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Li X, Wang J, Su M, Zhang M, Hu Y, Du J, Zhou H, Yang X, Zhang X, Jia H, Gao Z, Ye Z. Multiple-statistical genome-wide association analysis and genomic prediction of fruit aroma and agronomic traits in peaches. HORTICULTURE RESEARCH 2023; 10:uhad117. [PMID: 37577398 PMCID: PMC10419450 DOI: 10.1093/hr/uhad117] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Accepted: 05/21/2023] [Indexed: 08/15/2023]
Abstract
'Chinese Cling' is an important founder in peach breeding history due to the pleasant flavor. Genome-wide association studies (GWAS) combined with genomic selection are promising tools in fruit tree breeding, as there is a considerable time lapse between crossing and release of a cultivar. In this study, 242 peaches from Shanghai germplasm were genotyped with 145 456 single-nucleotide polymorphisms (SNPs). The six agronomic traits of fruit flesh color, fruit shape, fruit hairiness, flower type, pollen sterility, and soluble solids content, along with 14 key volatile odor compounds (VOCs), were recorded for multiple-statistical GWAS. Except the reported candidate genes, six novel genes were identified as associated with these traits. Thirty-nine significant SNPs were associated with eight VOCs. The putative candidate genes were confirmed for VOCs by RNA-seq, including three genes in the biosynthesis pathway found to be associated with linalool, soluble solids content, and cis-3-hexenyl acetate. Multiple-trait genomic prediction enhanced the predictive ability for γ-decalactone to 0.7415 compared with the single-trait model value of 0.1017. One PTS1-SSR marker was designed to predict the linalool content, and the favorable genotype 187/187 was confirmed, mainly existing in the 'Shanghai Shuimi' landrace. Overall, our findings will be helpful in determining peach accessions with the ideal phenotype and show the potential of multiple-trait genomic prediction to improve accuracy for highly correlated genetic traits. The diagnostic marker will be valuable for the breeder to bridge the gap between quantitative trait loci and marker-assisted selection for developing strong-aroma cultivars.
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Affiliation(s)
- Xiongwei Li
- Peach Research Department of Forest & Fruit Tree Institute, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China
| | - Jiabo Wang
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization (Southwest Minzu University, Ministry of Education), Chengdu, Sichuan 610041, China
| | - Mingshen Su
- Peach Research Department of Forest & Fruit Tree Institute, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China
| | - Minghao Zhang
- Peach Research Department of Forest & Fruit Tree Institute, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China
| | - Yang Hu
- Peach Research Department of Forest & Fruit Tree Institute, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China
| | - Jihong Du
- Peach Research Department of Forest & Fruit Tree Institute, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China
| | - Huijuan Zhou
- Peach Research Department of Forest & Fruit Tree Institute, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China
| | - Xiaofeng Yang
- Peach Group of Shanghai Runzhuang Agricultural Science and Technology Institute, Shanghai 201415, China
| | - Xianan Zhang
- Peach Research Department of Forest & Fruit Tree Institute, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China
| | - Huijuan Jia
- Department of Horticulture, Key Laboratory for Horticultural Plant Growth, Development and Quality Improvement of State Agriculture Ministry, Zhejiang Unihversity, Hangzhou 310058, China
| | - Zhongshan Gao
- Department of Horticulture, Key Laboratory for Horticultural Plant Growth, Development and Quality Improvement of State Agriculture Ministry, Zhejiang Unihversity, Hangzhou 310058, China
| | - Zhengwen Ye
- Peach Research Department of Forest & Fruit Tree Institute, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China
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Li M, Li J, Nie P, Li G, Liu W, Gong Q, Dong X, Gao X, Chen W, Zhang A. A high-quality assembled genome of a representative peach landrace, 'Feichenghongli', and analysis of distinct late florescence and narrow leaf traits. BMC PLANT BIOLOGY 2023; 23:230. [PMID: 37120546 PMCID: PMC10148998 DOI: 10.1186/s12870-023-04242-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Accepted: 04/22/2023] [Indexed: 05/03/2023]
Abstract
BACKGROUND Peach (Prunus persica L. Batsch) is one of the most popular fruits worldwide. Although the reference genome of 'Lovell' peach has been released, the diversity of genome-level variations cannot be explored with one genome. To detect these variations, it is necessary to assemble more genomes. RESULTS We sequenced and de novo assembled the genome of 'Feichenghongli' (FCHL), a representative landrace with strict self-pollination, which maintained the homozygosity of the genome as much as possible. The chromosome-level genome of FCHL was 239.06 Mb in size with a contig N50 of 26.93 Mb and only 4 gaps at the scaffold level. The alignment of the FCHL genome with the reference 'Lovell' genome enabled the identification of 432535 SNPs, 101244 insertions and deletions, and 7299 structural variants. Gene family analysis showed that the expanded genes in FCHL were enriched in sesquiterpenoids and triterpenoid biosynthesis. RNA-seq analyses were carried out to investigate the two distinct traits of late florescence and narrow leaves. Two key genes, PpDAM4 and PpAGL31, were identified candidates for the control of flower bud dormancy, and an F-box gene, PpFBX92, was identified as a good candidate gene in the regulation of leaf size. CONCLUSIONS The assembled high-quality genome could deepen our understanding of variations among diverse genomes and provide valuable information for identifying functional genes and improving the molecular breeding process.
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Affiliation(s)
- Miao Li
- Shandong Institute of Pomology, Taian City, 271000 Shandong Province China
| | - Jian Li
- Shandong Institute of Pomology, Taian City, 271000 Shandong Province China
| | - Peixian Nie
- Shandong Institute of Pomology, Taian City, 271000 Shandong Province China
| | - Guixiang Li
- Shandong Institute of Pomology, Taian City, 271000 Shandong Province China
| | - Wei Liu
- Shandong Institute of Pomology, Taian City, 271000 Shandong Province China
| | - Qingtao Gong
- Shandong Institute of Pomology, Taian City, 271000 Shandong Province China
| | - Xiaomin Dong
- Shandong Institute of Pomology, Taian City, 271000 Shandong Province China
| | - Xiaolan Gao
- Shandong Institute of Pomology, Taian City, 271000 Shandong Province China
| | - Wenyu Chen
- Feicheng peach Industry Development Center, Feicheng City, 271600 Shandong Province China
| | - Anning Zhang
- Shandong Institute of Pomology, Taian City, 271000 Shandong Province China
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Savoia MA, Del Faro L, Turco A, Fanelli V, Venerito P, Montemurro C, Sabetta W. Biodiversity Evaluation and Preservation of Italian Stone Fruit Germplasm (Peach and Apricot) in Southern Italy. PLANTS (BASEL, SWITZERLAND) 2023; 12:1279. [PMID: 36986967 PMCID: PMC10055517 DOI: 10.3390/plants12061279] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 02/27/2023] [Accepted: 03/09/2023] [Indexed: 06/19/2023]
Abstract
The Prunus genus encompasses a group of economically important and closely related crops, sharing an essentially common genome and, thereby, a high level of conserved and transferable microsatellite (SSR) loci. In Southern Italy, many of the local and/or neglected varieties are abandoned and at risk of extinction due to the high degree of urbanization and agricultural intensification, despite their value as genetic resources for crop improvement. This research aimed to genetically and morphologically characterize the traditional apricot (P. armenica) and peach (P. persica) germplasms collected in old family orchards. Most of the official descriptor categories were scored, thus revealing a rather high level of phenotypic variation in both collections. Genetic data allowed the discovery of diversity masked by morphological traits. Genotyping in 15 and 18 SSRs, eight of which were transferable across both species, showed an average polymorphic informativeness (PIC) of 0.44 and 0.59 for apricot and peach, respectively, and a total of 70 and 144 alleles. A reliable identification of each genotype was achieved, and the presence of possible mislabeling and/or erroneous denominations was solved. These results are encouraging for the valorization of the still poorly explored Italian Prunus germplasm, with significant economic consequences for bioresource conservation and management.
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Affiliation(s)
- Michele Antonio Savoia
- Department of Soil, Plant and Food Sciences, University of Bari Aldo Moro, Via Amendola 165/A, 70126 Bari, Italy
| | - Loredana Del Faro
- CRSFA-Centro Ricerca, Sperimentazione e Formazione in Agricoltura “Basile Caramia”, Via Cisternino 281, 70010 Locorotondo, Italy
| | - Andrea Turco
- CRSFA-Centro Ricerca, Sperimentazione e Formazione in Agricoltura “Basile Caramia”, Via Cisternino 281, 70010 Locorotondo, Italy
| | - Valentina Fanelli
- Department of Soil, Plant and Food Sciences, University of Bari Aldo Moro, Via Amendola 165/A, 70126 Bari, Italy
| | - Pasquale Venerito
- CRSFA-Centro Ricerca, Sperimentazione e Formazione in Agricoltura “Basile Caramia”, Via Cisternino 281, 70010 Locorotondo, Italy
| | - Cinzia Montemurro
- Department of Soil, Plant and Food Sciences, University of Bari Aldo Moro, Via Amendola 165/A, 70126 Bari, Italy
- Spin Off Sinagri s.r.l., University of Bari Aldo Moro, Via Amendola 165/A, 70126 Bari, Italy
- Institute for Sustainable Plant Protection–Support Unit Bari, National Research Council (IPSP-CNR), Via Amendola 165/A, 70126 Bari, Italy
| | - Wilma Sabetta
- Spin Off Sinagri s.r.l., University of Bari Aldo Moro, Via Amendola 165/A, 70126 Bari, Italy
- Institute of Biosciences and BioResources, National Research Council (IBBR-CNR), Via Amendola 165/A, 70126 Bari, Italy
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Mas-Gómez J, Cantín CM, Moreno MÁ, Martínez-García PJ. Genetic Diversity and Genome-Wide Association Study of Morphological and Quality Traits in Peach Using Two Spanish Peach Germplasm Collections. FRONTIERS IN PLANT SCIENCE 2022; 13:854770. [PMID: 35386674 PMCID: PMC8979248 DOI: 10.3389/fpls.2022.854770] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Accepted: 02/21/2022] [Indexed: 06/14/2023]
Abstract
Peach [Prunus persica (L.) Batsch] is one of the most important stone fruits species in world production. Spanish peach production is currently the second largest in the world and the available cultivars in Spain includes a great source of genetic diversity with variability in fruit quality traits and postharvest disorders tolerance. In order to explore the genetic diversity and single nucleotide polymorphism (SNP)-trait associations in the Spanish germplasm, the new peach 18K SNP v2 array was used to genotype 287 accessions belonging to the two National Peach Germplasm Collections placed at the Agrifood Research and Technology Centre of Aragon (CITA) and at the Experimental Station of Aula Dei (EEAD)-CSIC. The high density of the new SNP array allowed the identification of 30 groups of synonymies, which had not been identified before using low-density markers. In addition, a possible large-scale molecular event in 'Starcrest', a sport of 'Springcrest', was detected showing a possible chromosome replacement of a 13.5 Mb region. Previous suggestions about Spanish diversification regions agreed with our genetic diversity and linkage disequilibrium (LD) decay results using high-density markers. A genome-wide association study (GWAS) detected 34 significant SNP-trait association with the type of leaf glands (TLG), fruit hairiness (FH), and flesh texture (FT). The impact of the significant SNPs was studied with SnpEff. Candidate genes encode several important family proteins involved in trichome formation and powdery mildew resistance (linked to TLG in peach). The genetic distance among cultivars obtained, together with SNP-trait associations found, provide new knowledge for marker-assisted selection and crossing approaches in peach breeding programmes.
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Affiliation(s)
- Jorge Mas-Gómez
- Department of Plant Breeding, Centre of Edaphology and Applied Biology of Segura, Spanish National Research Council (CEBAS-CSIC), Murcia, Spain
| | - Celia M. Cantín
- Department of Pomology, Experimental Station of Aula Dei-CSIC, Spanish National Research Council, Zaragoza, Spain
- Department of Horticulture, Agrifood Research and Technology Centre of Aragon, Zaragoza, Spain
| | - María Ángeles Moreno
- Department of Pomology, Experimental Station of Aula Dei-CSIC, Spanish National Research Council, Zaragoza, Spain
| | - Pedro J. Martínez-García
- Department of Plant Breeding, Centre of Edaphology and Applied Biology of Segura, Spanish National Research Council (CEBAS-CSIC), Murcia, Spain
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Genetic Diversity of Peach Cultivars from the Collection of the Nikita Botanical Garden Based on SSR Markers. PLANTS 2021; 10:plants10122609. [PMID: 34961080 PMCID: PMC8704053 DOI: 10.3390/plants10122609] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 11/24/2021] [Accepted: 11/24/2021] [Indexed: 11/16/2022]
Abstract
The Nikita Botanical Garden (NBG) has a unique Prunus L. collection (peach, apricot, plum, cherry) comprising more than 3000 accessions. NBG is also a breeding center for stone fruits, including peach (Prunus persica (L.) Batsch). In the present study a set of 85 peach cultivars bred in NBG, Europe, and North America was analyzed using 12 SSR markers to assess their genetic diversity and relatedness. The detected polymorphism level was comparable to the previous estimates of genetic variability in peach cultivars. The average number of alleles per locus was 5.67, PIC value averaged 0.49, expected, and observed heterozygosity averaged 0.52 and 0.31, respectively. Among the detected alleles, 19 (27.94%) were rare and 12 (17.65%) were unique. All studied accessions except two could be identified with the used marker set. Cluster analysis revealed some groups according to the cultivars’ pedigrees. No clear differentiation of the studied sample according to geographic origin or fruit characteristics of peach cultivars was revealed. The results provide valuable information for identification and rational management of the material preserved in the NBG peach collection.
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Population-scale peach genome analyses unravel selection patterns and biochemical basis underlying fruit flavor. Nat Commun 2021; 12:3604. [PMID: 34127667 PMCID: PMC8203738 DOI: 10.1038/s41467-021-23879-2] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Accepted: 05/17/2021] [Indexed: 02/05/2023] Open
Abstract
A narrow genetic basis in modern cultivars and strong linkage disequilibrium in peach (Prunus persica) has restricted resolution power for association studies in this model fruit species, thereby limiting our understanding of economically important quality traits including fruit flavor. Here, we present a high-quality genome assembly for a Chinese landrace, Longhua Shui Mi (LHSM), a representative of the Chinese Cling peaches that have been central in global peach genetic improvement. We also map the resequencing data for 564 peach accessions to this LHSM assembly at an average depth of 26.34× per accession. Population genomic analyses reveal a fascinating history of convergent selection for sweetness yet divergent selection for acidity in eastern vs. western modern cultivars. Molecular-genetics and biochemical analyses establish that PpALMT1 (aluminum-activated malate transporter 1) contributes to their difference of malate content and that increases fructose content accounts for the increased sweetness of modern peach fruits, as regulated by PpERDL16 (early response to dehydration 6-like 16). Our study illustrates the strong utility of the genomics resources for both basic and applied efforts to understand and exploit the genetic basis of fruit quality in peach.
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7
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Jin J, Gan K, Zhao L, Jia H, Zhu Y, Li X, Yang Z, Ye Z, Cao K, Wang Z, Yu M, Zhang Y, Ma Z, Liu H, Arús P, Akkerdaas JH, Gao Z, van Ree R. Peach allergen Pru p 1 content is generally low in fruit but with large variation in different varieties. Clin Transl Allergy 2021; 11:e12034. [PMID: 34025984 PMCID: PMC8120414 DOI: 10.1002/clt2.12034] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Revised: 04/05/2021] [Accepted: 04/26/2021] [Indexed: 01/22/2023] Open
Abstract
Background Pru p 1 is a major allergen in peach and nectarine, and the different content in varieties may affect the degree of allergic reactions. This study aimed to quantify Pru p 1 levels in representative peach varieties and select hypoallergenic Pru p 1 varieties. Methods To obtain monoclonal and polyclonal antibodies, mice and rabbits, respectively, were immunized with recombinant Pru p 1.01 and Pru p 1.02. The Pru p 1 levels in fruits from 83 representative peach varieties was quantified by sandwich enzyme-linked immunosorbent assay (sELISA). nPru p 1 was obtained through specific monoclonal antibody affinity purification and confirmed by Western blot and mass spectrometry. The variable Pru p 1 content of selected varieties was evaluated by Western blot and the expression level of encoding Pru p 1 genes by quantitative polymerase chain reaction. Results A sELISA method with monoclonal and polyclonal antibodies was built for quantifying Pru p 1 levels in peach. Pru p 1 was mainly concentrated in the peel (0.20-73.44 μg/g, fresh weight), being very low in the pulp (0.05-9.62 μg/g) and not detected in wild peach. For the 78 peach and nectarine varieties, Pru p 1 content varied widely from 0.12 to 6.45 μg/g in whole fruit. We verified that natural Pru p 1 is composed of 1.01 and 1.02 isoallergens, and the Pru p 1 expression level and Pru p 1 band intensity in the immunoblots were in agreement with protein quantity determined by ELISA for some tested varieties. In some cases, the reduced levels of Pru p 1 did not coincide with low Pru p 3 in the same variety in whole fruit, while some ancient wild peach and nectarines contained low levels of both allergens, and late-ripening yellow flesh varieties were usually highly allergenic. Conclusion Pru p 1 content is generally low in peach compared to Pru p 3. Several hypoallergenic Pru p 1 and Pru p 3 varieties, "Zi Xue Tao," "Wu Yue Xian," and "May Fire," were identified, which could be useful in trials for peach allergy patients.
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Affiliation(s)
- Jing Jin
- Allergy Research Center Zhejiang University Hangzhou China.,College of Agriculture and Biotechnology Zhejiang University Hangzhou China
| | - Kexin Gan
- College of Agriculture and Biotechnology Zhejiang University Hangzhou China
| | - Lan Zhao
- Allergy Research Center Zhejiang University Hangzhou China.,College of Agriculture and Biotechnology Zhejiang University Hangzhou China
| | - Huijuan Jia
- College of Agriculture and Biotechnology Zhejiang University Hangzhou China
| | - Yifan Zhu
- College of Agriculture and Biotechnology Zhejiang University Hangzhou China
| | - Xiongwei Li
- Forest & Fruit Tree Institute Shanghai Academy of Agricultural Sciences Shanghai China
| | - Zhaowei Yang
- State Key Laboratory of Respiratory Disease The First Affiliated Hospital of Guangzhou Medical University Guangzhou China
| | - Zhengwen Ye
- Forest & Fruit Tree Institute Shanghai Academy of Agricultural Sciences Shanghai China
| | - Ke Cao
- Zhengzhou Fruit Research Institute China Academy of Agricultural Sciences Zhengzhou China
| | - Zhiqiang Wang
- Zhengzhou Fruit Research Institute China Academy of Agricultural Sciences Zhengzhou China
| | - Mingliang Yu
- Fruit Tree Institute Jiangsu Academy of Agricultural Sciences Nanjing China
| | - Yuyan Zhang
- Fruit Tree Institute Jiangsu Academy of Agricultural Sciences Nanjing China
| | - Zhisheng Ma
- Shijiazhuang Pomology Institute Hebei Academy of Agriculture and Forestry Sciences Shijiazhuang Hebei China
| | - Hangkong Liu
- College of Horticulture Northwest A&F University Yangling Shaanxi China
| | - Pere Arús
- IRTA Centre de Recerca en Agrigenòmica CSIC-IRTA-UAB-UB Campus UAB - Edifici CRAG Barcelona Spain
| | - Jaap H Akkerdaas
- Departments of Experimental Immunology and Otorhinolaryngology Amsterdam UMC University of Amsterdam Amsterdam The Netherlands
| | - Zhongshan Gao
- Allergy Research Center Zhejiang University Hangzhou China.,College of Agriculture and Biotechnology Zhejiang University Hangzhou China.,Departments of Experimental Immunology and Otorhinolaryngology Amsterdam UMC University of Amsterdam Amsterdam The Netherlands
| | - Ronald van Ree
- Departments of Experimental Immunology and Otorhinolaryngology Amsterdam UMC University of Amsterdam Amsterdam The Netherlands
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8
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Minamikawa MF, Kunihisa M, Noshita K, Moriya S, Abe K, Hayashi T, Katayose Y, Matsumoto T, Nishitani C, Terakami S, Yamamoto T, Iwata H. Tracing founder haplotypes of Japanese apple varieties: application in genomic prediction and genome-wide association study. HORTICULTURE RESEARCH 2021; 8:49. [PMID: 33642580 PMCID: PMC7917097 DOI: 10.1038/s41438-021-00485-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Revised: 12/28/2020] [Accepted: 01/03/2021] [Indexed: 05/21/2023]
Abstract
Haplotypes provide useful information for genomics-based approaches, genomic prediction, and genome-wide association study. As a small number of superior founders have contributed largely to the breeding history of fruit trees, the information of founder haplotypes may be relevant for performing the genomics-based approaches in these plants. In this study, we proposed a method to estimate 14 haplotypes from 7 founders and automatically trace the haplotypes forward to apple parental (185 varieties) and breeding (659 F1 individuals from 16 full-sib families) populations based on 11,786 single-nucleotide polymorphisms, by combining multiple algorithms. Overall, 92% of the single-nucleotide polymorphisms information in the parental and breeding populations was characterized by the 14 founder haplotypes. The use of founder haplotype information improved the accuracy of genomic prediction in 7 traits and the resolution of genome-wide association study in 13 out of 27 fruit quality traits analyzed in this study. We also visualized the significant propagation of the founder haplotype with the largest genetic effect in genome-wide association study over the pedigree tree of the parental population. These results suggest that the information of founder haplotypes can be useful for not only genetic improvement of fruit quality traits in apples but also for understanding the selection history of founder haplotypes in the breeding program of Japanese apple varieties.
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Affiliation(s)
- Mai F Minamikawa
- Laboratory of Biometry and Bioinformatics, 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
| | - Miyuki Kunihisa
- Institute of Fruit Tree and Tea Science, National Agriculture and Food Research Organization (NARO), 2-1 Fujimoto, Tsukuba, Ibaraki, 305-8605, Japan
| | - Koji Noshita
- Laboratory of Biometry and Bioinformatics, 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
| | - Shigeki Moriya
- Division of Apple Research, Institute of Fruit Tree and Tea Science, NARO, 92-24 Shimokuriyagawa Nabeyashiki, Morioka, Iwate, 020-0123, Japan
| | - Kazuyuki Abe
- Division of Apple Research, Institute of Fruit Tree and Tea Science, NARO, 92-24 Shimokuriyagawa Nabeyashiki, Morioka, Iwate, 020-0123, Japan
| | - Takeshi Hayashi
- Institute of Crop Science, NARO, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8518, Japan
| | - Yuichi Katayose
- Institute of Crop Science, NARO, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8518, Japan
| | - Toshimi Matsumoto
- Institute of Crop Science, NARO, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8518, Japan
- Institute of Agrobiological Sciences, NARO, 1-2 Owashi, Tsukuba, Ibaraki, 305-8634, Japan
| | - Chikako Nishitani
- Institute of Fruit Tree and Tea Science, National Agriculture and Food Research Organization (NARO), 2-1 Fujimoto, Tsukuba, Ibaraki, 305-8605, Japan
| | - Shingo Terakami
- Institute of Fruit Tree and Tea Science, National Agriculture and Food Research Organization (NARO), 2-1 Fujimoto, Tsukuba, Ibaraki, 305-8605, Japan
| | - Toshiya Yamamoto
- Institute of Fruit Tree and Tea Science, National Agriculture and Food Research Organization (NARO), 2-1 Fujimoto, Tsukuba, Ibaraki, 305-8605, Japan
| | - Hiroyoshi Iwata
- Laboratory of Biometry and Bioinformatics, 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.
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9
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Di Guardo M, Farneti B, Khomenko I, Modica G, Mosca A, Distefano G, Bianco L, Troggio M, Sottile F, La Malfa S, Biasioli F, Gentile A. Genetic characterization of an almond germplasm collection and volatilome profiling of raw and roasted kernels. HORTICULTURE RESEARCH 2021; 8:27. [PMID: 33518710 PMCID: PMC7848010 DOI: 10.1038/s41438-021-00465-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Revised: 12/11/2020] [Accepted: 12/17/2020] [Indexed: 05/16/2023]
Abstract
Almond is appreciated for its nutraceutical value and for the aromatic profile of the kernels. In this work, an almond collection composed of 96 Sicilian accessions complemented with 10 widely cultivated cultivars was phenotyped for the production of volatile organic compounds using a proton-transfer time-of-flight mass spectrometer and genotyped using the Illumina Infinium®18 K Peach SNP array. The profiling of the aroma was carried out on fresh and roasted kernels enabling the detection of 150 mass peaks. Sixty eight, for the most related with sulfur compounds, furan containing compounds, and aldehydes formed by Strecker degradation, significantly increased during roasting, while the concentration of fifty-four mass peaks, for the most belonging to alcohols and terpenes, significantly decreased. Four hundred and seventy-one robust SNPs were selected and employed for population genetic studies. Structure analysis detected three subpopulations with the Sicilian accessions characterized by a different genetic stratification compared to those collected in Apulia (South Italy) and the International cultivars. The linkage-disequilibrium (LD) decay across the genome was equal to r2 = 0.083. Furthermore, a high level of collinearity (r2 = 0.96) between almond and peach was registered confirming the high synteny between the two genomes. A preliminary application of a genome-wide association analysis allowed the detection of significant marker-trait associations for 31 fresh and 33 roasted almond mass peaks respectively. An accurate genetic and phenotypic characterization of novel germplasm can represent a valuable tool for the set-up of marker-assisted selection of novel cultivars with an enhanced aromatic profile.
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Affiliation(s)
- M Di Guardo
- Department of Agriculture, Food and Environment (Di3A), University of Catania, via Valdisavoia 5, 95123, Catania, Italy
| | - B Farneti
- Research and Innovation Centre, Fondazione Edmund Mach, San Michele all' Adige, Trento, Italy
| | - I Khomenko
- Research and Innovation Centre, Fondazione Edmund Mach, San Michele all' Adige, Trento, Italy
| | - G Modica
- Department of Agriculture, Food and Environment (Di3A), University of Catania, via Valdisavoia 5, 95123, Catania, Italy
| | - A Mosca
- Department of Agriculture, Food and Environment (Di3A), University of Catania, via Valdisavoia 5, 95123, Catania, Italy
| | - G Distefano
- Department of Agriculture, Food and Environment (Di3A), University of Catania, via Valdisavoia 5, 95123, Catania, Italy.
| | - L Bianco
- Research and Innovation Centre, Fondazione Edmund Mach, San Michele all' Adige, Trento, Italy
| | - M Troggio
- Research and Innovation Centre, Fondazione Edmund Mach, San Michele all' Adige, Trento, Italy
| | - F Sottile
- Dipartimento di Architettura, University of Palermo, Viale delle Scienze, Ed. 14 90128, Palermo, Italy
| | - S La Malfa
- Department of Agriculture, Food and Environment (Di3A), University of Catania, via Valdisavoia 5, 95123, Catania, Italy
| | - F Biasioli
- Research and Innovation Centre, Fondazione Edmund Mach, San Michele all' Adige, Trento, Italy
| | - A Gentile
- Department of Agriculture, Food and Environment (Di3A), University of Catania, via Valdisavoia 5, 95123, Catania, Italy
- National Center for Citrus Improvement, College of Horticulture and Landscape, Hunan Agricultural University, Changsha, China
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Li X, Wang J, Su M, Zhou J, Zhang M, Du J, Zhou H, Gan K, Jin J, Zhang X, Cao K, Fang W, Wang L, Jia H, Gao Z, Ye Z. Single Nucleotide Polymorphism Detection for Peach Gummosis Disease Resistance by Genome-Wide Association Study. FRONTIERS IN PLANT SCIENCE 2021; 12:763618. [PMID: 35197988 PMCID: PMC8858797 DOI: 10.3389/fpls.2021.763618] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Accepted: 12/28/2021] [Indexed: 05/05/2023]
Abstract
Peach gummosis is one of the most widespread and destructive diseases. It causes growth stunting, yield loss, branch, trunk, and tree death, and is becoming a restrictive factor in healthy and sustainable development of peach production. Although a locus has been identified based on bi-parental quantitative trait locus (QTL) mapping, selection of gummosis-resistant cultivars remains challenging due to the lack of resistant parents and of the complexity of an inducing factor. In this study, an integrated approach of genome-wide association study (GWAS) and comparative transcriptome was used to elucidate the genetic architecture associated with the disease using 195 accessions and 145,456 genome-wide single nucleotide polymorphisms (SNPs). The broad-sense and narrow-sense heritabilities were estimated using 2-year phenotypic data and genotypic data, which gave high values of 70 and 73%, respectively. Evaluation of population structure by neighbor-joining and principal components analysis (PCA) clustered all accessions into three major groups and six subgroups, mainly according to fruit shape, hairy vs. glabrous fruit skin, pedigree, geographic origin, and domestication history. Five SNPs were found to be significantly associated with gummosis disease resistance, of which SNPrs285957, located on chromosome6 across 28 Mb, was detected by both the BLINK and the FarmCPU model. Six candidate genes flanked by or harboring the significant SNPs, previously implicated in biotic stress tolerance, were significantly associated with this resistance. Two highly resistant accessions were identified with low disease severity, which could be potential sources of resistance genes for breeding. Our results provide a fresh insight into the genetic control of peach gummosis disease.
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Affiliation(s)
- Xiongwei Li
- Forest and Fruit Tree Institute, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Jiabo Wang
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization (Southwest Minzu University), Ministry of Education, Chengdu, China
| | - Mingshen Su
- Forest and Fruit Tree Institute, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Jingyi Zhou
- Horticultural Department, Shanghai Municipal Agricultural Technology Extension and Service Center, Shanghai, China
| | - Minghao Zhang
- Forest and Fruit Tree Institute, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Jihong Du
- Forest and Fruit Tree Institute, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Huijuan Zhou
- Forest and Fruit Tree Institute, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Kexin Gan
- Key Laboratory for Horticultural Plant Growth, Department of Horticulture, Development and Quality Improvement of State Agriculture Ministry, Zhejiang University, Hangzhou, China
| | - Jing Jin
- Key Laboratory for Horticultural Plant Growth, Department of Horticulture, Development and Quality Improvement of State Agriculture Ministry, Zhejiang University, Hangzhou, China
| | - Xianan Zhang
- Forest and Fruit Tree Institute, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Ke Cao
- Zhengzhou Fruit Research Institute, Chinese Academy of Agriculture Sciences, Zhengzhou, China
| | - Weichao Fang
- Zhengzhou Fruit Research Institute, Chinese Academy of Agriculture Sciences, Zhengzhou, China
| | - Lirong Wang
- Zhengzhou Fruit Research Institute, Chinese Academy of Agriculture Sciences, Zhengzhou, China
| | - Huijuan Jia
- Key Laboratory for Horticultural Plant Growth, Department of Horticulture, Development and Quality Improvement of State Agriculture Ministry, Zhejiang University, Hangzhou, China
| | - Zhongshan Gao
- Key Laboratory for Horticultural Plant Growth, Department of Horticulture, Development and Quality Improvement of State Agriculture Ministry, Zhejiang University, Hangzhou, China
- Zhongshan Gao,
| | - Zhengwen Ye
- Forest and Fruit Tree Institute, Shanghai Academy of Agricultural Sciences, Shanghai, China
- *Correspondence: Zhengwen Ye,
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Sganzerla WG, Ferreira ALA, Rosa GB, Azevedo MS, Ferrareze JP, Komatsu RA, Nunes MR, da Rosa CG, Schmit R, Costa MD, Ciotta MN, de Lima Veeck AP. Feijoa [Acca sellowiana (Berg) Burret] accessions characterization and discrimination by chemometrics. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2020; 100:5373-5384. [PMID: 32542666 DOI: 10.1002/jsfa.10585] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 06/07/2020] [Accepted: 06/15/2020] [Indexed: 06/11/2023]
Abstract
BACKGROUND Feijoa [Acca sellowiana (Berg) Burret] is a Brazilian native fruit with few commercial-level plantations and high agroindustrial potential. A genotype evaluation experiment was conducted from 1996 onward, aiming to obtain fruits based on the agronomical parameters; however, the selection based on chemical composition had not been evaluated with respect to developing a new cultivar. Accordingly, the present study aimed to discriminate seven accessions of feijoa in terms of nutritional composition, phenolic compounds and antioxidant activity using multivariate analysis (principal component analysis and multivariate contrast), targeting the potential production of a new cultivar with better nutritional value and high antioxidant capacity. RESULTS Feijoa husk presented high content of ashes, lipids, proteins, carbohydrates, phenolic compounds and antioxidant activity compared to feijoa pulp. However, only feijoa pulp was selected to multivariate analysis because it is the fruit edible part. Data variability was explained in 78% and the feijoa pulp accessions were discriminated into four groups related to their characteristics. The accession 5 discrimination can be explained by the high content of ashes, carbohydrates, soluble solids, phenolic compounds and antioxidant activity. Accession 6 was also discriminated by the high content of total acidity, pH and proteins, as well as a low content of soluble solids. CONCLUSION Feijoa accessions may be indicated for increasing plant selection via hybridization with the other accessions, aiming to produce new cultivars with better nutritional composition and antioxidant capacity. For example, accession 5 is the most suited fruit for human consumption and is a potential plant with respect to becoming a new cultivar. © 2020 Society of Chemical Industry.
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Affiliation(s)
- William Gustavo Sganzerla
- Federal Institute of Education, Science and Technology of Santa Catarina State, IFSC Campus Lages, R. Heitor Villa Lobos, 222, Lages, SC, 88506-400, Brazil
- School of Food Engineering (FEA), Post-Graduation Program in Food Engineering, University of Campinas (UNICAMP), Campinas, Brazil
| | - Ana Letícia Andrade Ferreira
- Federal Institute of Education, Science and Technology of Santa Catarina State, IFSC Campus Lages, R. Heitor Villa Lobos, 222, Lages, SC, 88506-400, Brazil
| | - Gabriel Bachega Rosa
- Federal Institute of Education, Science and Technology of Santa Catarina State, IFSC Campus Lages, R. Heitor Villa Lobos, 222, Lages, SC, 88506-400, Brazil
| | - Mônia Stremel Azevedo
- Federal Institute of Education, Science and Technology of Santa Catarina State, IFSC Campus Lages, R. Heitor Villa Lobos, 222, Lages, SC, 88506-400, Brazil
| | - Jocleita Peruzzo Ferrareze
- Federal Institute of Education, Science and Technology of Santa Catarina State, IFSC Campus Lages, R. Heitor Villa Lobos, 222, Lages, SC, 88506-400, Brazil
| | - Roberto Akitoshi Komatsu
- Federal Institute of Education, Science and Technology of Santa Catarina State, IFSC Campus Lages, R. Heitor Villa Lobos, 222, Lages, SC, 88506-400, Brazil
| | - Michael Ramos Nunes
- Federal Institute of Education, Science and Technology of Santa Catarina State, IFSC Campus Lages, R. Heitor Villa Lobos, 222, Lages, SC, 88506-400, Brazil
| | - Cleonice Gonçalves da Rosa
- Post-Graduation Program in Environment and Health, University of Planalto Catarinense (UNIPLAC), Lages, Brazil
| | - Rodolfo Schmit
- Federal Institute of Education, Science and Technology of Santa Catarina State, IFSC Campus Lages, R. Heitor Villa Lobos, 222, Lages, SC, 88506-400, Brazil
| | - Murilo Dalla Costa
- Company of Agricultural Research and Rural Extension of Santa Catarina State (EPAGRI), Lages Experimental Station, Lages, Brazil
| | - Marlise Nara Ciotta
- Company of Agricultural Research and Rural Extension of Santa Catarina State (EPAGRI), Lages Experimental Station, Lages, Brazil
| | - Ana Paula de Lima Veeck
- Federal Institute of Education, Science and Technology of Santa Catarina State, IFSC Campus Lages, R. Heitor Villa Lobos, 222, Lages, SC, 88506-400, Brazil
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Abdallah D, Baraket G, Perez V, Salhi Hannachi A, Hormaza JI. Self-compatibility in peach [ Prunus persica (L.) Batsch]: patterns of diversity surrounding the S-locus and analysis of SFB alleles. HORTICULTURE RESEARCH 2020; 7:170. [PMID: 33082976 PMCID: PMC7527504 DOI: 10.1038/s41438-020-00392-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 08/08/2020] [Accepted: 08/12/2020] [Indexed: 05/07/2023]
Abstract
Self-incompatibility (SI) to self-compatibility (SC) transition is one of the most frequent and prevalent evolutionary shifts in flowering plants. Prunus L. (Rosaceae) is a genus of over 200 species most of which exhibit a Gametophytic SI system. Peach [Prunus persica (L.) Batsch; 2n = 16] is one of the few exceptions in the genus known to be a fully self-compatible species. However, the evolutionary process of the complete and irreversible loss of SI in peach is not well understood and, in order to fill that gap, in this study 24 peach accessions were analyzed. Pollen tube growth was controlled in self-pollinated flowers to verify their self-compatible phenotypes. The linkage disequilibrium association between alleles at the S-locus and linked markers at the end of the sixth linkage group was not significant (P > 0.05), except with the closest markers suggesting the absence of a signature of negative frequency dependent selection at the S-locus. Analysis of SFB1 and SFB2 protein sequences allowed identifying the absence of some variable and hypervariable domains and the presence of additional α-helices at the C-termini. Molecular and evolutionary analysis of SFB nucleotide sequences showed a signature of purifying selection in SFB2, while the SFB1 seemed to evolve neutrally. Thus, our results show that the SFB2 allele diversified after P. persica and P. dulcis (almond) divergence, a period which is characterized by an important bottleneck, while SFB1 diversified at a transition time between the bottleneck and population expansion.
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Affiliation(s)
- Donia Abdallah
- Faculté des Sciences de Tunis, Département Biologie, Université de Tunis El Manar, 2092 Tunis, Tunisie
| | - Ghada Baraket
- Faculté des Sciences de Tunis, Département Biologie, Université de Tunis El Manar, 2092 Tunis, Tunisie
| | - Veronica Perez
- Laboratorio de Agrobiología Juan José Bravo Rodríguez (Cabildo Insular de La Palma), Unidad Técnica del Instituto de Productos Naturales y Agrobiología (IPNA-CSIC), 38700 S/C La Palma, Canary Islands, Spain
| | - Amel Salhi Hannachi
- Faculté des Sciences de Tunis, Département Biologie, Université de Tunis El Manar, 2092 Tunis, Tunisie
| | - Jose I. Hormaza
- Instituto de Hortofruticultura Subtropical y Mediterránea La Mayora (IHSM La Mayora-UMA-CSIC), 29750 Algarrobo-Costa, Malaga Spain
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13
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Eduardo I, Alegre S, Alexiou KG, Arús P. Resynthesis: Marker-Based Partial Reconstruction of Elite Genotypes in Clonally-Reproducing Plant Species. FRONTIERS IN PLANT SCIENCE 2020; 11:1205. [PMID: 32849747 PMCID: PMC7427350 DOI: 10.3389/fpls.2020.01205] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2020] [Accepted: 07/24/2020] [Indexed: 06/02/2023]
Abstract
We propose a method for marker-based selection of cultivars of clonally-reproducing plant species which keeps the basic genetic architecture of a top-performing cultivar (usually a partly heterozygous genotype), with the addition of some agronomically relevant differences (such as production time, product appearance or quality), providing added value to the product or cultivation process. The method is based on selecting a) two complementary nearly-inbred lines from successive selfing generations (ideally only F2 and F3) of large size, that may generate individuals with most of their genome identical to the original cultivar but being homozygous for either of the two component haplotypes in the rest, and b) individuals with such characteristics already occurring in the F2. Option a) allows for introgressing genes from other individuals in one or both of these nearly-inbred lines. Peach, a woody-perennial, clonally-reproduced species, was chosen as a model for a proof of concept of the Resynthesis process due to its biological characteristics: self-compatibility, compact and genetically well-known genome, low recombination rates and relatively short intergeneration time (3-4 years). From 416 F2 seedlings from cultivar Sweet Dream (SD), we obtained seven individuals with 76-94% identity with SD, and selected five pairs of complementary lines with average homozygosity of the two parents ≥0.70 such that crossing would produce some individuals highly similar to SD. The application of this scheme to other species with more complex genomes or biological features, including its generalization to F1 hybrids, is discussed.
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Affiliation(s)
- Iban Eduardo
- IRTA (Institut de Recerca i Tecnologia Agroalimentàries), Barcelona, Spain
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus UAB, Barcelona, Spain
| | - Simó Alegre
- IRTA (Institut de Recerca i Tecnologia Agroalimentàries), Barcelona, Spain
- Parc Científic i Tecnològic Agroalimentari de Lleida, Lleida, Spain
| | - Konstantinos G. Alexiou
- IRTA (Institut de Recerca i Tecnologia Agroalimentàries), Barcelona, Spain
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus UAB, Barcelona, Spain
| | - Pere Arús
- IRTA (Institut de Recerca i Tecnologia Agroalimentàries), Barcelona, Spain
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus UAB, Barcelona, Spain
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14
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Pavan S, Delvento C, Ricciardi L, Lotti C, Ciani E, D'Agostino N. Recommendations for Choosing the Genotyping Method and Best Practices for Quality Control in Crop Genome-Wide Association Studies. Front Genet 2020; 11:447. [PMID: 32587600 PMCID: PMC7299185 DOI: 10.3389/fgene.2020.00447] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2019] [Accepted: 04/14/2020] [Indexed: 12/19/2022] Open
Abstract
High-throughput genotyping boosts genome-wide association studies (GWAS) in crop species, leading to the identification of single-nucleotide polymorphisms (SNPs) associated with economically important traits. Choosing a cost-effective genotyping method for crop GWAS requires careful examination of several aspects, namely, the purpose and the scale of the study, crop-specific genomic features, and technical and economic matters associated with each genotyping option. Once genotypic data have been obtained, quality control (QC) procedures must be applied to avoid bias and false signals in genotype–phenotype association tests. QC for human GWAS has been extensively reviewed; however, QC for crop GWAS may require different actions, depending on the GWAS population type. Here, we review most popular genotyping methods based on next-generation sequencing (NGS) and array hybridization, and report observations that should guide the investigator in the choice of the genotyping method for crop GWAS. We provide recommendations to perform QC in crop species, and deliver an overview of bioinformatics tools that can be used to accomplish all needed tasks. Overall, this work aims to provide guidelines to harmonize those procedures leading to SNP datasets ready for crop GWAS.
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Affiliation(s)
- Stefano Pavan
- Department of Soil, Plant and Food Science, Section of Genetics and Plant Breeding, University of Bari Aldo Moro, Bari, Italy.,Institute of Biomedical Technologies, National Research Council (CNR), Bari, Italy
| | - Chiara Delvento
- Department of Soil, Plant and Food Science, Section of Genetics and Plant Breeding, University of Bari Aldo Moro, Bari, Italy
| | - Luigi Ricciardi
- Department of Soil, Plant and Food Science, Section of Genetics and Plant Breeding, University of Bari Aldo Moro, Bari, Italy
| | - Concetta Lotti
- Department of Agricultural, Food and Environmental Sciences, University of Foggia, Foggia, Italy
| | - Elena Ciani
- Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari Aldo Moro, Bari, Italy
| | - Nunzio D'Agostino
- Department of Agricultural Sciences, University of Naples Federico II, Naples, Italy
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15
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Jin J, Gao L, Zhao L, Gao Z, Li X, Xie H, Ni J, Gan K, Wu S, Ye Z, Luo J, Cao K, Ma R, Chen M, Arús P, Versteeg SA, Wang H, Liu ML, Jia H, Ree R. Selection of Pru p 3 hypoallergenic peach and nectarine varieties. Allergy 2020; 75:1256-1260. [PMID: 31710093 DOI: 10.1111/all.14102] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Revised: 10/22/2019] [Accepted: 10/27/2019] [Indexed: 01/02/2023]
Affiliation(s)
- Jing Jin
- College of Agriculture and Biotechnology Zhejiang University Hangzhou China
| | - Ling Gao
- College of Agriculture and Biotechnology Zhejiang University Hangzhou China
| | - Lan Zhao
- College of Agriculture and Biotechnology Zhejiang University Hangzhou China
| | - Zhong‐shan Gao
- College of Agriculture and Biotechnology Zhejiang University Hangzhou China
- Allergy Research Center Zhejiang University Hangzhou China
- Departments of Experimental Immunology and of Otorhinolaryngology Amsterdam UMC University of Amsterdam Amsterdam the Netherlands
| | - Xiong‐wei Li
- Forest & Fruit Tree Institute Shanghai Academy of Agricultural Sciences Shanghai China
| | - Han‐bing Xie
- College of Agriculture and Biotechnology Zhejiang University Hangzhou China
| | - Jun‐bei Ni
- College of Agriculture and Biotechnology Zhejiang University Hangzhou China
| | - Ke‐xin Gan
- College of Agriculture and Biotechnology Zhejiang University Hangzhou China
| | - Shan‐dong Wu
- Allergy Research Center Zhejiang University Hangzhou China
| | - Zheng‐wen Ye
- Forest & Fruit Tree Institute Shanghai Academy of Agricultural Sciences Shanghai China
| | - Jun Luo
- Forest & Fruit Tree Institute Shanghai Academy of Agricultural Sciences Shanghai China
| | - Ke Cao
- Zhengzhou Fruit Research Institute China Academy of Agricultural Sciences Zhengzhou China
| | - Rui‐juan Ma
- Horticultural Institute Jiangsu Academy of Agricultural Sciences Nanjing China
| | | | - Pere Arús
- IRTA Centre de Recerca en Agrigenòmica CSIC‐IRTA‐UAB‐UB, Campus UAB – Edifici CRAG Cerdanyola del Vallès (Bellaterra) Barcelona Spain
| | - Serge A. Versteeg
- Departments of Experimental Immunology and of Otorhinolaryngology Amsterdam UMC University of Amsterdam Amsterdam the Netherlands
| | - Hui‐ying Wang
- Department of Allergy the Second Affiliated Hospital School of Medicine Zhejiang University Hangzhou China
| | - Mei-ling Liu
- Department of Allergy The Third People’s Hospital of Datong Datong China
| | - Hui‐juan Jia
- College of Agriculture and Biotechnology Zhejiang University Hangzhou China
| | - Ronald Ree
- Departments of Experimental Immunology and of Otorhinolaryngology Amsterdam UMC University of Amsterdam Amsterdam the Netherlands
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16
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Detection and application of genome-wide variations in peach for association and genetic relationship analysis. BMC Genet 2019; 20:101. [PMID: 31888445 PMCID: PMC6937647 DOI: 10.1186/s12863-019-0799-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Accepted: 12/05/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Peach (Prunus persica L.) is a diploid species and model plant of the Rosaceae family. In the past decade, significant progress has been made in peach genetic research via DNA markers, but the number of these markers remains limited. RESULTS In this study, we performed a genome-wide DNA markers detection based on sequencing data of six distantly related peach accessions. A total of 650,693~1,053,547 single nucleotide polymorphisms (SNPs), 114,227~178,968 small insertion/deletions (InDels), 8386~12,298 structure variants (SVs), 2111~2581 copy number variants (CNVs) and 229,357~346,940 simple sequence repeats (SSRs) were detected and annotated. To demonstrate the application of DNA markers, 944 SNPs were filtered for association study of fruit ripening time and 15 highly polymorphic SSRs were selected to analyze the genetic relationship among 221 accessions. CONCLUSIONS The results showed that the use of high-throughput sequencing to develop DNA markers is fast and effective. Comprehensive identification of DNA markers, including SVs and SSRs, would be of benefit to genetic diversity evaluation, genetic mapping, and molecular breeding of peach.
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17
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Ying H, Shi J, Zhang S, Pingcuo G, Wang S, Zhao F, Cui Y, Zeng X. Transcriptomic and metabolomic profiling provide novel insights into fruit development and flesh coloration in Prunus mira Koehne, a special wild peach species. BMC PLANT BIOLOGY 2019; 19:463. [PMID: 31675926 PMCID: PMC6825364 DOI: 10.1186/s12870-019-2074-6] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Accepted: 10/14/2019] [Indexed: 05/21/2023]
Abstract
BACKGROUND Flesh color is one of the most important traits for the commercial value of peach fruit. To unravel the underlying regulatory network in Prunus mira, we performed an integrated analysis of the transcriptome and metabolome of 3 fruit types with various flesh pigmentations (milk-white, yellow and blood) at 3 developmental stages (pit-hardening, cell enlargement and fruit ripening). RESULTS Transcriptome analysis showed that an intense transcriptional adjustment is required for the transition from the pit-hardening to the cell enlargement stage. In contrast, few genes were differentially expressed (DEGs) from the cell enlargement to the fruit ripening stage and importantly, the 3 fruits displayed diverse transcriptional activities, indicating that difference in fruit flesh pigmentations mainly occurred during the ripening stage. We further investigated the DEGs between pairs of fruit types during the ripening stage and identified 563 DEGs representing the 'core transcriptome' associated with major differentiations between the 3 fruit types, including flesh pigmentation. Meanwhile, we analyzed the metabolome, particularly, at the ripening stage and uncovered 40 differential metabolites ('core metabolome') between the 3 fruit types including 5 anthocyanins, which may be the key molecules associated with flesh coloration. Finally, we constructed the regulatory network depicting the interactions between anthocyanins and important transcripts involved in fruit flesh coloration. CONCLUSIONS The major metabolites and transcripts involved in fruit flesh coloration in P. mira were unraveled in this study providing valuable information which will undoubtedly assist in breeding towards improved fruit quality in peach.
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Affiliation(s)
- Hong Ying
- The ministry of agriculture of Qinghai-Tibet plateau fruit trees scientific observation test station, Lhasa, 850032, Tibet, China
- Institute of Vegetables, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, 850002, Tibet, China
| | - Jian Shi
- Wuhan Metware Biotechnology Co., Ltd, Wuhan, 430070, China
| | - Shanshan Zhang
- The ministry of agriculture of Qinghai-Tibet plateau fruit trees scientific observation test station, Lhasa, 850032, Tibet, China
- Institute of Vegetables, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, 850002, Tibet, China
| | - Gesang Pingcuo
- The ministry of agriculture of Qinghai-Tibet plateau fruit trees scientific observation test station, Lhasa, 850032, Tibet, China
- Institute of Vegetables, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, 850002, Tibet, China
| | - Shuo Wang
- The ministry of agriculture of Qinghai-Tibet plateau fruit trees scientific observation test station, Lhasa, 850032, Tibet, China
- Institute of Vegetables, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, 850002, Tibet, China
| | - Fan Zhao
- The ministry of agriculture of Qinghai-Tibet plateau fruit trees scientific observation test station, Lhasa, 850032, Tibet, China
- Institute of Vegetables, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, 850002, Tibet, China
| | - Yongning Cui
- The ministry of agriculture of Qinghai-Tibet plateau fruit trees scientific observation test station, Lhasa, 850032, Tibet, China
- Institute of Vegetables, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, 850002, Tibet, China
| | - Xiuli Zeng
- The ministry of agriculture of Qinghai-Tibet plateau fruit trees scientific observation test station, Lhasa, 850032, Tibet, China.
- Institute of Vegetables, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, 850002, Tibet, China.
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18
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Sharma S, Kaur R, Solanke AKU, Dubey H, Tiwari S, Kumar K. Transcriptome sequencing of Himalayan Raspberry ( Rubus ellipticus) and development of simple sequence repeat markers. 3 Biotech 2019; 9:161. [PMID: 30944808 DOI: 10.1007/s13205-019-1685-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2018] [Accepted: 03/19/2019] [Indexed: 12/11/2022] Open
Abstract
KEY MESSAGE Rubus ellipticus is a wild crop having less number of EST-SSR markers. First attempt was made towards the transcriptomics data analysis and generation of EST-SSR markers which were used in genetic diversity and transferability studies. ABSTRACT Rubus ellipticus is a raspberry with yellow fruits, native to tropical and subtropical India and Asia. Leaves of Rubus ellipticus 'Kumarhatti' collection were utilized for cDNA library construction. More than 15 million sequencing reads were generated using NextSeq 500 Illumina RNA-seq technology. The DNASTAR software was used for de novo assembly from which 7777 unigenes with an average length of 500 bp was obtained. These unigenes were annotated using public databases, including NCBI non-redundant and gene ontology. De novo assembly of R. ellipticus unigenes found the highest similarity to apple than to other members of Rosaceae. This is the first attempt to use the Illumina platform of RNA sequencing and de novo assembly for R. ellipticus without a reference genome. In this study, unigenes were used for SSR marker development. ESTs containing SSR motifs were extracted using an online Microsatellite Identification Tool (MISA). SSR primers were designed from the SSR containing 704 EST sequences using the Websat software. Total 304 EST-SSRs primers were successfully designed, out of which 68 randomly selected primer pairs were custom synthesized and used for validation. Real-time PCR was also performed to analyze the relationship of transcriptional factors with fruit ripening. Out of 68 primer pairs, 61 were found to be informative in R. ellipticus, whereas 65 primer pairs were informative in the five tested genera of Rosaceae, i.e., pear, peach, apple, rose, and strawberry with 95.3% and 93.5% polymorphism, leading to the conclusion that these marker systems are very efficient to carryout diversity and cross transferability study in Rosaceae genera.
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Aranzana MJ, Decroocq V, Dirlewanger E, Eduardo I, Gao ZS, Gasic K, Iezzoni A, Jung S, Peace C, Prieto H, Tao R, Verde I, Abbott AG, Arús P. Prunus genetics and applications after de novo genome sequencing: achievements and prospects. HORTICULTURE RESEARCH 2019; 6:58. [PMID: 30962943 PMCID: PMC6450939 DOI: 10.1038/s41438-019-0140-8] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Revised: 03/10/2019] [Accepted: 03/13/2019] [Indexed: 05/04/2023]
Abstract
Prior to the availability of whole-genome sequences, our understanding of the structural and functional aspects of Prunus tree genomes was limited mostly to molecular genetic mapping of important traits and development of EST resources. With public release of the peach genome and others that followed, significant advances in our knowledge of Prunus genomes and the genetic underpinnings of important traits ensued. In this review, we highlight key achievements in Prunus genetics and breeding driven by the availability of these whole-genome sequences. Within the structural and evolutionary contexts, we summarize: (1) the current status of Prunus whole-genome sequences; (2) preliminary and ongoing work on the sequence structure and diversity of the genomes; (3) the analyses of Prunus genome evolution driven by natural and man-made selection; and (4) provide insight into haploblocking genomes as a means to define genome-scale patterns of evolution that can be leveraged for trait selection in pedigree-based Prunus tree breeding programs worldwide. Functionally, we summarize recent and ongoing work that leverages whole-genome sequences to identify and characterize genes controlling 22 agronomically important Prunus traits. These include phenology, fruit quality, allergens, disease resistance, tree architecture, and self-incompatibility. Translationally, we explore the application of sequence-based marker-assisted breeding technologies and other sequence-guided biotechnological approaches for Prunus crop improvement. Finally, we present the current status of publically available Prunus genomics and genetics data housed mainly in the Genome Database for Rosaceae (GDR) and its updated functionalities for future bioinformatics-based Prunus genetics and genomics inquiry.
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Affiliation(s)
- Maria José Aranzana
- IRTA, Centre de Recerca en Agrigenòmica CSIC-IRTA-UAB-UB, Campus UAB, Edifici CRAG, Cerdanyola del Vallès (Bellaterra), 08193 Barcelona, Spain
| | - Véronique Decroocq
- UMR 1332 BFP, INRA, University of Bordeaux, A3C and Virology Teams, 33882 Villenave-d’Ornon Cedex, France
| | - Elisabeth Dirlewanger
- UMR 1332 BFP, INRA, University of Bordeaux, A3C and Virology Teams, 33882 Villenave-d’Ornon Cedex, France
| | - Iban Eduardo
- IRTA, Centre de Recerca en Agrigenòmica CSIC-IRTA-UAB-UB, Campus UAB, Edifici CRAG, Cerdanyola del Vallès (Bellaterra), 08193 Barcelona, Spain
| | - Zhong Shan Gao
- Allergy Research Center, Zhejiang University, 310058 Hangzhou, China
| | | | - Amy Iezzoni
- Department of Horticulture, Michigan State University, 1066 Bogue Street, East Lansing, MI 48824-1325 USA
| | - Sook Jung
- Department of Horticulture, Washington State University, Pullman, WA 99164-6414 USA
| | - Cameron Peace
- Department of Horticulture, Washington State University, Pullman, WA 99164-6414 USA
| | - Humberto Prieto
- Biotechnology Laboratory, La Platina Research Station, Instituto de Investigaciones Agropecuarias, Santa Rosa, 11610 La Pintana, Santiago Chile
| | - Ryutaro Tao
- Laboratory of Pomology, Graduate School of Agriculture, Kyoto University, Kyoto, 606-8502 Japan
| | - Ignazio Verde
- Consiglio per la ricerca in agricoltura e l’analisi dell’economia agraria (CREA) – Centro di ricerca Olivicoltura, Frutticoltura e Agrumicoltura (CREA-OFA), Rome, Italy
| | - Albert G. Abbott
- University of Kentucky, 106 T. P. Cooper Hall, Lexington, KY 40546-0073 USA
| | - Pere Arús
- IRTA, Centre de Recerca en Agrigenòmica CSIC-IRTA-UAB-UB, Campus UAB, Edifici CRAG, Cerdanyola del Vallès (Bellaterra), 08193 Barcelona, Spain
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Pandian S, Satish L, Rameshkumar R, Muthuramalingam P, Rency AS, Rathinapriya P, Ramesh M. Analysis of population structure and genetic diversity in an exotic germplasm collection of Eleusine coracana (L.) Gaertn. using genic-SSR markers. Gene 2018; 653:80-90. [DOI: 10.1016/j.gene.2018.02.018] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2017] [Revised: 01/22/2018] [Accepted: 02/07/2018] [Indexed: 11/30/2022]
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21
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Genetic diversity of Spanish Prunus domestica L. germplasm reveals a complex genetic structure underlying. PLoS One 2018; 13:e0195591. [PMID: 29630655 PMCID: PMC5891032 DOI: 10.1371/journal.pone.0195591] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2017] [Accepted: 03/25/2018] [Indexed: 12/17/2022] Open
Abstract
European plum (Prunus domestica L.) is an ancient domesticated species cultivated in temperate areas worldwide whose genetic structure has been scarcely analyzed to date. In this study, a broad representation of Spanish European plum germplasm collected in Northeastern Spain and a representative set of reference cultivars were compared using nuclear and chloroplast markers. The number of alleles per locus detected with the SSR markers ranged from 8 to 39, with an average of 23.4 alleles, and 8 haplotypes were identified. Bayesian model-based clustering, minimum spanning networks, and the analysis of molecular variance showed the existence of a hierarchical structure. At the first level, two genetic groups were found, one containing 'Reine Claude' type reference cultivars altogether with ca. 25% of local genotypes, and a second one much more diverse. This latter group split in two groups, one containing most (ca. 70%) local genotypes and some old Spanish and French reference cultivars, whereas the other included 24 reference cultivars and only six local genotypes. A third partition level allowed a significant finer delineation into five groups. As a whole, the genetic structure of European plum from Northeastern Spain was shown to be complex and conditioned by a geographical proximity factor. This study not only contributes to genetic conservation and breeding for this species at the national level, but also supports the relevance of undertaking similar tasks of collection and characterization in other unexplored areas. Moreover, this kind of research could lead to future coordinated actions for the examination of the whole European plum diversity, to define conservation strategies, and could be used to better understand the genetic control of traits of horticultural interest through association mapping.
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Cirilli M, Flati T, Gioiosa S, Tagliaferri I, Ciacciulli A, Gao Z, Gattolin S, Geuna F, Maggi F, Bottoni P, Rossini L, Bassi D, Castrignanò T, Chillemi G. PeachVar-DB: A Curated Collection of Genetic Variations for the Interactive Analysis of Peach Genome Data. PLANT & CELL PHYSIOLOGY 2018; 59:e2. [PMID: 29216377 DOI: 10.1093/pcp/pcx183] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Accepted: 11/16/2017] [Indexed: 05/06/2023]
Abstract
Applying next-generation sequencing (NGS) technologies to species of agricultural interest has the potential to accelerate the understanding and exploration of genetic resources. The storage, availability and maintenance of huge quantities of NGS-generated data remains a major challenge. The PeachVar-DB portal, available at http://hpc-bioinformatics.cineca.it/peach, is an open-source catalog of genetic variants present in peach (Prunus persica L. Batsch) and wild-related species of Prunus genera, annotated from 146 samples publicly released on the Sequence Read Archive (SRA). We designed a user-friendly web-based interface of the database, providing search tools to retrieve single nucleotide polymorphism (SNP) and InDel variants, along with useful statistics and information. PeachVar-DB results are linked to the Genome Database for Rosaceae (GDR) and the Phytozome database to allow easy access to other external useful plant-oriented resources. In order to extend the genetic diversity covered by the PeachVar-DB further, and to allow increasingly powerful comparative analysis, we will progressively integrate newly released data.
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Affiliation(s)
- Marco Cirilli
- Department of Agricultural Science (DISAA), University of Milan, Milan, Italy
| | - Tiziano Flati
- Cineca, HPC High Performance Computing Department, Rome, Italy
- IBIOM-CNR, Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, Bari, Italy
| | - Silvia Gioiosa
- Cineca, HPC High Performance Computing Department, Rome, Italy
- IBIOM-CNR, Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, Bari, Italy
| | | | - Angelo Ciacciulli
- Department of Agricultural Science (DISAA), University of Milan, Milan, Italy
| | - Zhongshan Gao
- Department of Horticulture, College of Agriculture and Biotechnology, Zhejiang University, 310058, Hangzhou, China
| | - Stefano Gattolin
- Parco Tecnologico Padano, Via Einstein, Loc. C.na Codazza, Lodi, Italy
| | - Filippo Geuna
- Department of Agricultural Science (DISAA), University of Milan, Milan, Italy
| | - Francesco Maggi
- Department of Computer Science, 'Sapienza' University of Rome, Via Salaria 113, 00198 Rome, Italy
| | - Paolo Bottoni
- Department of Computer Science, 'Sapienza' University of Rome, Via Salaria 113, 00198 Rome, Italy
| | - Laura Rossini
- Department of Agricultural Science (DISAA), University of Milan, Milan, Italy
| | - Daniele Bassi
- Department of Agricultural Science (DISAA), University of Milan, Milan, Italy
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Cirilli M, Rossini L, Geuna F, Palmisano F, Minafra A, Castrignanò T, Gattolin S, Ciacciulli A, Babini AR, Liverani A, Bassi D. Genetic dissection of Sharka disease tolerance in peach (P. persica L. Batsch). BMC PLANT BIOLOGY 2017; 17:192. [PMID: 29100531 PMCID: PMC5670703 DOI: 10.1186/s12870-017-1117-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Accepted: 10/09/2017] [Indexed: 05/21/2023]
Abstract
BACKGROUND Plum pox virus (PPV), agent of Sharka disease, is the most important quarantine pathogen of peach (P. persica L. Batsch). Extensive evaluation of peach germplasm has highlighted the lack of resistant sources, while suggesting the presence of a quantitative disease resistance, expressed as reduction in the intensity of symptoms. Unravelling the genetic architecture of peach response to PPV infection is essential for pyramiding resistant genes and for developing more tolerant varieties. For this purpose, a genome-wide association (GWA) approach was applied in a panel of accessions phenotyped for virus susceptibility and genotyped with the IPSC peach 9 K SNP Array, and coupled with an high-coverage resequencing of the tolerant accession 'Kamarat'. RESULTS Genome-wide association identified three highly significant associated loci on chromosome 2 and 3, accounting for most of the reduction in PPV-M susceptibility within the analysed peach population. The exploration of associated intervals through whole-genome comparison of the tolerant accession 'Kamarat' and other susceptible accessions, including the PPV-resistant wild-related species P. davidiana, allow the identification of allelic variants in promising candidate genes, including an RTM2-like gene already characterized in A. thaliana. CONCLUSIONS The present study is the first effort to identify genetic factors involved in Sharka disease in peach germplasm through a GWA approach. We provide evidence of the presence of quantitative resistant loci in a collection of peach accessions, identifying major loci and highly informative SNPs that could be useful for marker assisted selection. These results could serve as reference bases for future research aimed at the comprehension of genetic mechanism regulating the complex peach-PPV interaction.
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Affiliation(s)
- Marco Cirilli
- Department of Agricultural and Environmental Sciences (DISAA), University of Milan, via Celoria 2, Milan, Italy
| | - Laura Rossini
- Department of Agricultural and Environmental Sciences (DISAA), University of Milan, via Celoria 2, Milan, Italy
- Parco Tecnologico Padano, via Einstein, Loc. C.na Codazza, Lodi, Italy
| | - Filippo Geuna
- Department of Agricultural and Environmental Sciences (DISAA), University of Milan, via Celoria 2, Milan, Italy
| | - Francesco Palmisano
- Centro di Ricerca, Sperimentazione e Formazione in Agricoltura Basile-Caramia (CRSFA), via Cisternino, 281 Locorotondo, Bari, Italy
| | - Angelantonio Minafra
- Istituto per la Protezione Sostenibile delle Piante (CNR-IPSP), via Amendola 122/D, Bari, Italy
| | - Tiziana Castrignanò
- CINECA, SCAI Super Computing Applications and Innovation, via dei Tizii 6, Rome, Italy
| | - Stefano Gattolin
- Parco Tecnologico Padano, via Einstein, Loc. C.na Codazza, Lodi, Italy
| | - Angelo Ciacciulli
- Department of Agricultural and Environmental Sciences (DISAA), University of Milan, via Celoria 2, Milan, Italy
| | | | - Alessandro Liverani
- CREA, Research Centre for Olive, Citrus and Tree Fruit, via La Canapona 1 bis, Forlì, Italy
| | - Daniele Bassi
- Department of Agricultural and Environmental Sciences (DISAA), University of Milan, via Celoria 2, Milan, Italy
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Guo LN, Gao XF. Genetic diversity and population structure of Indigofera szechuensis complex (Fabaceae) based on EST-SSR markers. Gene 2017; 624:26-33. [DOI: 10.1016/j.gene.2017.04.047] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2017] [Revised: 04/25/2017] [Accepted: 04/28/2017] [Indexed: 10/19/2022]
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25
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López-Girona E, Zhang Y, Eduardo I, Mora JRH, Alexiou KG, Arús P, Aranzana MJ. A deletion affecting an LRR-RLK gene co-segregates with the fruit flat shape trait in peach. Sci Rep 2017; 7:6714. [PMID: 28751691 PMCID: PMC5532255 DOI: 10.1038/s41598-017-07022-0] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2017] [Accepted: 06/20/2017] [Indexed: 01/01/2023] Open
Abstract
In peach, the flat phenotype is caused by a partially dominant allele in heterozygosis (Ss), fruits from homozygous trees (SS) abort a few weeks after fruit setting. Previous research has identified a SSR marker (UDP98-412) highly associated with the trait, found suitable for marker assisted selection (MAS). Here we report a ∼10 Kb deletion affecting the gene PRUPE.6G281100, 400 Kb upstream of UDP98-412, co-segregating with the trait. This gene is a leucine-rich repeat receptor-like kinase (LRR-RLK) orthologous to the Brassinosteroid insensitive 1-associated receptor kinase 1 (BAK1) group. PCR markers suitable for MAS confirmed its strong association with the trait in a collection of 246 cultivars. They were used to evaluate the DNA from a round fruit derived from a somatic mutation of the flat variety 'UFO-4', revealing that the mutation affected the flat associated allele (S). Protein BLAST alignment identified significant hits with genes involved in different biological processes. Best protein hit occurred with AtRLP12, which may functionally complement CLAVATA2, a key regulator that controls the stem cell population size. RT-PCR analysis revealed the absence of transcription of the partially deleted allele. The data support PRUPE.6G281100 as a candidate gene for flat shape in peach.
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Affiliation(s)
- Elena López-Girona
- IRTA (Institut de Recerca i Tecnologia Agroalimentàries), Barcelona, Spain
| | - Yu Zhang
- Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Campus UAB, Bellaterra, Barcelona, Spain
| | - Iban Eduardo
- IRTA (Institut de Recerca i Tecnologia Agroalimentàries), Barcelona, Spain
| | | | | | - Pere Arús
- IRTA (Institut de Recerca i Tecnologia Agroalimentàries), Barcelona, Spain
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26
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Hernández Mora JR, Micheletti D, Bink M, Van de Weg E, Cantín C, Nazzicari N, Caprera A, Dettori MT, Micali S, Banchi E, Campoy JA, Dirlewanger E, Lambert P, Pascal T, Troggio M, Bassi D, Rossini L, Verde I, Quilot-Turion B, Laurens F, Arús P, Aranzana MJ. Integrated QTL detection for key breeding traits in multiple peach progenies. BMC Genomics 2017; 18:404. [PMID: 28583082 PMCID: PMC5460339 DOI: 10.1186/s12864-017-3783-6] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2017] [Accepted: 05/10/2017] [Indexed: 01/23/2023] Open
Abstract
Background Peach (Prunus persica (L.) Batsch) is a major temperate fruit crop with an intense breeding activity. Breeding is facilitated by knowledge of the inheritance of the key traits that are often of a quantitative nature. QTLs have traditionally been studied using the phenotype of a single progeny (usually a full-sib progeny) and the correlation with a set of markers covering its genome. This approach has allowed the identification of various genes and QTLs but is limited by the small numbers of individuals used and by the narrow transect of the variability analyzed. In this article we propose the use of a multi-progeny mapping strategy that used pedigree information and Bayesian approaches that supports a more precise and complete survey of the available genetic variability. Results Seven key agronomic characters (data from 1 to 3 years) were analyzed in 18 progenies from crosses between occidental commercial genotypes and various exotic lines including accessions of other Prunus species. A total of 1467 plants from these progenies were genotyped with a 9 k SNP array. Forty-seven QTLs were identified, 22 coinciding with major genes and QTLs that have been consistently found in the same populations when studied individually and 25 were new. A substantial part of the QTLs observed (47%) would not have been detected in crosses between only commercial materials, showing the high value of exotic lines as a source of novel alleles for the commercial gene pool. Our strategy also provided estimations on the narrow sense heritability of each character, and the estimation of the QTL genotypes of each parent for the different QTLs and their breeding value. Conclusions The integrated strategy used provides a broader and more accurate picture of the variability available for peach breeding with the identification of many new QTLs, information on the sources of the alleles of interest and the breeding values of the potential donors of such valuable alleles. These results are first-hand information for breeders and a step forward towards the implementation of DNA-informed strategies to facilitate selection of new cultivars with improved productivity and quality. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3783-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- José R Hernández Mora
- IRTA, Centre de Recerca en Agrigenòmica CSIC-IRTA-UAB-UB; Campus UAB, Bellaterra (Cerdanyola del Vallès), 08193, Barcelona, Spain
| | - Diego Micheletti
- Research and Innovation Centre, Fondazione Edmund Mach (FEM), Via Mach 1, 38010, San Michele all'Adige, TN, Italy
| | - Marco Bink
- Hendrix Genetics Research, Technology & Services B.V., P.O. Box 114, 5830AC, Boxmeer, The Netherlands
| | - Eric Van de Weg
- Plant Breeding, Wageningen University and Research Droevendaalsesteeg 1, P.O. Box 386, 6700AJ, Wageningen, The Netherlands
| | - Celia Cantín
- IRTA, FruitCentreParc Cientific i Tecnològic Agroalimentari de Lleida (PCiTAL), Lleida, Spain
| | - Nelson Nazzicari
- PTP Science Park, Via Einstein, 26900, Lodi, Italy.,Council for Agricultural Research and Economics (CREA) Research Centre for Fodder Crops and Dairy Productions, Lodi, Italy
| | | | - Maria Teresa Dettori
- Consiglio per la Ricerca in Agricoltura e L'analisi Dell'economia Agraria (CREA) - Centro di Ricerca per la Frutticoltura, 00134, Roma, Italy
| | - Sabrina Micali
- Consiglio per la Ricerca in Agricoltura e L'analisi Dell'economia Agraria (CREA) - Centro di Ricerca per la Frutticoltura, 00134, Roma, Italy
| | - Elisa Banchi
- Research and Innovation Centre, Fondazione Edmund Mach (FEM), Via Mach 1, 38010, San Michele all'Adige, TN, Italy
| | | | | | | | | | - Michela Troggio
- Research and Innovation Centre, Fondazione Edmund Mach (FEM), Via Mach 1, 38010, San Michele all'Adige, TN, Italy
| | - Daniele Bassi
- Università degli Studi di Milano, DiSAA, Via Celoria 2, 20133, Milan, Italy
| | - Laura Rossini
- PTP Science Park, Via Einstein, 26900, Lodi, Italy.,Università degli Studi di Milano, DiSAA, Via Celoria 2, 20133, Milan, Italy
| | - Ignazio Verde
- Consiglio per la Ricerca in Agricoltura e L'analisi Dell'economia Agraria (CREA) - Centro di Ricerca per la Frutticoltura, 00134, Roma, Italy
| | | | | | - Pere Arús
- IRTA, Centre de Recerca en Agrigenòmica CSIC-IRTA-UAB-UB; Campus UAB, Bellaterra (Cerdanyola del Vallès), 08193, Barcelona, Spain
| | - Maria José Aranzana
- IRTA, Centre de Recerca en Agrigenòmica CSIC-IRTA-UAB-UB; Campus UAB, Bellaterra (Cerdanyola del Vallès), 08193, Barcelona, Spain.
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Ma B, Liao L, Peng Q, Fang T, Zhou H, Korban SS, Han Y. Reduced representation genome sequencing reveals patterns of genetic diversity and selection in apple. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2017; 59:190-204. [PMID: 28093854 DOI: 10.1111/jipb.12522] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2016] [Accepted: 01/15/2017] [Indexed: 05/02/2023]
Abstract
Identifying DNA sequence variations is a fundamental step towards deciphering the genetic basis of traits of interest. Here, a total of 20 cultivated and 10 wild apples were genotyped using specific-locus amplified fragment sequencing, and 39,635 single nucleotide polymorphisms with no missing genotypes and evenly distributed along the genome were selected to investigate patterns of genome-wide genetic variations between cultivated and wild apples. Overall, wild apples displayed higher levels of genetic diversity than cultivated apples. Linkage disequilibrium (LD) decays were observed quite rapidly in cultivated and wild apples, with an r2 -value below 0.2 at 440 and 280 bp, respectively. Moreover, bidirectional gene flow and different distribution patterns of LD blocks were detected between domesticated and wild apples. Most LD blocks unique to cultivated apples were located within QTL regions controlling fruit quality, thus suggesting that fruit quality had probably undergone selection during apple domestication. The genome of the earliest cultivated apple in China, Nai, was highly similar to that of Malus sieversii, and contained a small portion of genetic material from other wild apple species. This suggested that introgression could have been an important driving force during initial domestication of apple. These findings will facilitate future breeding and genetic dissection of complex traits in apple.
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Affiliation(s)
- Baiquan Ma
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden of the Chinese Academy of Sciences, Wuhan 430074, China
- Graduate University of Chinese Academy of Sciences, 19A Yuquanlu, Beijing 100049, China
| | - Liao Liao
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden of the Chinese Academy of Sciences, Wuhan 430074, China
- Sino-African Joint Research Center, Chinese Academy of Sciences, Wuhan 430074, China
| | - Qian Peng
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden of the Chinese Academy of Sciences, Wuhan 430074, China
- Graduate University of Chinese Academy of Sciences, 19A Yuquanlu, Beijing 100049, China
| | - Ting Fang
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden of the Chinese Academy of Sciences, Wuhan 430074, China
- Graduate University of Chinese Academy of Sciences, 19A Yuquanlu, Beijing 100049, China
| | - Hui Zhou
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden of the Chinese Academy of Sciences, Wuhan 430074, China
- Sino-African Joint Research Center, Chinese Academy of Sciences, Wuhan 430074, China
| | - Schuyler S Korban
- Department of Biology, University of Massachusetts Boston, Boston Massachusetts 02184, USA
| | - Yuepeng Han
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden of the Chinese Academy of Sciences, Wuhan 430074, China
- Sino-African Joint Research Center, Chinese Academy of Sciences, Wuhan 430074, China
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28
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Wang BQ, Liu JH, Gong XQ, Long CA, Li GH. Characterization of the expression of the stress-responsive PpERS1 gene from peach and analysis of its promoter using transgenic tomato. PLANT BIOTECHNOLOGY (TOKYO, JAPAN) 2016; 33:383-393. [PMID: 31274999 PMCID: PMC6587038 DOI: 10.5511/plantbiotechnology.16.1102a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2016] [Accepted: 11/02/2016] [Indexed: 06/09/2023]
Abstract
The PpERS1 gene, which encodes an ethylene receptor and responds to abiotic and biotic stresses, was cloned from peach (Prunus persica L. Batsch cv Okubao). The genomic DNA sequence of PpERS1 comprises seven exons which are separated by six introns, interestingly alternative splicing of the first intron produced three different PpERS1 transcripts. In addition, a 2.8-kb sequence including the promoter of PpERS1 was isolated and analyzed by placing expressing of the GUS reporter gene under its control. Several putative cis-elements were identified in the promoter of PpERS1, including two ethylene-responsive elements (EREs), five W boxes, and four putative binding sites for MYB-type transcription factors. Deletion analysis indicated the presence of an enhancer element in the PpERS1 promoter. Temporal and spatial expression analysis of the PpERS1 promoter using histochemical GUS staining showed GUS activity in all tissues examined throughout the development of transgenic tomato plants. Exposure to various stresses caused similar changes in expression patterns in peach and transgenic tomato plants. Overall, our results suggested that PpERS1 gene might play important roles in response to multiple stresses via signal transduction mediated by ethylene receptors. The characterization of the PpERS1 promoter contributes to our understanding of the transcriptional regulation of this ethylene receptor in peach.
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Affiliation(s)
- Bao-Quan Wang
- Key Laboratory of Horticultural Plant Biology of Ministry of Education College of Horticulture and Forestry Sciences Huazhong Agricultural University, Wuhan 430070, China
| | - Ji-Hong Liu
- Key Laboratory of Horticultural Plant Biology of Ministry of Education College of Horticulture and Forestry Sciences Huazhong Agricultural University, Wuhan 430070, China
| | - Xiao-Qing Gong
- Key Laboratory of Horticultural Plant Biology of Ministry of Education College of Horticulture and Forestry Sciences Huazhong Agricultural University, Wuhan 430070, China
| | - Chao-An Long
- Key Laboratory of Horticultural Plant Biology of Ministry of Education College of Horticulture and Forestry Sciences Huazhong Agricultural University, Wuhan 430070, China
| | - Guo-Huai Li
- Key Laboratory of Horticultural Plant Biology of Ministry of Education College of Horticulture and Forestry Sciences Huazhong Agricultural University, Wuhan 430070, China
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Abstract
The domesticated almond [Prunus dulcis (L.) Batsch] and peach [P. persica (Mill.) D. A. Webb] originated on opposite sides of Asia and were independently domesticated ∼5000 yr ago. While interfertile, they possess alternate mating systems and differ in a number of morphological and physiological traits. Here, we evaluated patterns of genome-wide diversity in both almond and peach to better understand the impacts of mating system, adaptation, and domestication on the evolution of these taxa. Almond has around seven times the genetic diversity of peach, and high genome-wide FST values support their status as separate species. We estimated a divergence time of ∼8 MYA (million years ago), coinciding with an active period of uplift in the northeast Tibetan Plateau and subsequent Asian climate change. We see no evidence of a bottleneck during domestication of either species, but identify a number of regions showing signatures of selection during domestication and a significant overlap in candidate regions between peach and almond. While we expected gene expression in fruit to overlap with candidate selected regions, instead we find enrichment for loci highly differentiated between the species, consistent with recent fossil evidence suggesting fruit divergence long preceded domestication. Taken together, this study tells us how closely related tree species evolve and are domesticated, the impact of these events on their genomes, and the utility of genomic information for long-lived species. Further exploration of this data will contribute to the genetic knowledge of these species and provide information regarding targets of selection for breeding application, and further the understanding of evolution in these species.
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Genome-wide association study of 12 agronomic traits in peach. Nat Commun 2016; 7:13246. [PMID: 27824331 PMCID: PMC5105138 DOI: 10.1038/ncomms13246] [Citation(s) in RCA: 111] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2015] [Accepted: 09/15/2016] [Indexed: 12/31/2022] Open
Abstract
Peach (Prunus persica L.) is a highly valuable crop species and is recognized by molecular researchers as a model fruit for the Rosaceae family. Using whole-genome sequencing data generated from 129 peach accessions, here we perform a comprehensive genome-wide association study for 12 key agronomic traits. We show that among the 10 qualitative traits investigated, nine exhibit consistent and more precise association signals than previously identified by linkage analysis. For two of the qualitative traits, we describe candidate genes, one potentially involved in cell death and another predicted to encode an auxin-efflux carrier, that are highly associated with fruit shape and non-acidity, respectively. Furthermore, we find that several genomic regions harbouring association signals for fruit weight and soluble solid content overlapped with predicted selective sweeps that occurred during peach domestication and improvement. Our findings contribute to the large-scale characterization of genes controlling agronomic traits in peach. Peach is both an economically important crop species and a model for Rosaceae fruit development research. Here, the authors perform genome-wide association analysis in peach and find candidate genes associated with variation in agronomically important fruit phenotypes.
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Urrestarazu J, Denancé C, Ravon E, Guyader A, Guisnel R, Feugey L, Poncet C, Lateur M, Houben P, Ordidge M, Fernandez-Fernandez F, Evans KM, Paprstein F, Sedlak J, Nybom H, Garkava-Gustavsson L, Miranda C, Gassmann J, Kellerhals M, Suprun I, Pikunova AV, Krasova NG, Torutaeva E, Dondini L, Tartarini S, Laurens F, Durel CE. Analysis of the genetic diversity and structure across a wide range of germplasm reveals prominent gene flow in apple at the European level. BMC PLANT BIOLOGY 2016; 16:130. [PMID: 27277533 PMCID: PMC4898379 DOI: 10.1186/s12870-016-0818-0] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2016] [Accepted: 05/23/2016] [Indexed: 05/18/2023]
Abstract
BACKGROUND The amount and structure of genetic diversity in dessert apple germplasm conserved at a European level is mostly unknown, since all diversity studies conducted in Europe until now have been performed on regional or national collections. Here, we applied a common set of 16 SSR markers to genotype more than 2,400 accessions across 14 collections representing three broad European geographic regions (North + East, West and South) with the aim to analyze the extent, distribution and structure of variation in the apple genetic resources in Europe. RESULTS A Bayesian model-based clustering approach showed that diversity was organized in three groups, although these were only moderately differentiated (FST = 0.031). A nested Bayesian clustering approach allowed identification of subgroups which revealed internal patterns of substructure within the groups, allowing a finer delineation of the variation into eight subgroups (FST = 0.044). The first level of stratification revealed an asymmetric division of the germplasm among the three groups, and a clear association was found with the geographical regions of origin of the cultivars. The substructure revealed clear partitioning of genetic groups among countries, but also interesting associations between subgroups and breeding purposes of recent cultivars or particular usage such as cider production. Additional parentage analyses allowed us to identify both putative parents of more than 40 old and/or local cultivars giving interesting insights in the pedigree of some emblematic cultivars. CONCLUSIONS The variation found at group and subgroup levels may reflect a combination of historical processes of migration/selection and adaptive factors to diverse agricultural environments that, together with genetic drift, have resulted in extensive genetic variation but limited population structure. The European dessert apple germplasm represents an important source of genetic diversity with a strong historical and patrimonial value. The present work thus constitutes a decisive step in the field of conservation genetics. Moreover, the obtained data can be used for defining a European apple core collection useful for further identification of genomic regions associated with commercially important horticultural traits in apple through genome-wide association studies.
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Affiliation(s)
- Jorge Urrestarazu
- IRHS, INRA, AGROCAMPUS-Ouest, Université d'Angers, SFR 4207 QUASAV, 42 rue Georges Morel, 49071, Beaucouzé cedex, France
- Department of Agricultural Sciences, University of Bologna, Viale Giuseppe Fanin 44, 40127, Bologna, Italy
- Public University of Navarre (UPNA), Campus Arrosadia, 31006, Pamplona, Spain
| | - Caroline Denancé
- IRHS, INRA, AGROCAMPUS-Ouest, Université d'Angers, SFR 4207 QUASAV, 42 rue Georges Morel, 49071, Beaucouzé cedex, France
| | - Elisa Ravon
- IRHS, INRA, AGROCAMPUS-Ouest, Université d'Angers, SFR 4207 QUASAV, 42 rue Georges Morel, 49071, Beaucouzé cedex, France
| | - Arnaud Guyader
- IRHS, INRA, AGROCAMPUS-Ouest, Université d'Angers, SFR 4207 QUASAV, 42 rue Georges Morel, 49071, Beaucouzé cedex, France
| | - Rémi Guisnel
- IRHS, INRA, AGROCAMPUS-Ouest, Université d'Angers, SFR 4207 QUASAV, 42 rue Georges Morel, 49071, Beaucouzé cedex, France
| | - Laurence Feugey
- IRHS, INRA, AGROCAMPUS-Ouest, Université d'Angers, SFR 4207 QUASAV, 42 rue Georges Morel, 49071, Beaucouzé cedex, France
| | - Charles Poncet
- Plateforme Gentyane, INRA UMR1095 Genetics, Diversity and Ecophysiology of Cereals, 63100, Clermont-Ferrand, France
| | - Marc Lateur
- CRA-W, Centre Wallon de Recherches Agronomiques, Plant Breeding & Biodiversity, Bâtiment Emile Marchal, Rue de Liroux, 4 - 5030, Gembloux, Belgium
| | - Patrick Houben
- CRA-W, Centre Wallon de Recherches Agronomiques, Plant Breeding & Biodiversity, Bâtiment Emile Marchal, Rue de Liroux, 4 - 5030, Gembloux, Belgium
| | - Matthew Ordidge
- School of Agriculture, Policy and Development, University of Reading, Whiteknights, Reading, RG6 6AR, UK
| | | | - Kate M Evans
- Washington State University Tree Fruit Research and Extension Center, 1100 N Western Ave, Wenatchee, WA, 98801, USA
| | - Frantisek Paprstein
- RBIPH, Research and Breeding Institute of Pomology Holovousy Ltd., 508 01, Horice, Czech Republic
| | - Jiri Sedlak
- RBIPH, Research and Breeding Institute of Pomology Holovousy Ltd., 508 01, Horice, Czech Republic
| | - Hilde Nybom
- Department of Plant Breeding, Balsgård, Fjälkestadsvägen 459, Swedish University of Agricultural Sciences, 291 94, Kristianstad, Sweden
| | - Larisa Garkava-Gustavsson
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Box 101, 230 53, Alnarp, Sweden
| | - Carlos Miranda
- Public University of Navarre (UPNA), Campus Arrosadia, 31006, Pamplona, Spain
| | - Jennifer Gassmann
- Agroscope, Institute for Plant Production Sciences IPS, Schloss 1, P.O. Box, 8820, Wädenswil, Switzerland
| | - Markus Kellerhals
- Agroscope, Institute for Plant Production Sciences IPS, Schloss 1, P.O. Box, 8820, Wädenswil, Switzerland
| | - Ivan Suprun
- NCRRIH&V, North Caucasian Regional Research Institute of Horticulture and Viticulture, 39, 40-letiya Pobedy street, Krasnodar, 350901, Russian Federation
| | - Anna V Pikunova
- VNIISPK, The All Russian Research Institute of Fruit Crop Breeding, 302530, p/o Zhilina, Orel district, Russian Federation
| | - Nina G Krasova
- VNIISPK, The All Russian Research Institute of Fruit Crop Breeding, 302530, p/o Zhilina, Orel district, Russian Federation
| | - Elnura Torutaeva
- Kyrgyz National Agrarian University, 68 Mederova Street, 720005, Bishkek, Kyrgyzstan
| | - Luca Dondini
- Department of Agricultural Sciences, University of Bologna, Viale Giuseppe Fanin 44, 40127, Bologna, Italy
| | - Stefano Tartarini
- Department of Agricultural Sciences, University of Bologna, Viale Giuseppe Fanin 44, 40127, Bologna, Italy
| | - François Laurens
- IRHS, INRA, AGROCAMPUS-Ouest, Université d'Angers, SFR 4207 QUASAV, 42 rue Georges Morel, 49071, Beaucouzé cedex, France
| | - Charles-Eric Durel
- IRHS, INRA, AGROCAMPUS-Ouest, Université d'Angers, SFR 4207 QUASAV, 42 rue Georges Morel, 49071, Beaucouzé cedex, France.
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Wang L, Peng Q, Zhao J, Ren F, Zhou H, Wang W, Liao L, Owiti A, Jiang Q, Han Y. Evolutionary origin of Rosaceae-specific active non-autonomous hAT elements and their contribution to gene regulation and genomic structural variation. PLANT MOLECULAR BIOLOGY 2016; 91:179-91. [PMID: 26941188 DOI: 10.1007/s11103-016-0454-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2015] [Accepted: 02/08/2016] [Indexed: 06/05/2023]
Abstract
Transposable elements account for approximately 30 % of the Prunus genome; however, their evolutionary origin and functionality remain largely unclear. In this study, we identified a hAT transposon family, termed Moshan, in Prunus. The Moshan elements consist of three types, aMoshan, tMoshan, and mMoshan. The aMoshan and tMoshan types contain intact or truncated transposase genes, respectively, while the mMoshan type is miniature inverted-repeat transposable element (MITE). The Moshan transposons are unique to Rosaceae, and the copy numbers of different Moshan types are significantly correlated. Sequence homology analysis reveals that the mMoshan MITEs are direct deletion derivatives of the tMoshan progenitors, and one kind of mMoshan containing a MuDR-derived fragment were amplified predominately in the peach genome. The mMoshan sequences contain cis-regulatory elements that can enhance gene expression up to 100-fold. The mMoshan MITEs can serve as potential sources of micro and long noncoding RNAs. Whole-genome re-sequencing analysis indicates that mMoshan elements are highly active, and an insertion into S-haplotype-specific F-box gene was reported to cause the breakdown of self-incompatibility in sour cherry. Taken together, all these results suggest that the mMoshan elements play important roles in regulating gene expression and driving genomic structural variation in Prunus.
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Affiliation(s)
- Lu Wang
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden of the Chinese Academy of Sciences, Wuhan, 430074, People's Republic of China
| | - Qian Peng
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden of the Chinese Academy of Sciences, Wuhan, 430074, People's Republic of China
- Graduate University of Chinese Academy of Sciences, 19A Yuquanlu, Beijing, 100049, People's Republic of China
| | - Jianbo Zhao
- Institute of Forestry and Pomology, Beijing Academy of Agriculture and Forestry Sciences, A12, Ruiwangfen, Beijing, 100093, People's Republic of China
| | - Fei Ren
- Institute of Forestry and Pomology, Beijing Academy of Agriculture and Forestry Sciences, A12, Ruiwangfen, Beijing, 100093, People's Republic of China
| | - Hui Zhou
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden of the Chinese Academy of Sciences, Wuhan, 430074, People's Republic of China
- Graduate University of Chinese Academy of Sciences, 19A Yuquanlu, Beijing, 100049, People's Republic of China
| | - Wei Wang
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden of the Chinese Academy of Sciences, Wuhan, 430074, People's Republic of China
| | - Liao Liao
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden of the Chinese Academy of Sciences, Wuhan, 430074, People's Republic of China
- Sino-African Joint Research Center, Chinese Academy of Sciences, Wuhan, 430074, People's Republic of China
| | - Albert Owiti
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden of the Chinese Academy of Sciences, Wuhan, 430074, People's Republic of China
- Graduate University of Chinese Academy of Sciences, 19A Yuquanlu, Beijing, 100049, People's Republic of China
| | - Quan Jiang
- Institute of Forestry and Pomology, Beijing Academy of Agriculture and Forestry Sciences, A12, Ruiwangfen, Beijing, 100093, People's Republic of China.
| | - Yuepeng Han
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden of the Chinese Academy of Sciences, Wuhan, 430074, People's Republic of China.
- Sino-African Joint Research Center, Chinese Academy of Sciences, Wuhan, 430074, People's Republic of China.
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Cirilli M, Bassi D, Ciacciulli A. Sugars in peach fruit: a breeding perspective. HORTICULTURE RESEARCH 2016; 3:15067. [PMID: 26816618 PMCID: PMC4720000 DOI: 10.1038/hortres.2015.67] [Citation(s) in RCA: 77] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2015] [Revised: 12/10/2015] [Accepted: 12/10/2015] [Indexed: 05/23/2023]
Abstract
The last decade has been characterized by a decrease in peach (Prunus persica) fruit consumption in many countries, foremost due to unsatisfactory quality. The sugar content is one of the most important quality traits perceived by consumers, and the development of novel peach cultivars with sugar-enhanced content is a primary objective of breeding programs to revert the market inertia. Nevertheless, the progress reachable through classical phenotypic selection is limited by the narrow genetic bases of peach breeding material and by the complex quantitative nature of the trait, which is deeply affected by environmental conditions and agronomical management. The development of molecular markers applicable in MAS or MAB has become an essential strategy to boost the selection efficiency. Despite the enormous advances in 'omics' sciences, providing powerful tools for plant genotyping, the identification of the genetic bases of sugar-related traits is hindered by the lack of adequate phenotyping methods that are able to address strong within-plant variability. This review provides an overview of the current knowledge of the metabolic pathways and physiological mechanisms regulating sugar accumulation in peach fruit, the main advances in phenotyping approaches and genetic background, and finally addressing new research priorities and prospective for breeders.
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Affiliation(s)
- Marco Cirilli
- Department of Agricultural and Environmental Sciences (DISAA), University of Milan, via Celoria 2, 20133 Milan, Italy
| | - Daniele Bassi
- Department of Agricultural and Environmental Sciences (DISAA), University of Milan, via Celoria 2, 20133 Milan, Italy
| | - Angelo Ciacciulli
- Department of Agricultural and Environmental Sciences (DISAA), University of Milan, via Celoria 2, 20133 Milan, Italy
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Pan L, Zeng W, Niu L, Lu Z, Liu H, Cui G, Zhu Y, Chu J, Li W, Fang W, Cai Z, Li G, Wang Z. PpYUC11, a strong candidate gene for the stony hard phenotype in peach (Prunus persica L. Batsch), participates in IAA biosynthesis during fruit ripening. JOURNAL OF EXPERIMENTAL BOTANY 2015; 66:7031-44. [PMID: 26307136 PMCID: PMC4765781 DOI: 10.1093/jxb/erv400] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
High concentrations of indole-3-acetic acid (IAA) are required for climacteric ethylene biosynthesis to cause fruit softening in melting flesh peaches at the late ripening stage. By contrast, the fruits of stony hard peach cultivars do not soften and produce little ethylene due to the low IAA concentrations. To investigate the regulation of IAA accumulation during peach ripening [the transition from stage S3 to stage S4 III (climacteric)], a digital gene expression (DGE) analysis was performed. The expression patterns of auxin-homeostasis-related genes were compared in fruits of the melting flesh peach 'Goldhoney 3' and the stony hard flesh peach 'Yumyeong' during the ripening stage. It is revealed here that a YUCCA flavin mono-oxygenase gene (PpYUC11, ppa008176m), a key gene in auxin biosynthesis, displayed an identical differential expression profile to the profiles of IAA accumulation and PpACS1 transcription: the mRNA transcripts increased at the late ripening stage in melting flesh peaches but were below the limit of detection in mature fruits of stony hard peaches. In addition, the strong association between intron TC microsatellite genotypes of PpYUC11 and the flesh texture (normal or stony hard) is described in 43 peach varieties, indicating that this locus may be responsible for the stony hard phenotype in peach. These findings support the hypothesis that PpYUC11 may play an essential role in auxin biosynthesis during peach fruit ripening and is a candidate gene for the control of the stony hard phenotype in peach.
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Affiliation(s)
- Lei Pan
- Key Laboratory of Fruit Breeding Technology, Ministry of Agriculture, Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou 450009, China Key Laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China
| | - Wenfang Zeng
- Key Laboratory of Fruit Breeding Technology, Ministry of Agriculture, Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou 450009, China
| | - Liang Niu
- Key Laboratory of Fruit Breeding Technology, Ministry of Agriculture, Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou 450009, China
| | - Zhenhua Lu
- Key Laboratory of Fruit Breeding Technology, Ministry of Agriculture, Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou 450009, China
| | - Hui Liu
- Key Laboratory of Fruit Breeding Technology, Ministry of Agriculture, Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou 450009, China
| | - Guochao Cui
- Key Laboratory of Fruit Breeding Technology, Ministry of Agriculture, Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou 450009, China
| | - Yunqin Zhu
- Key Laboratory of Fruit Breeding Technology, Ministry of Agriculture, Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou 450009, China
| | - Jinfang Chu
- National Centre for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Weiping Li
- National Centre for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Weichao Fang
- Key Laboratory of Fruit Breeding Technology, Ministry of Agriculture, Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou 450009, China
| | - Zuguo Cai
- Key Laboratory of Fruit Breeding Technology, Ministry of Agriculture, Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou 450009, China
| | - Guohuai Li
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China
| | - Zhiqiang Wang
- Key Laboratory of Fruit Breeding Technology, Ministry of Agriculture, Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou 450009, China
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Urrestarazu J, Royo JB, Santesteban LG, Miranda C. Evaluating the Influence of the Microsatellite Marker Set on the Genetic Structure Inferred in Pyrus communis L. PLoS One 2015; 10:e0138417. [PMID: 26382618 PMCID: PMC4575082 DOI: 10.1371/journal.pone.0138417] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2015] [Accepted: 08/29/2015] [Indexed: 12/19/2022] Open
Abstract
Fingerprinting information can be used to elucidate in a robust manner the genetic structure of germplasm collections, allowing a more rational and fine assessment of genetic resources. Bayesian model-based approaches are nowadays majorly preferred to infer genetic structure, but it is still largely unresolved how marker sets should be built in order to obtain a robust inference. The objective was to evaluate, in Pyrus germplasm collections, the influence of the SSR marker set size on the genetic structure inferred, also evaluating the influence of the criterion used to select those markers. Inferences were performed considering an increasing number of SSR markers that ranged from just two up to 25, incorporated one at a time into the analysis. The influence of the number of SSR markers used was evaluated comparing the number of populations and the strength of the signal detected, and also the similarity of the genotype assignments to populations between analyses. In order to test if those results were influenced by the criterion used to select the SSRs, several choosing scenarios based on the discrimination power or the fixation index values of the SSRs were tested. Our results indicate that population structure could be inferred accurately once a certain SSR number threshold was reached, which depended on the underlying structure within the genotypes, but the method used to select the markers included on each set appeared not to be very relevant. The minimum number of SSRs required to provide robust structure inferences and adequate measurements of the differentiation, even when low differentiation levels exist within populations, was proved similar to that of the complete list of recommended markers for fingerprinting. When a SSR set size similar to the minimum marker sets recommended for fingerprinting it is used, only major divisions or moderate (FST>0.05) differentiation of the germplasm are detected.
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Affiliation(s)
- Jorge Urrestarazu
- Departamento de Producción Agraria, Universidad Pública de Navarra, Pamplona, Navarra, Spain
| | - José B Royo
- Departamento de Producción Agraria, Universidad Pública de Navarra, Pamplona, Navarra, Spain
| | - Luis G Santesteban
- Departamento de Producción Agraria, Universidad Pública de Navarra, Pamplona, Navarra, Spain
| | - Carlos Miranda
- Departamento de Producción Agraria, Universidad Pública de Navarra, Pamplona, Navarra, Spain
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Dettori MT, Micali S, Giovinazzi J, Scalabrin S, Verde I, Cipriani G. Mining microsatellites in the peach genome: development of new long-core SSR markers for genetic analyses in five Prunus species. SPRINGERPLUS 2015; 4:337. [PMID: 26185739 PMCID: PMC4497997 DOI: 10.1186/s40064-015-1098-0] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/06/2015] [Accepted: 06/12/2015] [Indexed: 02/04/2023]
Abstract
A wide inventory of molecular markers is nowadays available for individual fingerprinting. Microsatellites, or simple sequence repeats (SSRs), play a relevant role due to their relatively ease of use, their abundance in the plant genomes, and their co-dominant nature, together with the availability of primer sequences in many important agricultural crops. Microsatellites with long-core motifs are more easily scored and were adopted long ago in human genetics but they were developed only in few crops, and Prunus species are not among them. In the present work the peach whole-genome sequence was used to select 216 SSRs containing long-core motifs with tri-, tetra- and penta-nucleotide repeats. Microsatellite primer pairs were designed and tested for polymorphism in the five diploid Prunus species of economic relevance (almond, apricot, Japanese plum, peach and sweet cherry). A set of 26 microsatellite markers covering all the eight chromosomes, was also selected and used in the molecular characterization, population genetics and structure analyses of a representative sample of the five diploid Prunus species, assessing their transportability and effectiveness. The combined probability of identity between two random individuals for the whole set of 26 SSRs was quite low, ranging from 2.30 × 10−7 in peach to 9.48 × 10−10 in almond, confirming the usefulness of the proposed set for fingerprinting analyses in Prunus species.
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Affiliation(s)
- Maria Teresa Dettori
- Consiglio per la Ricerca in Agricoltura e l'analisi dell'economia agraria, Centro di Ricerca per la Frutticoltura, Rome, Italy
| | - Sabrina Micali
- Consiglio per la Ricerca in Agricoltura e l'analisi dell'economia agraria, Centro di Ricerca per la Frutticoltura, Rome, Italy
| | - Jessica Giovinazzi
- Consiglio per la Ricerca in Agricoltura e l'analisi dell'economia agraria, Centro di Ricerca per la Frutticoltura, Rome, Italy
| | | | - Ignazio Verde
- Consiglio per la Ricerca in Agricoltura e l'analisi dell'economia agraria, Centro di Ricerca per la Frutticoltura, Rome, Italy
| | - Guido Cipriani
- Dipartimento di Scienze Agrarie e Ambientali, University of Udine, Udine, Italy
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Leforestier D, Ravon E, Muranty H, Cornille A, Lemaire C, Giraud T, Durel CE, Branca A. Genomic basis of the differences between cider and dessert apple varieties. Evol Appl 2015; 8:650-61. [PMID: 26240603 PMCID: PMC4516418 DOI: 10.1111/eva.12270] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2014] [Accepted: 04/15/2015] [Indexed: 12/26/2022] Open
Abstract
Unraveling the genomic processes at play during variety diversification is of fundamental interest for understanding evolution, but also of applied interest in crop science. It can indeed provide knowledge on the genetic bases of traits for crop improvement and germplasm diversity management. Apple is one of the most important fruit crops in temperate regions, having both great economic and cultural values. Sweet dessert apples are used for direct consumption, while bitter cider apples are used to produce cider. Several important traits are known to differentiate the two variety types, in particular fruit size, biennial versus annual fruit bearing, and bitterness, caused by a higher content in polyphenols. Here, we used an Illumina 8k SNP chip on two core collections, of 48 dessert and 48 cider apples, respectively, for identifying genomic regions responsible for the differences between cider and dessert apples. The genome-wide level of genetic differentiation between cider and dessert apples was low, although 17 candidate regions showed signatures of divergent selection, displaying either outlier FST values or significant association with phenotypic traits (bitter versus sweet fruits). These candidate regions encompassed 420 genes involved in a variety of functions and metabolic pathways, including several colocalizations with QTLs for polyphenol compounds.
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Affiliation(s)
- Diane Leforestier
- UMR 1345 Institut de Recherche en Horticulture et Semences, Université d'Angers Angers, France
| | - Elisa Ravon
- UMR 1345 Institut de Recherche en Horticulture et Semences, INRA Beaucouzé, France
| | - Hélène Muranty
- UMR 1345 Institut de Recherche en Horticulture et Semences, INRA Beaucouzé, France
| | - Amandine Cornille
- Ecologie, Systématique et Evolution, Université Paris-Sud Orsay, France ; Ecologie, Systématique et Evolution, CNRS Orsay, France
| | - Christophe Lemaire
- UMR 1345 Institut de Recherche en Horticulture et Semences, Université d'Angers Angers, France
| | - Tatiana Giraud
- Ecologie, Systématique et Evolution, Université Paris-Sud Orsay, France ; Ecologie, Systématique et Evolution, CNRS Orsay, France
| | - Charles-Eric Durel
- UMR 1345 Institut de Recherche en Horticulture et Semences, INRA Beaucouzé, France
| | - Antoine Branca
- Ecologie, Systématique et Evolution, Université Paris-Sud Orsay, France ; Ecologie, Systématique et Evolution, CNRS Orsay, France
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Jia HM, Jiao Y, Wang GY, Li YH, Jia HJ, Wu HX, Chai CY, Dong X, Guo Y, Zhang L, Gao QK, Chen W, Song LJ, van de Weg E, Gao ZS. Genetic diversity of male and female Chinese bayberry (Myrica rubra) populations and identification of sex-associated markers. BMC Genomics 2015; 16:394. [PMID: 25986380 PMCID: PMC4436740 DOI: 10.1186/s12864-015-1602-5] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2014] [Accepted: 05/01/2015] [Indexed: 11/25/2022] Open
Abstract
Background Chinese bayberry (Myrica rubra Sieb. & Zucc.) is an important subtropical evergreen fruit tree in southern China. Generally dioecious, the female plants are cultivated for fruit and have been studied extensively, but male plants have received very little attention. Knowledge of males may have a major impact on conservation and genetic improvement as well as on breeding. Using 84 polymorphic SSRs, we genotyped 213 M. rubra individuals (99 male individuals, 113 female varieties and 1 monoecious) and compared the difference in genetic diversity between the female and the male populations. Results Neighbour-joining cluster analysis separated M. rubra from three related species, and the male from female populations within M. rubra. By structure analysis, 178 M. rubra accessions were assigned to two subpopulations: Male dominated (98) and Female dominated (80). The well-known cultivars ‘Biqi’ and ‘Dongkui’, and the landraces ‘Fenhong’ are derived from three different gene pools. Female population had a slightly higher values of genetic diversity parameters (such as number of alleles and heterozygosity) than the male population, but not significantly different. The SSR loci ZJU062 and ZJU130 showed an empirical Fst value of 0.455 and 0.333, respectively, which are significantly above the 95 % confidence level, indicating that they are outlier loci related to sex separation. Conclusion The male and female populations of Chinese bayberry have similar genetic diversity in terms of average number of alleles and level of heterozygosity, but were clearly separated by genetic structure analysis due to two markers associated with sex type, ZJU062 and ZJU130. Zhejiang Province China could be the centre of diversity of M. rubra in China, with wide genetic diversity coverage; and the two representative cultivars ‘Biqi’ and ‘Dongkui’, and one landrace ‘Fenhong’ in three female subpopulations. This research provides genetic information on male and female Chinese bayberry and will act as a reference for breeding programs. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1602-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Hui-min Jia
- Department of Horticulture, College of Agriculture and Biotechnology, Zhejiang University, 310058, Hangzhou, Zhejiang, China.
| | - Yun Jiao
- Department of Horticulture, College of Agriculture and Biotechnology, Zhejiang University, 310058, Hangzhou, Zhejiang, China.
| | - Guo-yun Wang
- Fruit Research Institute, 315400, Yuyao, Ningbo, PR China.
| | - Ying-hui Li
- The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI)/Key Lab of Germplasm Utilization (MOA), Chinese Academy of Agricultural Sciences, Institute of Crop Science, 100081, Beijing, China.
| | - Hui-juan Jia
- Department of Horticulture, College of Agriculture and Biotechnology, Zhejiang University, 310058, Hangzhou, Zhejiang, China.
| | - Hong-xia Wu
- Department of Horticulture, College of Agriculture and Biotechnology, Zhejiang University, 310058, Hangzhou, Zhejiang, China.
| | - Chun-yan Chai
- Forestry Technology Extension Center, 315300, Cixi, Ningbo, China.
| | - Xiao Dong
- Department of Horticulture, College of Agriculture and Biotechnology, Zhejiang University, 310058, Hangzhou, Zhejiang, China.
| | - Yanping Guo
- Department of Horticulture, College of Agriculture and Biotechnology, Zhejiang University, 310058, Hangzhou, Zhejiang, China.
| | - Liping Zhang
- Department of Horticulture, College of Agriculture and Biotechnology, Zhejiang University, 310058, Hangzhou, Zhejiang, China.
| | - Qi-kang Gao
- Bio-Macromolecules Analysis Lab, Analysis Center of Agrobiology, Environmental Sciences of Zhejiang University, 310058, Hangzhou, China.
| | - Wei Chen
- Zhejiang Institute of Subtropical Crops, Wenzhou, 325005, China.
| | - Li-Juan Song
- Wenzhou Vocational and Technical College, 325035, Wenzhou, China.
| | - Eric van de Weg
- Plant Breeding-Wageningen University and Research Centre, P.O. Box 16, 6700 AA, Wageningen, The Netherlands.
| | - Zhong-shan Gao
- Department of Horticulture, College of Agriculture and Biotechnology, Zhejiang University, 310058, Hangzhou, Zhejiang, China.
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Micheletti D, Dettori MT, Micali S, Aramini V, Pacheco I, Da Silva Linge C, Foschi S, Banchi E, Barreneche T, Quilot-Turion B, Lambert P, Pascal T, Iglesias I, Carbó J, Wang LR, Ma RJ, Li XW, Gao ZS, Nazzicari N, Troggio M, Bassi D, Rossini L, Verde I, Laurens F, Arús P, Aranzana MJ. Whole-Genome Analysis of Diversity and SNP-Major Gene Association in Peach Germplasm. PLoS One 2015; 10:e0136803. [PMID: 26352671 PMCID: PMC4564248 DOI: 10.1371/journal.pone.0136803] [Citation(s) in RCA: 72] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2015] [Accepted: 08/07/2015] [Indexed: 12/24/2022] Open
Abstract
Peach was domesticated in China more than four millennia ago and from there it spread world-wide. Since the middle of the last century, peach breeding programs have been very dynamic generating hundreds of new commercial varieties, however, in most cases such varieties derive from a limited collection of parental lines (founders). This is one reason for the observed low levels of variability of the commercial gene pool, implying that knowledge of the extent and distribution of genetic variability in peach is critical to allow the choice of adequate parents to confer enhanced productivity, adaptation and quality to improved varieties. With this aim we genotyped 1,580 peach accessions (including a few closely related Prunus species) maintained and phenotyped in five germplasm collections (four European and one Chinese) with the International Peach SNP Consortium 9K SNP peach array. The study of population structure revealed the subdivision of the panel in three main populations, one mainly made up of Occidental varieties from breeding programs (POP1OCB), one of Occidental landraces (POP2OCT) and the third of Oriental accessions (POP3OR). Analysis of linkage disequilibrium (LD) identified differential patterns of genome-wide LD blocks in each of the populations. Phenotypic data for seven monogenic traits were integrated in a genome-wide association study (GWAS). The significantly associated SNPs were always in the regions predicted by linkage analysis, forming haplotypes of markers. These diagnostic haplotypes could be used for marker-assisted selection (MAS) in modern breeding programs.
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Affiliation(s)
- Diego Micheletti
- IRTA, Centre de Recerca en Agrigenòmica CSIC-IRTA-UAB-UB, Campus UAB, Bellaterra (Cerdanyola del Vallès), Barcelona, Spain
| | - Maria Teresa Dettori
- Consiglio per la ricerca in agricoltura e l’analisi dell’economia agraria (CRA), Centro di Ricerca per la Frutticoltura, Roma, Italy
| | - Sabrina Micali
- Consiglio per la ricerca in agricoltura e l’analisi dell’economia agraria (CRA), Centro di Ricerca per la Frutticoltura, Roma, Italy
| | - Valeria Aramini
- Consiglio per la ricerca in agricoltura e l’analisi dell’economia agraria (CRA), Centro di Ricerca per la Frutticoltura, Roma, Italy
| | - Igor Pacheco
- Università degli Studi di Milano, DiSAA, Milan, Italy
| | | | | | - Elisa Banchi
- Research and Innovation Centre, Fondazione Edmund Mach (FEM), San Michele all'Adige (TN), Italy
| | - Teresa Barreneche
- INRA, UMR 1332 de Biologie du Fruit et Pathologie, Villenave d’Ornon, France
- Univ. Bordeaux, UMR 1332 de Biologie du Fruit et Pathologie, Villenave d’Ornon, France
| | | | | | - Thierry Pascal
- INRA UR1052 GAFL, Domaine Saint Maurice, Montfavet, France
| | - Ignasi Iglesias
- IRTA, Estació Experimental de Lleida, Parc de Gardeny, Edifici Fruitcentre, Lleida, Spain
| | - Joaquim Carbó
- IRTA, Estacio Experimental Mas Badia, La Tallada d'Empordà, Girona, Spain
| | - Li-rong Wang
- Zhenzhou Fruit Research Institute, CAAS, Zhengzhou, China
| | - Rui-juan Ma
- Horticultural Institute, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Xiong-wei Li
- Department of Horticulture, Zhejiang University, Hangzhou, China
| | - Zhong-shan Gao
- Department of Horticulture, Zhejiang University, Hangzhou, China
| | | | - Michela Troggio
- Research and Innovation Centre, Fondazione Edmund Mach (FEM), San Michele all'Adige (TN), Italy
| | - Daniele Bassi
- Università degli Studi di Milano, DiSAA, Milan, Italy
| | - Laura Rossini
- Università degli Studi di Milano, DiSAA, Milan, Italy
- Parco Tecnologico Padano, Lodi, Italy
| | - Ignazio Verde
- Consiglio per la ricerca in agricoltura e l’analisi dell’economia agraria (CRA), Centro di Ricerca per la Frutticoltura, Roma, Italy
| | - François Laurens
- INRA, UMR 1345 Institut de Recherche en Horticulture et Semences, Beaucouzé, France
- Université d’Angers, UMR 1345 Institut de Recherche en Horticulture et Semences, SFR 4207 QUASAV, PRES L’UNAM, Angers, France
- AgroCampus-Ouest, UMR 1345 Institut de Recherche en Horticulture et Semences, Angers, France
| | - Pere Arús
- IRTA, Centre de Recerca en Agrigenòmica CSIC-IRTA-UAB-UB, Campus UAB, Bellaterra (Cerdanyola del Vallès), Barcelona, Spain
| | - Maria José Aranzana
- IRTA, Centre de Recerca en Agrigenòmica CSIC-IRTA-UAB-UB, Campus UAB, Bellaterra (Cerdanyola del Vallès), Barcelona, Spain
- * E-mail:
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Donoso JM, Eduardo I, Picañol R, Batlle I, Howad W, Aranzana MJ, Arús P. High-density mapping suggests cytoplasmic male sterility with two restorer genes in almond × peach progenies. HORTICULTURE RESEARCH 2015; 2:15016. [PMID: 26504569 PMCID: PMC4595988 DOI: 10.1038/hortres.2015.16] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2015] [Accepted: 04/09/2015] [Indexed: 05/18/2023]
Abstract
Peach (Prunus persica) and almond (Prunus dulcis) are two sexually compatible species that produce fertile offspring. Almond, a highly polymorphic species, is a potential source of new genes for peach that has a strongly eroded gene pool. Here we describe the genetics of a male sterile phenotype that segregated in two almond ('Texas') × peach ('Earlygold') progenies: an F2 (T×E) and a backcross one (T1E) to the 'Earlygold' parent. High-density maps were developed using a 9k peach SNP chip and 135 simple-sequence repeats. Three highly syntenic and collinear maps were obtained: one for the F2 (T×E) and two for the backcross, T1E (for the hybrid) and E (for 'Earlygold'). A major reduction of recombination was observed in the interspecific maps (T×E and T1E) compared to the intraspecific parent (E). The E map also had extensive monomorphic genomic regions suggesting the presence of large DNA fragments identical by descent. Our data for the male sterility character were consistent with the existence of cytoplasmic male sterility, where individuals having the almond cytoplasm required the almond allele in at least one of two independent restorer genes, Rf1 and Rf2, to be fertile. The restorer genes were located in a 3.4 Mbp fragment of linkage group 2 (Rf1) and 1.4 Mbp of linkage group 6 (Rf2). Both fragments contained several genes coding for pentatricopeptide proteins, demonstrated to be responsible for restoring fertility in other species. The implications of these results for using almond as a source of novel variability in peach are discussed.
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Affiliation(s)
- José Manuel Donoso
- IRTA, Centre de Recerca en Agrigenòmica CSIC-IRTA-UAB-UB; Campus UAB, Bellaterra (Cerdanyola del Vallès), 08193 Barcelona, Spain
| | - Iban Eduardo
- IRTA, Centre de Recerca en Agrigenòmica CSIC-IRTA-UAB-UB; Campus UAB, Bellaterra (Cerdanyola del Vallès), 08193 Barcelona, Spain
| | - Roger Picañol
- IRTA, Centre de Recerca en Agrigenòmica CSIC-IRTA-UAB-UB; Campus UAB, Bellaterra (Cerdanyola del Vallès), 08193 Barcelona, Spain
| | - Ignasi Batlle
- IRTA. Centre de Mas de Bover. Crta. De Reus – El Morell Km 3.8. 43120 Constantί, Tarragona, Spain
| | - Werner Howad
- IRTA, Centre de Recerca en Agrigenòmica CSIC-IRTA-UAB-UB; Campus UAB, Bellaterra (Cerdanyola del Vallès), 08193 Barcelona, Spain
| | - María José Aranzana
- IRTA, Centre de Recerca en Agrigenòmica CSIC-IRTA-UAB-UB; Campus UAB, Bellaterra (Cerdanyola del Vallès), 08193 Barcelona, Spain
| | - Pere Arús
- IRTA, Centre de Recerca en Agrigenòmica CSIC-IRTA-UAB-UB; Campus UAB, Bellaterra (Cerdanyola del Vallès), 08193 Barcelona, Spain
- E-mail:
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Development of Ty1-copia retrotransposon-based SSAP molecular markers for the study of genetic diversity in peach. BIOCHEM SYST ECOL 2014. [DOI: 10.1016/j.bse.2014.08.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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