Article
Biochemistry & Molecular Biology
Shuo Gao, Tiantian Lu, Hongbing She, Zhaosheng Xu, Helong Zhang, Zhiyuan Liu, Wei Qian
Summary: This study identified the RPF2 gene, which confers resistance against spinach downy mildew, through molecular marker analysis and sequence analysis. A molecular marker, RPF2-IN12821, was developed based on the sequence variation of the Spo12821 gene. These findings contribute to the understanding of the genetic basis of resistance against downy mildew in spinach and have implications for breeding resistant lines in the future.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biochemistry & Molecular Biology
Hongchen Lu, Hanfei Wu, Guangfeng Zhu, Caijun Yin, Lun Zhao, Jing Wen, Bin Yi, Chaozhi Ma, Jinxing Tu, Tingdong Fu, Jinxiong Shen
Summary: This study reveals that the imbalance of the CLV-WUS feedback loop may contribute to the abnormal development of multi-inflorescence in rapeseed. The BnaMI gene was successfully fine-mapped to a 55 kb genomic region using a traditional mapping approach, and five candidate genes were identified.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Plant Sciences
Abate Mekonnen Solomon, Tae-Gun Kim, Koeun Han, Hea-Young Lee, Abhinandan Patil, Muhammad Irfan Siddique, Jeonghwan Ahn, Byoung-Cheorl Kang
Summary: The orientation of pepper fruits is controlled by a dominant gene, which was identified and localized on chromosome 12 through QTL analysis and GWAS. The study narrowed down the region of interest based on two markers completely cosegregated with the phenotype, providing insights for understanding pepper fruit development and breeding for fruit orientation.
FRONTIERS IN PLANT SCIENCE
(2021)
Article
Biochemistry & Molecular Biology
Samar M. Esmail, Diego Jarquin, Andreas Boerner, Ahmed Sallam
Summary: This study evaluated the NB and PM resistance of 122 diverse barley genotypes from 34 countries and found high genetic variation among the genotypes. No significant correlation was found between PM and NB resistance, but 21 genotypes immune to both diseases were identified. Furthermore, GWAS identified SNP markers associated with increased resistance to PM and NB.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2023)
Article
Plant Sciences
Qibin Wu, Yachun Su, Yong-Bao Pan, Fu Xu, Wenhui Zou, Beibei Que, Peixia Lin, Tingting Sun, Michael P. P. Grisham, Liping Xu, Youxiong Que
Summary: In this study, a large number of progenies were generated by crossing different sugarcane varieties, and the differential gene expression between resistant and susceptible progenies was analyzed by RNA sequencing. SNP markers and candidate genes associated with smut resistance were identified, and a potential molecular mechanism of sugarcane's resistance to smut was proposed.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Plant Sciences
Shuangjuan Yang, Xinxin Tian, Zhiyong Wang, Xiaochun Wei, Yanyan Zhao, Henan Su, Xiaobin Zhao, Baoming Tian, Yuxiang Yuan, Xiao-Wei Zhang
Summary: This study successfully fine-mapped the white flower gene BrWF3 in Chinese cabbage and identified its most likely candidate gene. Functional and sequence analysis revealed that BrWF3 may be involved in the production of xanthophyll esters, impacting chromoplast development. Furthermore, a functional marker TXBH83 was developed for BrWF3, providing valuable information for breeding in Chinese cabbage.
FRONTIERS IN PLANT SCIENCE
(2021)
Article
Biochemistry & Molecular Biology
Bao Li, Tonghua Wang, Yiming Guo, Xinhong Liu, Lichao Deng, Liang Qu, Mei Li
Summary: In this study, a major QTL conferring branching-related traits was identified in rapeseed and eight candidate genes were discovered in the surrounding region. Comparative and expression analysis revealed four promising candidate genes, providing a foundation for unraveling the genetic and molecular mechanisms controlling branching in rapeseed.
MOLECULAR GENETICS AND GENOMICS
(2022)
Article
Agronomy
M. Mehnaz, P. Dracatos, A. Pham, T. March, A. Maurer, K. Pillen, K. Forrest, T. Kulkarni, M. Pourkheirandish, R. F. Park, D. Singh
Summary: A newly discovered gene Rph28 conferring resistance to barley leaf rust was fine-mapped on chromosome 5H from wild barley. The gene, identified in a Hordeum vulgare ssp. spontaneum-derived barley line, was found to be broadly effective against a diverse set of Australian P. hordei pathotypes. Further genetic analysis confirmed the presence of a single dominant gene for resistance in the identified barley line.
THEORETICAL AND APPLIED GENETICS
(2021)
Article
Agronomy
Feiyan Qi, Ziqi Sun, Hua Liu, Zheng Zheng, Li Qin, Lei Shi, Qingzheng Chen, Haidong Liu, Xiufang Lin, Lijuan Miao, Mengdi Tian, Xiao Wang, Bingyan Huang, Wenzhao Dong, Xinyou Zhang
Summary: This study fine mapped a major QTL qBWA12 for bacterial wilt resistance in peanut and identified a useful KASP marker for breeding disease-resistant varieties. The qBWA12 QTL was stably detected in multiple developmental stages and trial years and nine potential NBS-LRR genes were found in the candidate gene region.
THEORETICAL AND APPLIED GENETICS
(2022)
Article
Plant Sciences
Jian Ma, Congcong Li, Jiaxing Tian, Yanhong Qiu, Lihua Geng, Jianshe Wang
Summary: In this study, a GSB-resistant inbred line, H55R, was identified from screening 260 melon germplasm resources. Genetic analysis revealed that the GSB resistance in H55R was controlled by a single dominant gene, tentatively named Gsb-7(t). Through bulked segregant analysis and chromosome walking strategies, the Gsb-7(t) gene was delimited to a 140-kb interval on chromosome 7, with the MELO3C010403-T2 transcript as the most likely candidate gene. These findings provide new genetic resources for the development of GSB-resistant melon cultivars in the future.
Article
Plant Sciences
Yaping Wang, Antje Habekuss, Murukarthick Jayakodi, Martin Mascher, Rod J. Snowdon, Andreas Stahl, Janina Fuss, Frank Ordon, Dragan Perovic
Summary: In this study, 423 F-4 segmental recombinant inbred lines were developed from crosses of Chikurin Ibaraki 1 with two BaMMV-susceptible cultivars, Igri and Uschi. Using a set of 32 KASP assays, the target locus was narrowed down and several candidate genes were identified for further functional analysis.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Horticulture
Huangying Shu, Chengyao He, Muhammad Ali Mumtaz, Yuanyuan Hao, Yan Zhou, Weiheng Jin, Jie Zhu, Wenlong Bao, Shanhan Cheng, Guopeng Zhu, Zhiwei Wang
Summary: This study constructed a high-density genetic map using two different colored pepper germplasms, and found that fruit color is controlled by a single locus. By transforming two markers into dCAPS markers, a potential gene associated with fruit color was identified. These findings provide fundamental knowledge and a new resource for the genetic improvement and molecular breeding of pepper fruit color.
SCIENTIA HORTICULTURAE
(2023)
Article
Biology
Dominik Karl Lagler, Elisabeth Hannemann, Kim Eck, Juergen Klawatsch, Doris Seichter, Ingolf Russ, Christian Mendel, Gesine Luehken, Stefan Krebs, Helmut Blum, Maulik Upadhyay, Ivica Medugorac
Summary: This study aimed to analyze natural tail length variation in Merinolandschaf and identify causal alleles for the short tail phenotype segregating within long-tailed breeds. The research discovered a SNP in the first exon of HOXB13 and a SINE element in the promoter of HOXB13 as potential candidates. These findings have implications for breeding shorter-tailed sheep, improving animal welfare, and understanding differential embryonic development.
COMMUNICATIONS BIOLOGY
(2022)
Article
Agronomy
Nastacia Adler-Berke, Yitzchak Goldenberg, Yariv Brotman, Irina Kovalski, Amit Gal-On, Tirza Doniger, Rotem Harel-Beja, Christelle Troadec, Abdelhafid Bendahmane, Michel Pitrat, Catherine Dogimont, Nurit Katzir, Rafael Perl-Treves
Summary: This study successfully performed positional cloning of the Zym locus using multiple mapping populations, constructing a high-resolution genetic map and laying the foundation for functional studies of this important locus.
Article
Plant Sciences
Ruiqiong Li, Jianan Zou, Dongming Sun, Yan Jing, Depeng Wu, Ming Lian, Weili Teng, Yuhang Zhan, Wenbin Li, Xue Zhao, Yingpeng Han
Summary: This study identified 15 QTLs associated with soybean isoflavone content, with a novel locus qISO19-1 identified on chromosome 19. The candidate gene GmMT1 was found to positively correlate with isoflavone content, and overexpression of GmMT1 increased isoflavone contents in soybeans while also improving resistance to pathogenic infection.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Multidisciplinary Sciences
Murukarthick Jayakodi, Agnieszka A. Golicz, Jonathan Kreplak, Lavinia Fechete, Deepti Angra, Petr Bednar, Elesandro Bornhofen, Hailin Zhang, Raphael Boussageon, Sukhjiwan Kaur, Kwok Cheung, Jana Cizkova, Heidrun Gundlach, Asis Hallab, Baptiste Imbert, Gabriel Keeble-Gagnere, Andrea Koblizkova, Lucie Kobrlova, Petra Krejci, Troels W. Mouritzen, Pavel Neumann, Marcin Nadzieja, Linda Kaergaard Nielsen, Petr Novak, Jihad Orabi, Sudharsan Padmarasu, Tom Robertson-Shersby-Harvie, Laura Avila Robledillo, Andrea Schiemann, Jaakko Tanskanen, Petri Toronen, Ahmed O. Warsame, Alexander H. J. Wittenberg, Axel Himmelbach, Gregoire Aubert, Pierre-Emmanuel Courty, Jaroslav Dolezel, Liisa U. Holm, Luc L. Janss, Hamid Khazaei, Jiri Macas, Martin Mascher, Petr Smykal, Rod J. Snowdon, Nils Stein, Frederick L. Stoddard, Jens Stougaard, Nadim Tayeh, Ana M. Torres, Bjorn Usadel, Ingo Schubert, Donal Martin O'Sullivan, Alan H. Schulman, Stig Uggerhoj Andersen
Summary: Increasing the proportion of locally produced plant protein in diets could reduce greenhouse gas emissions and loss of biodiversity. However, plant protein production is hindered by the lack of a cool-season legume equivalent to soybean. This study presents a high-quality genome assembly of faba bean and demonstrates its potential for sustainable protein production.
Article
Biochemistry & Molecular Biology
Ivona Kubalova, Amanda Souza Camara, Petr Capal, Tomas Beseda, Jean-Marie Rouillard, Gina Marie Krause, Katerina Holusova, Helena Toegelova, Axel Himmelbach, Nils Stein, Andreas Houben, Jaroslav Dolezel, Martin Mascher, Hana Simkova, Veit Schubert
Summary: Hi-C analysis, biopolymer modeling, and structured illumination microscopy were used to reveal the chromonema, a helically-wound chromatin thread forming barley mitotic chromatids. The helical turn size varies along the chromosome length and intermingles chromatin from adjacent turns. The observable dimensions of sister chromatid exchanges further support the helical chromonema model.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Multidisciplinary Sciences
Yi-Tzu Kuo, Amanda Souza Camara, Veit Schubert, Pavel Neumann, Jiri Macas, Michael Melzer, Jianyong Chen, Jorg Fuchs, Simone Abel, Evelyn Klocke, Bruno Huettel, Axel Himmelbach, Dmitri Demidov, Frank Dunemann, Martin Mascher, Takayoshi Ishii, Andre Marques, Andreas Houben
Summary: This study reveals the holocentric characteristics of the lilioid plant Chionographis japonica, showing that its centromeres consist of evenly spaced units and differ from other known holocentric species. The study also finds that C. japonica forms clustered centromeres similar to monocentric species, but the large-scale chromatin arrangement is different. The formation of holocentromeres from interphase centromere clusters was simulated using polymer simulations.
NATURE COMMUNICATIONS
(2023)
Article
Multidisciplinary Sciences
Yongyu Huang, Roop Kamal, Nandhakumar Shanmugaraj, Twan Rutten, Venkatasubbu Thirulogachandar, Shuangshuang Zhao, Iris Hoffie, Goetz Hensel, Jeyaraman Rajaraman, Yudelsy Antonia Tandron Moya, Mohammad-Reza Hajirezaei, Axel Himmelbach, Naser Poursarebani, Udda Lundqvist, Jochen Kumlehn, Nils Stein, Nicolaus von Wiren, Martin Mascher, Michael Melzer, Thorsten Schnurbusch
Summary: Flowering plants with indeterminate inflorescences often produce more floral structures than necessary. In barley (Hordeum vulgare L.), the initiation and maturation of floral primordia are molecularly decoupled. Initiation is primarily controlled by flowering-time genes, while floral growth is regulated by barley CCT MOTIF FAMILY 4 (HvCMF4) through light signaling, chloroplast, and vascular developmental programs. Mutations in HvCMF4 result in increased primordia death and pollination failure due to reduced rachis greening and limited energy supply to floral tissues. HvCMF4 is proposed to be a light sensory factor that coordinates floral initiation and survival with the vascular-localized circadian clock. Notably, stacking beneficial alleles for primordia number and survival has positive implications for grain production. These findings offer insights into the molecular mechanisms of grain number determination in cereal crops.
Article
Biochemistry & Molecular Biology
Charlotte Ost, Hieu Xuan Cao, Thuy Linh Nguyen, Axel Himmelbach, Martin Mascher, Nils Stein, Klaus Humbeck
Summary: Plants respond to drought by reprogramming gene expression with the help of the phytohormone abscisic acid (ABA). This study investigated the response of barley plants to drought at both the epigenome and transcriptome levels. It was found that specific genes involved in ABA signaling and related pathways were induced in response to drought, including two members of the PP2C family. Histone modifications, such as H3K9 acetylation, were also found to be more sensitive to drought compared to H3K4 trimethylation.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Biographical-Item
Biotechnology & Applied Microbiology
Rajeev K. K. Varshney, Nils Stein, Jochen Reif
Summary: Professor Graner has made significant contributions to the field of international crop plant genomics research over the past four decades. His work includes the development of the first integrated RFLP map of barley and advancements in functional genomics. He has also played a key role in plant genetic resources conservation and utilization.
PLANT BIOTECHNOLOGY JOURNAL
(2023)
Article
Plant Sciences
Louis McLeod, Lorenzo Barchi, Giorgio Tumino, Pasquale Tripodi, Jeremy Salinier, Christophe Gros, Hatice Filiz Boyaci, Ramazan Ozalp, Yelena Borovsky, Roland Schafleitner, Derek Barchenger, Richard Finkers, Matthijs Brouwer, Nils Stein, Mark Timothy Rabanus-Wallace, Giovanni Giuliano, Roeland Voorrips, Ilan Paran, Veronique Lefebvre
Summary: Investigating crop diversity through GWAS on core collections helps in deciphering the genetic determinants of complex traits. The G2P-SOL project conducted multi-environment GWAS on a diverse subset of Capsicum annuum accessions and detected environment-specific and multi-environment QTLs for various agronomic traits. This study identified candidate genes potentially implicated in fruit flavor, color, size, shape, plant productivity, vigor, and earliness traits.
Article
Plant Sciences
Lorenzo Barchi, Giuseppe Aprea, M. Timothy Rabanus-Wallace, Laura Toppino, David Alonso, Ezio Portis, Sergio Lanteri, Luciana Gaccione, Emmanuel Omondi, Maarten van Zonneveld, Roland Schafleitner, Paola Ferrante, Andreas Boerner, Nils Stein, Maria Jose Diez, Veronique Lefebvre, Jeremy Salinier, Hatice Filiz Boyaci, Richard Finkers, Matthijs Brouwer, Arnaud G. Bovy, Giuseppe Leonardo Rotino, Jaime Prohens, Giovanni Giuliano
Summary: Eggplant is an important crop widely grown and consumed in Asia, the Mediterranean basin, and Southeast Europe. This study reports the largest collection of georeferenced and genotyped eggplant and its wild relatives to date, providing insights into its domestication centers and migration patterns. The data indicates the existence of at least two main domestication centers in Southeast Asia and the Indian subcontinent, with limited genetic exchange between them. The study also highlights the preservation of "local" phenotypic characteristics in eggplant populations.
Article
Agronomy
Ronja Wonneberger, Miriam Schreiber, Allison Haaning, Gary J. Muehlbauer, Robbie Waugh, Nils Stein
Summary: Plant breeding and selection have greatly improved agronomic and quality traits of modern crops. In this study, the genetic composition of barley cultivars from the past 190 years was characterized using SNP marker data. A distinct centromeric haplotype on chromosome 5H, introduced in the early to mid-twentieth century, has been under positive selection and non-recombining for the past 70 years. This haplotype carries genes conferring highly beneficial traits and is found in modern European barley germplasm and may have been introduced from North African landraces.
THEORETICAL AND APPLIED GENETICS
(2023)
Article
Agronomy
M. Timothy Rabanus-Wallace, Nils Stein
Summary: Accurate and complete taxonomic assignments are crucial for maximizing the benefits of genebank resources. Genebank genomics provides a potential solution by using genetic methods, but since the number of samples is too large, automation is necessary. A recent study on peppers sequenced over 10,000 genebank accessions and presented an opportunity to develop automated taxonomic correction methods.
THEORETICAL AND APPLIED GENETICS
(2023)
Article
Plant Sciences
Samira El Hanafi, Yong Jiang, Zakaria Kehel, Albert W. Schulthess, Yusheng Zhao, Martin Mascher, Max Haupt, Axel Himmelbach, Nils Stein, Ahmed Amri, Jochen C. Reif
Summary: Genome-wide prediction is a powerful tool in breeding and shows promise for enhancing the use of genebank material. By predicting the performance of plant genetic resources, the hidden potential and information gap in genebanks can be addressed, supporting prebreeding programs. Across-genebank predictions using different genebanks as training and test sets can significantly improve the predictive characterization of germplasm collections.
FRONTIERS IN PLANT SCIENCE
(2023)
Article
Biology
Patrick Koenig, Sebastian Beier, Martin Mascher, Nils Stein, Matthias Lange, Uwe Scholz
Summary: DivBrowse is a web application that allows interactive visualization and exploratory analysis of genomic diversity data stored in VCF files. It combines BLAST as an entry point with features like principal component analysis, providing a unique set of capabilities for studying genomic biodiversity datasets. The application also supports data interoperability and integration with existing web applications.
Correction
Biology
Patrick Konig, Sebastian Beier, Martin Mascher, Nils Stein, Matthias Lange, Uwe Scholz