | - Zhihao Liu
- Novogene Bioinformatics Technology Co., Ltd., Tianjin, China
| | - Qingqin Cao
- Beijing Collaborative Innovation Center for Eco-Environmental Improvement with Forestry and Fruit Trees, Beijing, China
- Department of Biological Science and Engineering, Key Laboratory of Urban Agriculture (North China), Ministry of Agriculture, Beijing University of Agriculture, Beijing, China
| | - Ling Qin
- Department of Plant Science and Technology, Beijing Key Laboratory of Agricultural Application and New Technique, Beijing University of Agriculture, Beijing, China
- Beijing Collaborative Innovation Center for Eco-Environmental Improvement with Forestry and Fruit Trees, Beijing, China
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26
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Torello Marinoni D, Valentini N, Portis E, Acquadro A, Beltramo C, Mehlenbacher SA, Mockler TC, Rowley ER, Botta R. High density SNP mapping and QTL analysis for time of leaf budburst in Corylus avellana L. PLoS One 2018; 13:e0195408. [PMID: 29608620 PMCID: PMC5880404 DOI: 10.1371/journal.pone.0195408] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2017] [Accepted: 03/21/2018] [Indexed: 01/25/2023] Open
Abstract
The growing area of European hazelnut (Corylus avellana L.) is increasing, as well as the number of producing countries, and there is a pressing need for new improved cultivars. Hazelnut conventional breeding process is slow, due to the length of juvenile phase and the high heterozygosity level. The development of genetic linkage maps and the identification of molecular markers tightly linked to QTL (quantitative trait loci) of agronomic interest are essential tools for speeding up the selection of seedlings carrying desired traits through marker-assisted selection. The objectives of this study were to enrich a previous linkage map and confirm QTL related to time of leaf budburst, using an F1 population obtained by crossing Tonda Gentile delle Langhe with Merveille de Bollwiller. Genotyping-by-Sequencing was used to identify a total of 9,999 single nucleotide polymorphism markers. Well saturated linkage maps were constructed for each parent using the double pseudo-testcross mapping strategy. A reciprocal translocation was detected in Tonda Gentile delle Langhe between two non-homologous chromosomes. Applying a bioinformatic approach, we were able to disentangle ‘pseudo-linkage’ between markers, removing markers around the translocation breakpoints and obtain a linear order of the markers for the two chromosomes arms, for each linkage group involved in the translocation. Twenty-nine QTL for time of leaf budburst were identified, including a stably expressed region on LG_02 of the Tonda Gentile delle Langhe map. The stability of these QTL and their coding sequence content indicates promise for the identification of specific chromosomal regions carrying key genes involved in leaf budburst.
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Affiliation(s)
- Daniela Torello Marinoni
- Dipartimento di Scienze Agrarie, Forestali e Alimentari, Università degli Studi di Torino, Grugliasco, Torino, Italy
| | - Nadia Valentini
- Dipartimento di Scienze Agrarie, Forestali e Alimentari, Università degli Studi di Torino, Grugliasco, Torino, Italy
| | - Ezio Portis
- Dipartimento di Scienze Agrarie, Forestali e Alimentari, Università degli Studi di Torino, Grugliasco, Torino, Italy
- * E-mail:
| | - Alberto Acquadro
- Dipartimento di Scienze Agrarie, Forestali e Alimentari, Università degli Studi di Torino, Grugliasco, Torino, Italy
| | - Chiara Beltramo
- Dipartimento di Scienze Agrarie, Forestali e Alimentari, Università degli Studi di Torino, Grugliasco, Torino, Italy
| | - Shawn A. Mehlenbacher
- Department of Horticulture, Oregon State University, Corvallis, Oregon, United States of America
| | - Todd C. Mockler
- Donald Danforth Plant Science Center, St. Louis, Missouri, United States of America
| | - Erik R. Rowley
- Donald Danforth Plant Science Center, St. Louis, Missouri, United States of America
| | - Roberto Botta
- Dipartimento di Scienze Agrarie, Forestali e Alimentari, Università degli Studi di Torino, Grugliasco, Torino, Italy
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27
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Genotyping by Sequencing in Almond: SNP Discovery, Linkage Mapping, and Marker Design. G3-GENES GENOMES GENETICS 2018; 8:161-172. [PMID: 29141988 PMCID: PMC5765344 DOI: 10.1534/g3.117.300376] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
In crop plant genetics, linkage maps provide the basis for the mapping of loci that affect important traits and for the selection of markers to be applied in crop improvement. In outcrossing species such as almond (Prunus dulcis Mill. D. A. Webb), application of a double pseudotestcross mapping approach to the F1 progeny of a biparental cross leads to the construction of a linkage map for each parent. Here, we report on the application of genotyping by sequencing to discover and map single nucleotide polymorphisms in the almond cultivars “Nonpareil” and “Lauranne.” Allele-specific marker assays were developed for 309 tag pairs. Application of these assays to 231 Nonpareil × Lauranne F1 progeny provided robust linkage maps for each parent. Analysis of phenotypic data for shell hardness demonstrated the utility of these maps for quantitative trait locus mapping. Comparison of these maps to the peach genome assembly confirmed high synteny and collinearity between the peach and almond genomes. The marker assays were applied to progeny from several other Nonpareil crosses, providing the basis for a composite linkage map of Nonpareil. Applications of the assays to a panel of almond clones and a panel of rootstocks used for almond production demonstrated the broad applicability of the markers and provide subsets of markers that could be used to discriminate among accessions. The sequence-based linkage maps and single nucleotide polymorphism assays presented here could be useful resources for the genetic analysis and genetic improvement of almond.
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Yan M, Byrne DH, Klein PE, Yang J, Dong Q, Anderson N. Genotyping-by-sequencing application on diploid rose and a resulting high-density SNP-based consensus map. HORTICULTURE RESEARCH 2018; 5:17. [PMID: 29619228 PMCID: PMC5878828 DOI: 10.1038/s41438-018-0021-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2017] [Revised: 10/03/2017] [Accepted: 01/22/2018] [Indexed: 05/09/2023]
Abstract
Roses, which have been cultivated for at least 5000 years, are one of the most important ornamental crops in the world. Because of the interspecific nature and high heterozygosity in commercial roses, the genetic resources available for rose are limited. To effectively identify markers associated with QTL controlling important traits, such as disease resistance, abundant markers along the genome and careful phenotyping are required. Utilizing genotyping by sequencing technology and the strawberry genome (Fragaria vesca v2.0.a1) as a reference, we generated thousands of informative single nucleotide polymorphism (SNP) markers. These SNPs along with known bridge simple sequence repeat (SSR) markers allowed us to create the first high-density integrated consensus map for diploid roses. Individual maps were first created for populations J06-20-14-3×"Little Chief" (J14-3×LC), J06-20-14-3×"Vineyard Song" (J14-3×VS) and "Old Blush"×"Red Fairy" (OB×RF) and these maps were linked with 824 SNPs and 13 SSR bridge markers. The anchor SSR markers were used to determine the numbering of the rose linkage groups. The diploid consensus map has seven linkage groups (LGs), a total length of 892.2 cM, and an average distance of 0.25 cM between 3527 markers. By combining three individual populations, the marker density and the reliability of the marker order in the consensus map was improved over a single population map. Extensive synteny between the strawberry and diploid rose genomes was observed. This consensus map will serve as the tool for the discovery of marker-trait associations in rose breeding using pedigree-based analysis. The high level of conservation observed between the strawberry and rose genomes will help further comparative studies within the Rosaceae family and may aid in the identification of candidate genes within QTL regions.
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Affiliation(s)
- Muqing Yan
- Department of Horticultural Sciences, Texas A&M University, College Station, TX 77843 USA
| | - David H. Byrne
- Department of Horticultural Sciences, Texas A&M University, College Station, TX 77843 USA
| | - Patricia E. Klein
- Department of Horticultural Sciences, Texas A&M University, College Station, TX 77843 USA
- Institute for Plant Genomics and Biotechnology, Texas A&M University, College Station, TX 77843 USA
| | - Jizhou Yang
- Institute for Plant Genomics and Biotechnology, Texas A&M University, College Station, TX 77843 USA
- Present Address: Department of Computer Science, San Francisco State University, San Francisco, CA 94132 USA
| | - Qianni Dong
- Department of Horticultural Sciences, Texas A&M University, College Station, TX 77843 USA
- Present Address: Monsanto Company, 700 Chesterfield Parkway West, Chesterfield, MO 63017 USA
| | - Natalie Anderson
- Department of Horticultural Sciences, Texas A&M University, College Station, TX 77843 USA
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Shirasawa K, Isuzugawa K, Ikenaga M, Saito Y, Yamamoto T, Hirakawa H, Isobe S. The genome sequence of sweet cherry (Prunus avium) for use in genomics-assisted breeding. DNA Res 2017; 24:499-508. [PMID: 28541388 PMCID: PMC5737369 DOI: 10.1093/dnares/dsx020] [Citation(s) in RCA: 130] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Accepted: 04/25/2017] [Indexed: 12/13/2022] Open
Abstract
We determined the genome sequence of sweet cherry (Prunus avium) using next-generation sequencing technology. The total length of the assembled sequences was 272.4 Mb, consisting of 10,148 scaffold sequences with an N50 length of 219.6 kb. The sequences covered 77.8% of the 352.9 Mb sweet cherry genome, as estimated by k-mer analysis, and included >96.0% of the core eukaryotic genes. We predicted 43,349 complete and partial protein-encoding genes. A high-density consensus map with 2,382 loci was constructed using double-digest restriction site–associated DNA sequencing. Comparing the genetic maps of sweet cherry and peach revealed high synteny between the two genomes; thus the scaffolds were integrated into pseudomolecules using map- and synteny-based strategies. Whole-genome resequencing of six modern cultivars found 1,016,866 SNPs and 162,402 insertions/deletions, out of which 0.7% were deleterious. The sequence variants, as well as simple sequence repeats, can be used as DNA markers. The genomic information helps us to identify agronomically important genes and will accelerate genetic studies and breeding programs for sweet cherries. Further information on the genomic sequences and DNA markers is available in DBcherry (http://cherry.kazusa.or.jp (8 May 2017, date last accessed)).
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Affiliation(s)
- Kenta Shirasawa
- Kazusa DNA Research Institute, Kisarazu, Chiba 292-0818, Japan
| | - Kanji Isuzugawa
- Horticultural Experiment Station, Yamagata Integrated Agricultural Research Center, Sagae, Yamagata 991-0043, Japan
| | - Mitsunobu Ikenaga
- Central Agricultural Experiment Station, Agricultural Research Department, Hokkaido Research Organization, Naganuma, Hokkaido 069-1395, Japan
| | - Yutaro Saito
- Horticultural Experiment Station, Yamagata Integrated Agricultural Research Center, Sagae, Yamagata 991-0043, Japan
| | - Toshiya Yamamoto
- Institute of Fruit Tree and Tea Science, National Agriculture and Food Research Organization, Tsukuba, Ibaraki 305-8605, Japan
| | - Hideki Hirakawa
- Kazusa DNA Research Institute, Kisarazu, Chiba 292-0818, Japan
| | - Sachiko Isobe
- Kazusa DNA Research Institute, Kisarazu, Chiba 292-0818, Japan
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Wu Y, Chen Y, Pan C, Xiao N, Yu L, Li Y, Zhang X, Pan X, Chen X, Liang C, Dai Z, Li A. Development and Evaluation of Near-Isogenic Lines with Different Blast Resistance Alleles at the Piz Locus in japonica Rice from the Lower Region of the Yangtze River, China. PLANT DISEASE 2017; 101:1283-1291. [PMID: 30682968 DOI: 10.1094/pdis-12-16-1855-re] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Rice blast, caused by Magnaporthe oryzae, threatens rice production in most of the rice-growing areas in China, especially in regions that have grown Oryza sativa subsp. japonica in recent years. The use of resistance genes is the most effective and economical approach for blast control. In our study, a set of six near-isogenic lines (NIL) were developed by introgression of six resistance alleles of the Piz locus (Pi2, Pigm, Pi40, Pi9, Piz, and Pizt) into a blast-susceptible, high-yielding, high-quality japonica '07GY31' via marker-assisted backcross breeding. Artificial inoculation using 144 M. oryzae isolates collected from the lower region of the Yangtze River, China, revealed that most of the NIL, including NIL-Pi2, NIL-Pigm, NIL-Pi40, NIL-Pi9, and NIL-Pizt, exhibited broad-spectrum resistance against rice blast at the seedling stage, with resistance frequencies (RF) of 93.06 to 98.61%. NIL-Piz was an exception, with an RF of 21.53%, which was slightly higher than the recurrent parent 07GY31. NIL-Pi40 and NIL-Pigm had broad-spectrum resistance (RF of 93.33 and 71.67%, respectively) at the heading stage following inoculation of 60 isolates of M. oryzae. Field trials with artificial inoculation at the seedling and heading stage showed that NIL-Pigm and NIL-Pi40 were highly resistant in four locations under high disease pressure. NIL-Pizt showed effective resistance in three locations from Zhejiang and Jiangsu Provinces. This study shows that O. sativa subsp. japonica alleles of the Piz locus confer resistance to M. oryzae, and provides an effective method to enhance seedling and panicle blast resistance in rice plants in the lower region of the Yangtze River, China.
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Affiliation(s)
- Yunyu Wu
- Lixiahe Agricultural Research Institute of Jiangsu Province, Yangzhou 225009, China; and Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing 210095, China
| | - Yu Chen
- Lixiahe Agricultural Research Institute of Jiangsu Province, Yangzhou; Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing; and Key Laboratory of Plant Functional Genomics, Ministry of Education, Yangzhou University, Yangzhou, 225009, China
| | - Cunhong Pan
- Lixiahe Agricultural Research Institute of Jiangsu Province, Yangzhou and Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing
| | - Ning Xiao
- Lixiahe Agricultural Research Institute of Jiangsu Province, Yangzhou and Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing
| | - Ling Yu
- Lixiahe Agricultural Research Institute of Jiangsu Province, Yangzhou and Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing
| | - Yuhong Li
- Lixiahe Agricultural Research Institute of Jiangsu Province, Yangzhou and Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing
| | - Xiaoxiang Zhang
- Lixiahe Agricultural Research Institute of Jiangsu Province, Yangzhou and Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing
| | - Xuebiao Pan
- Key Laboratory of Plant Functional Genomics, Ministry of Education, Yangzhou University, Yangzhou
| | - Xijun Chen
- Key Laboratory of Plant Functional Genomics, Ministry of Education, Yangzhou University, Yangzhou
| | - Chengzhi Liang
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Zhengyuan Dai
- Lixiahe Agricultural Research Institute of Jiangsu Province, Yangzhou 225009, China; and Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing 210095, China
| | - Aihong Li
- Lixiahe Agricultural Research Institute of Jiangsu Province, Yangzhou 225009, China; and Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing 210095, China
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31
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Hewitt S, Kilian B, Hari R, Koepke T, Sharpe R, Dhingra A. Evaluation of multiple approaches to identify genome-wide polymorphisms in closely related genotypes of sweet cherry ( Prunus avium L.). Comput Struct Biotechnol J 2017; 15:290-298. [PMID: 28392892 PMCID: PMC5376269 DOI: 10.1016/j.csbj.2017.03.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2016] [Revised: 03/02/2017] [Accepted: 03/08/2017] [Indexed: 11/25/2022] Open
Abstract
Identification of genetic polymorphisms and subsequent development of molecular markers is important for marker assisted breeding of superior cultivars of economically important species. Sweet cherry (Prunus avium L.) is an economically important non-climacteric tree fruit crop in the Rosaceae family and has undergone a genetic bottleneck due to breeding, resulting in limited genetic diversity in the germplasm that is utilized for breeding new cultivars. Therefore, it is critical to recognize the best platforms for identifying genome-wide polymorphisms that can help identify, and consequently preserve, the diversity in a genetically constrained species. For the identification of polymorphisms in five closely related genotypes of sweet cherry, a gel-based approach (TRAP), reduced representation sequencing (TRAPseq), a 6k cherry SNParray, and whole genome sequencing (WGS) approaches were evaluated in the identification of genome-wide polymorphisms in sweet cherry cultivars. All platforms facilitated detection of polymorphisms among the genotypes with variable efficiency. In assessing multiple SNP detection platforms, this study has demonstrated that a combination of appropriate approaches is necessary for efficient polymorphism identification, especially between closely related cultivars of a species. The information generated in this study provides a valuable resource for future genetic and genomic studies in sweet cherry, and the insights gained from the evaluation of multiple approaches can be utilized for other closely related species with limited genetic diversity in the breeding germplasm.
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Affiliation(s)
- Seanna Hewitt
- Molecular Plant Sciences Graduate Program, Washington State University, Pullman, WA 99164, United States; Department of Horticulture, Washington State University, Pullman, WA 99164-6414, United States
| | - Benjamin Kilian
- Molecular Plant Sciences Graduate Program, Washington State University, Pullman, WA 99164, United States; Department of Horticulture, Washington State University, Pullman, WA 99164-6414, United States
| | - Ramyya Hari
- Department of Horticulture, Washington State University, Pullman, WA 99164-6414, United States
| | - Tyson Koepke
- Molecular Plant Sciences Graduate Program, Washington State University, Pullman, WA 99164, United States; Department of Horticulture, Washington State University, Pullman, WA 99164-6414, United States
| | - Richard Sharpe
- Molecular Plant Sciences Graduate Program, Washington State University, Pullman, WA 99164, United States; Department of Horticulture, Washington State University, Pullman, WA 99164-6414, United States
| | - Amit Dhingra
- Molecular Plant Sciences Graduate Program, Washington State University, Pullman, WA 99164, United States; Department of Horticulture, Washington State University, Pullman, WA 99164-6414, United States
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32
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İpek A, İpek M, Ercişli S, Tangu NA. Transcriptome-based SNP discovery by GBS and the construction of a genetic map for olive. Funct Integr Genomics 2017; 17:493-501. [PMID: 28213629 DOI: 10.1007/s10142-017-0552-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2016] [Revised: 02/04/2017] [Accepted: 02/07/2017] [Indexed: 10/20/2022]
Abstract
Molecular markers located in the genic regions of plants are valuable tools for the identification of candidate genes of economically important traits and consequent use in marker-assisted selection (MAS). In the past, simple sequence repeat markers (SSRs) and single-nucleotide polymorphisms (SNPs) located in expressed sequence tags (ESTs) were developed by sequencing RNA derived from different plant tissues, which involves laborious RNA extraction, mRNA isolation, and cDNA synthesis. In order to develop SNP markers located in olive transcriptomes, we used the recently developed genotyping-by-sequencing (GBS) technique. An analysis was done for 125 olive DNA samples (123 DNA samples from a cross-pollinated F1 mapping population, and two samples from parents). From 45 to 66% of Illumina reads from GBS analysis were aligned to the olive transcriptome. A total of 22,033 transcriptome-based SNP markers were identified, and 3384 of these were mapped in the olive genome. The genetic linkage map constructed in this study consists of 1 cleaved amplified polymorphic sequence (CAPS), 19 SSR, and 3384 transcriptome-based SNP markers. The map covers 3340.8 cM of the olive genome in 23 linkage groups, with the length of the linkage groups ranging from 55.6 to 248.7 cM. Average map distance between flanking markers was 0.98 cM. This genetic linkage map is a saturated genetic map and will be a useful tool for the localization of quantitative trait loci (QTLs) and gene(s) of interest and for the identification of candidate genes for economically important traits.
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Affiliation(s)
- Ahmet İpek
- Faculty of Agriculture, Horticulture Department, Uludag University, Bursa, Turkey.
| | - Meryem İpek
- Faculty of Agriculture, Horticulture Department, Uludag University, Bursa, Turkey
| | - Sezai Ercişli
- Faculty of Agriculture, Horticulture Department, Atatürk University, Erzurum, Turkey
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33
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Scheben A, Batley J, Edwards D. Genotyping-by-sequencing approaches to characterize crop genomes: choosing the right tool for the right application. PLANT BIOTECHNOLOGY JOURNAL 2017; 15:149-161. [PMID: 27696619 PMCID: PMC5258866 DOI: 10.1111/pbi.12645] [Citation(s) in RCA: 124] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2016] [Revised: 09/24/2016] [Accepted: 09/28/2016] [Indexed: 05/18/2023]
Abstract
In the last decade, the revolution in sequencing technologies has deeply impacted crop genotyping practice. New methods allowing rapid, high-throughput genotyping of entire crop populations have proliferated and opened the door to wider use of molecular tools in plant breeding. These new genotyping-by-sequencing (GBS) methods include over a dozen reduced-representation sequencing (RRS) approaches and at least four whole-genome resequencing (WGR) approaches. The diversity of methods available, each often producing different types of data at different cost, can make selection of the best-suited method seem a daunting task. We review the most common genotyping methods used today and compare their suitability for linkage mapping, genomewide association studies (GWAS), marker-assisted and genomic selection and genome assembly and improvement in crops with various genome sizes and complexity. Furthermore, we give an outline of bioinformatics tools for analysis of genotyping data. WGR is well suited to genotyping biparental cross populations with complex, small- to moderate-sized genomes and provides the lowest cost per marker data point. RRS approaches differ in their suitability for various tasks, but demonstrate similar costs per marker data point. These approaches are generally better suited for de novo applications and more cost-effective when genotyping populations with large genomes or high heterozygosity. We expect that although RRS approaches will remain the most cost-effective for some time, WGR will become more widespread for crop genotyping as sequencing costs continue to decrease.
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Affiliation(s)
- Armin Scheben
- School of Plant Biology and Institute of AgricultureUniversity of Western AustraliaPerthWAAustralia
| | - Jacqueline Batley
- School of Plant Biology and Institute of AgricultureUniversity of Western AustraliaPerthWAAustralia
| | - David Edwards
- School of Plant Biology and Institute of AgricultureUniversity of Western AustraliaPerthWAAustralia
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Salazar JA, Pacheco I, Shinya P, Zapata P, Silva C, Aradhya M, Velasco D, Ruiz D, Martínez-Gómez P, Infante R. Genotyping by Sequencing for SNP-Based Linkage Analysis and Identification of QTLs Linked to Fruit Quality Traits in Japanese Plum ( Prunus salicina Lindl.). FRONTIERS IN PLANT SCIENCE 2017; 8:476. [PMID: 28443103 PMCID: PMC5386982 DOI: 10.3389/fpls.2017.00476] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2017] [Accepted: 03/20/2017] [Indexed: 05/21/2023]
Abstract
Marker-assisted selection (MAS) in stone fruit (Prunus species) breeding is currently difficult to achieve due to the polygenic nature of the most relevant agronomic traits linked to fruit quality. Genotyping by sequencing (GBS), however, provides a large quantity of useful data suitable for fine mapping using Single Nucleotide Polymorphisms (SNPs) from a reference genome. In this study, GBS was used to genotype 272 seedlings of three F1 Japanese plum (Prunus salicina Lindl) progenies derived from crossing "98-99" (as a common female parent) with "Angeleno," "September King," and "September Queen" as male parents. Raw sequences were aligned to the Peach genome v1, and 42,909 filtered SNPs were obtained after sequence alignment. In addition, 153 seedlings from the "98-99" × "Angeleno" cross were used to develop a genetic map for each parent. A total of 981 SNPs were mapped (479 for "98-99" and 502 for "Angeleno"), covering a genetic distance of 688.8 and 647.03 cM, respectively. Fifty five seedlings from this progeny were phenotyped for different fruit quality traits including ripening time, fruit weight, fruit shape, chlorophyll index, skin color, flesh color, over color, firmness, and soluble solids content in the years 2015 and 2016. Linkage-based QTL analysis allowed the identification of genomic regions significantly associated with ripening time (LG4 of both parents and both phenotyping years), fruit skin color (LG3 and LG4 of both parents and both years), chlorophyll degradation index (LG3 of both parents in 2015) and fruit weight (LG7 of both parents in 2016). These results represent a promising situation for GBS in the identification of SNP variants associated to fruit quality traits, potentially applicable in breeding programs through MAS, in a highly heterozygous crop species such as Japanese plum.
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Affiliation(s)
- Juan A. Salazar
- Departamento de Producción Agrícola, Universidad de ChileSantiago, Chile
| | - Igor Pacheco
- Laboratorio de Bioinformática y Expresión Génica, Instituto de Nutrición y Tecnología de Alimentos, Universidad de ChileSantiago, Chile
| | - Paulina Shinya
- Departamento de Producción Agrícola, Universidad de ChileSantiago, Chile
| | - Patricio Zapata
- Departamento de Producción Agrícola, Universidad de ChileSantiago, Chile
| | - Claudia Silva
- Laboratorio de Bioinformática y Expresión Génica, Instituto de Nutrición y Tecnología de Alimentos, Universidad de ChileSantiago, Chile
| | | | | | - David Ruiz
- National Clonal Germplasm Repository, ARS, USDADavis, CA, USA
| | | | - Rodrigo Infante
- Departamento de Producción Agrícola, Universidad de ChileSantiago, Chile
- *Correspondence: Rodrigo Infante
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Monden Y, Tahara M. Genetic linkage analysis using DNA markers in sweetpotato. BREEDING SCIENCE 2017; 67:41-51. [PMID: 28465667 PMCID: PMC5407921 DOI: 10.1270/jsbbs.16142] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2016] [Accepted: 10/03/2016] [Indexed: 05/23/2023]
Abstract
Sweetpotato is one of the most important food crop species in the world, with more than 104,000,000 tons produced each year, and the breeding of superior cultivars with agronomically important traits, such as improved disease resistance, yield, and nutrient richness, is necessary, especially in developing countries. However, as a result of the crop's complex genomic architecture, which results from its hexaploidy (2n = 6× = 90), high heterozygosity, huge genome, and outcrossing nature, the analysis of genetic linkage in sweetpotato has been challenging. In addition, the lack of whole genome sequences or gene annotations for cultivated hexaploids has interrupted the validation of mapped QTL regions and gene cloning. In spite of these technical difficulties, linkage map construction and QTL mapping analysis have been reported. This review summarizes the results of these linkage analyses, which used SSR, AFLP, and retrotransposon-based molecular markers, and describes future directions for the genetic analysis and marker-assisted breeding of this important but genetically complex crop species.
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Affiliation(s)
- Yuki Monden
- Graduate School of Environmental and Life Science, Okayama University,
1-1-1 Tsushimanaka Kitaku, Okayama, Okayama 700-8530,
Japan
| | - Makoto Tahara
- Graduate School of Environmental and Life Science, Okayama University,
1-1-1 Tsushimanaka Kitaku, Okayama, Okayama 700-8530,
Japan
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36
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Correia S, Schouten R, Silva AP, Gonçalves B. Factors Affecting Quality and Health Promoting Compounds during Growth and Postharvest Life of Sweet Cherry ( Prunus avium L.). FRONTIERS IN PLANT SCIENCE 2017; 8:2166. [PMID: 29312407 PMCID: PMC5742238 DOI: 10.3389/fpls.2017.02166] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2017] [Accepted: 12/08/2017] [Indexed: 05/13/2023]
Abstract
Sweet cherries are attractive fruits due to their taste, color, nutritional value, and beneficial health effects. Sweet cherry is a highly perishable fruit and all quality attributes and the level of health promoting compounds are affected by growth conditions, picking, packing, transport, and storage. During production, the correct combination of scion × rootstock will produce fruits with higher firmness, weight, sugars, vitamins, and phenolic compounds that boost the fruit antioxidant activity. Orchard management, such as applying drip irrigation and summer pruning, will increase fruit sugar levels and total phenolic content, while application of growth regulators can result in improved storability, increased red coloring, increased fruit size, and reduced cracking. Salicylic acid, oxalic acid, acetylsalicylic acid, and methyl salicylate are promising growth regulators as they also increase total phenolics, anthocyanins, and induce higher activity of antioxidant enzymes. These growth regulators are now also applied as fruit coatings that improve shelf-life with higher antioxidant enzyme activities and total phenolics. Optimizing storage and transport conditions, such as hydro cooling with added CaCl2, chain temperature and relative humidity control, are crucial for slowing down decay of quality attributes and increasing the antioxidant capacity. Application of controlled atmosphere during storage is successful in delaying quality attributes, but lowers ascorbic acid levels. The combination of low temperature storage in combination with modified atmosphere packaging (MAP) is successful in reducing the incidence of fruit decay, while preserving taste attributes and stem color with a higher antioxidant capacity. A new trend in MAP is the use of biodegradable films such as micro-perforated polylactic acid film that combine significant retention of quality attributes, high consumer acceptability, and a reduced environmental footprint. Another trend is to replace MAP with fruit edible coatings. Edible coatings, such as various lipid composite coatings, have advantages in retaining quality attributes and increasing the antioxidant activity (chitosan) and are regarded as approved food additives, although studies regarding consumer acceptance are needed. The recent publication of the sweet cherry genome will likely increase the identification of more candidate genes involved in growing and maintaining health related compounds and quality attributes.
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Affiliation(s)
- Sofia Correia
- Centre for the Research and Technology of Agro-Environmental and Biological Sciences, University of Trás-os-Montes e Alto Douro, Vila Real, Portugal
- *Correspondence: Sofia Correia
| | - Rob Schouten
- Horticulture and Product Physiology, Wageningen University, Wageningen, Netherlands
| | - Ana P. Silva
- Centre for the Research and Technology of Agro-Environmental and Biological Sciences, University of Trás-os-Montes e Alto Douro, Vila Real, Portugal
| | - Berta Gonçalves
- Centre for the Research and Technology of Agro-Environmental and Biological Sciences, University of Trás-os-Montes e Alto Douro, Vila Real, Portugal
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Xiao S, Wang P, Dong L, Zhang Y, Han Z, Wang Q, Wang Z. Whole-genome single-nucleotide polymorphism (SNP) marker discovery and association analysis with the eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA) content in Larimichthys crocea. PeerJ 2016; 4:e2664. [PMID: 28028455 PMCID: PMC5180582 DOI: 10.7717/peerj.2664] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2016] [Accepted: 10/07/2016] [Indexed: 12/30/2022] Open
Abstract
Whole-genome single-nucleotide polymorphism (SNP) markers are valuable genetic resources for the association and conservation studies. Genome-wide SNP development in many teleost species are still challenging because of the genome complexity and the cost of re-sequencing. Genotyping-By-Sequencing (GBS) provided an efficient reduced representative method to squeeze cost for SNP detection; however, most of recent GBS applications were reported on plant organisms. In this work, we used an EcoRI-NlaIII based GBS protocol to teleost large yellow croaker, an important commercial fish in China and East-Asia, and reported the first whole-genome SNP development for the species. 69,845 high quality SNP markers that evenly distributed along genome were detected in at least 80% of 500 individuals. Nearly 95% randomly selected genotypes were successfully validated by Sequenom MassARRAY assay. The association studies with the muscle eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA) content discovered 39 significant SNP markers, contributing as high up to ∼63% genetic variance that explained by all markers. Functional genes that involved in fat digestion and absorption pathway were identified, such as APOB, CRAT and OSBPL10. Notably, PPT2 Gene, previously identified in the association study of the plasma n-3 and n-6 polyunsaturated fatty acid level in human, was re-discovered in large yellow croaker. Our study verified that EcoRI-NlaIII based GBS could produce quality SNP markers in a cost-efficient manner in teleost genome. The developed SNP markers and the EPA and DHA associated SNP loci provided invaluable resources for the population structure, conservation genetics and genomic selection of large yellow croaker and other fish organisms.
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Affiliation(s)
- Shijun Xiao
- Fisheries College, Jimei University, Xiamen, Fujian, China
| | - Panpan Wang
- Fisheries College, Jimei University, Xiamen, Fujian, China
| | - Linsong Dong
- Fisheries College, Jimei University, Xiamen, Fujian, China
| | - Yaguang Zhang
- Fisheries College, Jimei University, Xiamen, Fujian, China
| | - Zhaofang Han
- Fisheries College, Jimei University, Xiamen, Fujian, China
| | - Qiurong Wang
- Fisheries College, Jimei University, Xiamen, Fujian, China
| | - Zhiyong Wang
- Fisheries College, Jimei University, Xiamen, Fujian, China
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38
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Gürcan K, Teber S, Ercisli S, Yilmaz KU. Genotyping by Sequencing (GBS) in Apricots and Genetic Diversity Assessment with GBS-Derived Single-Nucleotide Polymorphisms (SNPs). Biochem Genet 2016; 54:854-885. [PMID: 27465591 DOI: 10.1007/s10528-016-9762-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Accepted: 07/20/2016] [Indexed: 11/27/2022]
Abstract
Genotyping by sequencing (GBS), which is a highly promising technique for molecular breeding, has been implemented in apricots, including Turkish, European, and Plum Pox Virus-resistant accessions. DNA samples were digested with the ApeKI restriction enzyme to construct a genome-complexity-reduced 90-plex GBS library. After filtering the raw sequences, approximately 28 G of clean data were generated, and 17,842 high-quality single-nucleotide polymorphism (SNP) loci were discovered. A total of 561 SNP loci with 0 or 1 missing reads for the 90 accessions produced 1162 markers that were used for the cluster and population structure analysis of the same collection. The results of the SNP analysis indicated that the relation of the European accessions with the western Turkish apricots was accurately positioned. The resistant accessions from different sources were clustered together, confirming the previous finding that SEO/Harlayne-type resistance probably originated from the same source. The Malatya accessions produce most of the world's dried apricots and are likely to be a genetically distinct group. Simple sequence repeat (SSR) and self-incompatibly (SI) locus characterization of the accessions was also included. SI genotyping supported the SNP findings, demonstrating both the reliability of SNP genotyping and the usefulness of SI genotyping for understanding the history of apricot breeding. The SSR genotyping revealed a characterization similar to that of SNP genotyping with a slightly lower resolution in the dendrogram. In conclusion, the GBS approach was validated in apricots, with the discovery of a large number of SNPs, and was demonstrated to be reliable by fingerprinting the accessions in a more informative manner.
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Affiliation(s)
- Kahraman Gürcan
- Genome and Stem Cell Research Center, Erciyes University, Kayseri, Turkey.
- Department of Agricultural Biotechnology, Erciyes University, Kayseri, Turkey.
| | - Saffet Teber
- Genome and Stem Cell Research Center, Erciyes University, Kayseri, Turkey
- Department of Agricultural Biotechnology, Erciyes University, Kayseri, Turkey
| | - Sezai Ercisli
- Department of Horticulture, Faculty of Agriculture, Ataturk University, Erzurum, Turkey
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Mahoney LL, Sargent DJ, Abebe-Akele F, Wood DJ, Ward JA, Bassil NV, Hancock JF, Folta KM, Davis TM. A High-Density Linkage Map of the Ancestral Diploid Strawberry, , Constructed with Single Nucleotide Polymorphism Markers from the IStraw90 Array and Genotyping by Sequencing. THE PLANT GENOME 2016; 9. [PMID: 27898812 DOI: 10.3835/plantgenome2015.08.0071] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Makino is recognized as an ancestor of the octoploid strawberry species, which includes the cultivated strawberry, × Duchesne ex Rozier. Here we report the construction of the first high-density linkage map for . The linkage map (Fii map) is based on two high-throughput techniques of single nucleotide polymorphism (SNP) genotyping: the IStraw90 Array (hereafter "Array"), and genotyping by sequencing (GBS). The F generation mapping population was derived by selfing hybrid F1D, the product of a cross between two divergent accessions collected from Hokkaido, Japan. The Fii map consists of seven linkage groups (LGs) and has an overall length of 451.7 cM as defined by 496 loci populated by 4173 markers: 3280 from the Array and 893 from GBS. Comparisons with two versions of the ssp. L. 'Hawaii 4' pseudo-chromosome (PC) assemblies reveal substantial conservation of synteny and colinearity, yet identified differences that point to possible genomic divergences between and , and/or to genomic assembly errors. The Fii map provides a basis for anchoring a genome assembly as a prerequisite for constructing a second diploid reference genome for .
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40
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Berthouly-Salazar C, Mariac C, Couderc M, Pouzadoux J, Floc’h JB, Vigouroux Y. Genotyping-by-Sequencing SNP Identification for Crops without a Reference Genome: Using Transcriptome Based Mapping as an Alternative Strategy. FRONTIERS IN PLANT SCIENCE 2016; 7:777. [PMID: 27379109 PMCID: PMC4908121 DOI: 10.3389/fpls.2016.00777] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Accepted: 05/19/2016] [Indexed: 05/26/2023]
Abstract
Next-generation sequencing opens the way for genomic studies of diversity even for non-model crops and animals. Genome reduction techniques are becoming progressively more popular as they allow a fraction of the genome to be sequenced for multiple individuals and/or populations. These techniques are an efficient way to explore genome diversity in non-model crops and animals for which no reference genome is available. Genome reduction techniques emerged with the development of specific pipelines such as UNEAK (Universal Network Enabled Analysis Kit) and Stacks. However, even for non-model crops and animals, transcriptomes are easier to obtain, thereby making it possible to directly map reads. We investigate the direct use of transcriptome as an alternative strategy. Our specific objective was to compare SNPs obtained from the UNEAK pipeline as well as SNPs obtained by directly mapping genotyping-by-sequencing reads on a transcriptome. We assessed the feasibility of both SNP datasets, UNEAK and transcriptome mapping, to investigate the diversity of 91 samples of wild pearl millet sampled across its distribution area. Both approaches produced several tens of thousands of single nucleotide variants, but differed in the way the variants were identified, leading to differences in the frequency spectrum associated with marked differences in the assessment of diversity. Difference in the frequency spectrum significantly biased a large set of diversity analyses as well as detection of selection approaches. However, whatever the approach, we found very similar inference of genetic structure, with three major genetic groups from West, Central, and East Africa. For non-model crops, using transcriptome data as a reference is thus a particularly promising way to obtain a more thorough analysis of datasets generated using genome reduction techniques.
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İpek A, Yılmaz K, Sıkıcı P, Tangu NA, Öz AT, Bayraktar M, İpek M, Gülen H. SNP Discovery by GBS in Olive and the Construction of a High-Density Genetic Linkage Map. Biochem Genet 2016; 54:313-325. [PMID: 26902470 DOI: 10.1007/s10528-016-9721-5] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2015] [Accepted: 02/10/2016] [Indexed: 10/22/2022]
Abstract
Genetic linkage maps are valuable tools for genetic, genomic, and crop breeding studies. Several genetic linkage maps were constructed for the olive (Olea europaea L.) genome, mainly using amplified fragment length polymorphisms (AFLPs) and simple sequence repeat (SSR) markers. However, AFLPs and SSR markers were not enough to develop a high-density olive linkage map. Genotyping-by-sequencing (GBS), a recently developed single-nucleotide polymorphism (SNP) identification methodology based on next-generation sequencing (NGS) technologies, has been demonstrated to be useful for the identification of a high number of SNP markers and the construction of high-density genetic linkage maps. In the present study, we identified a total of 10,941 SNPs from a cross between the olive cultivars 'Gemlik' and 'Edincik Su' using GBS and de novo SNP discovery implemented in the computer program "Stacks." A high-density genetic linkage map for the olive genome was constructed using 121 cross-pollinated full-sib F1 progeny and 5643 markers (21 SSRs, 203 AFLPs, and 5736 SNPs). This linkage map was composed of 25 linkage groups, covering 3049 cM of the olive genome, and the mean distance between the flanking markers was 0.53 cM. To the best of our knowledge, this map is the most saturated genetic linkage map in olive to date. We demonstrated that GBS is a valuable tool for the identification of thousands of SNPs for the construction of a saturated genetic linkage map in olive. The high-density genetic map developed in this study is a useful tool for locating quantitative trait loci and other economically important traits in the olive genome.
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Affiliation(s)
- Ahmet İpek
- Department of Horticulture, Faculty of Agriculture, Uludag University, Bursa, Turkey.
| | - Kübra Yılmaz
- Department of Molecular Biology and Genetics, Faculty of Arts and Science, Uludag University, Bursa, Turkey
| | - Pelin Sıkıcı
- Department of Horticulture, Faculty of Agriculture, Uludag University, Bursa, Turkey
| | | | - Ayşe Tülin Öz
- Department of Food Engineering, Faculty of Engineering, Osmaniye Korkut Ata University, Osmaniye, Turkey
| | - Murat Bayraktar
- Department of Horticulture, Faculty of Agriculture, Uludag University, Bursa, Turkey
| | - Meryem İpek
- Department of Horticulture, Faculty of Agriculture, Uludag University, Bursa, Turkey
| | - Hatice Gülen
- Department of Horticulture, Faculty of Agriculture, Uludag University, Bursa, Turkey
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Nimmakayala P, Abburi VL, Saminathan T, Almeida A, Davenport B, Davidson J, Reddy CVCM, Hankins G, Ebert A, Choi D, Stommel J, Reddy UK. Genome-Wide Divergence and Linkage Disequilibrium Analyses for Capsicum baccatum Revealed by Genome-Anchored Single Nucleotide Polymorphisms. FRONTIERS IN PLANT SCIENCE 2016; 7:1646. [PMID: 27857720 PMCID: PMC5093146 DOI: 10.3389/fpls.2016.01646] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2016] [Accepted: 10/18/2016] [Indexed: 05/03/2023]
Abstract
Principal component analysis (PCA) with 36,621 polymorphic genome-anchored single nucleotide polymorphisms (SNPs) identified collectively for Capsicum annuum and Capsicum baccatum was used to characterize population structure and species domestication of these two important incompatible cultivated pepper species. Estimated mean nucleotide diversity (π) and Tajima's D across various chromosomes revealed biased distribution toward negative values on all chromosomes (except for chromosome 4) in cultivated C. baccatum, indicating a population bottleneck during domestication of C. baccatum. In contrast, C. annuum chromosomes showed positive π and Tajima's D on all chromosomes except chromosome 8, which may be because of domestication at multiple sites contributing to wider genetic diversity. For C. baccatum, 13,129 SNPs were available, with minor allele frequency (MAF) ≥0.05; PCA of the SNPs revealed 283 C. baccatum accessions grouped into 3 distinct clusters, for strong population structure. The fixation index (FST ) between domesticated C. annuum and C. baccatum was 0.78, which indicates genome-wide divergence. We conducted extensive linkage disequilibrium (LD) analysis of C. baccatum var. pendulum cultivars on all adjacent SNP pairs within a chromosome to identify regions of high and low LD interspersed with a genome-wide average LD block size of 99.1 kb. We characterized 1742 haplotypes containing 4420 SNPs (range 9-2 SNPs per haplotype). Genome-wide association study (GWAS) of peduncle length, a trait that differentiates wild and domesticated C. baccatum types, revealed 36 significantly associated genome-wide SNPs. Population structure, identity by state (IBS) and LD patterns across the genome will be of potential use for future GWAS of economically important traits in C. baccatum peppers.
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Affiliation(s)
- Padma Nimmakayala
- Department of Biology, Gus R. Douglass Institute, West Virginia State UniversityInstitute, WV, USA
| | - Venkata L. Abburi
- Department of Biology, Gus R. Douglass Institute, West Virginia State UniversityInstitute, WV, USA
| | - Thangasamy Saminathan
- Department of Biology, Gus R. Douglass Institute, West Virginia State UniversityInstitute, WV, USA
| | - Aldo Almeida
- Department of Biology, Gus R. Douglass Institute, West Virginia State UniversityInstitute, WV, USA
| | - Brittany Davenport
- Department of Biology, Gus R. Douglass Institute, West Virginia State UniversityInstitute, WV, USA
| | - Joshua Davidson
- Department of Biology, Gus R. Douglass Institute, West Virginia State UniversityInstitute, WV, USA
| | | | - Gerald Hankins
- Department of Biology, Gus R. Douglass Institute, West Virginia State UniversityInstitute, WV, USA
| | - Andreas Ebert
- Genetic Resources and Seed Unit, Asian Vegetable Research and Development Center-The World Vegetable CenterTainan, Taiwan
| | - Doil Choi
- Department of Plant Science, Plant Genomics and Breeding Institute, College of Agriculture and Life Sciences, Seoul National UniversitySeoul, South Korea
| | - John Stommel
- Genetic Improvement of Fruits and Vegetables Laboratory (United States Department of Agriculture, Agricultural Research Service)Beltsville, MD, USA
| | - Umesh K. Reddy
- Department of Biology, Gus R. Douglass Institute, West Virginia State UniversityInstitute, WV, USA
- *Correspondence: Umesh K. Reddy
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Yamamoto T, Terakami S. Genomics of pear and other Rosaceae fruit trees. BREEDING SCIENCE 2016; 66:148-59. [PMID: 27069399 PMCID: PMC4780798 DOI: 10.1270/jsbbs.66.148] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2015] [Accepted: 01/12/2016] [Indexed: 05/04/2023]
Abstract
The family Rosaceae includes many economically important fruit trees, such as pear, apple, peach, cherry, quince, apricot, plum, raspberry, and loquat. Over the past few years, whole-genome sequences have been released for Chinese pear, European pear, apple, peach, Japanese apricot, and strawberry. These sequences help us to conduct functional and comparative genomics studies and to develop new cultivars with desirable traits by marker-assisted selection in breeding programs. These genomics resources also allow identification of evolutionary relationships in Rosaceae, development of genome-wide SNP and SSR markers, and construction of reference genetic linkage maps, which are available through the Genome Database for the Rosaceae website. Here, we review the recent advances in genomics studies and their practical applications for Rosaceae fruit trees, particularly pear, apple, peach, and cherry.
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Affiliation(s)
- Toshiya Yamamoto
- NARO Institute of Fruit Tree Science,
2-1 Fujimoto, Tsukuba, Ibaraki 305-8605,
Japan
| | - Shingo Terakami
- NARO Institute of Fruit Tree Science,
2-1 Fujimoto, Tsukuba, Ibaraki 305-8605,
Japan
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Wang J, Zhang K, Zhang X, Yan G, Zhou Y, Feng L, Ni Y, Duan X. Construction of Commercial Sweet Cherry Linkage Maps and QTL Analysis for Trunk Diameter. PLoS One 2015; 10:e0141261. [PMID: 26516760 PMCID: PMC4627659 DOI: 10.1371/journal.pone.0141261] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2015] [Accepted: 10/05/2015] [Indexed: 12/03/2022] Open
Abstract
A cross between the sweet cherry (Prunus avium) cultivars ‘Wanhongzhu’ and ‘Lapins’ was performed to create a mapping population suitable for the construction of a linkage map. The specific-locus amplified fragment (SLAF) sequencing technique used as a single nucleotide polymorphism (SNP) discovery platform and generated 701 informative genotypic assays; these, along with 16 microsatellites (SSRs) and the incompatibility (S) gene, were used to build a map which comprised 8 linkage groups (LGs) and covered a genetic distance of 849.0 cM. The mean inter-marker distance was 1.18 cM and there were few gaps > 5 cM in length. Marker collinearity was maintained with the established peach genomic sequence. The map was used to show that trunk diameter (TD) is under the control of 4 loci, mapping to 3 different LGs. Different locus influenced TD at a varying stage of the tree’s development. The high density ‘W×L’ genetic linkage map has the potential to enable high-resolution identification of QTLs of agronomically relevant traits, and accelerate sweet cherry breeding.
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Affiliation(s)
- Jing Wang
- Institute of Forestry and Pomology, Beijing Academy of Agricultural and Forestry Sciences, Beijing, 100093, China
- Beijing Engineering Research Center for Deciduous Fruit Trees, Beijing, 100093, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, P.R. China, Beijing, 100093, China
| | - Kaichun Zhang
- Institute of Forestry and Pomology, Beijing Academy of Agricultural and Forestry Sciences, Beijing, 100093, China
- Beijing Engineering Research Center for Deciduous Fruit Trees, Beijing, 100093, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, P.R. China, Beijing, 100093, China
- * E-mail:
| | - Xiaoming Zhang
- Institute of Forestry and Pomology, Beijing Academy of Agricultural and Forestry Sciences, Beijing, 100093, China
- Beijing Engineering Research Center for Deciduous Fruit Trees, Beijing, 100093, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, P.R. China, Beijing, 100093, China
| | - Guohua Yan
- Institute of Forestry and Pomology, Beijing Academy of Agricultural and Forestry Sciences, Beijing, 100093, China
- Beijing Engineering Research Center for Deciduous Fruit Trees, Beijing, 100093, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, P.R. China, Beijing, 100093, China
| | - Yu Zhou
- Institute of Forestry and Pomology, Beijing Academy of Agricultural and Forestry Sciences, Beijing, 100093, China
- Beijing Engineering Research Center for Deciduous Fruit Trees, Beijing, 100093, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, P.R. China, Beijing, 100093, China
| | - Laibao Feng
- Laboratory of Photosynthesis and Environmental Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Xiangshan Nanxincun 20, Beijing, 100093, China
| | - Yang Ni
- Institute of Forestry and Pomology, Beijing Academy of Agricultural and Forestry Sciences, Beijing, 100093, China
- Beijing Engineering Research Center for Deciduous Fruit Trees, Beijing, 100093, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, P.R. China, Beijing, 100093, China
| | - Xuwei Duan
- Institute of Forestry and Pomology, Beijing Academy of Agricultural and Forestry Sciences, Beijing, 100093, China
- Beijing Engineering Research Center for Deciduous Fruit Trees, Beijing, 100093, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, P.R. China, Beijing, 100093, China
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