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Dujak C, Coleto-Alcudia V, Aranzana MJ. Genomic analysis of fruit size and shape traits in apple: unveiling candidate genes through GWAS analysis. Hortic Res 2024; 11:uhad270. [PMID: 38419968 PMCID: PMC10901474 DOI: 10.1093/hr/uhad270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Accepted: 12/05/2023] [Indexed: 03/02/2024]
Abstract
Genomic tools facilitate the efficient selection of improved genetic materials within a breeding program. Here, we focus on two apple fruit quality traits: shape and size. We utilized data from 11 fruit morphology parameters gathered across three years of harvest from 355 genotypes of the apple REFPOP collection, which serves as a representative sample of the genetic variability present in European-cultivated apples. The data were then employed for genome-wide association studies (GWAS) using the FarmCPU and the BLINK models. The analysis identified 59 SNPs associated with fruit size and shape traits (35 with FarmCPU and 45 with BLINK) responsible for 71 QTNs. These QTNs were distributed across all chromosomes except for chromosomes 10 and 15. Thirty-four QTNs, identified by 27 SNPs, were related for size traits, and 37 QTNs, identified by 26 SNPs, were related to shape attributes. The definition of the haploblocks containing the most relevant SNPs served to propose candidate genes, among them the genes of the ovate family protein MdOFP17 and MdOFP4 that were in a 9.7kb haploblock on Chromosome 11. RNA-seq data revealed low or null expression of these genes in the oblong cultivar "Skovfoged" and higher expression in the flat "Grand'mere." The Gene Ontology enrichment analysis support a role of OFPs and hormones in shape regulation. In conclusion, this comprehensive GWAS analysis of the apple REFPOP collection has revealed promising genetic markers and candidate genes associated with apple fruit shape and size attributes, providing valuable insights that could enhance the efficiency of future breeding programs.
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Affiliation(s)
- Christian Dujak
- Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UABUB, Plant and Animal Genomics, Campus UAB, 08193 Bellaterra, Barcelona, Spain
| | - Veredas Coleto-Alcudia
- Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UABUB, Plant and Animal Genomics, Campus UAB, 08193 Bellaterra, Barcelona, Spain
| | - Maria José Aranzana
- Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UABUB, Plant and Animal Genomics, Campus UAB, 08193 Bellaterra, Barcelona, Spain
- IRTA (Institut de Recerca i Tecnologia Agroalimentàries), Genomics and Biotechnology, 08140 Caldes de Montbui, Barcelona, Spain
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De Mori G, Cipriani G. Marker-Assisted Selection in Breeding for Fruit Trait Improvement: A Review. Int J Mol Sci 2023; 24:ijms24108984. [PMID: 37240329 DOI: 10.3390/ijms24108984] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 05/12/2023] [Accepted: 05/17/2023] [Indexed: 05/28/2023] Open
Abstract
Breeding fruit species is time-consuming and expensive. With few exceptions, trees are likely the worst species to work with in terms of genetics and breeding. Most are characterized by large trees, long juvenile periods, and intensive agricultural practice, and environmental variability plays an important role in the heritability evaluations of every single important trait. Although vegetative propagation allows for the production of a significant number of clonal replicates for the evaluation of environmental effects and genotype × environment interactions, the spaces required for plant cultivation and the intensity of work necessary for phenotypic surveys slow down the work of researchers. Fruit breeders are very often interested in fruit traits: size, weight, sugar and acid content, ripening time, fruit storability, and post-harvest practices, among other traits relevant to each individual species. The translation of trait loci and whole-genome sequences into diagnostic genetic markers that are effective and affordable for use by breeders, who must choose genetically superior parents and subsequently choose genetically superior individuals among their progeny, is one of the most difficult tasks still facing tree fruit geneticists. The availability of updated sequencing techniques and powerful software tools offered the opportunity to mine tens of fruit genomes to find out sequence variants potentially useful as molecular markers. This review is devoted to analysing what has been the role of molecular markers in assisting breeders in selection processes, with an emphasis on the fruit traits of the most important fruit crops for which examples of trustworthy molecular markers have been developed, such as the MDo.chr9.4 marker for red skin colour in apples, the CCD4-based marker CPRFC1, and LG3_13.146 marker for flesh colour in peaches, papayas, and cherries, respectively.
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Affiliation(s)
- Gloria De Mori
- Department of Agricultural, Food, Environmental and Animal Sciences, University of Udine, Via delle Scienze 206, 33100 Udine, Italy
| | - Guido Cipriani
- Department of Agricultural, Food, Environmental and Animal Sciences, University of Udine, Via delle Scienze 206, 33100 Udine, Italy
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Mignard P, Font i Forcada C, Giménez R, Moreno MÁ. Population Structure and Association Mapping for Agronomical and Biochemical Traits of a Large Spanish Apple Germplasm. Plants (Basel) 2023; 12:1249. [PMID: 36986937 PMCID: PMC10057825 DOI: 10.3390/plants12061249] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Revised: 03/04/2023] [Accepted: 03/06/2023] [Indexed: 06/19/2023]
Abstract
A basic knowledge of linkage disequilibrium and population structure is necessary in order to determine the genetic control and identify significant associations with agronomical and phytochemical compounds in apple (Malus × domestica Borkh). In this study, 186 apple accessions (Pop1), representing both Spanish native accessions (94) and non-Spanish cultivars (92) from the EEAD-CSIC apple core collection, were assessed using 23 SSRs markers. Four populations were considered: Pop1, Pop2, Pop3, and Pop4. The initial Pop1 was divided into 150 diploid (Pop2) and 36 triploid accessions (Pop3), while for the inter-chromosomal linkage disequilibrium and the association mapping analysis, 118 phenotype diploid accessions were considered Pop4. Thus, the average number of alleles per locus and observed heterozygosity for the overall sample set (Pop1) were 15.65 and 0.75, respectively. The population structure analysis identified two subpopulations in the diploid accessions (Pop2 and Pop4) and four in the triploids (Pop3). Regarding the Pop4, the population structure with K = 2 subpopulations segregation was in agreement with the UPGMA cluster analysis according to the genetic pairwise distances. Moreover, the accessions seemed to be segregated by their origin (Spanish/non-Spanish) in the clustering analysis. One of the two subpopulations encountered was quite-exclusively formed by non-Spanish accessions (30 out of 33). Furthermore, agronomical and basic fruit quality parameters, antioxidant traits, individual sugars, and organic acids were assessed for the association mapping analysis. A high level of biodiversity was exhibited in the phenotypic characterization of Pop4, and a total of 126 significant associations were found between the 23 SSR markers and the 21 phenotypic traits evaluated. This study also identified many new marker-locus trait associations for the first time, such as in the antioxidant traits or in sugars and organic acids, which may be useful for predictions and for a better understanding of the apple genome.
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Rymbai H, Verma VK, Talang H, Assumi SR, Devi MB, Vanlalruati, Sangma RHCH, Biam KP, Chanu LJ, Makdoh B, Singh AR, Mawleiñ J, Hazarika S, Mishra VK. Biochemical and antioxidant activity of wild edible fruits of the eastern Himalaya, India. Front Nutr 2023; 10:1039965. [PMID: 36937364 PMCID: PMC10014916 DOI: 10.3389/fnut.2023.1039965] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Accepted: 01/31/2023] [Indexed: 03/05/2023] Open
Abstract
The eastern Himalayas, one of the important hotspots of global biodiversity, have a rich diversity of wild edible fruit trees. The fruits of these tree species have been consumed by the tribal people since time immemorial. However, there is limited information available on the biochemical and antioxidant properties of the fruits. Therefore, the present investigation was undertaken to study the physico-chemical and antioxidant properties of the nine most important wild fruit trees. Among the species, Pyrus pashia had the maximum fruit weight (37.83 g), while the highest juice (43.72%) and pulp content (84.67%) were noted in Haematocarpus validus and Myrica esculenta, respectively. Maximum total soluble solids (18.27%), total sugar (11.27%), moisture content (88.39%), ascorbic acid content (63.82 mg/100 g), total carotenoids (18.47 mg/100 g), and total monomeric anthocyanin (354.04 mg/100 g) were recorded in H. validus. Docynia indica had the highest total phenolic content (19.37 mg GAE/g), while H. validus recorded the highest total flavonoids and flavanol content. The antioxidant activities of the different fruits ranged from 0.17 to 0.67 IC50 for DPPH activity and 3.59-13.82 mg AAE/g for FRAP. These fruits had attractive pigmentation of both pulp and juice and were a good potential source for the extraction of natural edible color in the food industry. The fruits also possess high market prices; Prunus nepalensis fetched $ 34.10-$ 141.5 per tree. Therefore, these fruits are rich sources of antioxidants, pigments and have a high market value for livelihood and nutritional security.
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Ban S, El-Sharkawy I, Zhao J, Fei Z, Xu K. An apple somatic mutation of delayed fruit maturation date is primarily caused by a retrotransposon insertion-associated large deletion. Plant J 2022; 111:1609-1625. [PMID: 35861682 DOI: 10.1111/tpj.15911] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Revised: 07/03/2022] [Accepted: 07/20/2022] [Indexed: 06/15/2023]
Abstract
Somatic mutations may alter important traits in tree fruits, such as fruit color, size and maturation date. Autumn Gala (AGala), a somatic mutation from apple cultivar Gala, matures 4 weeks later than Gala. To understand the mechanisms underlying the delayed maturation, RNA-seq analyses were conducted with fruit sampled at 13 (Gala) and 16 (AGala) time-points during their growth and development. Weighted gene co-expression network analysis (WGCNA) of 23 372 differentially expressed genes resulted in 25 WGCNA modules. Of these, modules 1 (r = -0.98, P = 2E-21) and 2 (r = -0.52, P = 0.004), which were suppressed in AGala, were correlated with fruit maturation date. Surprisingly, 77 of the 152 member genes in module 1 were harbored in a 2.8-Mb genomic region on chromosome 6 that was deleted and replaced by a 10.7-kb gypsy-like retrotransposon (Gy-36) from chromosome 7 in AGala. Among the 77 member genes, MdACT7 was the most suppressed (by 10.5-fold) in AGala due to a disruptive 2.5-kb insertion in coding sequence. Moreover, MdACT7 is the exclusive apple counterpart of Arabidopsis ACT7 known of essential roles in plant development, and the functional allele MdACT7, which was lost to the deletion in AGala, was associated with early fruit maturation in 268 apple accessions. Overexpressing alleles MdACT7 and Mdact7 in an Arabidopsis act7 line showed that MdACT7 largely rescued its stunted growth and delayed initial flowering while Mdact7 did not. Therefore, the 2.8-Mb hemizygous deletion is largely genetically causal for fruit maturation delay in AGala, and the total loss of MdACT7 might have contributed to the phenotype.
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Affiliation(s)
- Seunghyun Ban
- Horticulture Section, School of Integrative Plant Science, Cornell University, Cornell Agritech, Geneva, New York, USA
| | - Islam El-Sharkawy
- Horticulture Section, School of Integrative Plant Science, Cornell University, Cornell Agritech, Geneva, New York, USA
| | | | - Zhangjun Fei
- Boyce Thompson Institute, Ithaca, New York, USA
- US Department of Agriculture, Agricultural Research Service, Robert W. Holley Center for Agriculture and Health, Ithaca, New York, USA
| | - Kenong Xu
- Horticulture Section, School of Integrative Plant Science, Cornell University, Cornell Agritech, Geneva, New York, USA
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6
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Shen F, Bianco L, Wu B, Tian Z, Wang Y, Wu T, Xu X, Han Z, Velasco R, Fontana P, Zhang X. A bulked segregant analysis tool for out-crossing species (BSATOS) and QTL-based genomics-assisted prediction of complex traits in apple. J Adv Res 2022; 42:149-162. [PMID: 36513410 PMCID: PMC9788957 DOI: 10.1016/j.jare.2022.03.013] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Revised: 03/06/2022] [Accepted: 03/22/2022] [Indexed: 12/27/2022] Open
Abstract
INTRODUCTION Genomic heterozygosity, self-incompatibility, and rich-in somatic mutations hinder the molecular breeding efficiency of outcrossing plants. OBJECTIVES We attempted to develop an efficient integrated strategy to identify quantitative trait loci (QTLs) and trait-associated genes, to develop gene markers, and to construct genomics-assisted prediction (GAP) modes. METHODS A novel protocol, bulked segregant analysis tool for out-crossing species (BSATOS), is presented here, which is characterized by taking full advantage of all segregation patterns (including AB × AB markers) and haplotype information. To verify the effectiveness of the protocol in dealing with the complex traits of outbreeding species, three apple cross populations with 9,654 individuals were adopted. RESULTS By using BSATOS, 90, 60, and 77 significant QTLs were identified successfully and candidate genes were predicted for apple fruit weight (FW), fruit ripening date (FRD), and fruit soluble solid content (SSC), respectively. The gene-based markers were developed and genotyped for 1,396 individuals in a training population, including 145 Malus accessions and 1,251 F1 plants of the three full-sib families. GAP models were trained using marker genotype effect estimates of the training population. The prediction accuracy was 0.7658, 0.6455, and 0.3758 for FW, FRD, and SSC, respectively. CONCLUSION The BSATOS and GAP models provided a convenient and efficient methodology for candidate gene mining and molecular breeding in out-crossing plant species. The BSATOS pipeline can be freely downloaded from: https://github.com/maypoleflyn/BSATOS.
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Affiliation(s)
- Fei Shen
- College of Horticulture, China Agricultural University, Beijing 100193, China,Research and Innovation Center, Edmund Mach Foundation, 38010 S. Michele all’Adige, Italy,Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Luca Bianco
- Research and Innovation Center, Edmund Mach Foundation, 38010 S. Michele all’Adige, Italy
| | - Bei Wu
- College of Horticulture, China Agricultural University, Beijing 100193, China
| | - Zhendong Tian
- College of Horticulture, China Agricultural University, Beijing 100193, China
| | - Yi Wang
- College of Horticulture, China Agricultural University, Beijing 100193, China
| | - Ting Wu
- College of Horticulture, China Agricultural University, Beijing 100193, China
| | - Xuefeng Xu
- College of Horticulture, China Agricultural University, Beijing 100193, China
| | - Zhenhai Han
- College of Horticulture, China Agricultural University, Beijing 100193, China,Corresponding authors.
| | - Riccardo Velasco
- Research Centre for Viticulture and Enology, CREA, Conegliano, Italy
| | - Paolo Fontana
- Research and Innovation Center, Edmund Mach Foundation, 38010 S. Michele all’Adige, Italy,Corresponding authors.
| | - Xinzhong Zhang
- College of Horticulture, China Agricultural University, Beijing 100193, China,Corresponding authors.
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Jung M, Keller B, Roth M, Aranzana MJ, Auwerkerken A, Guerra W, Al-Rifaï M, Lewandowski M, Sanin N, Rymenants M, Didelot F, Dujak C, Font i Forcada C, Knauf A, Laurens F, Studer B, Muranty H, Patocchi A. Genetic architecture and genomic predictive ability of apple quantitative traits across environments. Hortic Res 2022; 9:uhac028. [PMID: 35184165 PMCID: PMC8976694 DOI: 10.1093/hr/uhac028] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 12/09/2021] [Accepted: 01/11/2022] [Indexed: 06/14/2023]
Abstract
Implementation of genomic tools is desirable to increase the efficiency of apple breeding. Recently, the multi-environment apple reference population (apple REFPOP) proved useful for rediscovering loci, estimating genomic predictive ability, and studying genotype by environment interactions (G × E). So far, only two phenological traits were investigated using the apple REFPOP, although the population may be valuable when dissecting genetic architecture and reporting predictive abilities for additional key traits in apple breeding. Here we show contrasting genetic architecture and genomic predictive abilities for 30 quantitative traits across up to six European locations using the apple REFPOP. A total of 59 stable and 277 location-specific associations were found using GWAS, 69.2% of which are novel when compared with 41 reviewed publications. Average genomic predictive abilities of 0.18-0.88 were estimated using main-effect univariate, main-effect multivariate, multi-environment univariate, and multi-environment multivariate models. The G × E accounted for up to 24% of the phenotypic variability. This most comprehensive genomic study in apple in terms of trait-environment combinations provided knowledge of trait biology and prediction models that can be readily applied for marker-assisted or genomic selection, thus facilitating increased breeding efficiency.
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Affiliation(s)
- Michaela Jung
- Agroscope, Breeding Research Group, 8820 Wädenswil, Switzerland
- Molecular Plant Breeding, Institute of Agricultural Sciences, ETH Zurich, 8092 Zurich, Switzerland
| | - Beat Keller
- Agroscope, Breeding Research Group, 8820 Wädenswil, Switzerland
- Molecular Plant Breeding, Institute of Agricultural Sciences, ETH Zurich, 8092 Zurich, Switzerland
| | - Morgane Roth
- Agroscope, Breeding Research Group, 8820 Wädenswil, Switzerland
- GAFL, INRAE, 84140 Montfavet, France
| | - Maria José Aranzana
- IRTA (Institut de Recerca i Tecnologia Agroalimentàries), 08140 Caldes de Montbui, Barcelona, Spain
- Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Campus UAB, 08193 Bellaterra, Barcelona, Spain
| | | | | | - Mehdi Al-Rifaï
- Univ Angers, Institut Agro, INRAE, IRHS, SFR QuaSaV, F-49000 Angers, France
| | - Mariusz Lewandowski
- The National Institute of Horticultural Research, Konstytucji 3 Maja 1/3, 96-100 Skierniewice, Poland
| | | | - Marijn Rymenants
- Better3fruit N.V., 3202 Rillaar, Belgium
- Laboratory for Plant Genetics and Crop Improvement, KU Leuven, B-3001 Leuven, Belgium
| | | | - Christian Dujak
- Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Campus UAB, 08193 Bellaterra, Barcelona, Spain
| | - Carolina Font i Forcada
- IRTA (Institut de Recerca i Tecnologia Agroalimentàries), 08140 Caldes de Montbui, Barcelona, Spain
| | - Andrea Knauf
- Agroscope, Breeding Research Group, 8820 Wädenswil, Switzerland
- Molecular Plant Breeding, Institute of Agricultural Sciences, ETH Zurich, 8092 Zurich, Switzerland
| | - François Laurens
- Univ Angers, Institut Agro, INRAE, IRHS, SFR QuaSaV, F-49000 Angers, France
| | - Bruno Studer
- Molecular Plant Breeding, Institute of Agricultural Sciences, ETH Zurich, 8092 Zurich, Switzerland
| | - Hélène Muranty
- Univ Angers, Institut Agro, INRAE, IRHS, SFR QuaSaV, F-49000 Angers, France
| | - Andrea Patocchi
- Agroscope, Breeding Research Group, 8820 Wädenswil, Switzerland
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Yáñez MA, González B, Espinoza SE, Vogel H, Doll U. Phenotypic variation of fruit and ecophysiological traits among maqui (Aristotelia chilensis [Molina] Stuntz) provenances established in a common garden. Sci Rep 2022; 12:185. [PMID: 34997037 DOI: 10.1038/s41598-021-04013-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Accepted: 12/09/2021] [Indexed: 01/04/2023] Open
Abstract
The domestication of forest species has traditionally relied on productivity issues. However, today there are concerns about the potential responses of natural populations and new cultivars to extreme climatic conditions derived from climate change and how to incorporate this knowledge into the domestication programs. Aristotelia chilensis (Molina) Stuntz ('Maqui') is a widely distributed native species in Chile. Its berry is considered a "super fruit" with an increasing interest in the food industry. This study investigated the phenotypic variation of growth, fruit, and ecophysiological traits of 20 A. chilensis clones originated from six provenances along the latitudinal gradient and established in a common-garden experiment in the Mediterranean zone of central Chile (center part of the species distribution). Differences among provenances were observed for most of the traits under study, especially between the northern and southernmost provenances (i.e., San Fernando versus Entre Lagos). Northern provenances showed higher development of vegetative tissue and fruit yield but lower intrinsic water use efficiency (WUEint) compared with southern ones. Clonal variation within provenances was found significant for the ripening index, WUEint, and fruit number and weight but not significant for traits related to the crown and leaf morphology. A genetic differentiation due to latitudinal cline was not evident in this study, but differences among provenances suggest local adaptation for some traits. The genotypic variation in productive traits must be considered in the outgoing domestication of the species and future selection programs.
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Blatt S, Hiltz K. A New Look at Cultivar Preference in Hoplocampa testudinea (Hymenoptera: Tenthredinidae) on Apple in the Annapolis Valley of Nova Scotia, Canada. Insects 2021; 12:insects12090769. [PMID: 34564209 PMCID: PMC8466372 DOI: 10.3390/insects12090769] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Revised: 08/20/2021] [Accepted: 08/25/2021] [Indexed: 11/29/2022]
Abstract
Simple Summary Many insect species show a preference for specific varieties or cultivars within a host plant type, e.g., apple. The European apple sawfly, Hoplocampa testudinea Klug was found to show preference for apple cultivars in Nova Scotia in 2013 and 2014. We hypothesized that this preference could result from either the female selecting specific cultivars for egg deposition or differential survival of the larvae on these cultivars. We studied 15 cultivars over a four-year period (2016–2019) to determine the distribution of egg deposition within the orchard, we bagged fruitlets to closely monitor the damage and impact of H. testudinea during the growing season and evaluated the fruitlets for soluble solids (sugars), acidity and firmness. We determined that female choice in combination with fruitlet chemistry is likely responsible for the cultivar preferences observed. Abstract (1) Background: The European apple sawfly, Hoplocampa testudinea Klug (Hymenoptera: Tenthredinidae), can be an economically important pest in eastern Canada and shows preference for apple cultivars in Nova Scotia, Canada. We hypothesized that this preference could be due to oviposition by female H. testudinea (preference-performance hypothesis) during the bloom period or differential larval survival during development due to fruitlet physicochemical properties. (2) Methods: Fifteen commercial and experimental apple (Malusdomestica Borkh.; Rosaceae) cultivars located at the Kentville Research and Development Centre (Kentville, Nova Scotia) were chosen and examined for H. testudinea oviposition, larval performance during fruitlet development, fruitlet physicochemical properties and damage assessment at harvest from 2016–2019, inclusive. (3) Results: H. testudinea showed significant cultivar preference during oviposition, during development and at harvest, but the ranking of these cultivars was not the same throughout the season. Total impact by H. testudinea was consistent for most cultivars over multiple years of the study. (4) Conclusion: Correlation of oviposition with damage provided weak evidence for the preference-performance hypothesis. We propose that this relationship is weak due to differential survival of larvae during development.
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Wu B, Shen F, Chen CJ, Liu L, Wang X, Zheng WY, Deng Y, Wang T, Huang ZY, Xiao C, Zhou Q, Wang Y, Wu T, Xu XF, Han ZH, Zhang XZ. Natural variations in a pectin acetylesterase gene, MdPAE10, contribute to prolonged apple fruit shelf life. Plant Genome 2021; 14:e20084. [PMID: 33605090 DOI: 10.1002/tpg2.20084] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Accepted: 12/13/2020] [Indexed: 05/18/2023]
Abstract
Room-temperature shelf life is a key factor in fresh market apple (Malus domestica Borkh.) quality and commercial value. To investigate the genetic and molecular mechanism underlying apple shelf life, quantitative trait loci (QTL) were identified using bulked segregant analysis via sequencing (BSA-seq). Ethylene emission, flesh firmness, or crispness of apple fruit from 1,273 F1 plants of M. asiatica Nakai 'Zisai Pearl' × M. domestica 'Golden Delicious' were phenotyped prior to and during 6 wk of room-temperature storage. Segregation of ethylene emission and the flesh firmness or crispness traits was detected in the population. Thirteen QTL, including three major ones, were identified on chromosome 03, 08, and 16. A candidate gene encoding pectin acetylesterase, MdPAE10, from the QTL Z16.1 negatively affected fruit shelf life. A 379-bp deletion in the coding sequence of MdPAE10 disrupted its function. A single nucleotide polymorphism (SNP) in the MdPAE10 promoter region reduced its transcription activity. These findings provided insight into the genetic control of fruit shelf life and can be potentially used in apple marker-assisted selection.
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Affiliation(s)
- Bei Wu
- College of Horticulture, China Agricultural University, No. 2 Yuanmingyuan West Road, Haidian District, Beijing, 100193, China
| | - Fei Shen
- College of Horticulture, China Agricultural University, No. 2 Yuanmingyuan West Road, Haidian District, Beijing, 100193, China
| | - Chi Jie Chen
- College of Horticulture, China Agricultural University, No. 2 Yuanmingyuan West Road, Haidian District, Beijing, 100193, China
| | - Li Liu
- College of Horticulture, China Agricultural University, No. 2 Yuanmingyuan West Road, Haidian District, Beijing, 100193, China
| | - Xuan Wang
- College of Horticulture, China Agricultural University, No. 2 Yuanmingyuan West Road, Haidian District, Beijing, 100193, China
| | - Wen Yan Zheng
- College of Horticulture, China Agricultural University, No. 2 Yuanmingyuan West Road, Haidian District, Beijing, 100193, China
| | - Yang Deng
- College of Horticulture, China Agricultural University, No. 2 Yuanmingyuan West Road, Haidian District, Beijing, 100193, China
| | - Ting Wang
- College of Horticulture, China Agricultural University, No. 2 Yuanmingyuan West Road, Haidian District, Beijing, 100193, China
| | - Zhen Yu Huang
- College of Horticulture, China Agricultural University, No. 2 Yuanmingyuan West Road, Haidian District, Beijing, 100193, China
| | - Chen Xiao
- College of Horticulture, China Agricultural University, No. 2 Yuanmingyuan West Road, Haidian District, Beijing, 100193, China
| | - Qian Zhou
- College of Horticulture, China Agricultural University, No. 2 Yuanmingyuan West Road, Haidian District, Beijing, 100193, China
| | - Yi Wang
- College of Horticulture, China Agricultural University, No. 2 Yuanmingyuan West Road, Haidian District, Beijing, 100193, China
| | - Ting Wu
- College of Horticulture, China Agricultural University, No. 2 Yuanmingyuan West Road, Haidian District, Beijing, 100193, China
| | - Xue Feng Xu
- College of Horticulture, China Agricultural University, No. 2 Yuanmingyuan West Road, Haidian District, Beijing, 100193, China
| | - Zhen Hai Han
- College of Horticulture, China Agricultural University, No. 2 Yuanmingyuan West Road, Haidian District, Beijing, 100193, China
| | - Xin Zhong Zhang
- College of Horticulture, China Agricultural University, No. 2 Yuanmingyuan West Road, Haidian District, Beijing, 100193, China
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Jung M, Roth M, Aranzana MJ, Auwerkerken A, Bink M, Denancé C, Dujak C, Durel CE, Font I Forcada C, Cantin CM, Guerra W, Howard NP, Keller B, Lewandowski M, Ordidge M, Rymenants M, Sanin N, Studer B, Zurawicz E, Laurens F, Patocchi A, Muranty H. The apple REFPOP-a reference population for genomics-assisted breeding in apple. Hortic Res 2020; 7:189. [PMID: 33328447 PMCID: PMC7603508 DOI: 10.1038/s41438-020-00408-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Revised: 08/25/2020] [Accepted: 09/06/2020] [Indexed: 05/16/2023]
Abstract
Breeding of apple is a long-term and costly process due to the time and space requirements for screening selection candidates. Genomics-assisted breeding utilizes genomic and phenotypic information to increase the selection efficiency in breeding programs, and measurements of phenotypes in different environments can facilitate the application of the approach under various climatic conditions. Here we present an apple reference population: the apple REFPOP, a large collection formed of 534 genotypes planted in six European countries, as a unique tool to accelerate apple breeding. The population consisted of 269 accessions and 265 progeny from 27 parental combinations, representing the diversity in cultivated apple and current European breeding material, respectively. A high-density genome-wide dataset of 303,239 SNPs was produced as a combined output of two SNP arrays of different densities using marker imputation with an imputation accuracy of 0.95. Based on the genotypic data, linkage disequilibrium was low and population structure was weak. Two well-studied phenological traits of horticultural importance were measured. We found marker-trait associations in several previously identified genomic regions and maximum predictive abilities of 0.57 and 0.75 for floral emergence and harvest date, respectively. With decreasing SNP density, the detection of significant marker-trait associations varied depending on trait architecture. Regardless of the trait, 10,000 SNPs sufficed to maximize genomic prediction ability. We confirm the suitability of the apple REFPOP design for genomics-assisted breeding, especially for breeding programs using related germplasm, and emphasize the advantages of a coordinated and multinational effort for customizing apple breeding methods in the genomics era.
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Affiliation(s)
- Michaela Jung
- Molecular Plant Breeding, Institute of Agricultural Sciences, ETH Zurich, 8092, Zurich, Switzerland
- Breeding Research group, Agroscope, 8820, Wädenswil, Switzerland
| | - Morgane Roth
- Breeding Research group, Agroscope, 8820, Wädenswil, Switzerland
- GAFL, INRAE, 84140, Montfavet, France
| | - Maria José Aranzana
- IRTA (Institut de Recerca i Tecnologia Agroalimentàries), 08140, Caldes de Montbui, Barcelona, Spain
- Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Campus UAB, 08193, Bellaterra, Barcelona, Spain
| | | | - Marco Bink
- Biometris, Wageningen University and Research, 6708 PB, Wageningen, The Netherlands
- Hendrix Genetics Research, Technology and Services B.V., PO Box 114, 5830AC, Boxmeer, The Netherlands
| | - Caroline Denancé
- IRHS, Université d'Angers, INRAE, Institut Agro, SFR 4207 QuaSaV, 49071, Beaucouzé, France
| | - Christian Dujak
- Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Campus UAB, 08193, Bellaterra, Barcelona, Spain
| | - Charles-Eric Durel
- IRHS, Université d'Angers, INRAE, Institut Agro, SFR 4207 QuaSaV, 49071, Beaucouzé, France
| | - Carolina Font I Forcada
- IRTA (Institut de Recerca i Tecnologia Agroalimentàries), 08140, Caldes de Montbui, Barcelona, Spain
| | - Celia M Cantin
- IRTA (Institut de Recerca i Tecnologia Agroalimentàries), 08140, Caldes de Montbui, Barcelona, Spain
- ARAID (Fundación Aragonesa para la Investigación y el Desarrollo), 50018, Zaragoza, Spain
| | | | - Nicholas P Howard
- Department of Horticultural Science, University of Minnesota, St. Paul, MN, 55108, USA
- Institute of Biology and Environmental Sciences, University of Oldenburg, 26129, Oldenburg, Germany
| | - Beat Keller
- Molecular Plant Breeding, Institute of Agricultural Sciences, ETH Zurich, 8092, Zurich, Switzerland
- Breeding Research group, Agroscope, 8820, Wädenswil, Switzerland
| | | | - Matthew Ordidge
- School of Agriculture, Policy and Development, University of Reading, Whiteknights, RG6 6AR, Reading, UK
| | - Marijn Rymenants
- Better3fruit N.V., 3202, Rillaar, Belgium
- Biometris, Wageningen University and Research, 6708 PB, Wageningen, The Netherlands
- Laboratory for Plant Genetics and Crop Improvement, KU Leuven, B-3001, Leuven, Belgium
| | - Nadia Sanin
- Research Centre Laimburg, 39040, Auer, Italy
| | - Bruno Studer
- Molecular Plant Breeding, Institute of Agricultural Sciences, ETH Zurich, 8092, Zurich, Switzerland
| | - Edward Zurawicz
- Research Institute of Horticulture, 96-100, Skierniewice, Poland
| | - François Laurens
- IRHS, Université d'Angers, INRAE, Institut Agro, SFR 4207 QuaSaV, 49071, Beaucouzé, France
| | - Andrea Patocchi
- Breeding Research group, Agroscope, 8820, Wädenswil, Switzerland
| | - Hélène Muranty
- IRHS, Université d'Angers, INRAE, Institut Agro, SFR 4207 QuaSaV, 49071, Beaucouzé, France.
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12
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Cirilli M, Micali S, Aranzana MJ, Arús P, Babini A, Barreneche T, Bink M, Cantin CM, Ciacciulli A, Cos-Terrer JE, Drogoudi P, Eduardo I, Foschi S, Giovannini D, Guerra W, Liverani A, Pacheco I, Pascal T, Quilot-Turion B, Verde I, Rossini L, Bassi D. The Multisite PeachRefPop Collection: A True Cultural Heritage and International Scientific Tool for Fruit Trees. Plant Physiol 2020; 184:632-646. [PMID: 32727910 PMCID: PMC7536698 DOI: 10.1104/pp.19.01412] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Accepted: 07/17/2020] [Indexed: 05/21/2023]
Abstract
Plants have evolved a range of adaptive mechanisms that adjust their development and physiology to variable external conditions, particularly in perennial species subjected to long-term interplay with the environment. Exploiting the allelic diversity within available germplasm and leveraging the knowledge of the mechanisms regulating genotype interaction with the environment are crucial to address climatic challenges and assist the breeding of novel cultivars with improved resilience. The development of multisite collections is of utmost importance for the conservation and utilization of genetic materials and will greatly facilitate the dissection of genotype-by-environment interaction. Such resources are still lacking for perennial trees, especially with the intrinsic difficulties of successful propagation, material exchange, and living collection maintenance. This work describes the concept, design, and realization of the first multisite peach (Prunus persica) reference collection (PeachRefPop) located across different European countries and sharing the same experimental design. Other than an invaluable tool for scientific studies in perennial species, PeachRefPop provides a milestone in an international collaborative project for the conservation and exploitation of European peach germplasm resources and, ultimately, as a true heritage for future generations.
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Affiliation(s)
- Marco Cirilli
- Department of Agricultural and Environmental Sciences, University of Milan, 20133 Milan, Italy
| | - Sabrina Micali
- Consiglio Per La Ricerca In Agricoltura E L'analisi Dell'Economia Agraria, Research Centre for Olive, Fruit, and Citrus Crops, 00134 Rome, Italy
| | - Maria José Aranzana
- Institut de Recerca i Tecnologia Agroalimentàries, Centre de Recerca en Agrigenòmica Consejo Superior de Investigaciones Científicas, Institut de Recerca i Tecnologia Agroalimentàries, Universitat Autònoma de Barcelona, Universitat de Barcelona, Campus UAB, 08193 Barcelona, Spain
| | - Pere Arús
- Institut de Recerca i Tecnologia Agroalimentàries, Centre de Recerca en Agrigenòmica Consejo Superior de Investigaciones Científicas, Institut de Recerca i Tecnologia Agroalimentàries, Universitat Autònoma de Barcelona, Universitat de Barcelona, Campus UAB, 08193 Barcelona, Spain
| | - Annarosa Babini
- Phytosanitary Service, Regione Emilia-Romagna, 40128 Bologna, Italy
| | - Teresa Barreneche
- Université de Bordeaux, Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement, Biologie du Fruit et Pathologie, F-33140 Villenave d'Ornon, France
| | - Marco Bink
- Hendrix Genetics Research, Technology, and Services, 5830 AC Boxmeer, The Netherlands
| | - Celia M Cantin
- Institut de Recerca i Tecnologia Agroalimentàries, Centre de Recerca en Agrigenòmica Consejo Superior de Investigaciones Científicas, Institut de Recerca i Tecnologia Agroalimentàries, Universitat Autònoma de Barcelona, Universitat de Barcelona, Campus UAB, 08193 Barcelona, Spain
| | - Angelo Ciacciulli
- Department of Agricultural and Environmental Sciences, University of Milan, 20133 Milan, Italy
| | | | - Pavlina Drogoudi
- Hellenic Agricultural Organization 'Demeter', Department of Deciduous Fruit Trees, Institute of Plant Breeding and Genetic Resources, 59200 Naoussa, Greece
| | - Iban Eduardo
- Institut de Recerca i Tecnologia Agroalimentàries, Centre de Recerca en Agrigenòmica Consejo Superior de Investigaciones Científicas, Institut de Recerca i Tecnologia Agroalimentàries, Universitat Autònoma de Barcelona, Universitat de Barcelona, Campus UAB, 08193 Barcelona, Spain
| | - Stefano Foschi
- Centro Ricerche Produzioni Vegetali, 47522 Cesena, Italy
| | - Daniela Giovannini
- Consiglio per la Ricerca in Agricoltura e L'Analisi Del'Economia Agraria, Research Centre for Olive, Fruit, and Citrus Crops, 47121 Forlì, Italy
| | | | - Alessandro Liverani
- Consiglio per la Ricerca in Agricoltura e L'Analisi Del'Economia Agraria, Research Centre for Olive, Fruit, and Citrus Crops, 47121 Forlì, Italy
| | - Igor Pacheco
- Instituto de Nutrición y Tecnología de los Alimentos, Universidad de Chile, 7830490 Macul, Chile
| | - Thierry Pascal
- Institut National de Recherche pour L'Agriculture, L'Alimentation et L'Environnement, Génétique et Amélioration des Fruits et Légumes, F-84143 Montfavet, France
| | - Benedicte Quilot-Turion
- Institut National de Recherche pour L'Agriculture, L'Alimentation et L'Environnement, Génétique et Amélioration des Fruits et Légumes, F-84143 Montfavet, France
| | - Ignazio Verde
- Consiglio Per La Ricerca In Agricoltura E L'analisi Dell'Economia Agraria, Research Centre for Olive, Fruit, and Citrus Crops, 00134 Rome, Italy
| | - Laura Rossini
- Department of Agricultural and Environmental Sciences, University of Milan, 20133 Milan, Italy
| | - Daniele Bassi
- Department of Agricultural and Environmental Sciences, University of Milan, 20133 Milan, Italy
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13
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Nybom H, Ahmadi-Afzadi M, Rumpunen K, Tahir I. Review of the Impact of Apple Fruit Ripening, Texture and Chemical Contents on Genetically Determined Susceptibility to Storage Rots. Plants (Basel) 2020; 9:plants9070831. [PMID: 32630736 PMCID: PMC7411992 DOI: 10.3390/plants9070831] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 06/18/2020] [Accepted: 06/29/2020] [Indexed: 12/17/2022]
Abstract
Fungal storage rots like blue mould, grey mould, bull's eye rot, bitter rot and brown rot destroy large amounts of the harvested apple crop around the world. Application of fungicides is nowadays severely restricted in many countries and production systems, and these problems are therefore likely to increase. Considerable variation among apple cultivars in resistance/susceptibility has been reported, suggesting that efficient defence mechanisms can be selected for and used in plant breeding. These are, however, likely to vary between pathogens, since some fungi are mainly wound-mediated while others attack through lenticels or by infecting blossoms. Since mature fruits are considerably more susceptible than immature fruits, mechanisms involving fruit-ripening processes are likely to play an important role. Significant associations have been detected between the susceptibility to rots in harvested fruit and various fruit maturation-related traits like ripening time, fruit firmness at harvest and rate of fruit softening during storage, as well as fruit biochemical contents like acidity, sugars and polyphenols. Some sources of resistance to blue mould have been described, but more research is needed on the development of spore inoculation methods that produce reproducible data and can be used for large screenings, especially for lenticel-infecting fungi.
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Affiliation(s)
- Hilde Nybom
- Department of Plant Breeding–Balsgård, Swedish University of Agricultural Sciences, Fjälkestadsvägen 459, 29194 Kristianstad, Sweden;
- Correspondence:
| | - Masoud Ahmadi-Afzadi
- Department of Biotechnology, Institute of Science, High Technology and Environmental Sciences, Graduate University of Advanced Technology, Kerman 7631818356, Iran;
| | - Kimmo Rumpunen
- Department of Plant Breeding–Balsgård, Swedish University of Agricultural Sciences, Fjälkestadsvägen 459, 29194 Kristianstad, Sweden;
| | - Ibrahim Tahir
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Box 101, 23053 Alnarp, Sweden;
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14
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Christeller JT, McGhie TK, Johnston JW, Carr B, Chagné D. Quantitative trait loci influencing pentacyclic triterpene composition in apple fruit peel. Sci Rep 2019; 9:18501. [PMID: 31811217 PMCID: PMC6898447 DOI: 10.1038/s41598-019-55070-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Accepted: 11/15/2019] [Indexed: 01/27/2023] Open
Abstract
The chemical composition of pentacyclic triterpenes was analysed using a ‘Royal Gala’ x ‘Granny Smith’ segregating population in 2013 and 2015, using apple peels extracted from mature fruit at harvest and after 12 weeks of cold storage. In 2013, 20 compound isoforms from nine unique compound classes were measured for both treatments. In 2015, 20 and 17 compound isoforms from eight unique compound classes were measured at harvest and after cold storage, respectively. In total, 68 quantitative trait loci (QTLs) were detected on 13 linkage groups (LG). Thirty two and 36 QTLs were detected for compounds measured at harvest and after cold storage, respectively. The apple chromosomes with the most QTLs were LG3, LG5, LG9 and LG17. The largest effect QTL was for trihydroxy-urs-12-ene-28-oic acid, located on LG5; this was measured in 2015 after storage, and was inherited from the ‘Royal Gala’ parent (24.9% of the phenotypic variation explained).
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Affiliation(s)
- John T Christeller
- The New Zealand Institute for Plant and Food Research Ltd (Plant & Food Research), Palmerston North Research Centre, Palmerston North, New Zealand
| | - Tony K McGhie
- The New Zealand Institute for Plant and Food Research Ltd (Plant & Food Research), Palmerston North Research Centre, Palmerston North, New Zealand
| | | | - Bridie Carr
- Plant & Food Research, Havelock North, New Zealand.,Department of Agriculture and Fisheries, Maroochy Research Station, 47 Mayers Road, Nambour, QLD 4560, Australia
| | - David Chagné
- The New Zealand Institute for Plant and Food Research Ltd (Plant & Food Research), Palmerston North Research Centre, Palmerston North, New Zealand.
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15
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Chagné D, Vanderzande S, Kirk C, Profitt N, Weskett R, Gardiner SE, Peace CP, Volz RK, Bassil NV. Validation of SNP markers for fruit quality and disease resistance loci in apple ( Malus × domestica Borkh.) using the OpenArray® platform. Hortic Res 2019; 6:30. [PMID: 30854208 PMCID: PMC6395728 DOI: 10.1038/s41438-018-0114-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Revised: 11/01/2018] [Accepted: 12/12/2018] [Indexed: 05/22/2023]
Abstract
Genome mapping has promised much to tree fruit breeding during the last 10 years. Nevertheless, one of the greatest challenges remaining to tree fruit geneticists is the translation of trait loci and whole genome sequences into diagnostic genetic markers that are efficient and cost-effective for use by breeders, who must select genetically optimal parents and subsequently select genetically superior individuals among their progeny. To take this translational step, we designed the apple International RosBREED SNP Consortium OpenArray v1.0 (IRSCOA v1.0) assay using a set of 128 apple single nucleotide polymorphisms (SNPs) linked to fruit quality and pest and disease resistance trait loci. The Thermo Fisher Scientific OpenArray® technology enables multiplexed screening of SNP markers using a real-time PCR instrument with fluorescent probe-based Taqman® assays. We validated the apple IRSCOA v1.0 multi-trait assay by screening 240 phenotyped individuals from the Plant & Food Research apple cultivar breeding programme. This set of individuals comprised commercial and heritage cultivars, elite selections, and families segregating for traits of importance to breeders. In total, 33 SNP markers of the IRSCOA v1.0 were validated for use in marker-assisted selection (MAS) for the scab resistances Rvi2/Vh2, Rvi4/Vh4, Rvi6/Vf, fire blight resistance MR5/RLP1, powdery mildew resistance Pl2, fruit firmness, skin colour, flavour intensity, and acidity. The availability of this set of validated trait-associated SNP markers, which can be used individually on multiple genotyping platforms available to various apple breeding programmes or re-designed using the flanking sequences, represents a large translational genetics step from genomics to crop improvement of apple.
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Affiliation(s)
- David Chagné
- The New Zealand Institute for Plant & Food Research Ltd (Plant & Food Research), Palmerston North Research Centre, Palmerston North, New Zealand
| | - Stijn Vanderzande
- Department of Horticulture, Washington State University, Pullman, WA USA
| | - Chris Kirk
- The New Zealand Institute for Plant & Food Research Ltd (Plant & Food Research), Palmerston North Research Centre, Palmerston North, New Zealand
| | - Natalie Profitt
- Plant & Food Research, Hawke’s Bay Research Centre, Havelock North, New Zealand
| | - Rosemary Weskett
- Plant & Food Research, Hawke’s Bay Research Centre, Havelock North, New Zealand
| | - Susan E. Gardiner
- The New Zealand Institute for Plant & Food Research Ltd (Plant & Food Research), Palmerston North Research Centre, Palmerston North, New Zealand
| | - Cameron P. Peace
- Department of Horticulture, Washington State University, Pullman, WA USA
| | - Richard K. Volz
- Plant & Food Research, Hawke’s Bay Research Centre, Havelock North, New Zealand
| | - Nahla V. Bassil
- USDA-ARS, National Clonal Germplasm Repository, Corvallis, OR USA
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16
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Da L, Liu Y, Yang J, Tian T, She J, Ma X, Xu W, Su Z. AppleMDO: A Multi-Dimensional Omics Database for Apple Co-Expression Networks and Chromatin States. Front Plant Sci 2019; 10:1333. [PMID: 31695717 PMCID: PMC6817610 DOI: 10.3389/fpls.2019.01333] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Accepted: 09/25/2019] [Indexed: 05/17/2023]
Abstract
As an economically important crop, apple is one of the most cultivated fruit trees in temperate regions worldwide. Recently, a large number of high-quality transcriptomic and epigenomic datasets for apple were made available to the public, which could be helpful in inferring gene regulatory relationships and thus predicting gene function at the genome level. Through integration of the available apple genomic, transcriptomic, and epigenomic datasets, we constructed co-expression networks, identified functional modules, and predicted chromatin states. A total of 112 RNA-seq datasets were integrated to construct a global network and a conditional network (tissue-preferential network). Furthermore, a total of 1,076 functional modules with closely related gene sets were identified to assess the modularity of biological networks and further subjected to functional enrichment analysis. The results showed that the function of many modules was related to development, secondary metabolism, hormone response, and transcriptional regulation. Transcriptional regulation is closely related to epigenetic marks on chromatin. A total of 20 epigenomic datasets, which included ChIP-seq, DNase-seq, and DNA methylation analysis datasets, were integrated and used to classify chromatin states. Based on the ChromHMM algorithm, the genome was divided into 620,122 fragments, which were classified into 24 states according to the combination of epigenetic marks and enriched-feature regions. Finally, through the collaborative analysis of different omics datasets, the online database AppleMDO (http://bioinformatics.cau.edu.cn/AppleMDO/) was established for cross-referencing and the exploration of possible novel functions of apple genes. In addition, gene annotation information and functional support toolkits were also provided. Our database might be convenient for researchers to develop insights into the function of genes related to important agronomic traits and might serve as a reference for other fruit trees.
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Liu J, Abdelfattah A, Norelli J, Burchard E, Schena L, Droby S, Wisniewski M. Apple endophytic microbiota of different rootstock/scion combinations suggests a genotype-specific influence. Microbiome 2018; 6:18. [PMID: 29374490 PMCID: PMC5787276 DOI: 10.1186/s40168-018-0403-x] [Citation(s) in RCA: 81] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2017] [Accepted: 01/18/2018] [Indexed: 05/19/2023]
Abstract
BACKGROUND High-throughput amplicon sequencing spanning conserved portions of microbial genomes (16s rRNA and ITS) was used in the present study to describe the endophytic microbiota associated with three apple varieties, "Royal Gala," "Golden Delicious," and "Honey Crisp," and two rootstocks, M.9 and M.M.111. The objectives were to (1) determine if the microbiota differs in different rootstocks and apple varieties and (2) determine if specific rootstock-scion combinations influence the microbiota composition of either component. RESULTS Results indicated that Ascomycota (47.8%), Zygomycota (31.1%), and Basidiomycota (11.6%) were the dominant fungal phyla across all samples. The majority of bacterial sequences were assigned to Proteobacteria (58.4%), Firmicutes (23.8%), Actinobacteria (7.7%), Bacteroidetes (2%), and Fusobacteria (0.4%). Rootstocks appeared to influence the microbiota of associated grafted scion, but the effect was not statistically significant. Pedigree also had an impact on the composition of the endophytic microbiota, where closely-related cultivars had a microbial community that was more similar to each other than it was to a scion cultivar that was more distantly-related by pedigree. The more vigorous rootstock (M.M.111) was observed to possess a greater number of growth-promoting bacterial taxa, relative to the dwarfing rootstock (M.9). CONCLUSIONS The mechanism by which an apple genotype, either rootstock or scion, has a determinant effect on the composition of a microbial community is not known. The similarity of the microbiota in samples with a similar pedigree suggests the possibility of some level of co-evolution or selection as proposed by the "holobiont" concept in which metaorganisms have co-evolved. Clearly, however, the present information is only suggestive, and a more comprehensive analysis is needed.
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Affiliation(s)
- Jia Liu
- Chongqing Key Laboratory of Economic Plant Biotechnology, Collaborative Innovation Center of Special Plant Industry in Chongqing, Institute of Special Plants/College of Forestry and Life Science, Chongqing University of Arts and Sciences, Yongchuan, Chongqing, 402160 China
| | - Ahmed Abdelfattah
- Dipartimento di Agraria, Università Mediterranea di Reggio Calabria, Località Feo di Vito, 89122 Reggio Calabria, Italy
| | - John Norelli
- US Department of Agriculture, Agricultural Research Service (USDA-ARS), Kearneysville, WV 25430 USA
| | - Erik Burchard
- US Department of Agriculture, Agricultural Research Service (USDA-ARS), Kearneysville, WV 25430 USA
| | - Leonardo Schena
- Dipartimento di Agraria, Università Mediterranea di Reggio Calabria, Località Feo di Vito, 89122 Reggio Calabria, Italy
| | - Samir Droby
- Agricultural Research Organization (ARO), the Volcani Center, 50250 Bet Dagan, Israel
| | - Michael Wisniewski
- US Department of Agriculture, Agricultural Research Service (USDA-ARS), Kearneysville, WV 25430 USA
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18
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Di Guardo M, Bink MCAM, Guerra W, Letschka T, Lozano L, Busatto N, Poles L, Tadiello A, Bianco L, Visser RGF, van de Weg E, Costa F. Deciphering the genetic control of fruit texture in apple by multiple family-based analysis and genome-wide association. J Exp Bot 2017; 68:1451-1466. [PMID: 28338805 PMCID: PMC5441909 DOI: 10.1093/jxb/erx017] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Fruit texture is a complex feature composed of mechanical and acoustic properties relying on the modifications occurring in the cell wall throughout fruit development and ripening. Apple is characterized by a large variation in fruit texture behavior that directly impacts both the consumer's appreciation and post-harvest performance. To decipher the genetic control of fruit texture comprehensively, two complementing quantitative trait locus (QTL) mapping approaches were employed. The first was represented by a pedigree-based analysis (PBA) carried out on six full-sib pedigreed families, while the second was a genome-wide association study (GWAS) performed on a collection of 233 apple accessions. Both plant materials were genotyped with a 20K single nucleotide polymorphism (SNP) array and phenotyped with a sophisticated high-resolution texture analyzer. The overall QTL results indicated the fundamental role of chromosome 10 in controlling the mechanical properties, while chromosomes 2 and 14 were more associated with the acoustic response. The latter QTL, moreover, showed a consistent relationship between the QTL-estimated genotypes and the acoustic performance assessed among seedlings. The in silico annotation of these intervals revealed interesting candidate genes potentially involved in fruit texture regulation, as suggested by the gene expression profile. The joint integration of these approaches sheds light on the specific control of fruit texture, enabling important genetic information to assist in the selection of valuable fruit quality apple varieties.
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Affiliation(s)
- Mario Di Guardo
- Fondazione Edmund Mach, via Mach 1, 38010 San Michele all'Adige, Trento, Italy
- Graduate School Experimental Plant Sciences, Wageningen University, PO Box 386, 6700 AJ Wageningen, The Netherlands
| | - Marco C A M Bink
- Biometris, Wageningen University and Research Centre, Wageningen, The Netherlands
| | - Walter Guerra
- Laimburg Research Centre for Agriculture and Forestry, via Laimburg 6, 39040 Ora (BZ),Italy
| | - Thomas Letschka
- Laimburg Research Centre for Agriculture and Forestry, via Laimburg 6, 39040 Ora (BZ),Italy
| | - Lidia Lozano
- Laimburg Research Centre for Agriculture and Forestry, via Laimburg 6, 39040 Ora (BZ),Italy
| | - Nicola Busatto
- Fondazione Edmund Mach, via Mach 1, 38010 San Michele all'Adige, Trento,Italy
| | - Lara Poles
- Innovation Fruit Consortium (CIF), via Mach 1, 38010 San Michele all'Adige, Trento, Italy
| | - Alice Tadiello
- Fondazione Edmund Mach, via Mach 1, 38010 San Michele all'Adige, Trento,Italy
| | - Luca Bianco
- Fondazione Edmund Mach, via Mach 1, 38010 San Michele all'Adige, Trento,Italy
| | - Richard G F Visser
- Wageningen UR Plant Breeding, Wageningen University and Research Centre, Droevendaalsesteeg 1, PO Box 386, 6700 AJ Wageningen, The Netherlands
| | - Eric van de Weg
- Wageningen UR Plant Breeding, Wageningen University and Research Centre, Droevendaalsesteeg 1, PO Box 386, 6700 AJ Wageningen, The Netherlands
| | - Fabrizio Costa
- Fondazione Edmund Mach, via Mach 1, 38010 San Michele all'Adige, Trento,Italy
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19
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Migault V, Pallas B, Costes E. Combining Genome-Wide Information with a Functional Structural Plant Model to Simulate 1-Year-Old Apple Tree Architecture. Front Plant Sci 2017; 7:2065. [PMID: 28127302 PMCID: PMC5226960 DOI: 10.3389/fpls.2016.02065] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Accepted: 12/26/2016] [Indexed: 05/26/2023]
Abstract
In crops, optimizing target traits in breeding programs can be fostered by selecting appropriate combinations of architectural traits which determine light interception and carbon acquisition. In apple tree, architectural traits were observed to be under genetic control. However, architectural traits also result from many organogenetic and morphological processes interacting with the environment. The present study aimed at combining a FSPM built for apple tree, MAppleT, with genetic determinisms of architectural traits, previously described in a bi-parental population. We focused on parameters related to organogenesis (phyllochron and immediate branching) and morphogenesis processes (internode length and leaf area) during the first year of tree growth. Two independent datasets collected in 2004 and 2007 on 116 genotypes, issued from a 'Starkrimson' × 'Granny Smith' cross, were used. The phyllochron was estimated as a function of thermal time and sylleptic branching was modeled subsequently depending on phyllochron. From a genetic map built with SNPs, marker effects were estimated on four MAppleT parameters with rrBLUP, using 2007 data. These effects were then considered in MAppleT to simulate tree development in the two climatic conditions. The genome wide prediction model gave consistent estimations of parameter values with correlation coefficients between observed values and estimated values from SNP markers ranging from 0.79 to 0.96. However, the accuracy of the prediction model following cross validation schemas was lower. Three integrative traits (the number of leaves, trunk length, and number of sylleptic laterals) were considered for validating MAppleT simulations. In 2007 climatic conditions, simulated values were close to observations, highlighting the correct simulation of genetic variability. However, in 2004 conditions which were not used for model calibration, the simulations differed from observations. This study demonstrates the possibility of integrating genome-based information in a FSPM for a perennial fruit tree. It also showed that further improvements are required for improving the prediction ability. Especially temperature effect should be extended and other factors taken into account for modeling GxE interactions. Improvements could also be expected by considering larger populations and by testing other genome wide prediction models. Despite these limitations, this study opens new possibilities for supporting plant breeding by in silico evaluations of the impact of genotypic polymorphisms on plant integrative phenotypes.
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Affiliation(s)
| | | | - Evelyne Costes
- INRA, UMR 1334 AGAP, Equipe Architecture et Fonctionnement des Espèces FruitièresMontpellier, France
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20
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Urrestarazu J, Muranty H, Denancé C, Leforestier D, Ravon E, Guyader A, Guisnel R, Feugey L, Aubourg S, Celton JM, Daccord N, Dondini L, Gregori R, Lateur M, Houben P, Ordidge M, Paprstein F, Sedlak J, Nybom H, Garkava-Gustavsson L, Troggio M, Bianco L, Velasco R, Poncet C, Théron A, Moriya S, Bink MCAM, Laurens F, Tartarini S, Durel CE. Genome-Wide Association Mapping of Flowering and Ripening Periods in Apple. Front Plant Sci 2017; 8:1923. [PMID: 29176988 PMCID: PMC5686452 DOI: 10.3389/fpls.2017.01923] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Accepted: 10/24/2017] [Indexed: 05/17/2023]
Abstract
Deciphering the genetic control of flowering and ripening periods in apple is essential for breeding cultivars adapted to their growing environments. We implemented a large Genome-Wide Association Study (GWAS) at the European level using an association panel of 1,168 different apple genotypes distributed over six locations and phenotyped for these phenological traits. The panel was genotyped at a high-density of SNPs using the Axiom®Apple 480 K SNP array. We ran GWAS with a multi-locus mixed model (MLMM), which handles the putatively confounding effect of significant SNPs elsewhere on the genome. Genomic regions were further investigated to reveal candidate genes responsible for the phenotypic variation. At the whole population level, GWAS retained two SNPs as cofactors on chromosome 9 for flowering period, and six for ripening period (four on chromosome 3, one on chromosome 10 and one on chromosome 16) which, together accounted for 8.9 and 17.2% of the phenotypic variance, respectively. For both traits, SNPs in weak linkage disequilibrium were detected nearby, thus suggesting the existence of allelic heterogeneity. The geographic origins and relationships of apple cultivars accounted for large parts of the phenotypic variation. Variation in genotypic frequency of the SNPs associated with the two traits was connected to the geographic origin of the genotypes (grouped as North+East, West and South Europe), and indicated differential selection in different growing environments. Genes encoding transcription factors containing either NAC or MADS domains were identified as major candidates within the small confidence intervals computed for the associated genomic regions. A strong microsynteny between apple and peach was revealed in all the four confidence interval regions. This study shows how association genetics can unravel the genetic control of important horticultural traits in apple, as well as reduce the confidence intervals of the associated regions identified by linkage mapping approaches. Our findings can be used for the improvement of apple through marker-assisted breeding strategies that take advantage of the accumulating additive effects of the identified SNPs.
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Affiliation(s)
- Jorge Urrestarazu
- Institut de Recherche en Horticulture et Semences UMR 1345, INRA, SFR 4207 QUASAV, Beaucouzé, France
- Department of Agricultural Sciences, University of Bologna, Bologna, Italy
- Department of Agricultural Sciences, Public University of Navarre, Pamplona, Spain
- *Correspondence: Jorge Urrestarazu
| | - Hélène Muranty
- Institut de Recherche en Horticulture et Semences UMR 1345, INRA, SFR 4207 QUASAV, Beaucouzé, France
| | - Caroline Denancé
- Institut de Recherche en Horticulture et Semences UMR 1345, INRA, SFR 4207 QUASAV, Beaucouzé, France
| | - Diane Leforestier
- Institut de Recherche en Horticulture et Semences UMR 1345, INRA, SFR 4207 QUASAV, Beaucouzé, France
| | - Elisa Ravon
- Institut de Recherche en Horticulture et Semences UMR 1345, INRA, SFR 4207 QUASAV, Beaucouzé, France
| | - Arnaud Guyader
- Institut de Recherche en Horticulture et Semences UMR 1345, INRA, SFR 4207 QUASAV, Beaucouzé, France
| | - Rémi Guisnel
- Institut de Recherche en Horticulture et Semences UMR 1345, INRA, SFR 4207 QUASAV, Beaucouzé, France
| | - Laurence Feugey
- Institut de Recherche en Horticulture et Semences UMR 1345, INRA, SFR 4207 QUASAV, Beaucouzé, France
| | - Sébastien Aubourg
- Institut de Recherche en Horticulture et Semences UMR 1345, INRA, SFR 4207 QUASAV, Beaucouzé, France
| | - Jean-Marc Celton
- Institut de Recherche en Horticulture et Semences UMR 1345, INRA, SFR 4207 QUASAV, Beaucouzé, France
| | - Nicolas Daccord
- Institut de Recherche en Horticulture et Semences UMR 1345, INRA, SFR 4207 QUASAV, Beaucouzé, France
| | - Luca Dondini
- Department of Agricultural Sciences, University of Bologna, Bologna, Italy
| | - Roberto Gregori
- Department of Agricultural Sciences, University of Bologna, Bologna, Italy
| | - Marc Lateur
- Plant Breeding and Biodiversity, Centre Wallon de Recherches Agronomiques, Gembloux, Belgium
| | - Patrick Houben
- Plant Breeding and Biodiversity, Centre Wallon de Recherches Agronomiques, Gembloux, Belgium
| | - Matthew Ordidge
- School of Agriculture, Policy and Development, University of Reading, Reading, United Kingdom
| | | | - Jiri Sedlak
- Research and Breeding Institute of Pomology Holovousy Ltd., Horice, Czechia
| | - Hilde Nybom
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Kristianstad, Sweden
| | | | | | - Luca Bianco
- Fondazione Edmund Mach, San Michele all'Adige, Italy
| | | | - Charles Poncet
- Plateforme Gentyane, INRA, UMR 1095 Genetics, Diversity and Ecophysiology of Cereals, Clermont-Ferrand, France
| | - Anthony Théron
- Plateforme Gentyane, INRA, UMR 1095 Genetics, Diversity and Ecophysiology of Cereals, Clermont-Ferrand, France
| | - Shigeki Moriya
- Institut de Recherche en Horticulture et Semences UMR 1345, INRA, SFR 4207 QUASAV, Beaucouzé, France
- Apple Research Station, Institute of Fruit Tree and Tea Science, National Agriculture and Food Research Organization (NARO), Morioka, Japan
| | - Marco C. A. M. Bink
- Wageningen UR, Biometris, Wageningen, Netherlands
- Hendrix Genetics, Boxmeer, Netherlands
| | - François Laurens
- Institut de Recherche en Horticulture et Semences UMR 1345, INRA, SFR 4207 QUASAV, Beaucouzé, France
| | - Stefano Tartarini
- Department of Agricultural Sciences, University of Bologna, Bologna, Italy
| | - Charles-Eric Durel
- Institut de Recherche en Horticulture et Semences UMR 1345, INRA, SFR 4207 QUASAV, Beaucouzé, France
- Charles-Eric Durel
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21
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Bouchet AS, Laperche A, Bissuel-Belaygue C, Baron C, Morice J, Rousseau-Gueutin M, Dheu JE, George P, Pinochet X, Foubert T, Maes O, Dugué D, Guinot F, Nesi N. Genetic basis of nitrogen use efficiency and yield stability across environments in winter rapeseed. BMC Genet 2016; 17:131. [PMID: 27628849 PMCID: PMC5024496 DOI: 10.1186/s12863-016-0432-z] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2016] [Accepted: 08/24/2016] [Indexed: 01/13/2023] Open
Abstract
Background Nitrogen use efficiency is an important breeding trait that can be modified to improve the sustainability of many crop species used in agriculture. Rapeseed is a major oil crop with low nitrogen use efficiency, making its production highly dependent on nitrogen input. This complex trait is suspected to be sensitive to genotype × environment interactions, especially genotype × nitrogen interactions. Therefore, phenotyping diverse rapeseed populations under a dense network of trials is a powerful approach to study nitrogen use efficiency in this crop. The present study aimed to determine the quantitative trait loci (QTL) associated with yield in winter oilseed rape and to assess the stability of these regions under contrasting nitrogen conditions for the purpose of increasing nitrogen use efficiency. Results Genome-wide association studies and linkage analyses were performed on two diversity sets and two doubled-haploid populations. These populations were densely genotyped, and yield-related traits were scored in a multi-environment design including seven French locations, six growing seasons (2009 to 2014) and two nitrogen nutrition levels (optimal versus limited). Very few genotype × nitrogen interactions were detected, and a large proportion of the QTL were stable across nitrogen nutrition conditions. In contrast, strong genotype × trial interactions in which most of the QTL were specific to a single trial were found. To obtain further insight into the QTL × environment interactions, genetic analyses of ecovalence were performed to identify the genomic regions contributing to the genotype × nitrogen and genotype × trial interactions. Fifty-one critical genomic regions contributing to the additive genetic control of yield-associated traits were identified, and the structural organization of these regions in the genome was investigated. Conclusions Our results demonstrated that the effect of the trial was greater than the effect of nitrogen nutrition levels on seed yield-related traits under our experimental conditions. Nevertheless, critical genomic regions associated with yield that were stable across environments were identified in rapeseed. Electronic supplementary material The online version of this article (doi:10.1186/s12863-016-0432-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | - Anne Laperche
- AGROCAMPUS OUEST, UMR 1349 IGEPP, BP 35327, 35650, le Rheu, France.
| | | | - Cécile Baron
- INRA, UMR 1349 IGEPP, BP 35327, 35650, le Rheu, France
| | - Jérôme Morice
- INRA, UMR 1349 IGEPP, BP 35327, 35650, le Rheu, France
| | | | - Jean-Eric Dheu
- Limagrain Europe, Ferme de l'Etang, 77390, Verneuil-l'Etang, France
| | - Pierre George
- Biogemma, Chemin de Panedautes, 31700, Mondonville, France
| | - Xavier Pinochet
- Terres Inovia, Avenue Lucien Brétignières, 78850, Thiverval Grignon, France
| | - Thomas Foubert
- Euralis, Chemin de Panedautes, 31700, Mondonville, France
| | - Olivier Maes
- Maisadour Semences, Route de Saint Sever, BP27, 40001, Mont de Marsan Cedex, France
| | - Damien Dugué
- RAGT R2n, Rue Emile Singla, BP 3331, 12033, Rodez, France
| | - Florent Guinot
- Syngenta, Chemin de l'Hobit, 31790, Saint-Sauveur, France
| | - Nathalie Nesi
- INRA, UMR 1349 IGEPP, BP 35327, 35650, le Rheu, France
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22
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McClure KA, Gardner KM, Toivonen PMA, Hampson CR, Song J, Forney CF, DeLong J, Rajcan I, Myles S. QTL analysis of soft scald in two apple populations. Hortic Res 2016; 3:16043. [PMID: 27651916 PMCID: PMC5022660 DOI: 10.1038/hortres.2016.43] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2016] [Revised: 08/13/2016] [Accepted: 08/14/2016] [Indexed: 05/29/2023]
Abstract
The apple (Malus×domestica Borkh.) is one of the world's most widely grown and valuable fruit crops. With demand for apples year round, storability has emerged as an important consideration for apple breeding programs. Soft scald is a cold storage-related disorder that results in sunken, darkened tissue on the fruit surface. Apple breeders are keen to generate new cultivars that do not suffer from soft scald and can thus be marketed year round. Traditional breeding approaches are protracted and labor intensive, and therefore marker-assisted selection (MAS) is a valuable tool for breeders. To advance MAS for storage disorders in apple, we used genotyping-by-sequencing (GBS) to generate high-density genetic maps in two F1 apple populations, which were then used for quantitative trait locus (QTL) mapping of soft scald. In total, 900 million DNA sequence reads were generated, but after several data filtering steps, only 2% of reads were ultimately used to create two genetic maps that included 1918 and 2818 single-nucleotide polymorphisms. Two QTL associated with soft scald were identified in one of the bi-parental populations originating from parent 11W-12-11, an advanced breeding line. This study demonstrates the utility of next-generation DNA sequencing technologies for QTL mapping in F1 populations, and provides a basis for the advancement of MAS to improve storability of apples.
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Affiliation(s)
- Kendra A McClure
- Department of Plant and Animal Sciences, Faculty of Agriculture, Dalhousie University, Truro, Nova Scotia B2N 5E3, Canada
- Department of Plant Agriculture, Crop Science Building, University of Guelph, Guelph, Ontario N1G 2W1, Canada
| | - Kyle M Gardner
- Agriculture and Agri-Food Canada, Fredericton Research and Development Centre, Fredericton, New Brunswick E3B 4Z7, Canada
| | - Peter MA Toivonen
- Agriculture and Agri-Food Canada, Summerland Research and Development Centre, Summerland, British Columbia V0H 1Z0, Canada
| | - Cheryl R Hampson
- Agriculture and Agri-Food Canada, Summerland Research and Development Centre, Summerland, British Columbia V0H 1Z0, Canada
| | - Jun Song
- Agriculture and Agri-Food Canada, Kentville Research and Development Centre, Kentville, Nova Scotia, Canada B4N 1J5
| | - Charles F Forney
- Agriculture and Agri-Food Canada, Kentville Research and Development Centre, Kentville, Nova Scotia, Canada B4N 1J5
| | - John DeLong
- Agriculture and Agri-Food Canada, Kentville Research and Development Centre, Kentville, Nova Scotia, Canada B4N 1J5
| | - Istvan Rajcan
- Department of Plant Agriculture, Crop Science Building, University of Guelph, Guelph, Ontario N1G 2W1, Canada
| | - Sean Myles
- Department of Plant and Animal Sciences, Faculty of Agriculture, Dalhousie University, Truro, Nova Scotia B2N 5E3, Canada
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23
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Igarashi M, Hatsuyama Y, Harada T, Fukasawa-Akada T. Biotechnology and apple breeding in Japan. Breed Sci 2016; 66:18-33. [PMID: 27069388 PMCID: PMC4780799 DOI: 10.1270/jsbbs.66.18] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2015] [Accepted: 12/23/2015] [Indexed: 05/11/2023]
Abstract
Apple is a fruit crop of significant economic importance, and breeders world wide continue to develop novel cultivars with improved characteristics. The lengthy juvenile period and the large field space required to grow apple populations have imposed major limitations on breeding. Various molecular biological techniques have been employed to make apple breeding easier. Transgenic technology has facilitated the development of apples with resistance to fungal or bacterial diseases, improved fruit quality, or root stocks with better rooting or dwarfing ability. DNA markers for disease resistance (scab, powdery mildew, fire-blight, Alternaria blotch) and fruit skin color have also been developed, and marker-assisted selection (MAS) has been employed in breeding programs. In the last decade, genomic sequences and chromosome maps of various cultivars have become available, allowing the development of large SNP arrays, enabling efficient QTL mapping and genomic selection (GS). In recent years, new technologies for genetic improvement, such as trans-grafting, virus vectors, and genome-editing, have emerged. Using these techniques, no foreign genes are present in the final product, and some of them show considerable promise for application to apple breeding.
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Affiliation(s)
- Megumi Igarashi
- Hirosaki Industrial Research Institute, Aomori Prefectural Industrial Technology Research Center,
Ogimachi 1-1-8, Hirosaki, Aomori 036-8104,
Japan
| | - Yoshimichi Hatsuyama
- Apple Research Institute, Aomori Prefectural Industrial Technology Research Center,
Fukutami 24, Botandaira, Kuroishi, Aomori 036-0332,
Japan
| | - Takeo Harada
- Department of Agriculture and Life Science, Hirosaki University,
Bunkyouchou 3, Hirosaki, Aomori 036-8563,
Japan
| | - Tomoko Fukasawa-Akada
- Hirosaki Industrial Research Institute, Aomori Prefectural Industrial Technology Research Center,
Ogimachi 1-1-8, Hirosaki, Aomori 036-8104,
Japan
- Corresponding author (e-mail: )
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24
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Iwata H, Minamikawa MF, Kajiya-Kanegae H, Ishimori M, Hayashi T. Genomics-assisted breeding in fruit trees. Breed Sci 2016; 66:100-15. [PMID: 27069395 PMCID: PMC4780794 DOI: 10.1270/jsbbs.66.100] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2015] [Accepted: 01/12/2016] [Indexed: 05/03/2023]
Abstract
Recent advancements in genomic analysis technologies have opened up new avenues to promote the efficiency of plant breeding. Novel genomics-based approaches for plant breeding and genetics research, such as genome-wide association studies (GWAS) and genomic selection (GS), are useful, especially in fruit tree breeding. The breeding of fruit trees is hindered by their long generation time, large plant size, long juvenile phase, and the necessity to wait for the physiological maturity of the plant to assess the marketable product (fruit). In this article, we describe the potential of genomics-assisted breeding, which uses these novel genomics-based approaches, to break through these barriers in conventional fruit tree breeding. We first introduce the molecular marker systems and whole-genome sequence data that are available for fruit tree breeding. Next we introduce the statistical methods for biparental linkage and quantitative trait locus (QTL) mapping as well as GWAS and GS. We then review QTL mapping, GWAS, and GS studies conducted on fruit trees. We also review novel technologies for rapid generation advancement. Finally, we note the future prospects of genomics-assisted fruit tree breeding and problems that need to be overcome in the breeding.
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Affiliation(s)
- Hiroyoshi Iwata
- Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo,
1-1-1 Yayoi, Bunkyo, Tokyo 113-8657,
Japan
- Corresponding author (e-mail: )
| | - Mai F. Minamikawa
- Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo,
1-1-1 Yayoi, Bunkyo, Tokyo 113-8657,
Japan
| | - Hiromi Kajiya-Kanegae
- Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo,
1-1-1 Yayoi, Bunkyo, Tokyo 113-8657,
Japan
| | - Motoyuki Ishimori
- Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo,
1-1-1 Yayoi, Bunkyo, Tokyo 113-8657,
Japan
| | - Takeshi Hayashi
- Agroinfomatics Division, NARO Agricultural Research Center (NARC),
3-1-1 Kannondai, Tsukuba, Ibaraki 305-8666,
Japan
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25
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Sun R, Chang Y, Yang F, Wang Y, Li H, Zhao Y, Chen D, Wu T, Zhang X, Han Z. A dense SNP genetic map constructed using restriction site-associated DNA sequencing enables detection of QTLs controlling apple fruit quality. BMC Genomics 2015; 16:747. [PMID: 26437648 PMCID: PMC4595315 DOI: 10.1186/s12864-015-1946-x] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2014] [Accepted: 09/22/2015] [Indexed: 02/05/2023] Open
Abstract
Background Genetic map based quantitative trait locus (QTL) analysis is an important method for studying important horticultural traits in apple. To facilitate molecular breeding studies of fruit quality traits in apple, we aim to construct a high density map which was efficient for QTL mapping and possible to search for candidate genes directly in mapped QTLs regions. Methods A total of 1733 F1 seedlings derived from ‘Jonathan’ × ‘Golden Delicious’ was used for the map constructionand QTL analysis. The SNP markers were developed by restriction site-associated DNA sequencing (RADseq). Phenotyping data of fruit quality traits were calculated in 2008-2011. Once QTLs were mapped, candidate genes were searched for in the corresponding regions of the apple genome sequence underlying the QTLs. Then some of the candidate genes were validated using real-time PCR. Results A high-density genetic map with 3441 SNP markers from 297 individuals was generated. Of the 3441 markers, 2017 were mapped to ‘Jonathan’ with a length of 1343.4 cM and the average distance between markers was 0.67 cM, 1932 were mapped to ‘Golden Delicious’ with a length of 1516.0 cM and the average distance between markers was 0.78 cM. Twelve significant QTLs linked to the control of fruit weight, fruit firmness, sugar content and fruit acidity were mapped to seven linkage groups. Based on gene annotation, 80, 64 and 17 genes related to fruit weight, fruit firmness and fruit acidity, respectively, were analyzed.Among the 17 candidate genes associated with control of fruit acidity, changes in the expression of MDP0000582174 (MdMYB4) were in agreement with the pattern of changes in malic acid content in apple during ripening, and the relative expression of MDP0000239624 (MdME) was significantly correlated withfruit acidity. Conclusions We demonstrated the construction of a dense SNP genetic map in apple using next generation sequencing and that the increased resolution enabled the detection of narrow interval QTLs linked to the three fruit quality traits assessed. The candidate genes MDP0000582174 and MDP0000239624 were found to be related to fruit acidity regulation. We conclude that application of RADseq for genetic map construction improved the precision of QTL detection and should be utilized in future studies on the regulatory mechanisms of important fruit traits in apple. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1946-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Rui Sun
- Institute for Horticultural Plants, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China.
| | - Yuansheng Chang
- Institute for Horticultural Plants, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China.
| | - Fengqiu Yang
- Changli Institute for Pomology, Hebei Academy of Agricultural and Forestry Science, Changli, Heibei 066600, China.
| | - Yi Wang
- Institute for Horticultural Plants, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China.
| | - Hui Li
- Institute for Horticultural Plants, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China.
| | - Yongbo Zhao
- Changli Institute for Pomology, Hebei Academy of Agricultural and Forestry Science, Changli, Heibei 066600, China.
| | - Dongmei Chen
- Changli Institute for Pomology, Hebei Academy of Agricultural and Forestry Science, Changli, Heibei 066600, China.
| | - Ting Wu
- Institute for Horticultural Plants, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China.
| | - Xinzhong Zhang
- Institute for Horticultural Plants, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China.
| | - Zhenhai Han
- Institute for Horticultural Plants, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China.
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