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Martina M, De Rosa V, Magon G, Acquadro A, Barchi L, Barcaccia G, De Paoli E, Vannozzi A, Portis E. Revitalizing agriculture: next-generation genotyping and -omics technologies enabling molecular prediction of resilient traits in the Solanaceae family. FRONTIERS IN PLANT SCIENCE 2024; 15:1278760. [PMID: 38375087 PMCID: PMC10875072 DOI: 10.3389/fpls.2024.1278760] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Accepted: 01/22/2024] [Indexed: 02/21/2024]
Abstract
This review highlights -omics research in Solanaceae family, with a particular focus on resilient traits. Extensive research has enriched our understanding of Solanaceae genomics and genetics, with historical varietal development mainly focusing on disease resistance and cultivar improvement but shifting the emphasis towards unveiling resilience mechanisms in genebank-preserved germplasm is nowadays crucial. Collecting such information, might help researchers and breeders developing new experimental design, providing an overview of the state of the art of the most advanced approaches for the identification of the genetic elements laying behind resilience. Building this starting point, we aim at providing a useful tool for tackling the global agricultural resilience goals in these crops.
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Affiliation(s)
- Matteo Martina
- Department of Agricultural, Forest and Food Sciences (DISAFA), Plant Genetics, University of Torino, Grugliasco, Italy
| | - Valeria De Rosa
- Department of Agricultural, Food, Environmental and Animal Sciences (DI4A), University of Udine, Udine, Italy
| | - Gabriele Magon
- Department of Agronomy, Food, Natural Resources, Animals and Environment (DAFNAE), Laboratory of Plant Genetics and Breeding, University of Padua, Legnaro, Italy
| | - Alberto Acquadro
- Department of Agricultural, Forest and Food Sciences (DISAFA), Plant Genetics, University of Torino, Grugliasco, Italy
| | - Lorenzo Barchi
- Department of Agricultural, Forest and Food Sciences (DISAFA), Plant Genetics, University of Torino, Grugliasco, Italy
| | - Gianni Barcaccia
- Department of Agronomy, Food, Natural Resources, Animals and Environment (DAFNAE), Laboratory of Plant Genetics and Breeding, University of Padua, Legnaro, Italy
| | - Emanuele De Paoli
- Department of Agricultural, Food, Environmental and Animal Sciences (DI4A), University of Udine, Udine, Italy
| | - Alessandro Vannozzi
- Department of Agronomy, Food, Natural Resources, Animals and Environment (DAFNAE), Laboratory of Plant Genetics and Breeding, University of Padua, Legnaro, Italy
| | - Ezio Portis
- Department of Agricultural, Forest and Food Sciences (DISAFA), Plant Genetics, University of Torino, Grugliasco, Italy
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Gaccione L, Martina M, Barchi L, Portis E. A Compendium for Novel Marker-Based Breeding Strategies in Eggplant. PLANTS (BASEL, SWITZERLAND) 2023; 12:1016. [PMID: 36903876 PMCID: PMC10005326 DOI: 10.3390/plants12051016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Revised: 02/06/2023] [Accepted: 02/21/2023] [Indexed: 06/18/2023]
Abstract
The worldwide production of eggplant is estimated at about 58 Mt, with China, India and Egypt being the major producing countries. Breeding efforts in the species have mainly focused on increasing productivity, abiotic and biotic tolerance/resistance, shelf-life, the content of health-promoting metabolites in the fruit rather than decreasing the content of anti-nutritional compounds in the fruit. From the literature, we collected information on mapping quantitative trait loci (QTLs) affecting eggplant's traits following a biparental or multi-parent approach as well as genome-wide association (GWA) studies. The positions of QTLs were lifted according to the eggplant reference line (v4.1) and more than 700 QTLs were identified, here organized into 180 quantitative genomic regions (QGRs). Our findings thus provide a tool to: (i) determine the best donor genotypes for specific traits; (ii) narrow down QTL regions affecting a trait by combining information from different populations; (iii) pinpoint potential candidate genes.
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Singh J, van der Knaap E. Unintended Consequences of Plant Domestication. PLANT & CELL PHYSIOLOGY 2022; 63:1573-1583. [PMID: 35715986 DOI: 10.1093/pcp/pcac083] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Revised: 05/12/2022] [Accepted: 06/17/2022] [Indexed: 06/15/2023]
Abstract
Human selection on wild populations mostly favored a common set of plant traits during domestication. This process of direct selection also altered other independent traits that were not directly perceived or desired during crop domestication and improvement. A deeper knowledge of the inadvertent and undesirable phenotypic effects and their underlying genetic causes can help design strategies to mitigate their effects and improve genetic gain in crop plants. We review different factors explaining the negative consequences of plant domestication at the phenotypic and genomic levels. We further describe the genetic causes of undesirable effects that originate from the selection of favorable alleles during plant domestication. In addition, we propose strategies that could be useful in attenuating such effects for crop improvement. With novel -omics and genome-editing tools, it is relatively approachable to understand and manipulate the genetic and biochemical mechanisms responsible for the undesirable phenotypes in domesticated plants.
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Affiliation(s)
- Jugpreet Singh
- Center for Applied Genetic Technologies, 111 Riverbend Road, University of Georgia, Athens, GA 30602, USA
| | - Esther van der Knaap
- Center for Applied Genetic Technologies, 111 Riverbend Road, University of Georgia, Athens, GA 30602, USA
- Institute for Plant Breeding, Genetics and Genomics, 111 Riverbend Road, University of Georgia, Athens, GA 30602, USA
- Department of Horticulture, University of Georgia, Athens, GA 30602, USA
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Ro N, Haile M, Kim B, Cho GT, Lee J, Lee YJ, Hyun DY. Genome-Wide Association Study for Agro-Morphological Traits in Eggplant Core Collection. PLANTS (BASEL, SWITZERLAND) 2022; 11:2627. [PMID: 36235493 PMCID: PMC9571982 DOI: 10.3390/plants11192627] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 10/01/2022] [Accepted: 10/04/2022] [Indexed: 06/16/2023]
Abstract
Eggplant is one of the most economically and nutritionally important vegetables worldwide. The study of the association of phenotypic traits with genetic factors is vital for the rapid and efficient identification and selection of eggplant genetic resources for breeding purposes with desired traits. The eggplant resources (587) collected from different countries, including Korea, were used for establishing the core collection. A total of 288 accessions were selected from 587 Solanum accessions based on 52 single nucleotide polymorphisms (SNPs) markers together with 17 morphological traits. This core collection was further used to analyze the genetic associations of eggplant morphological variations. A large variation was found among the evaluated eggplant accessions for some agro-morphological traits. Stem prickles and leaf prickles showed a significant positive correlation (r = 0.83***), followed by days to flowering and days to maturity (r = 0.64***). A total of 114,981 SNPs were filtered and used for phylogenetic tree analysis, population structure analysis, and genome-wide association study (GWAS). Among the agro-morphological traits, significantly associated SNPs were found for six traits. A total of 377 significantly associated SNPs with six agro-morphological traits were identified. These six traits and the number of SNPs were: days to maturity (51), flower size (121), fruit width (20), harvest fruit color (42), leaf prickles (38), and stem prickles (105). The largest fraction of significant SNPs (11.94%) was obtained on chromosome Ch01, followed by Ch07 and Ch06 with 11.67% and 10.08%, respectively. This study will help to develop markers linked to the most important agro-morphological traits of eggplant genetic resources and support the selection of desirable traits for eggplant breeding programs.
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Affiliation(s)
- Nayoung Ro
- National Agrobiodiversity Center, National Institute of Agricultural Sciences, Rural Development Administration, Jeonju 54874, Korea; (M.H.); (B.K.); (G.-T.C.); (J.L.); (Y.-J.L.)
| | - Mesfin Haile
- National Agrobiodiversity Center, National Institute of Agricultural Sciences, Rural Development Administration, Jeonju 54874, Korea; (M.H.); (B.K.); (G.-T.C.); (J.L.); (Y.-J.L.)
| | - Bichsaem Kim
- National Agrobiodiversity Center, National Institute of Agricultural Sciences, Rural Development Administration, Jeonju 54874, Korea; (M.H.); (B.K.); (G.-T.C.); (J.L.); (Y.-J.L.)
| | - Gyu-Taek Cho
- National Agrobiodiversity Center, National Institute of Agricultural Sciences, Rural Development Administration, Jeonju 54874, Korea; (M.H.); (B.K.); (G.-T.C.); (J.L.); (Y.-J.L.)
| | - Jungro Lee
- National Agrobiodiversity Center, National Institute of Agricultural Sciences, Rural Development Administration, Jeonju 54874, Korea; (M.H.); (B.K.); (G.-T.C.); (J.L.); (Y.-J.L.)
| | - Yoon-Jung Lee
- National Agrobiodiversity Center, National Institute of Agricultural Sciences, Rural Development Administration, Jeonju 54874, Korea; (M.H.); (B.K.); (G.-T.C.); (J.L.); (Y.-J.L.)
| | - Do Yoon Hyun
- Department of Crops and Forestry, Korea National University of Agriculture and Fisheries, Jeonju 54874, Korea;
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Guan W, Ke C, Tang W, Jiang J, Xia J, Xie X, Yang M, Duan C, Wu W, Zheng Y. Construction of a High-Density Recombination Bin-Based Genetic Map Facilitates High-Resolution Mapping of a Major QTL Underlying Anthocyanin Pigmentation in Eggplant. Int J Mol Sci 2022; 23:ijms231810258. [PMID: 36142175 PMCID: PMC9499331 DOI: 10.3390/ijms231810258] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 08/31/2022] [Accepted: 09/03/2022] [Indexed: 02/08/2023] Open
Abstract
High-density genetic maps can significantly improve the resolution of QTL mapping. We constructed a high-density recombination bin-based genetic map of eggplant based on 200 F2 plants from an interspecific cross (Solanum melongena × S. incanum) using the whole genome resequencing strategy. The map was 2022.8 cM long, covering near 99% of the eggplant genome. The map contained 3776 bins, with 3644 (96.5%) being effective (position non-redundant) ones, giving a nominal average distance of 0.54 cM and an effective average distance of 0.56 cM between adjacent bins, respectively. Using this map and 172 F2:3 lines, a major QTL with pleiotropic effects on two anthocyanin pigmentation-related traits, leaf vein color (LVC) and fruit pericarp color (FPC), was steadily detected in a bin interval of 2.28 cM (or 1.68 Mb) on chromosome E10 in two cropping seasons, explaining ~65% and 55% of the phenotypic variation in LVC and FPC, respectively. Genome-wide association analysis in this population validated the QTL and demonstrated the correctness of mapping two bins of chromosome E02 onto E10. Bioinformatics analysis suggested that a WDR protein gene inside the bin interval with reliable effective variation between the two parents could be a possible candidate gene of the QTL.
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Affiliation(s)
- Wenxiang Guan
- Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, College of Agriculture/College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Fujian Provincial Key Laboratory of Crop Breeding by Design, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Changjiao Ke
- Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, College of Agriculture/College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Fujian Provincial Key Laboratory of Crop Breeding by Design, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Weiqi Tang
- Marine and Agricultural Biotechnology Laboratory, Fuzhou Institute of Oceanography, Minjiang University, Fuzhou 350108, China
| | - Jialong Jiang
- Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, College of Agriculture/College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Fujian Provincial Key Laboratory of Crop Breeding by Design, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Jing Xia
- Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, College of Agriculture/College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Fujian Provincial Key Laboratory of Crop Breeding by Design, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Xiaofang Xie
- Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, College of Agriculture/College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Fujian Provincial Key Laboratory of Crop Breeding by Design, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Mei Yang
- Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, College of Agriculture/College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Chenfeng Duan
- Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, College of Agriculture/College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Weiren Wu
- Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, College of Agriculture/College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Fujian Provincial Key Laboratory of Crop Breeding by Design, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Correspondence: (W.W.); (Y.Z.)
| | - Yan Zheng
- Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, College of Agriculture/College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Fujian Provincial Key Laboratory of Crop Breeding by Design, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Correspondence: (W.W.); (Y.Z.)
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Hernández MA, Butler JB, Ammitzboll H, Weller JL, Vaillancourt RE, Potts BM. Genetic control of the operculum and capsule morphology of Eucalyptus globulus. ANNALS OF BOTANY 2022; 130:97-108. [PMID: 35652517 PMCID: PMC9295918 DOI: 10.1093/aob/mcac072] [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: 01/27/2022] [Accepted: 05/29/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND AND AIMS The petaline operculum that covers the inner whorls until anthesis and the woody capsule that develops after fertilization are reproductive structures of eucalypts that protect the flower and seeds. Although they are distinct organs, they both develop from flower buds and this common ontogeny suggests shared genetic control. In Eucalyptus globulus their morphology is variable and we aimed to identify the quantitative trait loci (QTL) underlying this variation and determine whether there is common genetic control of these ecologically and taxonomically important reproductive structures. METHODS Samples of opercula and capsules were collected from 206 trees that belong to a large outcrossed F2E. globulus mapping population. The morphological variation in these structures was characterized by measuring six operculum and five capsule traits. QTL analysis was performed using these data and a linkage map consisting of 480 markers. KEY RESULTS A total of 27 QTL were detected for operculum traits and 28 for capsule traits, with the logarithm of odds ranging from 2.8 to 11.8. There were many co-located QTL associated with operculum or capsule traits, generally reflecting allometric relationships. A key finding was five genomic regions where co-located QTL affected both operculum and capsule morphology, and the overall trend for these QTL was to affect elongation of both organs. Some of these QTL appear to have a significant effect on the phenotype, with the strongest QTL explaining 26.4 % of the variation in operculum shape and 16.4 % in capsule shape. Flower bud measurements suggest the expression of these QTL starts during bud development. Several candidate genes were found associated with the QTL and their putative function is discussed. CONCLUSIONS Variation in both operculum and capsule traits in E. globulus is under strong genetic control. Our results suggest that these reproductive structures share a common genetic pathway during flower bud development.
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Affiliation(s)
- Mariano A Hernández
- School of Natural Sciences, University of Tasmania, Hobart, Tasmania 7001, Australia
- ARC Training Centre for Forest Value, University of Tasmania, Hobart, Tasmania 7001, Australia
- Instituto Nacional de Tecnología Agropecuaria (INTA), Route 27 - Km 38.3, Bella Vista, Corrientes 3432, Argentina
| | | | - Hans Ammitzboll
- School of Natural Sciences, University of Tasmania, Hobart, Tasmania 7001, Australia
- ARC Training Centre for Forest Value, University of Tasmania, Hobart, Tasmania 7001, Australia
| | - James L Weller
- School of Natural Sciences, University of Tasmania, Hobart, Tasmania 7001, Australia
- Australian Research Council Centre of Excellence for Plant Success in Nature and Agriculture
| | - René E Vaillancourt
- School of Natural Sciences, University of Tasmania, Hobart, Tasmania 7001, Australia
- ARC Training Centre for Forest Value, University of Tasmania, Hobart, Tasmania 7001, Australia
| | - Brad M Potts
- School of Natural Sciences, University of Tasmania, Hobart, Tasmania 7001, Australia
- ARC Training Centre for Forest Value, University of Tasmania, Hobart, Tasmania 7001, Australia
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Gong H, Rehman F, Ma Y, A B, Zeng S, Yang T, Huang J, Li Z, Wu D, Wang Y. Germplasm Resources and Strategy for Genetic Breeding of Lycium Species: A Review. FRONTIERS IN PLANT SCIENCE 2022; 13:802936. [PMID: 35222468 PMCID: PMC8874141 DOI: 10.3389/fpls.2022.802936] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Accepted: 01/07/2022] [Indexed: 06/01/2023]
Abstract
Lycium species (goji), belonging to Solanaceae, are widely spread in the arid to semiarid environments of Eurasia, Africa, North and South America, among which most species have affinal drug and diet functions, resulting in their potential to be a superior healthy food. However, compared with other crop species, scientific research on breeding Lycium species lags behind. This review systematically introduces the present germplasm resources, cytological examination and molecular-assisted breeding progress in Lycium species. Introduction of the distribution of Lycium species around the world could facilitate germplasm collection for breeding. Karyotypes of different species could provide a feasibility analysis of fertility between species. The introduction of mapping technology has discussed strategies for quantitative trait locus (QTL) mapping in Lycium species according to different kinds of traits. Moreover, to extend the number of traits and standardize the protocols of trait detection, we also provide 1,145 potential traits (275 agronomic and 870 metabolic) in different organs based on different reference studies on Lycium, tomato and other Solanaceae species. Finally, perspectives on goji breeding research are discussed and concluded. This review will provide breeders with new insights into breeding Lycium species.
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Affiliation(s)
- Haiguang Gong
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Provincial Key Laboratory of Digital Botanical Garden and Public Science, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- School of Life Science, University of Chinese Academy of Sciences, Beijing, China
| | - Fazal Rehman
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Provincial Key Laboratory of Digital Botanical Garden and Public Science, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- School of Life Science, University of Chinese Academy of Sciences, Beijing, China
| | - Yun Ma
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Provincial Key Laboratory of Digital Botanical Garden and Public Science, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- School of Life Science, University of Chinese Academy of Sciences, Beijing, China
| | - Biao A
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Provincial Key Laboratory of Digital Botanical Garden and Public Science, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- School of Life Science, University of Chinese Academy of Sciences, Beijing, China
| | - Shaohua Zeng
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Provincial Key Laboratory of Digital Botanical Garden and Public Science, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- School of Life Science, University of Chinese Academy of Sciences, Beijing, China
| | - Tianshun Yang
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Provincial Key Laboratory of Digital Botanical Garden and Public Science, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Jianguo Huang
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Provincial Key Laboratory of Digital Botanical Garden and Public Science, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- School of Life Science, University of Chinese Academy of Sciences, Beijing, China
| | - Zhong Li
- Agricultural Comprehensive Development Center in Ningxia Hui Autonomous Region, Yinchuan, China
| | | | - Ying Wang
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Provincial Key Laboratory of Digital Botanical Garden and Public Science, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- School of Life Science, Gannan Normal University, Ganzhou, China
- School of Life Science, University of Chinese Academy of Sciences, Beijing, China
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Barchi L, Rabanus‐Wallace MT, Prohens J, Toppino L, Padmarasu S, Portis E, Rotino GL, Stein N, Lanteri S, Giuliano G. Improved genome assembly and pan-genome provide key insights into eggplant domestication and breeding. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 107:579-596. [PMID: 33964091 PMCID: PMC8453987 DOI: 10.1111/tpj.15313] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Revised: 04/30/2021] [Accepted: 05/04/2021] [Indexed: 05/20/2023]
Abstract
Eggplant (Solanum melongena L.) is an important horticultural crop and one of the most widely grown vegetables from the Solanaceae family. It was domesticated from a wild, prickly progenitor carrying small, round, non-anthocyanic fruits. We obtained a novel, highly contiguous genome assembly of the eggplant '67/3' reference line, by Hi-C retrofitting of a previously released short read- and optical mapping-based assembly. The sizes of the 12 chromosomes and the fraction of anchored genes in the improved assembly were comparable to those of a chromosome-level assembly. We resequenced 23 accessions of S. melongena representative of the worldwide phenotypic, geographic, and genetic diversity of the species, and one each from the closely related species Solanum insanum and Solanum incanum. The eggplant pan-genome contained approximately 51.5 additional megabases and 816 additional genes compared with the reference genome, while the pan-plastome showed little genetic variation. We identified 53 selective sweeps related to fruit color, prickliness, and fruit shape in the nuclear genome, highlighting selection leading to the emergence of present-day S. melongena cultivars from its wild ancestors. Candidate genes underlying the selective sweeps included a MYBL1 repressor and CHALCONE ISOMERASE (for fruit color), homologs of Arabidopsis GLABRA1 and GLABROUS INFLORESCENCE STEMS2 (for prickliness), and orthologs of tomato FW2.2, OVATE, LOCULE NUMBER/WUSCHEL, SUPPRESSOR OF OVATE, and CELL SIZE REGULATOR (for fruit size/shape), further suggesting that selection for the latter trait relied on a common set of orthologous genes in tomato and eggplant.
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Affiliation(s)
- Lorenzo Barchi
- DISAFA – Plant geneticsUniversity of TurinGrugliasco (TO)10095Italy
| | | | - Jaime Prohens
- COMAVUniversitat Politècnica de ValènciaCamino de Vera 14Valencia46022Spain
| | - Laura Toppino
- CREA Research Centre for Genomics and BioinformaticsVia Paullese 28Montanaso LombardoLO26836Italy
| | - Sudharsan Padmarasu
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)Corrensstr. 3Seeland06466Germany
| | - Ezio Portis
- DISAFA – Plant geneticsUniversity of TurinGrugliasco (TO)10095Italy
| | - Giuseppe Leonardo Rotino
- CREA Research Centre for Genomics and BioinformaticsVia Paullese 28Montanaso LombardoLO26836Italy
| | - Nils Stein
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)Corrensstr. 3Seeland06466Germany
- Department of Crop SciencesCenter for Integrated Breeding Research (CiBreed)Georg‐August‐UniversityVon Siebold Str. 8Göttingen37075Germany
| | - Sergio Lanteri
- DISAFA – Plant geneticsUniversity of TurinGrugliasco (TO)10095Italy
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Page AML, Chapman MA. Identifying genomic regions targeted during eggplant domestication using transcriptome data. J Hered 2021; 112:519-525. [PMID: 34130314 PMCID: PMC8634079 DOI: 10.1093/jhered/esab035] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Accepted: 06/11/2021] [Indexed: 11/15/2022] Open
Abstract
Identifying genes and traits that have diverged during domestication provides key information of importance for maintaining and even increasing yield and nutrients in existing crops. A “bottom-up” population genetics approach was used to identify signatures of selection across the eggplant genome, to better understand the process of domestication. RNA-seq data were obtained for 4 wild eggplants (Solanum insanum L.) and 16 domesticated eggplants (S. melongena L.) and mapped to the eggplant genome. Single-nucleotide polymorphism (SNPs) exhibiting signatures of selection in domesticates were identified as those exhibiting high FST between the 2 populations (evidence of significant divergence) and low π for the domesticated population (indicative of a selective sweep). Some of these regions appear to overlap with previously identified quantitative trait loci for domestication traits. Genes in regions of linkage disequilibrium surrounding these SNPs were searched against the Arabidopsis thaliana and tomato genomes to find orthologs. Subsequent gene ontology (GO) enrichment analysis identified over-representation of GO terms related to photosynthesis and response to the environment. This work reveals genomic changes involved in eggplant domestication and improvement, and how this compares to observed changes in the tomato genome, revealing shared chromosomal regions involved in the domestication of both species.
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Affiliation(s)
- Anna M L Page
- Biological Sciences, University of Southampton, Southampton, UK
| | - Mark A Chapman
- Biological Sciences, University of Southampton, Southampton, UK
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Sulli M, Barchi L, Toppino L, Diretto G, Sala T, Lanteri S, Rotino GL, Giuliano G. An Eggplant Recombinant Inbred Population Allows the Discovery of Metabolic QTLs Controlling Fruit Nutritional Quality. FRONTIERS IN PLANT SCIENCE 2021; 12:638195. [PMID: 34079565 PMCID: PMC8166230 DOI: 10.3389/fpls.2021.638195] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2020] [Accepted: 03/22/2021] [Indexed: 06/02/2023]
Abstract
Eggplant (Solanum melongena L.) represents the third most important crop of the Solanaceae family and is an important component of our daily diet. A population of 164 F6 recombinant inbred lines (RILs), derived from two eggplant lines differing with respect to several key agronomic traits, "305E40" and "67/3," was grown to the commercial maturation stage, and fruits were harvested, separated into peel and flesh, and subjected to liquid chromatography Liquid Chromatography/Mass Spectrometry (LC/MS) analysis. Through a combination of untargeted and targeted metabolomics approaches, a number of metabolites belonging to the glycoalkaloid, anthocyanin, and polyamine classes and showing a differential accumulation in the two parental lines and F1 hybrid were identified. Through metabolic profiling of the RILs, we identified several metabolomic quantitative trait loci (mQTLs) associated with the accumulation of those metabolites. Each of the metabolic traits proved to be controlled by one or more quantitative trait loci (QTLs); for most of the traits, one major mQTL (phenotypic variation explained [PVE] ≥ 10%) was identified. Data on mQTL mapping and dominance-recessivity relationships of measured compounds in the parental lines and F1 hybrid, as well as an analysis of the candidate genes underlying the QTLs and of their sequence differences in the two parental lines, suggested a series of candidate genes underlying the traits under study.
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Affiliation(s)
- Maria Sulli
- Italian National Agency for New Technologies, Energy and Sustainable Economic Development (ENEA), Casaccia Research Centre, Rome, Italy
| | - Lorenzo Barchi
- Department of Agricultural, Forest and Food Sciences (DISAFA), Plant Genetics and Breeding, University of Turin, Grugliasco, Italy
| | - Laura Toppino
- CREA, Council for Agricultural and Economics Research, Research Centre for Genomics and Bioinformatics, Montanaso Lombardo, Italy
| | - Gianfranco Diretto
- Italian National Agency for New Technologies, Energy and Sustainable Economic Development (ENEA), Casaccia Research Centre, Rome, Italy
| | - Tea Sala
- CREA, Council for Agricultural and Economics Research, Research Centre for Genomics and Bioinformatics, Montanaso Lombardo, Italy
| | - Sergio Lanteri
- Department of Agricultural, Forest and Food Sciences (DISAFA), Plant Genetics and Breeding, University of Turin, Grugliasco, Italy
| | - Giuseppe Leonardo Rotino
- CREA, Council for Agricultural and Economics Research, Research Centre for Genomics and Bioinformatics, Montanaso Lombardo, Italy
| | - Giovanni Giuliano
- Italian National Agency for New Technologies, Energy and Sustainable Economic Development (ENEA), Casaccia Research Centre, Rome, Italy
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11
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Nyadanu D, Lowor ST, Akpertey A, Tchokponhoué DA, Pobee P, Dogbatse JA, Okyere D, Amon-Armah F, Brako-Marfo M. Genetic variability of bioactive compounds and selection for nutraceutical quality in kola [Cola nitida (Vent) Schott. and Endl.]. PLoS One 2020; 15:e0242972. [PMID: 33270707 PMCID: PMC7714174 DOI: 10.1371/journal.pone.0242972] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Accepted: 11/12/2020] [Indexed: 11/18/2022] Open
Abstract
Cola nitida known as Kola serves as flavouring ingredient in the food industry and is also of great importance during traditional rites in Africa. Despite the well-known pharmaceutical values of the species, efforts to develop improved varieties with enhanced nutraceutical quality is limited due to unavailability of information on variation of genotypes in bioactive compounds in the nuts. The objectives of this research were to evaluate 25 genotypes of kola for bioactive contents, determine relationship between nutritional and phenolic traits and to identify kola genotypes with good nutraceutical quality for use in developing improved varieties. The kola genotypes were established in the field using a randomized complete block design with three replicates. Nuts harvested from the blocks, were bulked and used to quantify soluble and insoluble sugars, total protein, moisture, ash, fats, pH, polyphenols, tannins and flavonoids using completely randomized design with three replicates in the laboratory. Data were analysed by combining Analysis of Variance, Kruskal-Wallis test, correlation test and multivariate analysis. Significant variations (P < 0.05) were observed among the kola genotypes for the bioactive traits evaluated. Phenolic traits were more heritable than nutritional traits. Although not significant (P > 0.05), correlation between nutritional and phenolic traits was negative, whereas correlations among nutritional traits were weak. On the contrary, significant and positive correlations (P < 0.05) were observed among phenolic traits. The hierarchical clustering analysis based on the traits evaluated grouped the 25 genotypes of kola evaluated into four clusters. Genotypes A12, JB4, JB19, JB36, P2-1b, and P2-1c were identified as potential parental lines for phenolic traits selection in kola whereas genotypes A10, Club, Atta1 and JB10 can be considered for soluble and insoluble sugar-rich variety development. These findings represent an important step towards improving nutritional and nutraceutical quality of kola nuts.
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Affiliation(s)
| | | | | | - Dèdéou Apocalypse Tchokponhoué
- Faculty of Agronomic Sciences, Laboratory of Genetics, Biotechnology and Seed Science, University of Abomey-Calvi, Abomey-Calavi, Republic of Benin
| | - Prince Pobee
- Cocoa Research Institute of Ghana, New Tafo-Akim, Ghana
| | | | - Daniel Okyere
- Department of Crop and Soil Sciences, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
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12
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A New Intra-Specific and High-Resolution Genetic Map of Eggplant Based on a RIL Population, and Location of QTLs Related to Plant Anthocyanin Pigmentation and Seed Vigour. Genes (Basel) 2020; 11:genes11070745. [PMID: 32635424 PMCID: PMC7397344 DOI: 10.3390/genes11070745] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Revised: 07/01/2020] [Accepted: 07/02/2020] [Indexed: 12/16/2022] Open
Abstract
Eggplant is the second most important solanaceous berry-producing crop after tomato. Despite mapping studies based on bi-parental progenies and GWAS approaches having been performed, an eggplant intraspecific high-resolution map is still lacking. We developed a RIL population from the intraspecific cross ‘305E40’, (androgenetic introgressed line carrying the locus Rfo-Sa1 conferring Fusarium resistance) x ‘67/3’ (breeding line whose genome sequence was recently released). One hundred and sixty-three RILs were genotyped by a genotype-by-sequencing (GBS) approach, which allowed us to identify 10,361 polymorphic sites. Overall, 267 Gb of sequencing data were generated and ~773 M Illumina paired end (PE) reads were mapped against the reference sequence. A new linkage map was developed, including 7249 SNPs assigned to the 12 chromosomes and spanning 2169.23 cM, with iaci@liberoan average distance of 0.4 cM between adjacent markers. This was used to elucidate the genetic bases of seven traits related to anthocyanin content in different organs recorded in three locations as well as seed vigor. Overall, from 7 to 17 QTLs (at least one major QTL) were identified for each trait. These results demonstrate that our newly developed map supplies valuable information for QTL fine mapping, candidate gene identification, and the development of molecular markers for marker assisted selection (MAS) of favorable alleles.
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13
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Performance of a Set of Eggplant (Solanum melongena) Lines With Introgressions From Its Wild Relative S. incanum Under Open Field and Screenhouse Conditions and Detection of QTLs. AGRONOMY-BASEL 2020. [DOI: 10.3390/agronomy10040467] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Introgression lines (ILs) of eggplant (Solanum melongena) represent a resource of high value for breeding and the genetic analysis of important traits. We have conducted a phenotypic evaluation in two environments (open field and screenhouse) of 16 ILs from the first set of eggplant ILs developed so far. Each of the ILs carries a single marker-defined chromosomal segment from the wild eggplant relative S. incanum (accession MM577) in the genetic background of S. melongena (accession AN-S-26). Seventeen agronomic traits were scored to test the performance of ILs compared to the recurrent parent and of identifying QTLs for the investigated traits. Significant morphological differences were found between parents, and the hybrid was heterotic for vigour-related traits. Despite the presence of large introgressed fragments from a wild exotic parent, individual ILs did not display differences with respect to the recipient parent for most traits, although significant genotype × environment interaction (G × E ) was detected for most traits. Heritability values for the agronomic traits were generally low to moderate. A total of ten stable QTLs scattered across seven chromosomes was detected. For five QTLs, the S. incanum introgression was associated with higher mean values for plant- and flower-related traits, including vigour prickliness and stigma length. For one flower- and four fruit-related-trait QTLs, including flower peduncle and fruit pedicel lengths and fruit weight, the S. incanum introgression was associated with lower mean values for fruit-related traits. Evidence of synteny to other previously reported in eggplant populations was found for three of the fruit-related QTLs. The other seven stable QTLs are new, demonstrating that eggplant ILs are of great interest for eggplant breeding under different environments.
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14
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Wei Q, Wang W, Hu T, Hu H, Wang J, Bao C. Construction of a SNP-Based Genetic Map Using SLAF-Seq and QTL Analysis of Morphological Traits in Eggplant. Front Genet 2020; 11:178. [PMID: 32218801 PMCID: PMC7078336 DOI: 10.3389/fgene.2020.00178] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Accepted: 02/13/2020] [Indexed: 01/09/2023] Open
Abstract
Eggplant (Solanum melongena; 2n = 24) is an economically important fruit crop of the family Solanaceae that was domesticated in India and Southeast Asia. Construction of a high-resolution genetic map and map-based gene mining in eggplant have lagged behind other crops within the family such as tomato and potato. In this study, we conducted high-throughput single nucleotide polymorphism (SNP) discovery in the eggplant genome using specific length amplified fragment (SLAF) sequencing and constructed a high-density genetic map for the quantitative trait locus (QTL) analysis of multiple traits. An interspecific F2 population of 121 individuals was developed from the cross between cultivated eggplant "1836" and the wild relative S. linnaeanum "1809." Genomic DNA extracted from parental lines and the F2 population was subjected to high-throughput SLAF sequencing. A total of 111.74 Gb of data and 487.53 million pair-end reads were generated. A high-resolution genetic map containing 2,122 SNP markers and 12 linkage groups was developed for eggplant, which spanned 1530.75 cM, with an average distance of 0.72 cM between adjacent markers. A total of 19 QTLs were detected for stem height and fruit and leaf morphology traits of eggplant, explaining 4.08-55.23% of the phenotypic variance. These QTLs were distributed on nine linkage groups (LGs), but not on LG2, 4, and 9. The number of SNPs ranged from 2 to 11 within each QTL, and the genetic interval varied from 0.15 to 10.53 cM. Overall, the results establish a foundation for the fine mapping of complex QTLs, candidate gene identification, and marker-assisted selection of favorable alleles in eggplant breeding.
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Affiliation(s)
| | | | | | | | | | - Chonglai Bao
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
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15
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Rinaldi R, Van Deynze A, Portis E, Rotino GL, Toppino L, Hill T, Ashrafi H, Barchi L, Lanteri S. New Insights on Eggplant/Tomato/Pepper Synteny and Identification of Eggplant and Pepper Orthologous QTL. FRONTIERS IN PLANT SCIENCE 2016; 7:1031. [PMID: 27486463 PMCID: PMC4948011 DOI: 10.3389/fpls.2016.01031] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Accepted: 06/30/2016] [Indexed: 05/20/2023]
Abstract
Eggplant, pepper, and tomato are the most exploited berry-producing vegetables within the Solanaceae family. Their genomes differ in size, but each has 12 chromosomes which have undergone rearrangements causing a redistribution of loci. The genome sequences of all three species are available but differ in coverage, assembly quality and percentage of anchorage. Determining their syntenic relationship and QTL orthology will contribute to exploit genomic resources and genetic data for key agronomic traits. The syntenic analysis between tomato and pepper based on the alignment of 34,727 tomato CDS to the pepper genome sequence, identified 19,734 unique hits. The resulting synteny map confirmed the 14 inversions and 10 translocations previously documented, but also highlighted 3 new translocations and 4 major new inversions. Furthermore, each of the 12 chromosomes exhibited a number of rearrangements involving small regions of 0.5-0.7 Mbp. Due to high fragmentation of the publicly available eggplant genome sequence, physical localization of most eggplant QTL was not possible, thus, we compared the organization of the eggplant genetic map with the genome sequence of both tomato and pepper. The eggplant/tomato syntenic map confirmed all the 10 translocations but only 9 of the 14 known inversions; on the other hand, a newly detected inversion was recognized while another one was not confirmed. The eggplant/pepper syntenic map confirmed 10 translocations and 8 inversions already detected and suggested a putative new translocation. In order to perform the assessment of eggplant and pepper QTL orthology, the eggplant and pepper sequence-based markers located in their respective genetic map were aligned onto the pepper genome. GBrowse in pepper was used as reference platform for QTL positioning. A set of 151 pepper QTL were located as well as 212 eggplant QTL, including 76 major QTL (PVE ≥ 10%) affecting key agronomic traits. Most were confirmed to cluster in orthologous chromosomal regions. Our results highlight that the availability of genome sequences for an increasing number of crop species and the development of "ultra-dense" physical maps provide new and key tools for detailed syntenic and orthology studies between related plant species.
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Affiliation(s)
- Riccardo Rinaldi
- DISAFA Plant Genetics and Breeding, University of TurinTurin, Italy
- Seed Biotechnology Center, University of California, DavisDavis, CA, USA
| | - Allen Van Deynze
- Seed Biotechnology Center, University of California, DavisDavis, CA, USA
| | - Ezio Portis
- DISAFA Plant Genetics and Breeding, University of TurinTurin, Italy
| | | | - Laura Toppino
- CREA-ORL Research Unit for Vegetable CropsMontanaso Lombardo, Italy
| | - Theresa Hill
- Seed Biotechnology Center, University of California, DavisDavis, CA, USA
| | - Hamid Ashrafi
- Seed Biotechnology Center, University of California, DavisDavis, CA, USA
| | - Lorenzo Barchi
- DISAFA Plant Genetics and Breeding, University of TurinTurin, Italy
- *Correspondence: Lorenzo Barchi
| | - Sergio Lanteri
- DISAFA Plant Genetics and Breeding, University of TurinTurin, Italy
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16
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Toppino L, Barchi L, Lo Scalzo R, Palazzolo E, Francese G, Fibiani M, D'Alessandro A, Papa V, Laudicina VA, Sabatino L, Pulcini L, Sala T, Acciarri N, Portis E, Lanteri S, Mennella G, Rotino GL. Mapping Quantitative Trait Loci Affecting Biochemical and Morphological Fruit Properties in Eggplant (Solanum melongena L.). FRONTIERS IN PLANT SCIENCE 2016; 7:256. [PMID: 26973692 PMCID: PMC4777957 DOI: 10.3389/fpls.2016.00256] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/24/2015] [Accepted: 02/15/2016] [Indexed: 05/19/2023]
Abstract
Eggplant berries are a source of health-promoting metabolites including antioxidant and nutraceutical compounds, mainly anthocyanins and chlorogenic acid; however, they also contain some anti-nutritional compounds such as steroidal glycoalkaloids (SGA) and saponins, which are responsible for the bitter taste of the flesh and with potential toxic effects on humans. Up to now, Quantitative Trait Loci (QTL) for the metabolic content are far from being characterized in eggplant, thus hampering the application of breeding programs aimed at improving its fruit quality. Here we report on the identification of some QTL for the fruit metabolic content in an F2 intraspecific mapping population of 156 individuals, obtained by crossing the eggplant breeding lines "305E40" × "67/3." The same population was previously employed for the development of a RAD-tag based linkage map and the identification of QTL associated to morphological and physiological traits. The mapping population was biochemically characterized for both fruit basic qualitative data, like dry matter, °Brix, sugars, and organic acids, as well as for health-related compounds such chlorogenic acid, (the main flesh monomeric phenol), the two peel anthocyanins [i.e., delphinidin-3-rutinoside (D3R) and delphinidin-3-(p- coumaroylrutinoside)-5-glucoside (nasunin)] and the two main steroidal glycoalkaloids, solasonine, and solamargine. For most of the traits, one major QTL (PVE ≥10%) was spotted and putative orthologies with other Solanaceae crops are discussed. The present results supply valuable information to eggplant breeders on the inheritance of key fruit quality traits, thus providing potential tools to assist future breeding programs.
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Affiliation(s)
- Laura Toppino
- Consiglio per la Ricerca in Agricoltura e l'Analisi dell'Economia Agraria-ORL, Unità di Ricerca per l'OrticolturaMontanaso Lombardo, Italy
| | - Lorenzo Barchi
- Dipartimento di Scienze Agrarie, Forestali e Alimentari, Plant Genetics and Breeding, University of TurinTurin, Italy
| | - Roberto Lo Scalzo
- Consiglio per la Ricerca in Agricoltura e l'Analisi dell'Economia Agraria-IAA, Unità di Ricerca per i Processi dell'Industria AgroalimentareMilano, Italy
| | - Eristanna Palazzolo
- Dipartimento di Scienze Agrarie e Forestali, Università degli Studi di PalermoPalermo, Italy
| | - Gianluca Francese
- Consiglio per la Ricerca in Agricoltura e l'Analisi dell'Economia Agraria-ORT, Centro di Ricerca per l'OrticolturaPontecagnano-Faiano, Italy
| | - Marta Fibiani
- Consiglio per la Ricerca in Agricoltura e l'Analisi dell'Economia Agraria-IAA, Unità di Ricerca per i Processi dell'Industria AgroalimentareMilano, Italy
| | - Antonietta D'Alessandro
- Consiglio per la Ricerca in Agricoltura e l'Analisi dell'Economia Agraria-ORT, Centro di Ricerca per l'OrticolturaPontecagnano-Faiano, Italy
| | - Vincenza Papa
- Consiglio per la Ricerca in Agricoltura e l'Analisi dell'Economia Agraria-IAA, Unità di Ricerca per i Processi dell'Industria AgroalimentareMilano, Italy
| | - Vito A. Laudicina
- Dipartimento di Scienze Agrarie e Forestali, Università degli Studi di PalermoPalermo, Italy
| | - Leo Sabatino
- Dipartimento di Scienze Agrarie e Forestali, Università degli Studi di PalermoPalermo, Italy
| | - Laura Pulcini
- Consiglio per la Ricerca in Agricoltura e l'Analisi dell'Economia Agraria-ORA, Unità di Ricerca per l'OrticolturaMonsampolo del Tronto, Italy
| | - Tea Sala
- Consiglio per la Ricerca in Agricoltura e l'Analisi dell'Economia Agraria-ORL, Unità di Ricerca per l'OrticolturaMontanaso Lombardo, Italy
| | - Nazzareno Acciarri
- Consiglio per la Ricerca in Agricoltura e l'Analisi dell'Economia Agraria-ORA, Unità di Ricerca per l'OrticolturaMonsampolo del Tronto, Italy
| | - Ezio Portis
- Dipartimento di Scienze Agrarie, Forestali e Alimentari, Plant Genetics and Breeding, University of TurinTurin, Italy
| | - Sergio Lanteri
- Dipartimento di Scienze Agrarie, Forestali e Alimentari, Plant Genetics and Breeding, University of TurinTurin, Italy
| | - Giuseppe Mennella
- Consiglio per la Ricerca in Agricoltura e l'Analisi dell'Economia Agraria-ORT, Centro di Ricerca per l'OrticolturaPontecagnano-Faiano, Italy
| | - Giuseppe L. Rotino
- Consiglio per la Ricerca in Agricoltura e l'Analisi dell'Economia Agraria-ORL, Unità di Ricerca per l'OrticolturaMontanaso Lombardo, Italy
- *Correspondence: Giuseppe L. Rotino
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17
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Portis E, Cericola F, Barchi L, Toppino L, Acciarri N, Pulcini L, Sala T, Lanteri S, Rotino GL. Association Mapping for Fruit, Plant and Leaf Morphology Traits in Eggplant. PLoS One 2015; 10:e0135200. [PMID: 26284782 PMCID: PMC4540451 DOI: 10.1371/journal.pone.0135200] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2015] [Accepted: 07/18/2015] [Indexed: 11/18/2022] Open
Abstract
An eggplant (Solanum melongena) association panel of 191 accessions, comprising a mixture of breeding lines, old varieties and landrace selections was SNP genotyped and phenotyped for key breeding fruit and plant traits at two locations over two seasons. A genome-wide association (GWA) analysis was performed using the mixed linear model, which takes into account both a kinship matrix and the sub-population membership of the accessions. Overall, 194 phenotype/genotype associations were uncovered, relating to 30 of the 33 measured traits. These associations involved 79 SNP loci mapping to 39 distinct chromosomal regions distributed over all 12 eggplant chromosomes. A comparison of the map positions of these SNPs with those of loci derived from conventional linkage mapping showed that GWA analysis both validated many of the known controlling loci and detected a large number of new marker/trait associations. Exploiting established syntenic relationships between eggplant chromosomes and those of tomato and pepper recognized orthologous regions in ten eggplant chromosomes harbouring genes influencing breeders’ traits.
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Affiliation(s)
- Ezio Portis
- Dipartimento di Scienze Agrarie, Forestali ed Alimentari (DISAFA)—Plant Genetics and Breeding, University of Torino, I-10095 Grugliasco, Torino, Italy
| | - Fabio Cericola
- Dipartimento di Scienze Agrarie, Forestali ed Alimentari (DISAFA)—Plant Genetics and Breeding, University of Torino, I-10095 Grugliasco, Torino, Italy
- Consiglio per la ricerca in agricoltura e l’analisi dell’economia agraria—CREA, Research Unit for Vegetable Crops, I-26836 Montanaso Lombardo, Lodi, Italy
| | - Lorenzo Barchi
- Dipartimento di Scienze Agrarie, Forestali ed Alimentari (DISAFA)—Plant Genetics and Breeding, University of Torino, I-10095 Grugliasco, Torino, Italy
| | - Laura Toppino
- Consiglio per la ricerca in agricoltura e l’analisi dell’economia agraria—CREA, Research Unit for Vegetable Crops, I-26836 Montanaso Lombardo, Lodi, Italy
| | - Nazzareno Acciarri
- Consiglio per la ricerca in agricoltura e l’analisi dell’economia agraria—CREA, Research Unit for Vegetable Crops, I-63030 Monsampolo del Tronto, Ascoli Piceno, Italy
| | - Laura Pulcini
- Consiglio per la ricerca in agricoltura e l’analisi dell’economia agraria—CREA, Research Unit for Vegetable Crops, I-63030 Monsampolo del Tronto, Ascoli Piceno, Italy
| | - Tea Sala
- Consiglio per la ricerca in agricoltura e l’analisi dell’economia agraria—CREA, Research Unit for Vegetable Crops, I-26836 Montanaso Lombardo, Lodi, Italy
| | - Sergio Lanteri
- Dipartimento di Scienze Agrarie, Forestali ed Alimentari (DISAFA)—Plant Genetics and Breeding, University of Torino, I-10095 Grugliasco, Torino, Italy
| | - Giuseppe Leonardo Rotino
- Consiglio per la ricerca in agricoltura e l’analisi dell’economia agraria—CREA, Research Unit for Vegetable Crops, I-26836 Montanaso Lombardo, Lodi, Italy
- * E-mail:
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18
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Ferris KG, Rushton T, Greenlee AB, Toll K, Blackman BK, Willis JH. Leaf shape evolution has a similar genetic architecture in three edaphic specialists within the Mimulus guttatus species complex. ANNALS OF BOTANY 2015; 116:213-23. [PMID: 26070644 PMCID: PMC4512191 DOI: 10.1093/aob/mcv080] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2015] [Revised: 03/06/2015] [Accepted: 04/24/2015] [Indexed: 05/13/2023]
Abstract
BACKGROUND AND AIMS The genetic basis of leaf shape has long interested botanists because leaf shape varies extensively across the plant kingdom and this variation is probably adaptive. However, knowledge of the genetic architecture of leaf shape variation in natural populations remains limited. This study examined the genetic architecture of leaf shape diversification among three edaphic specialists in the Mimulus guttatus species complex. Lobed and narrow leaves have evolved from the entire, round leaves of M. guttatus in M. laciniatus, M. nudatus and a polymorphic serpentine M. guttatus population (M2L). METHODS Bulk segregant analysis and next-generation sequencing were used to map quantitative trait loci (QTLs) that underlie leaf shape in an M. laciniatus × M. guttatus F2 population. To determine whether the same QTLs contribute to leaf shape variation in M. nudatus and M2L, F2s from M. guttatus × M. nudatus and lobed M2L × unlobed M. guttatus crosses were genotyped at QTLs from the bulk segregant analysis. KEY RESULTS Narrow and lobed leaf shapes in M. laciniatus, M. nudatus and M. guttatus are controlled by overlapping genetic regions. Several promising leaf shape candidate genes were found under each QTL. CONCLUSIONS The evolution of divergent leaf shape has taken place multiple times in the M. guttatus species complex and is associated with the occupation of dry, rocky environments. The genetic architecture of elongated and lobed leaves is similar across three species in this group. This may indicate that parallel genetic evolution from standing variation or new mutations is responsible for the putatively adaptive leaf shape variation in Mimulus.
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Affiliation(s)
- Kathleen G Ferris
- Department of Biology, Duke University, 125 Science Drive, Durham, NC 27705, USA and
| | - Tullia Rushton
- Department of Biology, Duke University, 125 Science Drive, Durham, NC 27705, USA and
| | - Anna B Greenlee
- Department of Biology, University of Virginia, 485 McCormick Road Charlottesville, VA 22904, USA
| | - Katherine Toll
- Department of Biology, Duke University, 125 Science Drive, Durham, NC 27705, USA and
| | - Benjamin K Blackman
- Department of Biology, University of Virginia, 485 McCormick Road Charlottesville, VA 22904, USA
| | - John H Willis
- Department of Biology, Duke University, 125 Science Drive, Durham, NC 27705, USA and
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19
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Wang L, Li J, Zhao J, He C. Evolutionary developmental genetics of fruit morphological variation within the Solanaceae. FRONTIERS IN PLANT SCIENCE 2015; 6:248. [PMID: 25918515 PMCID: PMC4394660 DOI: 10.3389/fpls.2015.00248] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2014] [Accepted: 03/27/2015] [Indexed: 05/20/2023]
Abstract
Morphological variations of fruits such as shape and size, and color are a result of adaptive evolution. The evolution of morphological novelties is particularly intriguing. An understanding of these evolutionary processes calls for the elucidation of the developmental and genetic mechanisms that result in particular fruit morphological characteristics, which determine seed dispersal. The genetic and developmental basis for fruit morphological variation was established at a microevolutionary time scale. Here, we summarize the progress on the evolutionary developmental genetics of fruit size, shape and color in the Solanaceae. Studies suggest that the recruitment of a pre-existing gene and subsequent modification of its interaction and regulatory networks are frequently involved in the evolution of morphological diversity. The basic mechanisms underlying changes in plant morphology are alterations in gene expression and/or gene function. We also deliberate on the future direction in evolutionary developmental genetics of fruit morphological variation such as fruit type. These studies will provide insights into plant developmental processes and will help to improve the productivity and fruit quality of crops.
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Affiliation(s)
- Li Wang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany – Chinese Academy of Sciences, BeijingChina
| | - Jing Li
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany – Chinese Academy of Sciences, BeijingChina
- Graduate University of Chinese Academy of Sciences, BeijingChina
| | - Jing Zhao
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany – Chinese Academy of Sciences, BeijingChina
- Graduate University of Chinese Academy of Sciences, BeijingChina
| | - Chaoying He
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany – Chinese Academy of Sciences, BeijingChina
- *Correspondence: Chaoying He, State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany – Chinese Academy of Sciences, Nanxincun 20, Xiangshan, 100093 Beijing, China
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20
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Portis E, Cericola F, Barchi L, Toppino L, Acciarri N, Pulcini L, Sala T, Lanteri S, Rotino GL. Association Mapping for Fruit, Plant and Leaf Morphology Traits in Eggplant. PLoS One 2015. [PMID: 26284782 DOI: 10.1371/jounal.pone.0135200] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/27/2023] Open
Abstract
An eggplant (Solanum melongena) association panel of 191 accessions, comprising a mixture of breeding lines, old varieties and landrace selections was SNP genotyped and phenotyped for key breeding fruit and plant traits at two locations over two seasons. A genome-wide association (GWA) analysis was performed using the mixed linear model, which takes into account both a kinship matrix and the sub-population membership of the accessions. Overall, 194 phenotype/genotype associations were uncovered, relating to 30 of the 33 measured traits. These associations involved 79 SNP loci mapping to 39 distinct chromosomal regions distributed over all 12 eggplant chromosomes. A comparison of the map positions of these SNPs with those of loci derived from conventional linkage mapping showed that GWA analysis both validated many of the known controlling loci and detected a large number of new marker/trait associations. Exploiting established syntenic relationships between eggplant chromosomes and those of tomato and pepper recognized orthologous regions in ten eggplant chromosomes harbouring genes influencing breeders' traits.
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Affiliation(s)
- Ezio Portis
- Dipartimento di Scienze Agrarie, Forestali ed Alimentari (DISAFA)-Plant Genetics and Breeding, University of Torino, I-10095 Grugliasco, Torino, Italy
| | - Fabio Cericola
- Dipartimento di Scienze Agrarie, Forestali ed Alimentari (DISAFA)-Plant Genetics and Breeding, University of Torino, I-10095 Grugliasco, Torino, Italy; Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria-CREA, Research Unit for Vegetable Crops, I-26836 Montanaso Lombardo, Lodi, Italy
| | - Lorenzo Barchi
- Dipartimento di Scienze Agrarie, Forestali ed Alimentari (DISAFA)-Plant Genetics and Breeding, University of Torino, I-10095 Grugliasco, Torino, Italy
| | - Laura Toppino
- Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria-CREA, Research Unit for Vegetable Crops, I-26836 Montanaso Lombardo, Lodi, Italy
| | - Nazzareno Acciarri
- Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria-CREA, Research Unit for Vegetable Crops, I-63030 Monsampolo del Tronto, Ascoli Piceno, Italy
| | - Laura Pulcini
- Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria-CREA, Research Unit for Vegetable Crops, I-63030 Monsampolo del Tronto, Ascoli Piceno, Italy
| | - Tea Sala
- Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria-CREA, Research Unit for Vegetable Crops, I-26836 Montanaso Lombardo, Lodi, Italy
| | - Sergio Lanteri
- Dipartimento di Scienze Agrarie, Forestali ed Alimentari (DISAFA)-Plant Genetics and Breeding, University of Torino, I-10095 Grugliasco, Torino, Italy
| | - Giuseppe Leonardo Rotino
- Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria-CREA, Research Unit for Vegetable Crops, I-26836 Montanaso Lombardo, Lodi, Italy
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Cericola F, Portis E, Lanteri S, Toppino L, Barchi L, Acciarri N, Pulcini L, Sala T, Rotino GL. Linkage disequilibrium and genome-wide association analysis for anthocyanin pigmentation and fruit color in eggplant. BMC Genomics 2014; 15:896. [PMID: 25311640 PMCID: PMC4210512 DOI: 10.1186/1471-2164-15-896] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2014] [Accepted: 10/06/2014] [Indexed: 11/26/2022] Open
Abstract
Background The genome-wide association (GWA) approach represents an alternative to biparental linkage mapping for determining the genetic basis of trait variation. Both approaches rely on recombination to re-arrange the genome, and seek to establish correlations between phenotype and genotype. The major advantages of GWA lie in being able to sample a much wider range of the phenotypic and genotypic variation present, in being able to exploit multiple rounds of historical recombination in many different lineages and to include multiple accessions of direct relevance to crop improvement. Results A 191 accessions eggplant (Solanum melongena L.) association panel, comprising a mixture of breeding lines, old varieties and landrace selections originating from Asia and the Mediterranean Basin, was SNP genotyped and scored for anthocyanin pigmentation and fruit color at two locations over two years. The panel formed two major clusters, reflecting geographical provenance and fruit type. The global level of linkage disequilibrium was 3.4 cM. A mixed linear model appeared to be the most appropriate for GWA. A set of 56 SNP locus/phenotype associations was identified and the genomic regions harboring these loci were distributed over nine of the 12 eggplant chromosomes. The associations were compared with the location of known QTL for the same traits. Conclusion The GWA mapping approach was effective in validating a number of established QTL and, thanks to the wide diversity captured by the panel, was able to detect a series of novel marker/trait associations. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-896) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | - Ezio Portis
- Dipartimento di Scienze Agrarie, Forestali e Alimentari (DISAFA) - Plant Genetics and Breeding, University of Torino, Largo P, Braccini 2, I-10095 Grugliasco, Torino, Italy.
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22
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Portis E, Barchi L, Toppino L, Lanteri S, Acciarri N, Felicioni N, Fusari F, Barbierato V, Cericola F, Valè G, Rotino GL. QTL mapping in eggplant reveals clusters of yield-related loci and orthology with the tomato genome. PLoS One 2014; 9:e89499. [PMID: 24586828 PMCID: PMC3931786 DOI: 10.1371/journal.pone.0089499] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2013] [Accepted: 01/21/2014] [Indexed: 11/18/2022] Open
Abstract
In spite of its widespread cultivation and nutritional and economic importance, the eggplant (Solanum melongena L.) genome has not been extensively explored. A lack of knowledge of the patterns of inheritance of key agronomic traits has hindered the exploitation of marker technologies to accelerate its genetic improvement. An already established F2 intraspecific population of eggplant bred from the cross ‘305E40’ x ‘67/3’ was phenotyped for 20 agronomically relevant traits at two sites. Up to seven quantitative trait loci (QTL) per trait were identified and the percentage of the phenotypic variance (PV) explained per QTL ranged from 4 to 93%. Not all the QTL were detectable at both sites, but for each trait at least one major QTL (PV explained ≥10%) was identified. Although no detectable QTL x environment interaction was found, some QTL identified were location-specific. Many of the fruit-related QTL clustered within specific chromosomal regions, reflecting either linkage and/or pleiotropy. Evidence for putative tomato orthologous QTL/genes was obtained for several of the eggplant QTL. Information regarding the inheritance of key agronomic traits was obtained. Some of the QTL, along with their respective linked markers, may be useful in the context of marker-assisted breeding.
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Affiliation(s)
- Ezio Portis
- DISAFA - Plant Genetics and Breeding, University of Torino, Grugliasco, Torino, Italy
| | - Lorenzo Barchi
- DISAFA - Plant Genetics and Breeding, University of Torino, Grugliasco, Torino, Italy
| | - Laura Toppino
- Consiglio per la Ricerca e Sperimentazione in Agricoltura - CRA-ORL, Research Unit for Vegetable Crops, Montanaso Lombardo, Lodi, Italy
| | - Sergio Lanteri
- DISAFA - Plant Genetics and Breeding, University of Torino, Grugliasco, Torino, Italy
| | - Nazzareno Acciarri
- Consiglio per la Ricerca e Sperimentazione in Agricoltura - CRA-ORA, Research Unit for Vegetable Crops, Monsampolo del Tronto, Ascoli Piceno, Italy
| | - Nazzareno Felicioni
- Consiglio per la Ricerca e Sperimentazione in Agricoltura - CRA-ORA, Research Unit for Vegetable Crops, Monsampolo del Tronto, Ascoli Piceno, Italy
| | - Fabio Fusari
- Consiglio per la Ricerca e Sperimentazione in Agricoltura - CRA-ORA, Research Unit for Vegetable Crops, Monsampolo del Tronto, Ascoli Piceno, Italy
| | - Valeria Barbierato
- Consiglio per la Ricerca e Sperimentazione in Agricoltura - CRA-ORL, Research Unit for Vegetable Crops, Montanaso Lombardo, Lodi, Italy
| | - Fabio Cericola
- DISAFA - Plant Genetics and Breeding, University of Torino, Grugliasco, Torino, Italy
| | - Giampiero Valè
- Consiglio per la Ricerca e Sperimentazione in Agricoltura - CRA-GPG, Genomic Research Centre, Fiorenzuola d'Arda, Piacenza, Italy ; Consiglio per la Ricerca e Sperimentazione in Agricoltura - CRA-RIS, Rice Research Unit, Vercelli, Italy
| | - Giuseppe Leonardo Rotino
- Consiglio per la Ricerca e Sperimentazione in Agricoltura - CRA-ORL, Research Unit for Vegetable Crops, Montanaso Lombardo, Lodi, Italy
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Genome-wide identification, phylogeny and expression analysis of SUN, OFP and YABBY gene family in tomato. Mol Genet Genomics 2013; 288:111-29. [PMID: 23371549 DOI: 10.1007/s00438-013-0733-0] [Citation(s) in RCA: 123] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2012] [Accepted: 01/09/2013] [Indexed: 01/25/2023]
Abstract
Members of the plant-specific gene families IQD/SUN, OFP and YABBY are thought to play important roles in plant growth and development. YABBY family members are involved in lateral organ polarity and growth; OFP members encode transcriptional repressors, whereas the role of IQD/SUN members is less clear. The tomato fruit shape genes SUN, OVATE, and FASCIATED belong to IQD/SUN, OFP and the YABBY gene family, respectively. A gene duplication resulting in high expression of SUN leads to elongated fruit, whereas a premature stop codon in OVATE and a large inversion within FASCIATED control fruit elongation and a flat fruit shape, respectively. In this study, we identified 34 SlSUN, 31 SlOFP and 9 SlYABBY genes in tomato and identified their position on 12 chromosomes. Genome mapping analysis showed that the SlSUN, SlOFP, and SlYABBY genes were enriched on the top and bottom segments of several chromosomes. In particular, on chromosome 10, a cluster of SlOFPs were found to originate from tandem duplication events. We also constructed three phylogenetic trees based on the protein sequences of the IQ67, OVATE and YABBY domains, respectively, from members of these families in Arabidopsis and tomato. The closest putative orthologs of the Arabidopsis and tomato genes were determined by the position on the phylogenetic tree and sequence similarity. Furthermore, expression analysis showed that some family members exhibited tissue-specific expression, whereas others were more ubiquitously expressed. Also, certain family members overlapped with known QTLs controlling fruit shape in Solanaceous plants. Combined, these results may help elucidate the roles of SUN, OFP and YABBY family members in plant growth and development.
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Liao PC, Tsai CC, Chou CH, Chiang YC. Introgression between cultivars and wild populations of Momordica charantia L. (Cucurbitaceae) in Taiwan. Int J Mol Sci 2012; 13:6469-6491. [PMID: 22754378 PMCID: PMC3382758 DOI: 10.3390/ijms13056469] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2012] [Revised: 05/16/2012] [Accepted: 05/18/2012] [Indexed: 11/16/2022] Open
Abstract
The landrace strains of Momordica charantia are widely cultivated vegetables throughout the tropics and subtropics, but not in Taiwan, a continental island in Southeast Asia, until a few hundred years ago. In contrast, the related wild populations with smaller fruit sizes are native to Taiwan. Because of the introduction of cultivars for agricultural purposes, these two accessions currently exhibit a sympatric or parapatric distribution in Taiwan. In this study, the cultivars and wild samples from Taiwan, India, and Korea were collected for testing of their hybridization and evolutionary patterns. The cpDNA marker showed a clear distinction between accessions of cultivars and wild populations of Taiwan and a long divergence time. In contrast, an analysis of eight selectively neutral nuclear microsatellite loci did not reveal a difference between the genetic structures of these two accessions. A relatively short divergence time and frequent but asymmetric gene flows were estimated based on the isolation-with-migration model. Historical and current introgression from cultivars to wild populations of Taiwan was also inferred using MIGRATE-n and BayesAss analyses. Our results showed that these two accessions shared abundant common ancestral polymorphisms, and the timing of the divergence and colonization of the Taiwanese wild populations is consistent with the geohistory of the Taiwan Strait land bridge of the Last Glacial Maximum (LGM). Long-term and recurrent introgression between accessions indicated the asymmetric capacity to receive foreign genes from other accessions. The modern introduction of cultivars of M. charantia during the colonization of Taiwan by the Han Chinese ethnic group enhanced the rate of gene replacement in the native populations and resulted in the loss of native genes.
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Affiliation(s)
- Pei-Chun Liao
- Department of Biological Science and Technology, National Pingtung University of Science and Technology, Pingtung 912, Taiwan; E-Mail:
| | - Chi-Chu Tsai
- Kaohsiung District Agricultural Research and Extension Station, Council of Agriculture, Pingtung 908, Taiwan; E-Mail:
| | - Chang-Hung Chou
- Research Center for Biodiversity, China Medical University, Taichung 404, Taiwan; E-Mail:
| | - Yu-Chung Chiang
- Department of Biological Sciences, National Sun Yat-sen University, Kaohsiung 804, Taiwan
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Miyatake K, Saito T, Negoro S, Yamaguchi H, Nunome T, Ohyama A, Fukuoka H. Development of selective markers linked to a major QTL for parthenocarpy in eggplant (Solanum melongena L.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2012; 124:1403-13. [PMID: 22301906 DOI: 10.1007/s00122-012-1796-8] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2011] [Accepted: 01/05/2012] [Indexed: 05/23/2023]
Abstract
Parthenocarpy, the ability to set fruits without pollination, is a useful trait for setting fruit under unfavorable conditions. To identify the loci controlling parthenocarpy in eggplant (Solanum melongena L.), we constructed linkage maps by using co-dominant simple sequence repeat and single nucleotide polymorphism markers in F(2) populations derived from intraspecific crosses between two non-parthenocarpic lines (LS1934 and Nakate-Shinkuro) and a parthenocarpic line (AE-P03). Total map distances were 1,414.6 cM (ALF2: LS1934 x AE-P03) and 1,153.8 cM (NAF2: Nakate-Shinkuro x AE-P03), respectively. Quantitative trait locus (QTL) analyses revealed two QTLs on chromosomes 3 and 8, which we denoted as Controlling parthenocarpy3.1 (Cop3.1) and Cop8.1, respectively. The percentage of phenotypic variance explained (PVE) of Cop3.1 was 6.3% in ALF2 (LOD = 4.2) and 10.6% in NAF2 (LOD = 3.0). The PVE of Cop8.1 was 45.7% in ALF2 (LOD = 23.8) and 29.7% in NAF2 (LOD = 7.9). Using a population of backcross inbred lines, we confirmed the effect of Cop8.1, but there was no evidence to support the contribution of Cop3.1. We need to verify the effect of Cop3.1 under various temperature conditions. In addition, we clarified the effectiveness of selective SSR markers, emf21H22 and emh11J10, mapped on each side of Cop8.1 in other F(2) populations derived from various parental combinations. This is the first report concerning QTL analysis of parthenocarpy in eggplant using molecular markers. It will be useful in marker-assisted selection and in revealing the genomic mechanism underlying parthenocarpy in eggplant.
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Affiliation(s)
- Koji Miyatake
- NARO Institute of Vegetable and Tea Science, 360 Kusawa, Ano, Tsu, Mie 514-2392, Japan.
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26
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Remigereau MS, Lakis G, Rekima S, Leveugle M, Fontaine MC, Langin T, Sarr A, Robert T. Cereal domestication and evolution of branching: evidence for soft selection in the Tb1 orthologue of pearl millet (Pennisetum glaucum [L.] R. Br.). PLoS One 2011; 6:e22404. [PMID: 21799845 PMCID: PMC3142148 DOI: 10.1371/journal.pone.0022404] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2011] [Accepted: 06/21/2011] [Indexed: 01/13/2023] Open
Abstract
BACKGROUND During the Neolithic revolution, early farmers altered plant development to domesticate crops. Similar traits were often selected independently in different wild species; yet the genetic basis of this parallel phenotypic evolution remains elusive. Plant architecture ranks among these target traits composing the domestication syndrome. We focused on the reduction of branching which occurred in several cereals, an adaptation known to rely on the major gene Teosinte-branched1 (Tb1) in maize. We investigate the role of the Tb1 orthologue (Pgtb1) in the domestication of pearl millet (Pennisetum glaucum), an African outcrossing cereal. METHODOLOGY/PRINCIPAL FINDINGS Gene cloning, expression profiling, QTL mapping and molecular evolution analysis were combined in a comparative approach between pearl millet and maize. Our results in pearl millet support a role for PgTb1 in domestication despite important differences in the genetic basis of branching adaptation in that species compared to maize (e.g. weaker effects of PgTb1). Genetic maps suggest this pattern to be consistent in other cereals with reduced branching (e.g. sorghum, foxtail millet). Moreover, although the adaptive sites underlying domestication were not formerly identified, signatures of selection pointed to putative regulatory regions upstream of both Tb1 orthologues in maize and pearl millet. However, the signature of human selection in the pearl millet Tb1 is much weaker in pearl millet than in maize. CONCLUSIONS/SIGNIFICANCE Our results suggest that some level of parallel evolution involved at least regions directly upstream of Tb1 for the domestication of pearl millet and maize. This was unanticipated given the multigenic basis of domestication traits and the divergence of wild progenitor species for over 30 million years prior to human selection. We also hypothesized that regular introgression of domestic pearl millet phenotypes by genes from the wild gene pool could explain why the selective sweep in pearl millet is softer than in maize.
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Affiliation(s)
- Marie-Stanislas Remigereau
- Laboratoire Ecologie, Systématique et Evolution, Université Paris-Sud XI, Orsay, France
- Institut de Biotechnologie des Plantes, Université Paris-Sud XI, Orsay, France
| | - Ghayas Lakis
- Laboratoire Ecologie, Systématique et Evolution, Université Paris-Sud XI, Orsay, France
| | - Samah Rekima
- Laboratoire Ecologie, Systématique et Evolution, Université Paris-Sud XI, Orsay, France
| | - Magalie Leveugle
- Laboratoire Ecologie, Systématique et Evolution, Université Paris-Sud XI, Orsay, France
| | - Michaël C. Fontaine
- Laboratoire Ecologie, Systématique et Evolution, Université Paris-Sud XI, Orsay, France
| | - Thierry Langin
- Institut de Biotechnologie des Plantes, Université Paris-Sud XI, Orsay, France
| | - Aboubakry Sarr
- Laboratoire Ecologie, Systématique et Evolution, Université Paris-Sud XI, Orsay, France
- Université Pierre et Marie Curie, Paris, France
| | - Thierry Robert
- Laboratoire Ecologie, Systématique et Evolution, Université Paris-Sud XI, Orsay, France
- Université Pierre et Marie Curie, Paris, France
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Pérez-Pérez JM, Esteve-Bruna D, Micol JL. QTL analysis of leaf architecture. JOURNAL OF PLANT RESEARCH 2010; 123:15-23. [PMID: 19885640 DOI: 10.1007/s10265-009-0267-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2009] [Accepted: 09/16/2009] [Indexed: 05/09/2023]
Abstract
Leaf size and shape define the photosynthetic capability of a plant and have a significant impact on important agronomic traits, such as yield, quality, disease resistance and stress responses. Cultivated varieties of many plant species show remarkable variations in leaf morphology. Such variation usually exhibits a continuous phenotypic distribution and is controlled by the interaction of multiple genes known as quantitative trait loci (QTL). Here, we review several studies that evaluate natural variations in the leaf morphologies of crop species, as well as in the model plant Arabidopsis thaliana. The use of high-throughput, genome-wide approaches such as transcriptomics and metabolomics is helping to identify the nucleotide polymorphism(s) responsible for the phenotypic differences attributed to some of these QTL.
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Grover A, Ramesh B, Sharma PC. Development of microsatellite markers in potato and their transferability in some members of Solanaceae. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2009; 15:343-58. [PMID: 23572945 PMCID: PMC3550351 DOI: 10.1007/s12298-009-0039-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
We have developed thirty new microsatellite markers in potato by screening genomic libraries and ESTs. Genomic libraries of potato cultivar Kufri Bahar were screened for sequences containing microsatellite motifs GA, GT, ACA, ATC, GAA, TAA and GATA. Using flanking sequences, PCR primers were designed for microsatellites identified from genomic libraries and ESTs. Sixteen new primer pairs from genomic libraries and fourteen from ESTs along with seven previously published primer pairs amplified PCR products in the selected genotypes comprising of 65 Solanum tuberosum lines and 14 other species of the potato gene pool. Neighbor-joining tree based on genetic distance matrix developed using microsatellite markers successfully distinguished all these genotypes in the expected size range. Seventeen microsatellites could also be cross-amplified in at least one of the five members of solanaceae, namely tomato, eggplant, pepper, petunia and tobacco. The new microsatellite markers obtained in this study will be useful in various genetic and taxonomic studies in potato and related genomes.
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Affiliation(s)
- Atul Grover
- />University School of Biotechnology, Guru Gobind Singh Indraprastha University, Kashmere Gate, Delhi, 110 403 India
| | - B. Ramesh
- />Department of Genetics and Plant Breeding, Chaudhary Charan Singh University, Meerut, 250 004 India
| | - P. C. Sharma
- />University School of Biotechnology, Guru Gobind Singh Indraprastha University, Kashmere Gate, Delhi, 110 403 India
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Gupta V, Mathur S, Solanke AU, Sharma MK, Kumar R, Vyas S, Khurana P, Khurana JP, Tyagi AK, Sharma AK. Genome analysis and genetic enhancement of tomato. Crit Rev Biotechnol 2009; 29:152-81. [PMID: 19319709 DOI: 10.1080/07388550802688870] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The Solanaceae is an important family of vegetable crops, ornamentals and medicinal plants. Tomato has served as a model member of this family largely because of its enriched cytogenetic, genetic, as well as physical, maps. Mapping has helped in cloning several genes of importance such as Pto, responsible for resistance against bacterial speck disease, Mi-1.2 for resistance against nematodes, and fw2.2 QTL for fruit weight. A high-throughput genome-sequencing program has been initiated by an international consortium of 10 countries. Since heterochromatin has been found to be concentrated near centromeres, the consortium is focusing on sequencing only the gene-rich euchromatic region. Genomes of the members of Solanaceae show a significant degree of synteny, suggesting that the tomato genome sequence would help in the cloning of genes for important traits from other Solanaceae members as well. ESTs from a large number of cDNA libraries have been sequenced, and microarray chips, in conjunction with wide array of ripening mutants, have contributed immensely to the understanding of the fruit-ripening phenomenon. Work on the analysis of the tomato proteome has also been initiated. Transgenic tomato plants with improved abiotic stress tolerance, disease resistance and insect resistance, have been developed. Attempts have also been made to develop tomato as a bioreactor for various pharmaceutical proteins. However, control of fruit quality and ripening remains an active and challenging area of research. Such efforts should pave the way to improve not only tomato, but also other solanaceous crops.
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Affiliation(s)
- Vikrant Gupta
- Interdisciplinary Centre for Plant Genomics, Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, India
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Barchi L, Lefebvre V, Sage-Palloix AM, Lanteri S, Palloix A. QTL analysis of plant development and fruit traits in pepper and performance of selective phenotyping. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2009; 118:1157-71. [PMID: 19219599 DOI: 10.1007/s00122-009-0970-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2008] [Accepted: 01/15/2009] [Indexed: 05/03/2023]
Abstract
A QTL analysis was performed to determine the genetic basis of 13 horticultural traits conditioning yield in pepper (Capsicum annuum). The mapping population was a large population of 297 recombinant inbred lines (RIL) originating from a cross between the large-fruited bell pepper cultivar 'Yolo Wonder' and the small-fruited chilli pepper 'Criollo de Morelos 334'. A total of 76 QTLs were detected for 13 fruit and plant traits, grouped in 28 chromosome regions. These QTLs explained together between 7% (internode growth time) and 91% (fruit diameter) of the phenotypic variation. The QTL analysis was also performed on two subsets of 141 and 93 RILs sampled using the MapPop software. The smaller populations allowed for the detection of a reduced set of QTLs and reduced the overall percentage of trait variation explained by QTLs. The frequency of false positives as well as the individual effect of QTLs increased in reduced population sets as a result of reduced sampling. The results from the QTL analysis permitted an overall glance over the genetic architecture of traits considered by breeders for selection. Colinearities between clusters of QTLs controlling fruit traits and/or plant development in distinct pepper species and in related solanaceous crop species (tomato and eggplant) suggests that shared mechanisms control the shape and growth of different organs throughout these species.
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Affiliation(s)
- Lorenzo Barchi
- INRA-Avignon, UR 1052, Génétique et Amélioration des Fruits et Légumes, BP 94, 84143, Montfavet Cedex, France
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Rothan C, Causse M. Natural and artificially induced genetic variability in crop and model plant species for plant systems biology. EXS 2007; 97:21-53. [PMID: 17432262 DOI: 10.1007/978-3-7643-7439-6_2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
The sequencing of plant genomes which was completed a few years ago for Arabidopsis thaliana and Oryza sativa is currently underway for numerous crop plants of commercial value such as maize, poplar, tomato grape or tobacco. In addition, hundreds of thousands of expressed sequence tags (ESTs) are publicly available that may well represent 40-60% of the genes present in plant genomes. Despite its importance for life sciences, genome information is only an initial step towards understanding gene function (functional genomics) and deciphering the complex relationships between individual genes in the framework of gene networks. In this chapter we introduce and discuss means of generating and identifying genetic diversity, i.e., means to genetically perturb a biological system and to subsequently analyse the systems response, e.g., the changes in plant morphology and chemical composition. Generating and identifying genetic diversity is in its own right a highly powerful resource of information and is established as an invaluable tool for systems biology.
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Affiliation(s)
- Christophe Rothan
- INRA-UMR 619 Biologie des Fruits, IBVI-INRA Bordeaux, BP 81, 71 Av. EdouardBourlaux, 33883 Villenave d'Ornon, France.
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Hancock JF. Contributions of domesticated plant studies to our understanding of plant evolution. ANNALS OF BOTANY 2005; 96:953-63. [PMID: 16159942 PMCID: PMC4247096 DOI: 10.1093/aob/mci259] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2005] [Revised: 06/08/2005] [Accepted: 07/29/2005] [Indexed: 05/04/2023]
Abstract
BACKGROUND Plant evolutionary theory has been greatly enriched by studies on crop species. Over the last century, important information has been generated on many aspects of population biology, speciation and polyploid genetics. SCOPE Searches for quantitative trait loci (QTL) in crop species have uncovered numerous blocks of genes that have dramatic effects on adaptation, particularly during the domestication process. Many of these QTL have epistatic and pleiotropic effects making rapid evolutionary change possible. Most of the pioneering work on the molecular basis of self-incompatibility has been conducted on crop species, along with the sequencing of the phytopathogenic resistance genes (R genes) responsible for the 'gene-to-gene' relations of coevolution observed in host-pathogen relationships. Some of the better examples of co-adaptation and early acting inbreeding depression have also been elucidated in crops. Crop-wild progenitor interactions have provided rich opportunities to study the evolution of novel adaptations subsequent to hybridization. Most crop/wild F1 hybrids have reduced fitness, but in some instances the crop relatives have acquired genes that make them more efficient weeds through crop mimicry. Studies on autopolyploid alfalfa and potato have uncovered the means by which polyploid gametes are formed and have led to hypotheses about how multiallelic interactions are associated with fitness and self-fertility. Research on the cole crops and wheat has discovered that newly formed polyploids can undergo dramatic genome rearrangements that could lead to rapid evolutionary change. CONCLUSIONS Many more important evolutionary discoveries are on the horizon, now that the whole genome sequence is available of the two major subspecies of rice Oryza sativa ssp. japonica and O. sativa ssp. indica. The rice sequence data can be used to study the origin of genes and gene families, track rates of sequence divergence over time, and provide hints about how genes evolve and generate products with novel biological properties. The rice sequence data has already been mined to show that transposable elements often carry fragments of cellular genes. This type of genome shuffling could play a role in creating novel, reorganized genes with new adaptive properties.
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Affiliation(s)
- James F Hancock
- Department of Horticulture, Michigan State University, East Lansing, MI 49924, USA.
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Moore S, Payton P, Wright M, Tanksley S, Giovannoni J. Utilization of tomato microarrays for comparative gene expression analysis in the Solanaceae. JOURNAL OF EXPERIMENTAL BOTANY 2005; 56:2885-95. [PMID: 16216847 DOI: 10.1093/jxb/eri283] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Transcriptional profiling allows for the assessment and comparison of cross-species gene activity and function on a comprehensive scale. The Solanaceae is a large, diverse dicot family, with well-established genetic relationships between major crop species (tomato, potato, pepper, eggplant, and tobacco). Although Arabidopsis thaliana is often the model of choice for anchoring comparative studies, certain biological processes are better examined in other plants. The ripening of fleshy fruits is not tractable in Arabidopsis; however, it has received considerable attention in tomato. As a member of the Solanaceae, tomato provides a well-characterized system to anchor transcriptional profiles of fruit ripening and development in related species. By utilizing different stages of tomato, pepper, and eggplant fruit, the use of tomato microarrays for expression analysis has been demonstrated in closely related heterologous species, and groups of candidate expressed sequence tags, which are useful as orthologous markers, have been identified, as well as genes implicated in fruit ripening and development in the Solanaceae.
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Affiliation(s)
- Shanna Moore
- Department of Plant Biology, Cornell University, Ithaca, NY 14853, USA
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Abstract
Plant domestication ranks as one of the most important developments in human history, giving human populations the potential to harness unprecedented quantities of the earth's resources. But domestication has also played a more subtle historical role as the foundation of the modern study of evolution and adaptation. Until recently, however, researchers interested in domestication were limited to studying phenotypic changes or the genetics of simple Mendelian traits, when often the characters of most interest--fruit size, yield, height, flowering time, etc.--are quantitative in nature. The goals of this paper are to review some of the recent work on the quantitative genetics of plant domestication, identify some of the common trends found in this literature, and offer some novel interpretations of the data that is currently available.
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Ruffel S, Gallois JL, Lesage ML, Caranta C. The recessive potyvirus resistance gene pot-1 is the tomato orthologue of the pepper pvr2-eIF4E gene. Mol Genet Genomics 2005; 274:346-53. [PMID: 15971038 DOI: 10.1007/s00438-005-0003-x] [Citation(s) in RCA: 101] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2005] [Accepted: 04/27/2005] [Indexed: 10/25/2022]
Abstract
The translation initiation factor 4E (eIF4E) has been implicated in naturally occurring resistance to Potato virus Y (PVY) determined by the pvr2 locus in pepper (Capsicum annuum). Here, the molecular basis of the recessive resistance to PVY and Tobacco etch virus (TEV) controlled by the pot-1 locus in tomato (Lycopersicon esculentum; now Solanum lycopersicum) was investigated. On the basis of genetic mapping data that indicated that pot-1 and pvr2 are located in syntenic regions of the tomato and pepper genomes, the possible involvement of eIF4E in pot-1-mediated resistance was assessed. Genetic mapping of members of the eIF4E multigenic family in tomato introgression lines revealed that an eIF4E locus indeed maps in the same genomic region as pot-1. By comparing eIF4E coding sequences between resistant and susceptible Lycopersicon genotypes, a small number of polymorphisms that co-segregate with the pot-1 locus were identified, suggesting that this gene could be involved in resistance to potyviruses. Functional complementation experiments using Potato virus X-mediated transient expression of eIF4E from a susceptible genotype in a resistant pepper genotype confirmed that a small number of amino acid substitutions in the eIF4E protein indeed account for resistance/susceptibility to both the PVY and TEV, and consequently that pot-1 and pvr2 are orthologues. Taken together, these results support the role of this eIF4E gene as a key component of recessive resistance to potyviruses, and validate the comparative genomic approach for the molecular characterization of recessive resistance genes.
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Affiliation(s)
- S Ruffel
- Institut National de la Recherche Agronomique, Genetics and Breeding of Fruits and Vegetables, Dom. St Maurice, BP94, 84143, Montfavet Cedex, France
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Frary A, Fritz LA, Tanksley SD. A comparative study of the genetic bases of natural variation in tomato leaf, sepal, and petal morphology. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2004; 109:523-33. [PMID: 15150691 DOI: 10.1007/s00122-004-1669-x] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2004] [Accepted: 03/20/2004] [Indexed: 05/22/2023]
Abstract
In an effort to better understand the dramatic differences in vegetative and floral morphology that differentiate species within the genus Lycopersicon, quantitative trait loci (QTL) for leaflet and perianth size and shape characters were mapped in an interspecific F2 population of tomato (Lycopersicon esculentum x L. pennellii). Thirty-six highly significant (P < or = 0.001) QTL were associated with 18 separate traits. QTL for correlated traits were generally not colocalized in the genome unless there was a clear codependence between the traits (e.g., organ length and area). Little or no overlap in QTL positioning between different organs was observed, suggesting that the genes determining the size and shape of leaflets, sepals, and petals are organ specific. Thus, while leaves are considered the developmental and evolutionary precursors to floral organs, genes acting late in development to determine certain aspects of morphology (namely shape and size) must have specialized to exert control over individual organs. Five of the leaflet-trait QTL map to analogous regions in the genome of eggplant, and therefore it appears there has been some conservation in the genes controlling leaf morphology within the Solanaceae.
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Affiliation(s)
- Amy Frary
- Department of Biological Sciences, Mount Holyoke College, South Hadley, MA 01075, USA.
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Frary A, Fulton TM, Zamir D, Tanksley SD. Advanced backcross QTL analysis of a Lycopersicon esculentum x L. pennellii cross and identification of possible orthologs in the Solanaceae. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2004; 108:485-496. [PMID: 14740082 DOI: 10.1007/s00122-003-1422-x] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2003] [Accepted: 07/04/2003] [Indexed: 05/24/2023]
Abstract
In this study, the advanced backcross QTL (AB-QTL) mapping strategy was used to identify loci for yield, processing and fruit quality traits in a population derived from the interspecific cross Lycopersicon esculentum E6203 x Lycopersicon pennellii accession LA1657. A total of 175 BC(2) plants were genotyped with 150 molecular markers and BC(2)F(1) plots were grown and phenotyped for 25 traits in three locations in Israel and California, U.S.A. A total of 84 different QTLs were identified, 45% of which have been possibly identified in other wild-species-derived populations of tomato. Moreover, three fruit-weight/size and shape QTLs ( fsz2b.1, fw3.1/ fsz3.1 and fs8.1) appear to have putative orthologs in the related solanaceous species, pepper and eggplant. For the 23 traits for which allelic effects could be deemed as favorable or unfavorable, 26% of the identified loci had L. pennellii alleles that enhanced the performance of the elite parent. Alleles that could be targeted for further introgression into cultivated tomato were also identified.
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Affiliation(s)
- A Frary
- Department of Biology, Izmir Institute of Technology, Urla, 35437, Izmir, Turkey
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Doganlar S, Frary A, Daunay MC, Lester RN, Tanksley SD. Conservation of gene function in the solanaceae as revealed by comparative mapping of domestication traits in eggplant. Genetics 2002. [PMID: 12196413 DOI: 10.1007/s10681-014-1234-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/27/2023] Open
Abstract
Quantitative trait loci (QTL) for domestication-related traits were identified in an interspecific F(2) population of eggplant (Solanum linnaeanum x S. melongena). Although 62 quantitative trait loci (QTL) were identified in two locations, most of the dramatic phenotypic differences in fruit weight, shape, color, and plant prickliness that distinguish cultivated eggplant from its wild relative could be attributed to six loci with major effects. Comparison of the genomic locations of the eggplant fruit weight, fruit shape, and color QTL with the positions of similar loci in tomato, potato, and pepper revealed that 40% of the different loci have putative orthologous counterparts in at least one of these other crop species. Overall, the results suggest that domestication of the Solanaceae has been driven by mutations in a very limited number of target loci with major phenotypic effects, that selection pressures were exerted on the same loci despite the crops' independent domestications on different continents, and that the morphological diversity of these four crops can be explained by divergent mutations at these loci.
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Affiliation(s)
- Sami Doganlar
- Department of Plant Breeding and Department of Plant Biology, Cornell University, Ithaca, New York 14853, USA
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