Article
Agronomy
Norain Jamalluddin, Festo J. Massawe, Sean Mayes, Wai Kuan Ho, Ajit Singh, Rachael C. Symonds
Summary: Through two drought screening trials, this study identified eight drought-tolerant germplasms in Amaranthus tricolor with stable performance across the two trials, and revealed that change in stem biomass may be a key adaptation mechanism for drought tolerance. They also found that dark-adapted quantum yield could be a useful parameter for identifying drought tolerance in amaranth.
Article
Agronomy
Roland Schafleitner, Chen-Yu Lin, Ya-Ping Lin, Tien-Hor Wu, Cian-Huei Hung, Chooi-Lin Phooi, Shu-Hui Chu, Yu-Cen Jhong, Yun-Yin Hsiao
Summary: Okra is a heat tolerant vegetable crop with high economic and nutritional importance in certain regions. A core collection of 166 okra accessions was selected for their response to flooding stress, with specific accessions showing maintained growth and health under flooding being chosen for further analysis and breeding purposes.
Article
Food Science & Technology
Ester Murube, Romina Beleggia, Deborah Pacetti, Ancuta Nartea, Giulia Frascarelli, Giovanna Lanzavecchia, Elisa Bellucci, Laura Nanni, Tania Gioia, Ugo Marciello, Stefania Esposito, Giacomo Foresi, Giuseppina Logozzo, Giuseppe Natale Frega, Elena Bitocchi, Roberto Papa
Summary: Food legumes play a crucial role in agriculture, contributing to nutrition and soil fertility. Characterizing morphological and compositional traits of seeds can help identify nutritional properties, but heritability estimates suggest considering environmental effects on genetic traits is also important.
Article
Multidisciplinary Sciences
Muraleedhar S. Aski, Neha Rai, Venkata Ravi Prakash Reddy, Gayacharan, Harsh Kumar Dikshit, Gyan Prakash Mishra, Dharmendra Singh, Arun Kumar, Renu Pandey, Madan Pal Singh, Aditya Pratap, Ramakrishnan M. Nair, Roland Schafleitner
Summary: Mungbean is an important food grain legume, but its production capacity is threatened by global warming. The research identified new variations of key root traits in mungbean and identified germplasm with potentially favorable root traits for further studies and breeding.
Article
Horticulture
Ken Hoshikawa, Ya-Ping Lin, Roland Schafleitner, Kenta Shirasawa, Sachiko Isobe, Duc Chinh Nguyen, Ryo Ohsawa, Yosuke Yoshioka
Summary: This study analyzed the genetic diversity and population structure of 465 Amaranthus tricolor accessions held by the World Vegetable Center genebank. A total of 10,509 SNPs were found, and 5,638 SNPs without missing data were identified in 440 accessions. These findings contribute to the research and breeding of this species.
SCIENTIA HORTICULTURAE
(2023)
Article
Plant Sciences
Evan B. Craine, Alathea Davies, Daniel Packer, Nathan D. Miller, Sandra M. Schmoeckel, Edgar P. Spalding, Mark Tester, Kevin M. Murphy
Summary: This study aimed to characterize the phenotypic relationships and variation within a quinoa world core collection. The results of this study establish a practical resource for plant breeders to leverage as they strategically develop germplasm in support of the global expansion of quinoa.
FRONTIERS IN PLANT SCIENCE
(2023)
Article
Agronomy
Sun Mi Huh, Ara Cho, Bomi Yim, Jiin Kim, Jin Gyu Jeong, Hoyeol Jang, Jeong-Hwan Mun, Hee-Ju Yu
Summary: Whole-genome resequencing and multi-sample genotyping analyses identified 796,294 high-quality single-nucleotide polymorphisms. High-depth variation data from 100 radish accessions classified the accessions into three main groups. These resources will enhance research on the trait genetic system, breeding, and diversity conservation of radishes.
Article
Plant Sciences
Siyu Hou, Xuemei Ren, Yang Yang, Donghang Wang, Wei Du, Xinfang Wang, Hongying Li, Yuanhuai Han, Longlong Liu, Zhaoxia Sun
Summary: In this study, genome-wide screening was performed to develop SSR markers associated with agronomic traits and rutin contents in Tartary buckwheat (TB). The polymorphic SSR markers and candidate genes identified in this study can be utilized for molecular characterization, marker-assisted breeding, and functional gene cloning in TB.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Plant Sciences
Dionysia-Angeliki Lyra, Anitha Raman, Aly Hozayen, Rashyd Zaaboul, Fouad O. Abou-Zaid, Ahmed El-Naggar, Sherine Mansoor, Henda Mahmoudi, Khalil Ammar
Summary: Climate change has greatly affected the quality of soil and water, leading to increased salinity in reservoirs in desert regions like the UAE and Egypt. Saline farming, specifically the cultivation of salt-tolerant crops and halophytes, offers a promising solution. The study evaluated six genotypes of Salicornia bigelovii, a widely consumed halophyte, in Dubai and Egypt, and found that ICBA-10 performed well in terms of biomass, seed yield, ion accumulation, amino acids, and unsaturated fatty acids content.
Article
Plant Sciences
Shizhuo Xiao, Xibin Dai, Lingxiao Zhao, Zhilin Zhou, Lukuan Zhao, Pan Xu, Bingqian Gao, An Zhang, Donglan Zhao, Rui Yuan, Yao Wang, Jie Wang, Qinglian Li, Qinghe Cao
Summary: This study deeply sequenced 314 sweetpotato germplasms and obtained high-quality SNPs and InDels. Genome-wide marker primers were designed based on the Indels, and high-confidence loci associated with important agronomic traits were detected. These results will contribute to genetic and breeding studies in sweetpotato.
HORTICULTURE RESEARCH
(2023)
Article
Plant Sciences
Sameh Boukail, Mercy Macharia, Mara Miculan, Alberto Masoni, Alessandro Calamai, Enrico Palchetti, Matteo Dell'Acqua
Summary: The study investigated the genomic and phenotypic diversity of a global proso millet collection, identifying 13 MTAs for key agronomic and seed traits with potential for application in breeding programs.
Article
Multidisciplinary Sciences
Charles Andiku, Hussein Shimelis, Admire I. T. Shayanowako, Prakash I. Gangashetty, Eric Manyasa
Summary: This study aimed to determine the genetic diversity among East African sorghum germplasm collections through agronomic and nutritional quality traits. Significant variations were detected, allowing for genetic gains through selection of promising lines for direct production or breeding.
Article
Agricultural Engineering
Vikender Kaur, Sunil S. Gomashe, J. Aravind, Shashank K. Yadav, Devender Dsingh, Shubhendra Singh Chauhan, Vinay Kumar, Balram Jat, Nandan Ramesh Tayade, Ankit Saroha, Nutan Kaushik, Sapna Langyan, Mamta Singh, Dhammaprakash Pandhari Wankhede, Kuldeep Singh, Ashok Kumar, Gyanendra Pratap Singh
Summary: India has the largest collection of linseed genetic resources, including a multi-purpose core collection that represents the maximum genetic diversity and representativeness. This core collection will provide important materials for linseed breeders and germplasm curators.
INDUSTRIAL CROPS AND PRODUCTS
(2023)
Article
Plant Sciences
Fatoumata Farida Traore, Adil El-Baouchi, Youness En-nahli, Kamal Hejjaoui, Mohamed Louay Metougui, Aladdin Hamwieh, Quahir Sohail, Tawffiq Istanbuli, Said Boughribil, Moez Amri
Summary: This study evaluated the agronomic performances and nutritional quality values of 282 advanced chickpea lines and found that only 4 genotypes exhibited both good agronomic performances and high nutritional quality. Significant differences and correlations were observed among the tested genotypes, with negative correlation between protein content and zinc concentration and positive correlations between grain filling time and micronutrients zinc, copper, and manganese, as well as macroelements potassium and magnesium.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Agronomy
Kehu Li, Lily Yan Wang, Huanhuan Ren, Yongyi Ge
Summary: This study conducted genotyping of functional marker genes for the USDA rice mini-core collection, and the results will contribute to the selection of parental materials with desired allele/gene combinations and phenotypes in rice breeding programs.
GENETIC RESOURCES AND CROP EVOLUTION
(2022)
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
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
Horticulture
Ken Hoshikawa, Ya-Ping Lin, Roland Schafleitner, Kenta Shirasawa, Sachiko Isobe, Duc Chinh Nguyen, Ryo Ohsawa, Yosuke Yoshioka
Summary: This study analyzed the genetic diversity and population structure of 465 Amaranthus tricolor accessions held by the World Vegetable Center genebank. A total of 10,509 SNPs were found, and 5,638 SNPs without missing data were identified in 440 accessions. These findings contribute to the research and breeding of this species.
SCIENTIA HORTICULTURAE
(2023)
Article
Plant Sciences
Ya-Ping Lin, Hung-Wei Chen, Pei-Min Yeh, Shashi S. Anand, Jiunn Lin, Juan Li, Thomas Noble, Ramakrishnan Nair, Roland Schafleitner, Maria Samsononova, Eric Bishop-von-Wettberg, Sergey Nuzhdin, Chau-Ti Ting, Robert J. Lawn, Cheng-Ruei Lee
Summary: By resequencing the whole genome of mungbean, this study investigated the global demographic history and molecular footprints of genes underlying 2 key domestication traits. The results revealed contrasting evolutionary patterns between the shattering resistance trait and stem determinacy trait in mungbean. This study highlights the complex genetic architecture of domestication and the limitations of genome-scan methods relying on hard selective sweeps.
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.