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Ke C, Guan W, Jiang J, Huang L, Li H, Li W, Lin Y, Lin L, Xie X, Wu W, Gao W, Zheng Y. Map-based cloning of LPD, a major gene positively regulates leaf prickle development in eggplant. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2024; 137:216. [PMID: 39249556 DOI: 10.1007/s00122-024-04726-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2024] [Accepted: 08/21/2024] [Indexed: 09/10/2024]
Abstract
KEY MESSAGE A critical gene for leaf prickle development (LPD) in eggplant was mapped on chromosome E06 and was confirmed to be SmARF10B through RNA interference using a new genetic transformation technique called SACI developed in this study Prickles on eggplant pose challenges for agriculture and are undesirable in cultivated varieties. This study aimed to uncover the genetic mechanisms behind prickle formation in eggplant. Using the F2 and F2:3 populations derived from a cross between the prickly wild eggplant, YQ, and the prickle-free cultivated variety, YZQ, we identified a key genetic locus (LPD, leaf prickle development) on chromosome E06 associated with leaf prickle development through BSA-seq and QTL mapping. An auxin response factor gene, SmARF10B, was predicted as the candidate gene as it exhibited high expression in YQ's mature leaves, while being significantly low in YZQ. Downregulating SmARF10B in YQ through RNAi using a simple and efficient Agrobacterium-mediated genetic transformation method named Seedling Apical Cut Infection (SACI) developed in this study substantially reduced the size and density of leaf prickles, confirming the role of this gene in prickle development. Besides, an effective SNP was identified in SmARF10B, resulting in an amino acid change between YQ and YZQ. However, this SNP did not consistently correlate with prickle formation in eight other eggplant materials examined. This study sheds light on the pivotal role of SmARF10B in eggplant prickle development and introduces a new genetic transformation method for eggplant, paving the way for future research in this field.
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Affiliation(s)
- Changjiao Ke
- Fujian Provincial Key Laboratory of Crop Breeding by Design, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
- College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Wenxiang Guan
- Fujian Provincial Key Laboratory of Crop Breeding by Design, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
- College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Jialong Jiang
- Fujian Provincial Key Laboratory of Crop Breeding by Design, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
- College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Likun Huang
- Fujian Provincial Key Laboratory of Crop Breeding by Design, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
- College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Hui Li
- Fujian Provincial Key Laboratory of Crop Breeding by Design, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Wenjing Li
- Fujian Provincial Key Laboratory of Crop Breeding by Design, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
- College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yanyu Lin
- Fujian Provincial Key Laboratory of Crop Breeding by Design, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Lihui Lin
- Fujian Provincial Key Laboratory of Crop Breeding by Design, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
- College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Xiaofang Xie
- Fujian Provincial Key Laboratory of Crop Breeding by Design, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Weiren Wu
- Fujian Provincial Key Laboratory of Crop Breeding by Design, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China.
- Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China.
| | - Wenxia Gao
- College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China.
| | - Yan Zheng
- Fujian Provincial Key Laboratory of Crop Breeding by Design, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China.
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China.
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Zhang L, Zhang R, Yan P, Zeng L, Zhao W, Feng H, Mu R, Hou W. PE ( Prickly Eggplant) encoding a cytokinin-activating enzyme responsible for the formation of prickles in eggplant. HORTICULTURE RESEARCH 2024; 11:uhae134. [PMID: 38974191 PMCID: PMC11226868 DOI: 10.1093/hr/uhae134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/28/2024] [Accepted: 04/27/2024] [Indexed: 07/09/2024]
Abstract
Eggplant is one of the most important vegetables worldwide, with some varieties displaying prickles. These prickles, present on the leaves, stems, and fruit calyxes, posing challenges during cultivation, harvesting, and transportation, making them an undesirable agronomic trait. However, the genetic mechanisms underlying prickle morphogenesis in eggplant remain poorly understood, impeding genetic improvements. In this study, genetic analyses revealed that prickle morphogenesis is governed by a single dominant nuclear gene, termed PE (Prickly Eggplant). Subsequent bulk segregant RNA-sequencing (BSR-seq) and linkage analysis preliminarily mapped PE to chromosome 6. This locus was then fine mapped to a 9233 bp interval in a segregating population of 1109 plants, harboring only one candidate gene, SmLOG1, which encodes a LONELY GUY (LOG)-family cytokinin biosynthetic enzyme. Expression analyses via transcriptome and qRT-PCR demonstrate that SmLOG1 is predominantly expressed in immature prickles. CRISPR-Cas9 knockout experiments targeting SmLOG1 in prickly parental line 'PI 381159' abolished prickles across all tissues, confirming its critical role in prickle morphogenesis. Sequence analysis of SmLOG1 pinpointed variations solely within the non-coding region. We developed a cleaved amplified polymorphic sequences (CAPS) marker from a distinct SNP located at -735-bp within the SmLOG1 promoter, finding significant association with prickle variation in 190 eggplant germplasms. These findings enhance our understanding of the molecular mechanisms governing prickle development in eggplant and facilitate the use of marker-assisted selection (MAS) for breeding prickleless cultivars.
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Affiliation(s)
- Lei Zhang
- Jiangsu Key Laboratory of Phylogenomics and Comparative Genomics, Jiangsu International Joint Center of Genomics, School of Life Sciences, Jiangsu Normal University, Xuzhou 221100, Jiangsu Province, China
| | - Runzhi Zhang
- Jiangsu Key Laboratory of Phylogenomics and Comparative Genomics, Jiangsu International Joint Center of Genomics, School of Life Sciences, Jiangsu Normal University, Xuzhou 221100, Jiangsu Province, China
| | - Ping Yan
- Jiangsu Key Laboratory of Phylogenomics and Comparative Genomics, Jiangsu International Joint Center of Genomics, School of Life Sciences, Jiangsu Normal University, Xuzhou 221100, Jiangsu Province, China
| | - Liqian Zeng
- Jiangsu Key Laboratory of Phylogenomics and Comparative Genomics, Jiangsu International Joint Center of Genomics, School of Life Sciences, Jiangsu Normal University, Xuzhou 221100, Jiangsu Province, China
| | - Weiwei Zhao
- Jiangsu Key Laboratory of Phylogenomics and Comparative Genomics, Jiangsu International Joint Center of Genomics, School of Life Sciences, Jiangsu Normal University, Xuzhou 221100, Jiangsu Province, China
| | - Huiqian Feng
- Jiangsu Key Laboratory of Phylogenomics and Comparative Genomics, Jiangsu International Joint Center of Genomics, School of Life Sciences, Jiangsu Normal University, Xuzhou 221100, Jiangsu Province, China
| | - Ruyu Mu
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Wenqian Hou
- Jiangsu Key Laboratory of Phylogenomics and Comparative Genomics, Jiangsu International Joint Center of Genomics, School of Life Sciences, Jiangsu Normal University, Xuzhou 221100, Jiangsu Province, China
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Gramazio P, Alonso D, Arrones A, Villanueva G, Plazas M, Toppino L, Barchi L, Portis E, Ferrante P, Lanteri S, Rotino GL, Giuliano G, Vilanova S, Prohens J. Conventional and new genetic resources for an eggplant breeding revolution. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:6285-6305. [PMID: 37419672 DOI: 10.1093/jxb/erad260] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Accepted: 07/05/2023] [Indexed: 07/09/2023]
Abstract
Eggplant (Solanum melongena) is a major vegetable crop with great potential for genetic improvement owing to its large and mostly untapped genetic diversity. It is closely related to over 500 species of Solanum subgenus Leptostemonum that belong to its primary, secondary, and tertiary genepools and exhibit a wide range of characteristics useful for eggplant breeding, including traits adaptive to climate change. Germplasm banks worldwide hold more than 19 000 accessions of eggplant and related species, most of which have yet to be evaluated. Nonetheless, eggplant breeding using the cultivated S. melongena genepool has yielded significantly improved varieties. To overcome current breeding challenges and for adaptation to climate change, a qualitative leap forward in eggplant breeding is necessary. The initial findings from introgression breeding in eggplant indicate that unleashing the diversity present in its relatives can greatly contribute to eggplant breeding. The recent creation of new genetic resources such as mutant libraries, core collections, recombinant inbred lines, and sets of introgression lines will be another crucial element and will require the support of new genomics tools and biotechnological developments. The systematic utilization of eggplant genetic resources supported by international initiatives will be critical for a much-needed eggplant breeding revolution to address the challenges posed by climate change.
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Affiliation(s)
- Pietro Gramazio
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de València, Camino de Vera 14, 46022 Valencia, Spain
| | - David Alonso
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de València, Camino de Vera 14, 46022 Valencia, Spain
| | - Andrea Arrones
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de València, Camino de Vera 14, 46022 Valencia, Spain
| | - Gloria Villanueva
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de València, Camino de Vera 14, 46022 Valencia, Spain
| | - Mariola Plazas
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de València, Camino de Vera 14, 46022 Valencia, Spain
| | - Laura Toppino
- CREA Research Centre for Genomics and Bioinformatics, Via Paullese 28, 26836 Montanaso Lombardo, LO, Italy
| | - Lorenzo Barchi
- Dipartimento di Scienze Agrarie, Forestali e Alimentari (DISAFA), Plant Genetics, University of Turin, Largo P. Braccini 2, 10095 Grugliasco, TO, Italy
| | - Ezio Portis
- Dipartimento di Scienze Agrarie, Forestali e Alimentari (DISAFA), Plant Genetics, University of Turin, Largo P. Braccini 2, 10095 Grugliasco, TO, Italy
| | - Paola Ferrante
- Agenzia Nazionale Per Le Nuove Tecnologie, L'energia e Lo Sviluppo Economico Sostenibile (ENEA), Casaccia Research Centre, Rome, Italy
| | - Sergio Lanteri
- Dipartimento di Scienze Agrarie, Forestali e Alimentari (DISAFA), Plant Genetics, University of Turin, Largo P. Braccini 2, 10095 Grugliasco, TO, Italy
| | - Giuseppe Leonardo Rotino
- CREA Research Centre for Genomics and Bioinformatics, Via Paullese 28, 26836 Montanaso Lombardo, LO, Italy
| | - Giovanni Giuliano
- Agenzia Nazionale Per Le Nuove Tecnologie, L'energia e Lo Sviluppo Economico Sostenibile (ENEA), Casaccia Research Centre, Rome, Italy
| | - Santiago Vilanova
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de València, Camino de Vera 14, 46022 Valencia, Spain
| | - Jaime Prohens
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de València, Camino de Vera 14, 46022 Valencia, Spain
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Villanueva G, Plazas M, Gramazio P, Moya RD, Prohens J, Vilanova S. Evaluation of three sets of advanced backcrosses of eggplant with wild relatives from different gene pools under low N fertilization conditions. HORTICULTURE RESEARCH 2023; 10:uhad141. [PMID: 37575654 PMCID: PMC10421729 DOI: 10.1093/hr/uhad141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Accepted: 07/08/2023] [Indexed: 08/15/2023]
Abstract
The development of new cultivars with improved nitrogen use efficiency (NUE) is key for implementing sustainable agriculture practices. Crop wild relatives (CWRs) provide valuable genetic resources for breeding programs aimed at achieving this goal. In this study, three eggplant (Solanum melongena) accessions together with their advanced backcrosses (ABs; BC3 to BC5 generations) were evaluated for 22 morpho-agronomic, physiological, and NUE traits under low nitrogen (LN) fertilization conditions. The ABs were developed with introgressions from the wild relatives Solanum insanum, Solanum dasyphyllum, and Solanum elaeagnifolium. The AB population comprised a total of 25, 59, and 59 genotypes, respectively, with overall donor wild relative genome coverage percentages of 58.8%, 46.3%, and 99.2%. The three S. melongena recurrent parents were also evaluated under control (normal) N fertilization. Reduction of N fertilization in the parents resulted in decreased chlorophyll content-related traits, aerial biomass, stem diameter, and yield and increased NUE, nitrogen uptake efficiency (NUpE), and nitrogen utilization efficiency (NUtE). However, the decrease in yield was moderate, ranging between 62.6% and 72.6%. A high phenotypic variation was observed within each of the three sets of ABs under LN conditions, with some individuals displaying improved transgressive characteristics over the recurrent parents. Using the single primer enrichment technology 5 k probes platform for high-throughput genotyping, we observed a variable but high degree of recurrent parent genome recovery in the ABs attributable to the lines recombination, allowing the successful identification of 16 quantitative trait loci (QTL). Different allelic effects were observed for the introgressed QTL alleles. Several candidate genes were identified in the QTL regions associated with plant growth, yield, fruit size, and NUE-related parameters. Our results show that eggplant materials with introgressions from CWRs can result in a dramatic impact in eggplant breeding for a more sustainable agriculture.
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Affiliation(s)
- Gloria Villanueva
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de València, Camino de Vera 14, 46022, Valencia, Spain
| | - Mariola Plazas
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de València, Camino de Vera 14, 46022, Valencia, Spain
| | - Pietro Gramazio
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de València, Camino de Vera 14, 46022, Valencia, Spain
| | - Reyes D Moya
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de València, Camino de Vera 14, 46022, Valencia, Spain
| | - Jaime Prohens
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de València, Camino de Vera 14, 46022, Valencia, Spain
| | - Santiago Vilanova
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de València, Camino de Vera 14, 46022, Valencia, Spains
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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: 3] [Impact Index Per Article: 3.0] [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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You Q, Li H, Wu J, Li T, Wang Y, Sun G, Li Z, Sun B. Mapping and validation of the epistatic D and P genes controlling anthocyanin biosynthesis in the peel of eggplant ( Solanum melongena L.) fruit. HORTICULTURE RESEARCH 2023; 10:uhac268. [PMID: 36789254 PMCID: PMC9923212 DOI: 10.1093/hr/uhac268] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Accepted: 11/27/2022] [Indexed: 06/18/2023]
Abstract
Fruit color is an important trait influencing the commercial value of eggplant fruits. Three dominant genes (D, P and Y) cooperatively control the anthocyanin coloration in eggplant fruits, but none has been mapped. In this study, two white-fruit accessions (19 141 and 19 147) and their F2 progeny, with 9:7 segregation ratio of anthocyanin pigmented versus non-pigmented fruits, were used for mapping the D and P genes. A high-density genetic map was constructed with 5270 SNPs spanning 1997.98 cM. Three QTLs were identified, including two genes on chromosome 8 and one on chromosome 10. Gene expression analyses suggested that the SmANS on chromosome 8 and SmMYB1 on chromosome 10 were the putative candidate genes for P and D, respectively. We further identified (1) a SNP leading to a premature stop codon within the conserved PLN03176 domain of SmANS in 19 141, (2) a G base InDel in the promoter region leading to an additional cis-regulatory element and (3) a 6-bp InDel within the R2-MYB DNA binding domain of SmMYB1, in 19 147. Subsequently, these three variations were validated by PARMS technology as related to phenotypes in the F2 population. Moreover, silencing of SmANS or SmMYB1 in the purple red fruits of F1 (E3316) led to inhibition of anthocyanin biosynthesis in the peels. Conversely, overexpression of SmANS or SmMYB1 restored anthocyanin biosynthesis in the calli of 19 141 and 19 147 respectively. Our findings demonstrated the epistatic interactions underlying the white color of eggplant fruits, which can be potentially applied to breeding of eggplant fruit peel color.
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Affiliation(s)
| | | | | | - Tao Li
- Guangdong Key Laboratory for New Technology Research of Vegetables, Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, Guangdong 510640, China
| | - Yikui Wang
- Institute of Vegetable, Guangxi Academy of Agricultural Sciences, Nanning, Guangxi 530007, China
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Systematic trait dissection in oilseed rape provides a comprehensive view, further insight, and exact roadmap for yield determination. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2022; 15:38. [PMID: 35440054 PMCID: PMC9019968 DOI: 10.1186/s13068-022-02134-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Accepted: 04/03/2022] [Indexed: 11/10/2022]
Abstract
Background Yield is the most important and complex trait that is influenced by numerous relevant traits with very complicated interrelations. While there are a large number of studies on the phenotypic relationship and genetic basis of yield traits, systematic studies with further dissection focusing on yield are limited. Therefore, there is still lack of a comprehensive and in-depth understanding of the determination of yield. Results In this study, yield was systematically dissected at the phenotypic, genetic to molecular levels in oilseed rape (Brassica napus L.). The analysis of correlation, network, and principal component for 21 traits in BnaZN-RIL population showed that yield was determined by a complex trait network with key contributors. The analysis of the constructed high-density single nucleotide polymorphism (SNP) linkage map revealed the concentrated distribution of distorted and heterozygous markers, likely due to selection on genes controlling the growth period and yield heterosis. A total of 134 consensus quantitative trait loci (QTL) were identified for 21 traits, of which all were incorporated into an interconnecting QTL network with dozens of hub-QTL. Four representative hub-QTL were further dissected to the target or candidate genes that governed the causal relationships between the relevant traits. Conclusions The highly consistent results at the phenotypic, genetic, and molecular dissecting demonstrated that yield was determined by a multilayer composite network that involved numerous traits and genes showing complex up/down-stream and positive/negative regulation. This provides a systematic view, further insight, and exact roadmap for yield determination, which represents a significant advance toward the understanding and dissection of complex traits. Supplementary Information The online version contains supplementary material available at 10.1186/s13068-022-02134-w.
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Arrones A, Mangino G, Alonso D, Plazas M, Prohens J, Portis E, Barchi L, Giuliano G, Vilanova S, Gramazio P. Mutations in the SmAPRR2 transcription factor suppressing chlorophyll pigmentation in the eggplant fruit peel are key drivers of a diversified colour palette. FRONTIERS IN PLANT SCIENCE 2022; 13:1025951. [PMID: 36388476 PMCID: PMC9647125 DOI: 10.3389/fpls.2022.1025951] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Accepted: 10/03/2022] [Indexed: 06/01/2023]
Abstract
Understanding the mechanisms by which chlorophylls are synthesized in the eggplant (Solanum melongena) fruit peel is of great relevance for eggplant breeding. A multi-parent advanced generation inter-cross (MAGIC) population and a germplasm collection have been screened for green pigmentation in the fruit peel and used to identify candidate genes for this trait. A genome-wide association study (GWAS) performed with 420 MAGIC individuals revealed a major association on chromosome 8 close to a gene similar to APRR2. Two variants in SmAPRR2, predicted as having a high impact effect, were associated with the absence of fruit chlorophyll pigmentation in the MAGIC population, and a large deletion of 5.27 kb was found in two reference genomes of accessions without chlorophyll in the fruit peel. The validation of the candidate gene SmAPRR2 was performed by its sequencing in a set of MAGIC individuals and through its de novo assembly in 277 accessions from the G2P-SOL eggplant core collection. Two additional mutations in SmAPRR2 associated with the lack of chlorophyll were identified in the core collection set. The phylogenetic analysis of APRR2 reveals orthology within Solanaceae and suggests that specialization of APRR2-like genes occurred independently in Cucurbitaceae and Solanaceae. A strong geographical differentiation was observed in the frequency of predominant mutations in SmAPRR2, resulting in a lack of fruit chlorophyll pigmentation and suggesting that this phenotype may have arisen and been selected independently several times. This study represents the first identification of a major gene for fruit chlorophyll pigmentation in the eggplant fruit.
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Affiliation(s)
- Andrea Arrones
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de València, Valencia, Spain
| | - Giulio Mangino
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de València, Valencia, Spain
| | - David Alonso
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de València, Valencia, Spain
| | - Mariola Plazas
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de València, Valencia, Spain
| | - Jaime Prohens
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de València, Valencia, Spain
| | - Ezio Portis
- Dipartimento di Scienze Agrarie, Forestali e Alimentari (DISAFA), Plant Genetics and Breeding, University of Turin, Grugliasco, Italy
| | - Lorenzo Barchi
- Dipartimento di Scienze Agrarie, Forestali e Alimentari (DISAFA), Plant Genetics and Breeding, University of Turin, Grugliasco, Italy
| | - Giovanni Giuliano
- Agenzia Nazionale Per Le Nuove Tecnologie, L’energia e Lo Sviluppo Economico Sostenibile (ENEA), Casaccia Research Centre, Rome, Italy
| | - Santiago Vilanova
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de València, Valencia, Spain
| | - Pietro Gramazio
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-Universitat Politècnica de València, Valencia, Spain
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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: 2] [Impact Index Per Article: 1.0] [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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10
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Tassone MR, Bagnaresi P, Desiderio F, Bassolino L, Barchi L, Florio FE, Sunseri F, Sirangelo TM, Rotino GL, Toppino L. A Genomic BSAseq Approach for the Characterization of QTLs Underlying Resistance to Fusarium oxysporum in Eggplant. Cells 2022; 11:2548. [PMID: 36010625 PMCID: PMC9406753 DOI: 10.3390/cells11162548] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Revised: 08/12/2022] [Accepted: 08/12/2022] [Indexed: 11/17/2022] Open
Abstract
Eggplant (Solanum melongena L.), similar to many other crops, suffers from soil-borne diseases, including Fusarium oxysporum f. sp. melongenae (Fom), causing wilting and heavy yield loss. To date, the genetic factors underlying plant responses to Fom are not well known. We previously developed a Recombinant Inbred Lines (RILs) population using as a female parent the fully resistant line '305E40' and as a male parent the partially resistant line '67/3'. The fully resistant trait to Fom was introgressed from the allied species S. aethiopicum. In this work, the RIL population was assessed for the responses to Fom and by using a genomic mapping approach, two major QTLs on chromosomes CH02 and CH11 were identified, associated with the full and partial resistance trait to Fom, respectively. A targeted BSAseq procedure in which Illumina reads bulks of RILs grouped according to their resistance score was aligned to the appropriate reference genomes highlighted differentially enriched regions between resistant/susceptible progeny in the genomic regions underlying both QTLs. The characterization of such regions allowed us to identify the most reliable candidate genes for the two resistance traits. With the aim of revealing exclusive species-specific contigs and scaffolds inherited from the allied species and thus associated with the full resistance trait, a draft de-novo assembly of available Illumina sequences of the '305E40' parent was developed to better resolve the non-recombining genomic region on its CH02 carrying the introgressed Fom resistance locus from S. aethiopicum.
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Affiliation(s)
- Maria Rosaria Tassone
- Council for Agricultural Research and Economics, Genomics and Bioinformatics Research Center, 26836 Montanaso Lombardo, Italy
- Department of Agricultural Science, University Mediterranea of Reggio Calabria, 89124 Reggio Calabria, Italy
| | - Paolo Bagnaresi
- Council for Agricultural Research and Economics, Genomics and Bioinformatics Research Center, 29017 Fiorenzuola d’Arda, Italy
| | - Francesca Desiderio
- Council for Agricultural Research and Economics, Genomics and Bioinformatics Research Center, 29017 Fiorenzuola d’Arda, Italy
| | - Laura Bassolino
- Council for Agricultural Research and Economics, Genomics and Bioinformatics Research Center, 26836 Montanaso Lombardo, Italy
- Council for Agricultural Research and Economics, Cereal and Industrial Crops Research Center, 40128 Bologna, Italy
| | - Lorenzo Barchi
- DISAFA, Plant Genetics and Breeding, University of Turin, 10095 Grugliasco, Italy
| | - Francesco Elia Florio
- Council for Agricultural Research and Economics, Genomics and Bioinformatics Research Center, 26836 Montanaso Lombardo, Italy
| | - Francesco Sunseri
- Department of Agricultural Science, University Mediterranea of Reggio Calabria, 89124 Reggio Calabria, Italy
| | - Tiziana Maria Sirangelo
- Council for Agricultural Research and Economics, Genomics and Bioinformatics Research Center, 26836 Montanaso Lombardo, Italy
| | - Giuseppe Leonardo Rotino
- Council for Agricultural Research and Economics, Genomics and Bioinformatics Research Center, 26836 Montanaso Lombardo, Italy
| | - Laura Toppino
- Council for Agricultural Research and Economics, Genomics and Bioinformatics Research Center, 26836 Montanaso Lombardo, Italy
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11
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Florio FE, Gattolin S, Toppino L, Bassolino L, Fibiani M, Lo Scalzo R, Rotino GL. A SmelAAT Acyltransferase Variant Causes a Major Difference in Eggplant ( Solanum melongena L.) Peel Anthocyanin Composition. Int J Mol Sci 2021; 22:ijms22179174. [PMID: 34502081 PMCID: PMC8431300 DOI: 10.3390/ijms22179174] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 08/18/2021] [Accepted: 08/21/2021] [Indexed: 12/15/2022] Open
Abstract
Eggplant berries are rich in anthocyanins like delphinidin-3-rutinoside (D3R) and nasunin (NAS), which are accumulated at high amounts in the peel. NAS is derived by D3R through acylation and glycosylation steps. The presence of D3R or NAS is usually associated with black-purple or lilac fruit coloration of the most cultivated varieties, respectively. Building on QTL mapping position, a candidate gene approach was used to investigate the involvement of a BAHD anthocyanin acyltransferase (SmelAAT) in determining anthocyanin type. The cDNA sequence comparison revealed the presence of a single-base deletion in D3R-type line ‘305E40’ (305E40_aat) with respect to the NAS-type reference line ‘67/3’. This is predicted to cause a frame shift mutation, leading to a loss of SmelAAT function and, thus, D3R retention. RT-qPCR analyses confirmed SmelAAT and 305E40_aat expression during berry maturation. In D3R-type lines, ‘305E40’ and ‘DR2’, overexpressing the functional SmelAAT allele from ‘67/3’, the transcript levels of the transgene correlated with the accumulation of NAS in fruit peel. Furthermore, it was also found a higher expression of the transcript for glucosyltransferase Smel5GT1, putatively involved with SmelAAT in the last steps of anthocyanin decoration. Finally, an indel marker matching with anthocyanin type in the ‘305E40’ × ’67/3’ segregating population was developed and validated in a wide number of accessions, proving its usefulness for breeding purposes.
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Affiliation(s)
- Francesco Elia Florio
- CREA, Research Centre for Genomics and Bioinformatics, 26836 Montanaso Lombardo, Italy; (F.E.F.); (L.T.); (L.B.)
- Department of Agricultural and Environmental Sciences (DISAA), University of Milan, 20133 Milan, Italy
| | - Stefano Gattolin
- CREA, Research Centre for Genomics and Bioinformatics, 26836 Montanaso Lombardo, Italy; (F.E.F.); (L.T.); (L.B.)
- CNR—National Research Council of Italy, Institute of Agricultural Biology and Biotechnology (IBBA), 20133 Milan, Italy
- Correspondence: (S.G.); (G.L.R.); Tel.: +39-037-1466-2507 (S.G.); +39-33-9548-4825 (G.L.R.)
| | - Laura Toppino
- CREA, Research Centre for Genomics and Bioinformatics, 26836 Montanaso Lombardo, Italy; (F.E.F.); (L.T.); (L.B.)
| | - Laura Bassolino
- CREA, Research Centre for Genomics and Bioinformatics, 26836 Montanaso Lombardo, Italy; (F.E.F.); (L.T.); (L.B.)
- CREA, Research Centre for Cereal and Industrial Crops, 40128 Bologna, Italy
| | - Marta Fibiani
- CREA, Research Centre for Engineering and Agro-Food Processing, 20133 Milan, Italy; (M.F.); (R.L.S.)
| | - Roberto Lo Scalzo
- CREA, Research Centre for Engineering and Agro-Food Processing, 20133 Milan, Italy; (M.F.); (R.L.S.)
| | - Giuseppe Leonardo Rotino
- CREA, Research Centre for Genomics and Bioinformatics, 26836 Montanaso Lombardo, Italy; (F.E.F.); (L.T.); (L.B.)
- Correspondence: (S.G.); (G.L.R.); Tel.: +39-037-1466-2507 (S.G.); +39-33-9548-4825 (G.L.R.)
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12
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Mir R, Calabuig-Serna A, Seguí-Simarro JM. Doubled Haploids in Eggplant. BIOLOGY 2021; 10:685. [PMID: 34356540 PMCID: PMC8301345 DOI: 10.3390/biology10070685] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 07/15/2021] [Accepted: 07/15/2021] [Indexed: 11/17/2022]
Abstract
Eggplant is a solanaceous crop cultivated worldwide for its edible fruit. Eggplant breeding programs are mainly aimed to the generation of F1 hybrids by crossing two highly homozygous, pure lines, which are traditionally obtained upon several self crossing generations, which is an expensive and time consuming process. Alternatively, fully homozygous, doubled haploid (DH) individuals can be induced from haploid cells of the germ line in a single generation. Several attempts have been made to develop protocols to produce eggplant DHs principally using anther culture and isolated microspore culture. Eggplant could be considered a moderately recalcitrant species in terms of ability for DH production. Anther culture stands nowadays as the most valuable technology to obtain eggplant DHs. However, the theoretical possibility of having plants regenerated from somatic tissues of the anther walls cannot be ruled out. For this reason, the use of isolated microspores is recommended when possible. This approach still has room for improvement, but it is largely genotype-dependent. In this review, we compile the most relevant advances made in DH production in eggplant, their application to breeding programs, and the future perspectives for the development of other, less genotype-dependent, DH technologies.
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Affiliation(s)
| | | | - Jose M. Seguí-Simarro
- Cell Biology Group—COMAV Institute, Universitat Politècnica de València, 46011 Valencia, Spain; (R.M.); (A.C.-S.)
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13
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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: 45] [Impact Index Per Article: 15.0] [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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14
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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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15
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Mauceri A, Abenavoli MR, Toppino L, Panda S, Mercati F, Aci MM, Aharoni A, Sunseri F, Rotino GL, Lupini A. Transcriptomics reveal new insights into molecular regulation of nitrogen use efficiency in Solanum melongena. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:4237-4253. [PMID: 33711100 DOI: 10.1093/jxb/erab121] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Accepted: 03/11/2021] [Indexed: 06/12/2023]
Abstract
Nitrogen-use efficiency (NUE) is a complex trait of great interest in breeding programs because through its improvement, high crop yields can be maintained whilst N supply is reduced. In this study, we report a transcriptomic analysis of four NUE-contrasting eggplant (Solanum melongena) genotypes following short- and long-term exposure to low N, to identify key genes related to NUE in the roots and shoots. The differentially expressed genes in the high-NUE genotypes are involved in the light-harvesting complex and receptor, a ferredoxin-NADP reductase, a catalase and WRKY33. These genes were then used as bait for a co-expression gene network analysis in order to identify genes with the same trends in expression. This showed that up-regulation of WRKY33 triggered higher expression of a cluster of 21 genes and also of other genes, many of which were related to N-metabolism, that were able to improve both nitrogen uptake efficiency and nitrogen utilization efficiency, the two components of NUE. We also conducted an independent de novo experiment to validate the significantly higher expression of WRKY33 and its gene cluster in the high-NUE genotypes. Finally, examination of an Arabidopsis transgenic 35S::AtWRKY33 overexpression line showed that it had a bigger root system and was more efficient at taking up N from the soil, confirming the pivotal role of WRKY33 for NUE improvement.
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Affiliation(s)
- Antonio Mauceri
- Dipartimento Agraria, Università degli Studi Mediterranea di Reggio Calabria, Loc. Feo di Vito, Reggio Calabria, Italy
| | - Maria Rosa Abenavoli
- Dipartimento Agraria, Università degli Studi Mediterranea di Reggio Calabria, Loc. Feo di Vito, Reggio Calabria, Italy
| | - Laura Toppino
- CREA - Research Centre for Genomics and Bioinformatics, Via Paullese 28, Montanaso Lombardo, Italy
| | - Sayantan Panda
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Francesco Mercati
- Istituto di Bioscienze e Biorisorse CNR - Consiglio Nazionale Ricerche, Corso Calatafimi 414, Palermo, Italy
| | - Meriem Miyassa Aci
- Dipartimento Agraria, Università degli Studi Mediterranea di Reggio Calabria, Loc. Feo di Vito, Reggio Calabria, Italy
| | - Asaph Aharoni
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Francesco Sunseri
- Dipartimento Agraria, Università degli Studi Mediterranea di Reggio Calabria, Loc. Feo di Vito, Reggio Calabria, Italy
| | - Giuseppe Leonardo Rotino
- CREA - Research Centre for Genomics and Bioinformatics, Via Paullese 28, Montanaso Lombardo, Italy
| | - Antonio Lupini
- Dipartimento Agraria, Università degli Studi Mediterranea di Reggio Calabria, Loc. Feo di Vito, Reggio Calabria, Italy
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16
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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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17
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Comparative Transcriptome Analysis Reveals Key Genes and Pathways Involved in Prickle Development in Eggplant. Genes (Basel) 2021; 12:genes12030341. [PMID: 33668977 PMCID: PMC7996550 DOI: 10.3390/genes12030341] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Revised: 02/12/2021] [Accepted: 02/23/2021] [Indexed: 12/02/2022] Open
Abstract
Eggplant is one of the most important vegetables worldwide. Prickles on the leaves, stems and fruit calyxes of eggplant may cause difficulties during cultivation, harvesting and transportation, and therefore is an undesirable agronomic trait. However, limited knowledge about molecular mechanisms of prickle morphogenesis has hindered the genetic improvement of eggplant. In this study, we performed the phenotypic characterization and transcriptome analysis on prickly and prickleless eggplant genotypes to understand prickle development at the morphological and molecular levels. Morphological analysis revealed that eggplant prickles were multicellular, lignified and layered organs. Comparative transcriptome analysis identified key pathways and hub genes involved in the cell cycle as well as flavonoid biosynthetic, photosynthetic, and hormone metabolic processes during prickle development. Interestingly, genes associated with flavonoid biosynthesis were up-regulated in developing prickles, and genes associated with photosynthesis were down-regulated in developing and matured prickles. It was also noteworthy that several development-related transcription factors such as bHLH, C2H2, MYB, TCP and WRKY were specifically down- or up-regulated in developing prickles. Furthermore, four genes were found to be differentially expressed within the Pl locus interval. This study provides new insights into the regulatory molecular mechanisms underlying prickle morphogenesis in eggplant, and the genes identified might be exploited in breeding programs to develop prickleless eggplant cultivars.
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18
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Qian Z, Zhang B, Chen H, Lu L, Duan M, Zhou J, Cui Y, Li D. Identification of Quantitative Trait Loci Controlling the Development of Prickles in Eggplant by Genome Re-sequencing Analysis. FRONTIERS IN PLANT SCIENCE 2021; 12:731079. [PMID: 34567042 PMCID: PMC8457335 DOI: 10.3389/fpls.2021.731079] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2021] [Accepted: 08/06/2021] [Indexed: 05/17/2023]
Abstract
Eggplant (Solanum melongena L.) is the third most important crop in the family of Solanaceae. Prickles are considered as the undesirable traits during the plantation of eggplant and the transportation of fruits. In this study, we constructed a high-quality genetic linkage Bin map derived from the re-sequencing analysis on a cross of a prickly wild landrace, 17C01, and a cultivated variety, 17C02. The major quantitative trait locus (QTL) controlling the development of prickles on the calyx (explained 30.42% of the phenotypic variation), named as qPC.12, was identified on a ~7 kb region on chromosome 12. A gene within qPC.12, which encodes a WUSCHEL-related homeobox-like protein, with higher expression levels in 17C01 calyx and 22-bp deletion in 17C02 was probably the functional gene for prickle formation. Results from this study would ultimately facilitate uncovering the molecular regulatory mechanisms underlying the development of a prickle in eggplant.
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Affiliation(s)
- Zongwei Qian
- National Engineering Research Center for Vegetables, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Science, Beijing, China
- Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture and Rural Affairs of the P. R. China, Beijing, China
| | - Bin Zhang
- National Engineering Research Center for Vegetables, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Science, Beijing, China
- Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture and Rural Affairs of the P. R. China, Beijing, China
| | - Haili Chen
- National Engineering Research Center for Vegetables, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Science, Beijing, China
- Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture and Rural Affairs of the P. R. China, Beijing, China
| | - Lei Lu
- College of Life Science and Technology, Jining Normal University, Ulanqab, China
| | - Mengqi Duan
- Turf Research Institute, Beijing Forestry University, Beijing, China
| | - Jun Zhou
- College of Life Sciences, Shandong Normal University, Jinan, China
| | - Yanling Cui
- National Engineering Research Center for Vegetables, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Science, Beijing, China
- Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture and Rural Affairs of the P. R. China, Beijing, China
- *Correspondence: Yanling Cui
| | - Dayong Li
- National Engineering Research Center for Vegetables, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Science, Beijing, China
- Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture and Rural Affairs of the P. R. China, Beijing, China
- College of Life Sciences, Shandong Normal University, Jinan, China
- Dayong Li
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19
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Wei Q, Wang J, Wang W, Hu T, Hu H, Bao C. A high-quality chromosome-level genome assembly reveals genetics for important traits in eggplant. HORTICULTURE RESEARCH 2020; 7:153. [PMID: 33024567 PMCID: PMC7506008 DOI: 10.1038/s41438-020-00391-0] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Revised: 08/19/2020] [Accepted: 08/23/2020] [Indexed: 05/04/2023]
Abstract
Eggplant (Solanum melongena L.) is an economically important vegetable crop in the Solanaceae family, with extensive diversity among landraces and close relatives. Here, we report a high-quality reference genome for the eggplant inbred line HQ-1315 (S. melongena-HQ) using a combination of Illumina, Nanopore and 10X genomics sequencing technologies and Hi-C technology for genome assembly. The assembled genome has a total size of ~1.17 Gb and 12 chromosomes, with a contig N50 of 5.26 Mb, consisting of 36,582 protein-coding genes. Repetitive sequences comprise 70.09% (811.14 Mb) of the eggplant genome, most of which are long terminal repeat (LTR) retrotransposons (65.80%), followed by long interspersed nuclear elements (LINEs, 1.54%) and DNA transposons (0.85%). The S. melongena-HQ eggplant genome carries a total of 563 accession-specific gene families containing 1009 genes. In total, 73 expanded gene families (892 genes) and 34 contraction gene families (114 genes) were functionally annotated. Comparative analysis of different eggplant genomes identified three types of variations, including single-nucleotide polymorphisms (SNPs), insertions/deletions (indels) and structural variants (SVs). Asymmetric SV accumulation was found in potential regulatory regions of protein-coding genes among the different eggplant genomes. Furthermore, we performed QTL-seq for eggplant fruit length using the S. melongena-HQ reference genome and detected a QTL interval of 71.29-78.26 Mb on chromosome E03. The gene Smechr0301963, which belongs to the SUN gene family, is predicted to be a key candidate gene for eggplant fruit length regulation. Moreover, we anchored a total of 210 linkage markers associated with 71 traits to the eggplant chromosomes and finally obtained 26 QTL hotspots. The eggplant HQ-1315 genome assembly can be accessed at http://eggplant-hq.cn. In conclusion, the eggplant genome presented herein provides a global view of genomic divergence at the whole-genome level and powerful tools for the identification of candidate genes for important traits in eggplant.
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Affiliation(s)
- Qingzhen Wei
- Institute of Vegetable Research, Zhejiang Academy of Agricultural Sciences, Hangzhou, 30021 China
| | - Jinglei Wang
- Institute of Vegetable Research, Zhejiang Academy of Agricultural Sciences, Hangzhou, 30021 China
| | - Wuhong Wang
- Institute of Vegetable Research, Zhejiang Academy of Agricultural Sciences, Hangzhou, 30021 China
| | - Tianhua Hu
- Institute of Vegetable Research, Zhejiang Academy of Agricultural Sciences, Hangzhou, 30021 China
| | - Haijiao Hu
- Institute of Vegetable Research, Zhejiang Academy of Agricultural Sciences, Hangzhou, 30021 China
| | - Chonglai Bao
- Institute of Vegetable Research, Zhejiang Academy of Agricultural Sciences, Hangzhou, 30021 China
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Miyatake K, Saito T, Nunome T, Yamaguchi H, Negoro S, Ohyama A, Wu J, Katayose Y, Fukuoka H. Fine mapping of a major locus representing the lack of prickles in eggplant revealed the availability of a 0.5-kb insertion/deletion for marker-assisted selection. BREEDING SCIENCE 2020; 70:438-448. [PMID: 32968346 PMCID: PMC7495204 DOI: 10.1270/jsbbs.20004] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Accepted: 04/02/2020] [Indexed: 05/29/2023]
Abstract
As prickles cause labour inefficiency during cultivation and scratches on the skin of fruits during transportation, they are considered undesirable traits of eggplant (Solanum melongena L.). Because the molecular basis of prickle emergence has not been entirely revealed in plants, we mapped an eggplant semi-dominant Prickle (Pl) gene locus, which causes the absence of prickles, on chromosome 6 of a linkage map of the F2 population derived from crossing the no-prickly cultivar 'Togenashi-senryo-nigo' and the prickly line LS1934. By performing synteny mapping with tomato, the genomic region corresponding to the eggplant Pl locus was identified. Through bacterial artificial chromosome (BAC) screening, positive BAC clones and the contig sequence that harbour the Pl locus in the prickly eggplant genome were revealed. The BAC contig length was 133 kb, and it contained 16 predicted genes. Among them, a characteristic 0.5-kb insertion/deletion was detected. As the 0.5-kb insertion was commonly identified with the prickly phenotype worldwide, a primer pair that amplifies the insertion/deletion could be used for marker-assisted selection of the no-prickly phenotype. Such findings contribute to map-based-cloning of the Pl gene and the understanding of gene function, ultimately providing new insights into the regulatory molecular mechanisms underlying prickle emergence in plants.
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Affiliation(s)
- Koji Miyatake
- Institute of Vegetable and Floriculture Science (NIVFS), National Agriculture and Food Research Organization (NARO), 360 Kusawa, Ano, Tsu, Mie 514-2392, Japan
| | - Takeo Saito
- Institute of Vegetable and Floriculture Science (NIVFS), National Agriculture and Food Research Organization (NARO), 360 Kusawa, Ano, Tsu, Mie 514-2392, Japan
| | - Tsukasa Nunome
- Institute of Vegetable and Floriculture Science (NIVFS), National Agriculture and Food Research Organization (NARO), 360 Kusawa, Ano, Tsu, Mie 514-2392, Japan
| | - Hirotaka Yamaguchi
- Institute of Vegetable and Floriculture Science (NIVFS), National Agriculture and Food Research Organization (NARO), 360 Kusawa, Ano, Tsu, Mie 514-2392, Japan
| | - Satomi Negoro
- Institute of Vegetable and Floriculture Science (NIVFS), National Agriculture and Food Research Organization (NARO), 360 Kusawa, Ano, Tsu, Mie 514-2392, Japan
| | - Akio Ohyama
- Institute of Vegetable and Floriculture Science (NIVFS), National Agriculture and Food Research Organization (NARO), 360 Kusawa, Ano, Tsu, Mie 514-2392, Japan
| | - Jianzhong Wu
- Institute of Crop Science (NICS), National Agriculture and Food Research Organization (NARO), 1-2 Owashi, Tsukuba, Ibaraki 305-8634, Japan
| | - Yuichi Katayose
- Institute of Crop Science (NICS), National Agriculture and Food Research Organization (NARO), 1-2 Owashi, Tsukuba, Ibaraki 305-8634, Japan
| | - Hiroyuki Fukuoka
- Institute of Vegetable and Floriculture Science (NIVFS), National Agriculture and Food Research Organization (NARO), 360 Kusawa, Ano, Tsu, Mie 514-2392, Japan
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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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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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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: 25] [Impact Index Per Article: 6.3] [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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24
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Page A, Gibson J, Meyer RS, Chapman MA. Eggplant Domestication: Pervasive Gene Flow, Feralization, and Transcriptomic Divergence. Mol Biol Evol 2020; 36:1359-1372. [PMID: 31039581 DOI: 10.1093/molbev/msz062] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
In the context of food security, examining the genomics of domestication will help identify genes underlying adaptive and economically important phenotypes, for example, larger fruit, improved taste, and loss of agronomically inferior phenotypes. Examination of genome-scale single nucleotide polymorphisms demonstrates the relationships between wild ancestors of eggplant (Solanum melongena L.), confirming that Solanum insanum L. is the wild progenitor. This species is split roughly into an Eastern (Malaysian, Thai, and Vietnamese) and Western (Indian, Madagascan, and Sri Lankan) group, with domesticates derived from the former. Additional "wild" accessions from India appear to be feral escapes, derived multiple times from domesticated varieties through admixture. Accessions with small egg-shaped fruit are generally found intermixed with East Asian Solanum insanum confirming they are primitive relative to the large-fruited domesticates. Comparative transcriptomics was used to track the loci under selection. Sequence analysis revealed a genetic bottleneck reducing variation by almost 50% in the primitive accessions relative to the wild species and a further 10% in the landraces. We also show evidence for selection on genes with a role in response to wounding and apoptosis. Genes showing a significant difference in expression between wild and primitive or between primitive and landrace genepools were mostly (>75%) downregulated in the derived populations and enriched for gene ontologies related to defense, flowering, signaling, and response to biotic and abiotic stimuli. This work reveals genomic changes involved in crop domestication and improvement, and the population genetics work explains why defining the eggplant domestication trajectory has been so challenging.
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Affiliation(s)
- Anna Page
- Biological Sciences, University of Southampton, Southampton, United Kingdom
| | - Jane Gibson
- Biological Sciences, University of Southampton, Southampton, United Kingdom
| | - Rachel S Meyer
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA
| | - Mark A Chapman
- Biological Sciences, University of Southampton, Southampton, United Kingdom
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Solanum aethiopicum gr. gilo and Its Interspecific Hybrid with S. melongena as Alternative Rootstocks for Eggplant: Effects on Vigor, Yield, and Fruit Physicochemical Properties of Cultivar ′Scarlatti′. AGRONOMY-BASEL 2019. [DOI: 10.3390/agronomy9050223] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Grafting is generally considered effective in ameliorating vegetable crop tolerance to biotic and abiotic stresses. The use of interspecific hybrid as rootstock for eggplant may represent a valid alternative approach to enhance eggplant performance. However, studies on the effects of different rootstocks on eggplant plant vigor, yield, and fruit quality traits often show conflicting results. Thus, an experiment was performed in two spring–summer growing seasons (2014 and 2015) by grafting eggplant ′Scarlatti′ F1 hybrid on two accessions of S. aethiopicum gr. gilo and on the interspecific hybrid S. melongena × S. aehtiopicumgr. gilo in comparison to the most common eggplant rootstock S. torvum. Results indicate that S. melongena × S. aethiopicum gr. gilo interspecific hybrid and S. torvum improved grafting success, plant vigor, early flowering and yield in ′Scarlatti′ F1 scion. All rootstocks tested did not negatively influence fruit apparent quality traits and fruit quality composition. Moreover, fruit glycoalkaloids content remained below the recommended threshold value. These findings suggest that the use of S. melongena × S. aethiopicum gr. gilo interspecific hybrid as rootstock may be a good alternative to the most commonly used S. torvum.
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N’Diaye A, Haile JK, Nilsen KT, Walkowiak S, Ruan Y, Singh AK, Clarke FR, Clarke JM, Pozniak CJ. Haplotype Loci Under Selection in Canadian Durum Wheat Germplasm Over 60 Years of Breeding: Association With Grain Yield, Quality Traits, Protein Loss, and Plant Height. FRONTIERS IN PLANT SCIENCE 2018; 9:1589. [PMID: 30455711 PMCID: PMC6230583 DOI: 10.3389/fpls.2018.01589] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Accepted: 10/15/2018] [Indexed: 05/21/2023]
Abstract
Durum wheat was introduced in the southern prairies of western Canada in the late nineteenth century. Breeding efforts have mainly focused on improving quality traits to meet the pasta industry demands. For this study, 192 durum wheat lines were genotyped using the Illumina 90K Infinium iSelect assay, and resulted in a total of 14,324 polymorphic SNPs. Genetic diversity changed over time, declining during the first 20 years of breeding in Canada, then increased in the late 1980s and early 1990s. We scanned the genome for signatures of selection, using the total variance Fst-based outlier detection method (Lositan), the hierarchical island model (Arlequin) and the Bayesian genome scan method (BayeScan). A total of 407 outliers were identified and clustered into 84 LD-based haplotype loci, spanning all 14 chromosomes of the durum wheat genome. The association analysis detected 54 haplotype loci, of which 39% contained markers with a complete reversal of allelic state. This tendency to fixation of favorable alleles corroborates the success of the Canadian durum wheat breeding programs over time. Twenty-one haplotype loci were associated with multiple traits. In particular, hap_4B_1 explained 20.6, 17.9 and 16.6% of the phenotypic variance of pigment loss, pasta b∗ and dough extensibility, respectively. The locus hap_2B_9 explained 15.9 and 17.8% of the variation of protein content and protein loss, respectively. All these pleiotropic haplotype loci offer breeders the unique opportunity for further improving multiple traits, facilitating marker-assisted selection in durum wheat, and could help in identifying genes as functional annotations of the wheat genome become available.
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Affiliation(s)
- Amidou N’Diaye
- Department of Plant Sciences, Crop Development Centre, University of Saskatchewan, Saskatoon, SK, Canada
| | - Jemanesh K. Haile
- Department of Plant Sciences, Crop Development Centre, University of Saskatchewan, Saskatoon, SK, Canada
| | - Kirby T. Nilsen
- Department of Plant Sciences, Crop Development Centre, University of Saskatchewan, Saskatoon, SK, Canada
| | - Sean Walkowiak
- Department of Plant Sciences, Crop Development Centre, University of Saskatchewan, Saskatoon, SK, Canada
| | - Yuefeng Ruan
- Agriculture and Agri-Food Canada, Swift Current Research and Development Centre, Swift Current, SK, Canada
| | - Asheesh K. Singh
- Department of Agronomy, Iowa State University, Ames, IA, United States
| | - Fran R. Clarke
- Agriculture and Agri-Food Canada, Swift Current Research and Development Centre, Swift Current, SK, Canada
| | - John M. Clarke
- Department of Plant Sciences, Crop Development Centre, University of Saskatchewan, Saskatoon, SK, Canada
| | - Curtis J. Pozniak
- Department of Plant Sciences, Crop Development Centre, University of Saskatchewan, Saskatoon, SK, Canada
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Acquadro A, Barchi L, Gramazio P, Portis E, Vilanova S, Comino C, Plazas M, Prohens J, Lanteri S. Coding SNPs analysis highlights genetic relationships and evolution pattern in eggplant complexes. PLoS One 2017; 12:e0180774. [PMID: 28686642 PMCID: PMC5501601 DOI: 10.1371/journal.pone.0180774] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2017] [Accepted: 06/21/2017] [Indexed: 11/18/2022] Open
Abstract
Brinjal (Solanum melongena), scarlet (S. aethiopicum) and gboma (S. macrocarpon) eggplants are three Old World domesticates. The genomic DNA of a collection of accessions belonging to the three cultivated species, along with a representation of various wild relatives, was characterized for the presence of single nucleotide polymorphisms (SNPs) using a genotype-by-sequencing approach. A total of 210 million useful reads were produced and were successfully aligned to the reference eggplant genome sequence. Out of the 75,399 polymorphic sites identified among the 76 entries in study, 12,859 were associated with coding sequence. A genetic relationships analysis, supported by the output of the FastSTRUCTURE software, identified four major sub-groups as present in the germplasm panel. The first of these clustered S. aethiopicum with its wild ancestor S. anguivi; the second, S. melongena, its wild progenitor S. insanum, and its relatives S. incanum, S. lichtensteinii and S. linneanum; the third, S. macrocarpon and its wild ancestor S. dasyphyllum; and the fourth, the New World species S. sisymbriifolium, S. torvum and S. elaeagnifolium. By applying a hierarchical FastSTRUCTURE analysis on partitioned data, it was also possible to resolve the ambiguous membership of the accessions of S. campylacanthum, S. violaceum, S. lidii, S. vespertilio and S. tomentsum, as well as to genetically differentiate the three species of New World Origin. A principal coordinates analysis performed both on the entire germplasm panel and also separately on the entries belonging to sub-groups revealed a clear separation among species, although not between each of the domesticates and their respective wild ancestors. There was no clear differentiation between either distinct cultivar groups or different geographical provenance. Adopting various approaches to analyze SNP variation provided support for interpretation of results. The genotyping-by-sequencing approach showed to be highly efficient for both quantifying genetic diversity and establishing genetic relationships among and within cultivated eggplants and their wild relatives. The relevance of these results to the evolution of eggplants, as well as to their genetic improvement, is discussed.
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Affiliation(s)
- Alberto Acquadro
- University of Turin—DISAFA—Plant Genetics and Breeding, University of Turin, Largo Braccini 2, Grugliasco, Torino, Italy
| | - Lorenzo Barchi
- University of Turin—DISAFA—Plant Genetics and Breeding, University of Turin, Largo Braccini 2, Grugliasco, Torino, Italy
| | - Pietro Gramazio
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de València, Camino de Vera 14, Valencia, Spain
| | - Ezio Portis
- University of Turin—DISAFA—Plant Genetics and Breeding, University of Turin, Largo Braccini 2, Grugliasco, Torino, Italy
| | - Santiago Vilanova
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de València, Camino de Vera 14, Valencia, Spain
| | - Cinzia Comino
- University of Turin—DISAFA—Plant Genetics and Breeding, University of Turin, Largo Braccini 2, Grugliasco, Torino, Italy
| | - Mariola Plazas
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-Universitat Politècnica de València, Camino de Vera 14, Valencia, Spain
| | - Jaime Prohens
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de València, Camino de Vera 14, Valencia, Spain
| | - Sergio Lanteri
- University of Turin—DISAFA—Plant Genetics and Breeding, University of Turin, Largo Braccini 2, Grugliasco, Torino, Italy
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Tweneboah S, Oh SK. Biological roles of NAC transcription factors in the regulation of biotic and abiotic stress responses in solanaceous crops. ACTA ACUST UNITED AC 2017. [DOI: 10.5010/jpb.2017.44.1.001] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
- Solomon Tweneboah
- Department of Applied Biology, College of Agriculture & Life Sciences, Chungnam National University, Daejeon, 34134, Republic of Korea
| | - Sang-Keun Oh
- Department of Applied Biology, College of Agriculture & Life Sciences, Chungnam National University, Daejeon, 34134, Republic of Korea
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Gebhardt C. The historical role of species from the Solanaceae plant family in genetic research. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2016; 129:2281-2294. [PMID: 27744490 PMCID: PMC5121179 DOI: 10.1007/s00122-016-2804-1] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2016] [Accepted: 09/12/2016] [Indexed: 05/20/2023]
Abstract
This article evaluates the main contributions of tomato, tobacco, petunia, potato, pepper and eggplant to classical and molecular plant genetics and genomics since the beginning of the twentieth century. Species from the Solanaceae family form integral parts of human civilizations as food sources and drugs since thousands of years, and, more recently, as ornamentals. Some Solanaceous species were subjects of classical and molecular genetic research over the last 100 years. The tomato was one of the principal models in twentieth century classical genetics and a pacemaker of genome analysis in plants including molecular linkage maps, positional cloning of disease resistance genes and quantitative trait loci (QTL). Besides that, tomato is the model for the genetics of fruit development and composition. Tobacco was the major model used to establish the principals and methods of plant somatic cell genetics including in vitro propagation of cells and tissues, totipotency of somatic cells, doubled haploid production and genetic transformation. Petunia was a model for elucidating the biochemical and genetic basis of flower color and development. The cultivated potato is the economically most important Solanaceous plant and ranks third after wheat and rice as one of the world's great food crops. Potato is the model for studying the genetic basis of tuber development. Molecular genetics and genomics of potato, in particular association genetics, made valuable contributions to the genetic dissection of complex agronomic traits and the development of diagnostic markers for breeding applications. Pepper and eggplant are horticultural crops of worldwide relevance. Genetic and genomic research in pepper and eggplant mostly followed the tomato model. Comparative genome analysis of tomato, potato, pepper and eggplant contributed to the understanding of plant genome evolution.
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Carletti G, Carra A, Allegro G, Vietto L, Desiderio F, Bagnaresi P, Gianinetti A, Cattivelli L, Valè G, Nervo G. QTLs for Woolly Poplar Aphid (Phloeomyzus passerinii L.) Resistance Detected in an Inter-Specific Populus deltoides x P. nigra Mapping Population. PLoS One 2016; 11:e0152569. [PMID: 27022954 PMCID: PMC4811529 DOI: 10.1371/journal.pone.0152569] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2015] [Accepted: 03/16/2016] [Indexed: 02/08/2023] Open
Abstract
The genus Populus represents one of the most economically important groups of forest trees. It is composed by approximately 30 species used for wood and non-wood products, phytoremediation and biomass. Poplar is subjected to several biological and environmental threats although, compared to annual crops, we know far less about the genetic bases of biotic stress resistance. Woolly poplar aphid (Phloeomyzus passerinii) is considered a main pest of cultivated poplars in European and American countries. In this work we present two high density linkage maps in poplar obtained by a genotyping by sequencing (GBS) approach and the identification of QTLs involved in Ph. passerinii resistance. A total of 5,667 polymorphic markers (5,606 SNPs and 61 SSRs) identified on expressed sequences have been used to genotype 131 plants of an F1 population P ×canadensis obtained by an interspecific mate between Populus deltoides (resistant to woolly poplar aphid) and Populus nigra (susceptible to woolly poplar aphid). The two linkage maps, obtained following the two-way pseudo-testcross mapping strategy, have been used to investigate the genetic bases of woolly poplar aphid resistance. One major QTL and two QTLs with minor effects (mapped on LGV, LGXVI and LG XIX) explaining the 65.8% of the genetic variance observed in the progeny in response to Ph. passerinii attack were found. The high density coverage of functional markers allowed the identification of three genes belonging to disease resistance pathway as putative candidates for P. deltoides resistance to woolly poplar aphid. This work is the first report on genetic of woolly poplar aphid genetic resistance and the resistant loci associated markers identified represent a valuable tool in resistance poplar breeding programs.
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Affiliation(s)
- Giorgia Carletti
- Council for Agricultural Research and Economics (CREA)-Research Unit for Intensive Wood Production, Casale Monferrato (AL), Italy
| | - Andrea Carra
- Council for Agricultural Research and Economics (CREA)-Research Unit for Intensive Wood Production, Casale Monferrato (AL), Italy
| | - Gianni Allegro
- Council for Agricultural Research and Economics (CREA)-Research Unit for Intensive Wood Production, Casale Monferrato (AL), Italy
| | - Lorenzo Vietto
- Council for Agricultural Research and Economics (CREA)-Research Unit for Intensive Wood Production, Casale Monferrato (AL), Italy
| | - Francesca Desiderio
- Council for Agricultural Research and Economics (CREA)-Genomics Research Centre, Fiorenzuola d'Arda (PC), Italy
| | - Paolo Bagnaresi
- Council for Agricultural Research and Economics (CREA)-Genomics Research Centre, Fiorenzuola d'Arda (PC), Italy
| | - Alberto Gianinetti
- Council for Agricultural Research and Economics (CREA)-Genomics Research Centre, Fiorenzuola d'Arda (PC), Italy
| | - Luigi Cattivelli
- Council for Agricultural Research and Economics (CREA)-Genomics Research Centre, Fiorenzuola d'Arda (PC), Italy
| | - Giampiero Valè
- Council for Agricultural Research and Economics (CREA)-Genomics Research Centre, Fiorenzuola d'Arda (PC), Italy
- Council for Agricultural Research and Economics (CREA)-Rice Research Unit, Vercelli, Italy
| | - Giuseppe Nervo
- Council for Agricultural Research and Economics (CREA)-Research Unit for Intensive Wood Production, Casale Monferrato (AL), Italy
- * E-mail:
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Miyatake K, Saito T, Negoro S, Yamaguchi H, Nunome T, Ohyama A, Fukuoka H. Detailed mapping of a resistance locus against Fusarium wilt in cultivated eggplant (Solanum melongena). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2016; 129:357-67. [PMID: 26582508 DOI: 10.1007/s00122-015-2632-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2015] [Accepted: 10/09/2015] [Indexed: 05/07/2023]
Abstract
KEY MESSAGE This is the first report on genetic mapping of a resistance locus against Fusarium wilt caused by the plant pathogen Fusarium oxysporum f. sp. melongenae in cultivated eggplant. ABSTRACT Fusarium wilt, caused by the plant pathogen Fusarium oxysporum f. sp. melongenae, is a major soil-borne disease threatening stable production in eggplant (Solanum melongena). Although three eggplant germplasms, LS1934, LS174, and LS2436, are known to be highly resistant to the pathogen, their resistance loci have not been mapped. In this study, we performed quantitative trait locus analyses in F2:3 populations and detected a resistance locus, FM1, at the end of chromosome 2, with two alleles, Fm1(L) and Fm1(E), in the F2 populations LWF2 [LS1934 × WCGR112-8 (susceptible)] and EWF2 [EPL-1 (derived from LS174) × WCGR112-8], respectively. The percentage of phenotypic variance explained by Fm1(L) derived from LS1934 was 75.0% [Logarithm of the odds (LOD) = 29.3], and that explained by Fm1(E) derived from EPL-1 was 92.2% (LOD = 65.8). Using backcrossed inbred lines, we mapped FM1 between two simple sequence repeat markers located ~4.881 cM apart from each other. Comparing the location of the above locus to those of previously reported ones, the resistance locus Rfo-sa1 from an eggplant ally (Solanum aethiopicum gr. Gilo) was mapped very close to FM1, whereas another resistance locus, from LS2436, was mapped to the middle of chromosome 4. This is the first report of mapping of a Fusarium resistance locus in cultivated eggplant. The availability of resistance-linked markers will enable the application of marker-assisted selection to overcome problems posed by self-incompatibility and introduction of negative traits because of linkage drag, and will lead to clear understanding of genetic mechanism of Fusarium resistance.
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Affiliation(s)
- Koji Miyatake
- NARO Institute of Vegetable and Tea Science (NIVTS), 360 Kusawa, Ano, Tsu, Mie, 514-2392, Japan.
| | - Takeo Saito
- NARO Institute of Vegetable and Tea Science (NIVTS), 360 Kusawa, Ano, Tsu, Mie, 514-2392, Japan
| | - Satomi Negoro
- NARO Institute of Vegetable and Tea Science (NIVTS), 360 Kusawa, Ano, Tsu, Mie, 514-2392, Japan
| | - Hirotaka Yamaguchi
- NARO Institute of Vegetable and Tea Science (NIVTS), 360 Kusawa, Ano, Tsu, Mie, 514-2392, Japan
| | - Tsukasa Nunome
- NARO Institute of Vegetable and Tea Science (NIVTS), 360 Kusawa, Ano, Tsu, Mie, 514-2392, Japan
| | - Akio Ohyama
- NARO Institute of Vegetable and Tea Science (NIVTS), 360 Kusawa, Ano, Tsu, Mie, 514-2392, Japan
| | - Hiroyuki Fukuoka
- NARO Institute of Vegetable and Tea Science (NIVTS), 360 Kusawa, Ano, Tsu, Mie, 514-2392, Japan
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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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Barabaschi D, Tondelli A, Desiderio F, Volante A, Vaccino P, Valè G, Cattivelli L. Next generation breeding. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2016; 242:3-13. [PMID: 26566820 DOI: 10.1016/j.plantsci.2015.07.010] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2015] [Revised: 07/10/2015] [Accepted: 07/11/2015] [Indexed: 05/18/2023]
Abstract
The genomic revolution of the past decade has greatly improved our understanding of the genetic make-up of living organisms. The sequencing of crop genomes has completely changed our vision and interpretation of genome organization and evolution. Re-sequencing allows the identification of an unlimited number of markers as well as the analysis of germplasm allelic diversity based on allele mining approaches. High throughput marker technologies coupled with advanced phenotyping platforms provide new opportunities for discovering marker-trait associations which can sustain genomic-assisted breeding. The availability of genome sequencing information is enabling genome editing (site-specific mutagenesis), to obtain gene sequences desired by breeders. This review illustrates how next generation sequencing-derived information can be used to tailor genomic tools for different breeders' needs to revolutionize crop improvement.
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Affiliation(s)
- Delfina Barabaschi
- Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria, Genomics Research Centre, Via San Protaso 302, 29017 Fiorenzuola d'Arda, Italy
| | - Alessandro Tondelli
- Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria, Genomics Research Centre, Via San Protaso 302, 29017 Fiorenzuola d'Arda, Italy
| | - Francesca Desiderio
- Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria, Genomics Research Centre, Via San Protaso 302, 29017 Fiorenzuola d'Arda, Italy
| | - Andrea Volante
- Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria, Rice Research Unit, SS 11 to Torino Km 2.5, 13100 Vercelli, Italy
| | - Patrizia Vaccino
- Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria, Research Unit for Cereal Selection in Continental areas, via R. Forlani, e, 26866 S. Angelo Lodigiano, Italy
| | - Giampiero Valè
- Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria, Rice Research Unit, SS 11 to Torino Km 2.5, 13100 Vercelli, Italy
| | - Luigi Cattivelli
- Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria, Genomics Research Centre, Via San Protaso 302, 29017 Fiorenzuola d'Arda, Italy.
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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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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: 29] [Impact Index Per Article: 3.2] [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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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: 25] [Impact Index Per Article: 2.8] [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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38
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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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Gramazio P, Prohens J, Plazas M, Andújar I, Herraiz FJ, Castillo E, Knapp S, Meyer RS, Vilanova S. Location of chlorogenic acid biosynthesis pathway and polyphenol oxidase genes in a new interspecific anchored linkage map of eggplant. BMC PLANT BIOLOGY 2014; 14:350. [PMID: 25491265 PMCID: PMC4279458 DOI: 10.1186/s12870-014-0350-z] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2014] [Accepted: 11/25/2014] [Indexed: 05/21/2023]
Abstract
BACKGROUND Eggplant is a powerful source of polyphenols which seems to play a key role in the prevention of several human diseases, such as cancer and diabetes. Chlorogenic acid is the polyphenol most present in eggplant, comprising between the 70% and 90% of the total polyphenol content. Introduction of the high chlorogenic acid content of wild relatives, such as S. incanum, into eggplant varieties will be of great interest. A potential side effect of the increased level polyphenols could be a decrease on apparent quality due to browning caused by the polyphenol oxidase enzymes mediated oxidation of polyphenols. We report the development of a new interspecific S. melongena × S. incanum linkage map based on a first backcross generation (BC1) towards the cultivated S. melongena as a tool for introgressing S. incanum alleles involved in the biosynthesis of chlorogenic acid in the genetic background of S. melongena. RESULTS The interspecific genetic linkage map of eggplant developed in this work anchor the most informative previously published genetic maps of eggplant using common markers. The 91 BC1 plants of the mapping population were genotyped with 42 COSII, 99 SSRs, 88 AFLPs, 9 CAPS, 4 SNPs and one morphological polymorphic markers. Segregation marker data resulted in a map encompassing 1085 cM distributed in 12 linkage groups. Based on the syntheny with tomato, the candidate genes involved in the core chlorogenic acid synthesis pathway in eggplant (PAL, C4H, 4CL, HCT, C3'H, HQT) as well as five polyphenol oxidase (PPO1, PPO2, PPO3, PPO4, PPO5) were mapped. Except for 4CL and HCT chlorogenic acid genes were not linked. On the contrary, all PPO genes clustered together. Candidate genes important in domestication such as fruit shape (OVATE, SISUN1) and prickliness were also located. CONCLUSIONS The achievements in location of candidate genes will allow the search of favorable alleles employing marker-assisted selection in order to develop new varieties with higher chlorogenic content alongside a lower polyphenol oxidase activity. This will result into an enhanced product showing a lower fruit flesh browning with improved human health properties.
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Affiliation(s)
- Pietro Gramazio
- />Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de València, Camino de Vera 14, 46022 Valencia, Spain
| | - Jaime Prohens
- />Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de València, Camino de Vera 14, 46022 Valencia, Spain
| | - Mariola Plazas
- />Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de València, Camino de Vera 14, 46022 Valencia, Spain
| | - Isabel Andújar
- />Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de València, Camino de Vera 14, 46022 Valencia, Spain
| | - Francisco Javier Herraiz
- />Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de València, Camino de Vera 14, 46022 Valencia, Spain
| | - Elena Castillo
- />Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de València, Camino de Vera 14, 46022 Valencia, Spain
| | - Sandra Knapp
- />Department of Life Sciences, Natural History Museum, Cromwell Road, London, SW7 5BD UK
| | - Rachel S Meyer
- />Center for Genomics and Systems Biology, New York University, 12 Waverly Place, New York, NY 10003 USA
- />Center for Genomics and Systems Biology, New York University Abu Dhabi Research Institute, Abu Dhabi, United Arab Emirates
| | - Santiago Vilanova
- />Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de València, Camino de Vera 14, 46022 Valencia, Spain
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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: 44] [Impact Index Per Article: 4.4] [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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