Article
Plant Sciences
Lara Pereira, Manoj Sapkota, Michael Alonge, Yi Zheng, Youjun Zhang, Hamid Razifard, Nathan K. Taitano, Michael C. Schatz, Alisdair R. Fernie, Ying Wang, Zhangjun Fei, Ana L. Caicedo, Denise M. Tieman, Esther van Der Knaap
Summary: The study revealed that the quality of tomato fruit in the red-fruited tomato clade is influenced by multiple genes controlling the balance of sugars, acids, and volatile compounds in the fruit. These genes exhibit high genetic diversity at specific loci, with novel haplotypes that could be used in breeding programs to enhance modern tomato quality. Additionally, gene expression patterns varied among phylogenetically diverse tomato accessions, with no clear relationship between expression and metabolite levels.
FRONTIERS IN PLANT SCIENCE
(2021)
Article
Agriculture, Multidisciplinary
Anoush Miriam Ficiciyan, Jacqueline Loos, Teja Tscharntke
Summary: Replacing traditional crop varieties with commercial, high-yielding varieties has led to a decline in farmland and crop diversity. Organic breeding organizations in Europe aim to conserve local, traditional varieties and develop new varieties that can adapt to harsh cultivation conditions and mixed cropping. The study found that organic varieties performed better in mixed cropping systems and showed higher fruit weight stability under weed stress when grown as single plants.
AGROECOLOGY AND SUSTAINABLE FOOD SYSTEMS
(2022)
Article
Agronomy
T. A. Anderson, S. M. Zitter, D. M. De Jong, D. M. Francis, M. A. Mutschler
Summary: This study identified cryptic early blight resistance introgressions in tomato breeding lines, demonstrated efficient genotypic selection for resistance, and validated several QTL associated with early blight resistance across different market classes. The development of near-isogenic fresh market tomato lines with high resistance to early blight, mediated largely by two QTLs, showcases the potential of mining introgressions in tomato lines for enhanced disease resistance.
THEORETICAL AND APPLIED GENETICS
(2021)
Article
Plant Sciences
Agustina P. Fortuny, Rodrigo A. Bueno, Javier H. Pereira da Costa, Maria Ines Zanor, Gustavo R. Rodriguez
Summary: This study found that in tomato fruits, heterosis and reciprocal effects were more pronounced at the metabolite level, being more influenced by genotypes than agronomic traits. Hybrids showed higher phenotypic diversity, with metabolites mainly being amino acids displaying more reciprocal effects and heterosis.
JOURNAL OF EXPERIMENTAL BOTANY
(2021)
Article
Horticulture
Ibrahim Makhadmeh, Ammar A. Albalasmeh, Mohammed Ali, Samar G. Thabet, Walaa Ali Darabseh, Saied Jaradat, Ahmad M. Alqudah
Summary: Exploring the genetic diversity among plant accessions is crucial for plant genetic resource conservation and management. This study evaluated the performance and genetic diversity of 46 tomato accessions in Jordan, revealing a wide range of variations. The analysis of molecular markers identified SSR primers associated with specific genes. These findings provide valuable information for plant breeding programs and future molecular analysis.
Article
Food Science & Technology
Anoush Miriam Ficiciyan, Jacqueline Loos, Teja Tscharntke
Summary: Global agrobiodiversity is threatened by the replacement of traditional, locally adapted crop varieties with high-yielding and hybrid varieties, leading to losses in diversity. European organic vegetable breeding organizations aim to increase the range of varieties for sustainable cultivation under sub-optimal conditions. Research on the performance of organic vegetable varieties compared to conventional high-yielding and hybrid varieties in different environmental conditions is still lacking.
FRONTIERS IN SUSTAINABLE FOOD SYSTEMS
(2021)
Article
Biology
Svetlana Nekoval, Anastasia Zakharchenko, Anastasia Sadovaya, Arina Churikova, Irina Fedoryanskaya
Summary: An assessment of 27 mutant tomato lines from four countries revealed that mutant lines obtained from the United States showed greater resistance to Alternaria alternata, while mutant lines from other countries demonstrated moderate resistance. These findings suggest a potential correlation between geographic origin and resistance levels in tomato mutant lines.
SAUDI JOURNAL OF BIOLOGICAL SCIENCES
(2022)
Article
Multidisciplinary Sciences
Shai Torgeman, Dani Zamir
Summary: Controlled population development and genome-wide association studies are powerful methods for identifying genes and alleles that contribute to complex traits. However, the contribution of nonadditive interactions between quantitative trait loci (QTLs) has been understudied. In this study, the researchers used a population of backcross inbred lines (BILs) to examine epistasis. They found that nonadditive interactions can improve crop productivity by increasing fruit yield in hybrids.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Plant Sciences
Ljiljana Kuzmanovic, Gloria Giovenali, Roberto Ruggeri, Francesco Rossini, Carla Ceoloni
Summary: This study evaluated the breeding potential of six recombinant lines (RLs) of durum wheat-Thinopyrum spp., which included high-efficiency QTL for resistance to Fusarium head blight and Fusarium crown rot. The RLs showed excellent genetic stability and yield performance under both rainfed and irrigated conditions, making them promising candidates for breeding programs to enhance crop security and safety.
Article
Agronomy
Manni Marefatzadeh-Khameneh, Sedigeh Fabriki-Ourang, Behzad Sorkhilalehloo, Jahangir Abbasi-Kohpalekani, Jafar Ahmadi
Summary: The study revealed that the tomato germplasm in the National Plant Gene Bank of Iran has abundant genetic diversity, which can be used for selecting tomato breeding lines. The studied tomato germplasm was classified into nine main clusters based on hierarchical cluster analysis, and fruit shape index and proximal/distal fruit end shape played important roles in the first two components explaining 50% of the total data variation.
GENETIC RESOURCES AND CROP EVOLUTION
(2021)
Article
Biotechnology & Applied Microbiology
Mariangela Arca, Brigitte Gouesnard, Tristan Mary-Huard, Marie-Christine Le Paslier, Cyril Bauland, Valerie Combes, Delphine Madur, Alain Charcosset, Stephane D. Nicolas
Summary: In this study, a novel DNA pooling strategy was used to identify promising traditional varieties and genomic regions to enhance the genetic diversity of modern breeds. The research found that most traditional varieties do not have closely related lines and that only 10 varieties account for more than half of the total contribution to inbred lines. Comparison with more advanced breeding cycles showed that landraces with limited contributions enriched the haplotype diversity of reference inbred lines more than those with a high contribution.
PLANT BIOTECHNOLOGY JOURNAL
(2023)
Article
Plant Sciences
Eleni Avramidou, Efi Sarri, Ioannis Ganopoulos, Panagiotis Madesis, Leonidas Kougiteas, Evgenia-Anna Papadopoulou, Konstantinos A. Aliferis, Eleni M. Abraham, Eleni Tani
Summary: This study compared the genetic diversity and seed metabolite profiles of five genetic materials of faba bean. Genetic diversity was assessed by SCoT markers and genetic distances were estimated by UPGMA dendrogram. The advanced line KK18 displayed the best nutritional profile and showed the highest potential for further exploration in breeding programs.
Article
Plant Sciences
Almudena Lazaro, Laura Ruiz-Aceituno
Summary: Consumers prefer firm tomatoes with soft skin due to their low level of springiness and resilience. Texture traits of tomatoes vary significantly among different genotypes and are strongly influenced by environmental factors.
PLANT FOODS FOR HUMAN NUTRITION
(2021)
Article
Food Science & Technology
Luis Felipe V. Ferrao, Haley Sater, Paul Lyrene, Rodrigo R. Amadeu, Charles A. Sims, Denise M. Tieman, Patricio R. Munoz
Summary: The study investigated the main components of blueberry aroma and identified a group of terpenoid volatiles associated with floral and sweet aroma notes preferred by consumers. The importance of metabolomic data for flavor-assisted selection was demonstrated, offering new avenues to explore flavor in blueberries.
FOOD RESEARCH INTERNATIONAL
(2022)
Article
Multidisciplinary Sciences
Jens Keilwagen, Heike Lehnert, Thomas Berner, Ekaterina Badaeva, Axel Himmelbach, Andreas Borner, Benjamin Kilian
Summary: This study developed a method to detect introgressions and predict the donor species using wheat genome sequences. The results showed that introgressions played a significant role in wheat breeding and evolution, and carried resistance genes.
SCIENTIFIC REPORTS
(2022)
Article
Agronomy
Roland Schafleitner, Ya-ping Lin, Fekadu Fufa Dinssa, Sognigbe N'Danikou, Richard Finkers, Ruth Minja, Mary Abukutsa-Onyango, Winnie Akinyi Nyonje, Chen-yu Lin, Tien-hor Wu, Jeremiah Phanuel Sigalla, Maarten van Zonneveld, Yun-yin Hsiao, Sanjeet Kumar, Wan-jen Wu, Hsin- Wang, Shou Lin, Ray-yu Yang
Summary: Amaranth is a crop with high nutritional value that is gaining popularity. The lack of improved cultivars limits its use, but the creation of a core collection is helping to overcome this limitation.
Article
Biochemistry & Molecular Biology
Genevieve Hoopes, Xiaoxi Meng, John P. Hamilton, Sai Reddy Achakkagari, Fernanda de Alves Freitas Guesdes, Marie E. Bolger, Joseph J. Coombs, Danny Esselink, Natalie R. Kaiser, Linda Kodde, Maria Kyriakidou, Brian Lavrijssen, Natascha van Lieshout, Rachel Shereda, Heather K. Tuttle, Brieanne Vaillancourt, Joshua C. Wood, Jan M. de Boer, Nolan Bornowski, Peter Bourke, David Douches, Herman J. van Eck, Dave Ellis, Max J. Feldman, Kyle M. Gardner, Johannes C. P. Hopman, Jiming Jiang, Walter S. De Jong, Joseph C. Kuhl, Richard G. Novy, Stan Oome, Vidyasagar Sathuvalli, Ek Han Tan, Remco A. Ursum, M. Isabel Vales, Kelly Vining, Richard G. F. Visser, Jack Vossen, G. Craig Yencho, Noelle L. Anglin, Christian W. B. Bachem, Jeffrey B. Endelman, Laura M. Shannon, Martina Stromvik, Helen H. Tai, Bjorn Usadel, C. Robin Buell, Richard Finkers
Summary: Cultivated potato is a clonally propagated autotetraploid species with a highly heterogeneous genome. Phased assemblies of six cultivars revealed extensive allelic diversity and structural variation, resulting in a complex transcriptome and predicted proteome. Wild species contribute to the allelic diversity in tetraploid cultivars. Understanding the complexity of the potato genome is key for precision breeding and hybridization.
Article
Genetics & Heredity
Natascha van Lieshout, Martijn van Kaauwen, Linda Kodde, Paul Arens, Marinus J. M. Smulders, Richard G. F. Visser, Richard Finkers
Summary: This study presents the most complete and contiguous chrysanthemum de novo assembly published so far, providing an important step forward in understanding the chrysanthemum genome, evolution, and history.
G3-GENES GENOMES GENETICS
(2022)
Article
Plant Sciences
Jose Blanca, Clara Pons, Javier Montero-Pau, David Sanchez-Matarredona, Peio Ziarsolo, Lilian Fontanet, Josef Fisher, Mariola Plazas, Joan Casals, Jose Luis Rambla, Alessandro Riccini, Samuela Pombarella, Alessandra Ruggiero, Maria Sulli, Stephania Grillo, Angelos Kanellis, Giovanni Giuliano, Richard Finkers, Maria Cammareri, Silvana Grandillo, Andrea Mazzucato, Mathilde Causse, Maria Jose Diez, Jaime Prohens, Dani Zamir, Joaquin Canizares, Antonio Jose Monforte, Antonio Granell
Summary: A study on European traditional tomato varieties found that high phenotypic diversity was created by traditional farmer-driven selection, inadvertently combining a few polymorphic loci. Analysis of 1254 tomato accessions revealed a continuous genetic gradient between traditional and modern varieties, with low genetic diversity and distinct genetic groups among traditional European tomatoes. Spanish and Italian varieties showed higher genetic diversity, possibly indicating independent secondary centers of diversity, while other varieties may be the result of recent migrations and hybridizations among European regions. A few highly polymorphic loci were associated with fruit morphological traits in the European traditional collection, suggesting a history of balancing selection by tomato farmers to maintain morphological variation.
JOURNAL OF EXPERIMENTAL BOTANY
(2022)
Article
Plant Sciences
Clara Pons, Joan Casals, Samuela Palombieri, Lilian Fontanet, Alessandro Riccini, Jose Luis Rambla, Alessandra Ruggiero, Maria del Rosario Figas, Mariola Plazas, Athanasios Koukounaras, Maurizio E. Picarella, Maria Sulli, Josef Fisher, Peio Ziarsolo, Jose Blanca, Joaquin Canizares, Maria Cammareri, Antonella Vitiello, Giorgia Batelli, Angelos Kanellis, Matthijs Brouwer, Richard Finkers, Konstantinos Nikoloudis, Salvador Soler, Giovanni Giuliano, Stephania Grillo, Silvana Grandillo, Dani Zamir, Andrea Mazzucato, Mathilde Causse, Maria Jose Diez, Jaime Prohens, Antonio Jose Monforte, Antonio Granell
Summary: This study evaluated a large traditional tomato collection from Southern Europe, revealing a wide range of phenotypic variability and differences among countries. By integrating phenotypic data and origin information, eight main tomato types were defined and 159 novel loci associations were identified.
HORTICULTURE RESEARCH
(2022)
Article
Multidisciplinary Sciences
Sven Schrinner, Rebecca Serra Mari, Richard Finkers, Paul Arens, Bjoern Usadel, Tobias Marschall, Gunnar W. Klau
Summary: This article presents a genetic phasing method for plant breeding that can phase the haplotype sequences of parental samples using a large number of low-depth progeny samples. By integrating weak Mendelian progeny signals with a Bayesian log-likelihood model and utilizing an interval scheduling approach, the method can compute high-quality sparse phasings.
Article
Plant Sciences
Xing Wang, Xueping Chen, Shuangxia Luo, Wei Ma, Na Li, Weiwei Zhang, Yury Tikunov, Shuxin Xuan, Jianjun Zhao, Yanhua Wang, Gengdi Zheng, Ping Yu, Yuling Bai, Arnaud Bovy, Shuxing Shen
Summary: Anthocyanins are important pigments that determine color in plants. Our study found that alternative splicing of the DFR gene and natural variations in the promoter region are closely related to anthocyanin accumulation. These variations have occurred during the domestication of spiny Solanum plants, resulting in altered anthocyanin accumulation.
Article
Chemistry, Applied
Hua Li, Dorthe H. Larsen, Ruimin Cao, Arjen C. van de Peppel, Yury M. Tikunov, Leo F. M. Marcelis, Ernst J. Woltering, Jan A. L. van Kan, Rob E. Schouten
Summary: The study investigated the relationship between the physical and chemical characteristics of red ripe strawberry fruit and the natural spoilage caused by Botrytis cinerea. It was found that genotypes with intense red coloration, high levels of anthocyanins, ascorbic acid, and malic acid had a lower susceptibility to B. cinerea. There were no clear correlations between spoilage rates and soluble sugars, most volatiles, firmness, and dry weight percentage. However, high levels of ethyl butanoate and 1-hexanol were correlated with high spoilage rates.
Article
Plant Sciences
Yi Wu, Sigal Popovsky-Sarid, Yury Tikunov, Yelena Borovsky, Kobi Baruch, Richard G. F. Visser, Ilan Paran, Arnaud Bovy
Summary: The genetic basis of flavonoid variation in pepper fruit was explored, and a major regulatory gene CaMYB12-like was identified. The study revealed the important role of CaMYB12-like in the regulation of flavonoid content in pepper fruit, and demonstrated the potential for breeding high-flavonoid content in cultivated pepper through transgenic technology.
Article
Plant Sciences
Chengcheng Cai, Alexandre Pele, Johan Bucher, Richard Finkers, Guusje Bonnema
Summary: Meiotic recombination is crucial for proper chromosome segregation and allelic combination generation. In this study, we analyzed 20 crosses of Brassica oleracea and produced high-resolution recombination maps. The results revealed similar recombination landscapes among different cross combinations and between sexes. We also found that gene density and large structural variations strongly influenced recombination formation in B. oleracea, and there were extensive variations in recombination number depending on the initial parents crossed with.
Article
Agronomy
Corentin R. Clot, Xulan Wang, Joey Koopman, Alejandro Therese Navarro, Johan Bucher, Richard G. F. Visser, Richard Finkers, Herman J. van Eck
Summary: The reinvention of potato as a diploid hybrid crop requires understanding of mutational load, recombination landscape, and genetic basis of fertility. In this study, the OutcrossSeq pipeline was implemented in R for analyzing a large diploid potato population. This pipeline allowed for marker inference, linkage map construction, and QTL mapping, leading to new insights for diploid potato breeding.
Article
Genetics & Heredity
Alejandro Therese Navarro, Peter M. Bourke, Eric van de Weg, Corentin R. Clot, Paul Arens, Richard Finkers, Chris Maliepaard
Summary: Linkage mapping is a method for ordering markers based on recombination events, but genotyping errors are common in high-throughput genotyping data. In this study, an algorithm called Smooth Descent (SD) was developed to improve the accuracy of genetic mapping and correct genotyping errors. SD is able to handle any marker type and autopolyploids, and it performs well in the presence of genotyping errors with error rates between 5% and 20% and non-homogeneous error rates among markers or individuals.
FRONTIERS IN GENETICS
(2023)
Article
Plant Sciences
Clara Pons, Joan Casals, Matthijs Brower, Adriana Sacco, Alessandro Riccini, Patrick Hendrickx, Maria del Rosario Figas, Josef Fisher, Silvana Grandillo, Andrea Mazzucato, Salvador Soler, Dani Zamir, Mathilde Causse, Maria Jose Diez, Richard Finkers, Jaime Prohens, Antonio Jose Monforte, Antonio Granell
Summary: European traditional tomato varieties have shown excellent agronomic performance and stability, even outperforming modern varieties. Genome-wide association studies have identified 141 QTLs associated with agro-morphological traits and revealed the genetic basis of stability. This study enhances our understanding of the genetic diversity available in European traditional tomato germplasm.
JOURNAL OF EXPERIMENTAL BOTANY
(2023)
Article
Multidisciplinary Sciences
Evangelia A. Papoutsoglou, Ioannis N. Athanasiadis, Richard G. F. Visser, Richard Finkers
Summary: Plant phenotyping experiments produce heterogeneous and poorly documented data, making it difficult to reuse. This study explores the challenges and benefits of making data FAIR, using potato developmental traits as a case study. By integrating and verifying datasets with environmental data, we discuss the potential for reproducibility and reusability of FAIR data, along with the challenges encountered in this process.
Correction
Plant Sciences
Jose Blanca, Clara Pons, Javier Montero-Pau, David Sanchez-Matarredona, Peio Ziarsolo, Lilian Fontanet, Josef Fisher, Mariola Plazas, Joan Casals, Jose Luis Rambla, Alessandro Riccini, Samuela Palombieri, Alessandra Ruggiero, Maria Sulli, Stephania Grillo, Angelos Kanellis, Giovanni Giuliano, Richard Finkers, Maria Cammareri, Silvana Grandillo, Andrea Mazzucato, Mathilde Causse, Maria Jose Diez, Jaime Prohens, Dani Zamir, Joaquin Canizares, Antonio Jose Monforte, Antonio Granell
JOURNAL OF EXPERIMENTAL BOTANY
(2022)