Article
Genetics & Heredity
Chin Jian Yang, Rodney N. Edmondson, Hans-Peter Piepho, Wayne Powell, Ian Mackay
Summary: This paper introduces the importance of multiparental Advanced Generation Inter-Cross (MAGIC) populations and the impact of various designs. To address the issues in current MAGIC population designs, the magicdesign R package and its Shiny app version have been developed to provide solutions for the future. Through this package, it is demonstrated that innovative MAGIC population designs can effectively increase haplotype diversity without the need for large crossing programs.
G3-GENES GENOMES GENETICS
(2021)
Article
Genetics & Heredity
Kathryn J. Michel, Dayane C. Lima, Hope Hundley, Vasanth Singan, Yuko Yoshinaga, Chris Daum, Kerrie Barry, Karl W. Broman, C. Robin Buell, Natalia de Leon, Shawn M. Kaeppler
Summary: The Stiff Stalk heterotic pool is an important germplasm resource in US maize breeding and has been widely used. Significant loci for flowering time and plant height traits were identified in a multi-parent population. Genomic prediction was used to effectively predict hybrid phenotypes without hybrid data.
Article
Genetics & Heredity
Karl W. Broman
Summary: A common step in the analysis of multiparent populations is genotype reconstruction, which involves identifying the origin of haplotypes using dense marker data. This process often utilizes a probability model to represent the distribution of founder alleles along chromosomes, considering their relative frequencies and the likelihood of exchanges among them. The model relies on the meiotic recombination process and mating design for the population. We present an approximate model that can be applied to various multiparent populations, implemented in the R/qtl2 software and demonstrated using publicly available data on Diversity Outbred and Collaborative Cross mice.
G3-GENES GENOMES GENETICS
(2022)
Article
Genetics & Heredity
Basten L. Snoek, Mark G. Sterken, Harm Nijveen, Rita J. M. Volkers, Joost Riksen, Philip C. Rosenstiel, Hinrich Schulenburg, Jan E. Kammenga
Summary: Studying genetic variation in gene expression is crucial for understanding complex traits, and the analysis of the mpRIL population in C. elegans reveals a large number of genes are influenced by polymorphic regulators, offering the potential to discover novel gene expression regulatory loci.
G3-GENES GENOMES GENETICS
(2021)
Article
Genetics & Heredity
Sarah G. Odell, Asher Hudson, Sebastien Praud, Pierre Dubreuil, Marie-Helene Tixier, Jeffrey Ross-Ibarra, Daniel E. Runcie
Summary: The search for quantitative trait loci is important in understanding complex traits in crops. This study compares different methods, including multiparent advanced generation intercross populations, for mapping quantitative trait loci in maize. The results show that each method has its own advantages and limitations in detecting quantitative trait loci for different agronomic traits. The study highlights the importance of considering different approaches and datasets in analyzing genetic information.
G3-GENES GENOMES GENETICS
(2022)
Article
Biochemistry & Molecular Biology
Laura Schmidt, John Jacobs, Thomas Schmutzer, Ahmad M. Alqudah, Wiebke Sannemann, Klaus Pillen, Andreas Maurer
Summary: To understand the natural variation of nitrogen uptake efficiency (UPE), a winter wheat population was phenotyped under different nitrogen levels and analyzed using a genome-wide association study. A total of 543 QTL related to nitrogen were identified, with 42 stable QTL detected across multiple weeks. Candidate genes associated with gibberellic acid-regulated growth and nitrate transporters were also identified. The results suggest that selection for UPE is beneficial under nitrogen-limited conditions.
Article
Genetics & Heredity
Chaozhi Zheng, Rodrigo R. Amadeu, Patricio R. Munoz, Jeffrey B. Endelman
Summary: A statistical framework for haplotype reconstruction in connected tetraploid F1 populations has been developed and implemented in PolyOrigin. This software is capable of handling populations with different numbers of parents and mating designs, reconstructing parental and offspring haplotypes based on genetic or physical maps, and demonstrating robustness to errors in input data and marker maps.
Article
Plant Sciences
Laura Schmidt, Kerstin A. Nagel, Anna Galinski, Wiebke Sannemann, Klaus Pillen, Andreas Maurer
Summary: This study analyzed the genetic control of root system architecture in a winter wheat population under different nitrogen treatments. The research found that 60 quantitative trait loci were specific to nitrogen treatments. Additionally, this study revealed a disparity in the genetic control of root development under low and high nitrogen supply, suggesting the need for targeted gene selection in breeding wheat varieties with improved nitrogen uptake efficiency.
Article
Genetics & Heredity
Brett A. Haines, Francesca Barradale, Beth L. Dumont
Summary: The study revealed that more than one-third of the Collaborative Cross (CC) mouse population exhibits significant sex ratio distortion (SRD) at wean, with twice as many male-biased strains than female-biased ones. These pervasive sex biases are stable over time and persist across different breeding environments, suggesting they may result from multilocus combinations of alleles. The mechanisms behind SRD are complex and diverse, with no single explanation for the population-wide phenomenon.
Article
Genetics & Heredity
Alexandra K. Lobo, Lindsay L. Traeger, Mark P. Keller, Alan D. Attie, Federico E. Rey, Karl W. Broman
Summary: In a Diversity Outbred mouse project with genotype data on 500 mice, including 297 with microbiome data, sample mix-ups and mixtures were identified using shotgun sequencing reads from fecal DNA, indicating the presence of mixtures of DNA from two mice in some microbiome samples.
G3-GENES GENOMES GENETICS
(2021)
Article
Genetics & Heredity
James R. Adams, Michiel E. de Vries, Chaozhi Zheng, Fred A. van Eeuwijk
Summary: This study investigates the genetic components of complex traits in hybrid potato populations. The results show the presence of nonadditive genetic effects in hybrid potato yield, with general combining ability effects being greater than specific combining ability effects. Tuber number is highly correlated with the genetic components of total yield. Tuber volume has the largest proportion of additive and nonadditive genetic variation.
G3-GENES GENOMES GENETICS
(2022)
Article
Genetics & Heredity
Luke M. Noble, Matthew Rockman, Henrique Teotonio
Summary: The Caenorhabditis elegans multiparental experimental evolution (CeMEE) panel is a collection of genome-sequenced, cryopreserved recombinant inbred lines useful for mapping the evolution and genetic basis of quantitative traits. The genotype and haplotype composition of CeMEE version 2 have been reported, with additive quantitative trait loci explaining 4% of trait variance detected.
G3-GENES GENOMES GENETICS
(2021)
Article
Genetics & Heredity
Matthew Vincent, Isabela Gerdes Gyuricza, Gregory R. Keele, Daniel M. Gatti, Mark P. Keller, Karl W. Broman, Gary A. Churchill
Summary: The Collaborative Cross and the Diversity Outbred mouse populations are related multiparental populations that are ideal for mapping genetic loci that regulate phenotypes. The QTLViewer software and website provide a graphical exploration of quantitative trait locus mapping and increase accessibility to these genetic resources.
G3-GENES GENOMES GENETICS
(2022)
Article
Genetics & Heredity
Yajie Duan, Qin Chen, Quanjia Chen, Kai Zheng, Yongsheng Cai, Yilei Long, Jieyin Zhao, Yaping Guo, Fenglei Sun, Yanying Qu
Summary: This study identified quantitative trait loci related to fiber strength in Gossypium barbadense and performed RNA sequencing and gene expression analysis to discover genes that regulate fiber strength. The findings provide insights into the genetic mechanism of fiber strength and offer new directions for improving cotton fiber strength.
G3-GENES GENOMES GENETICS
(2022)
Article
Biotechnology & Applied Microbiology
Waltram Ravelombola, Ainong Shi, Bao-Lam Huynh, Jun Qin, Haizheng Xiong, Aurora Manley, Lingdi Dong, Dotun Olaoye, Gehendra Bhattarai, Bazgha Zia, Huda Alshaya, Ibtisam Alatawi
Summary: This study evaluated salt tolerance in a cowpea population and identified SNP markers and candidate genes associated with salt tolerance. The results showed large variation in salt tolerance among cowpea lines and identified epistatic interactions. These findings have direct applications in breeding programs aiming to improve salt tolerance in cowpea through marker-assisted selection.
Article
Biochemistry & Molecular Biology
Fred A. van Eeuwijk, Daniela Bustos-Korts, Emilie J. Millet, Martin P. Boer, Willem Kruijer, Addie Thompson, Marcos Malosetti, Hiroyoshi Iwata, Roberto Quiroz, Christian Kuppe, Onno Muller, Konstantinos N. Blazakis, Kang Yu, Francois Tardieu, Scott C. Chapman
Article
Plant Sciences
Gregor Perich, Andreas Hund, Jonas Anderegg, Lukas Roth, Martin P. Boer, Achim Walter, Frank Liebisch, Helge Aasen
FRONTIERS IN PLANT SCIENCE
(2020)
Article
Agronomy
George Korontzis, Marcos Malosetti, Chaozhi Zheng, Chris Maliepaard, Han A. Mulder, Pim Lindhout, Roel F. Veerkamp, Fred A. van Eeuwijk
Article
Biology
Martin P. Boer, Hans-Peter Piepho, Emlyn R. Williams
JOURNAL OF AGRICULTURAL BIOLOGICAL AND ENVIRONMENTAL STATISTICS
(2020)
Article
Plant Sciences
Lukas Kronenberg, Steven Yates, Martin P. Boer, Norbert Kirchgessner, Achim Walter, Andreas Hund
Summary: This study investigates the genetic response of wheat stem elongation to temperature fluctuations, revealing a positive correlation between temperature response and the timing and height of stem elongation. Genome-wide association mapping identified temperature-responsive and temperature-irresponsive quantitative trait loci, with candidate genes related to flowering and growth pathways. Together with other genetic factors, these loci explained 71% of height variability, showcasing the potential of high-throughput field phenotyping for climate-resilient crop selection.
JOURNAL OF EXPERIMENTAL BOTANY
(2021)
Article
Automation & Control Systems
Puneet Mishra, Roy Sadeh, Maxime Ryckewaert, Ehud Bino, Gerrit Polder, Martin P. Boer, Douglas N. Rutledge, Ittai Herrmann
Summary: A generic data processing workflow combining chemometric approaches and deep learning is introduced for analyzing spectral imaging data in digital plant phenotyping experiments, extracting meaningful information for decision making by plant breeders. This approach accelerates the breeding of drought tolerant plant varieties.
CHEMOMETRICS AND INTELLIGENT LABORATORY SYSTEMS
(2021)
Article
Agriculture, Multidisciplinary
Puneet Mishra, Roy Sadeh, Ehud Bino, Gerrit Polder, Martin P. Boer, Douglas N. Rutledge, Ittai Herrmann
Summary: Close range spectra imaging of agricultural plants is commonly used for digital plant phenotyping, and a key challenge is separating plants from the background. This study proposes a novel approach combining chemometrics with deep learning for efficient segmentation of tall and wide spectral images. The results show high intersection over union (IoU) scores and efficient handling of the deep learning segmentation model.
COMPUTERS AND ELECTRONICS IN AGRICULTURE
(2021)
Article
Instruments & Instrumentation
Nur Fauzana Mohd Kasim, Puneet Mishra, Rob E. Schouten, Ernst J. Woltering, Martin P. Boer
Summary: This study compared a laboratory-based and a pocket-sized near-infrared spectrophotometer in predicting mango fruit firmness, finding similar performances between the two devices. The performance of batch specific models was improved by utilizing the BOSS variable selection routine.
INFRARED PHYSICS & TECHNOLOGY
(2021)
Article
Agronomy
Wenhao Li, Martin P. Boer, Chaozhi Zheng, Ronny V. L. Joosen, Fred A. van Eeuwijk
Summary: The study introduced an IBD-based mixed model approach for detecting QTLs and accounting for multilevel relatedness in various MPP designs. Through simulated and real data case studies, the method was found to be widely applicable and showed advantages over other tools in terms of mapping power and resolution.
THEORETICAL AND APPLIED GENETICS
(2021)
Article
Plant Sciences
Stefan Wilson, Chaozhi Zheng, Chris Maliepaard, Han A. Mulder, Richard G. F. Visser, Ate van der Burgt, Fred van Eeuwijk
Summary: The use of genomic prediction in tetraploid potato is increasing, prompting a comparison of different GP models. The study found that differences between shrinkage penalties and variable selection in GP models were negligible, and the inclusion of dominance effects could improve prediction accuracy for traits like tuber count. This highlights the potential for GP in tetraploid potato breeding.
FRONTIERS IN PLANT SCIENCE
(2021)
Article
Genetics & Heredity
Rodrigo R. Amadeu, Patricio R. Munoz, Chaozhi Zheng, Jeffrey B. Endelman
Summary: The study aimed to develop software for quantitative trait locus (QTL) mapping in autotetraploids and found that the number of progeny per parental haplotype (pph) largely determined the statistical power for QTL detection and accuracy of the estimated haplotype effects. The software also enables comparison of models with multiple QTL and nonadditive effects, with practical impacts in breeding programs.
Article
Genetics & Heredity
James R. Adams, Michiel E. de Vries, Chaozhi Zheng, Fred A. van Eeuwijk
Summary: This study investigates the genetic components of complex traits in hybrid potato populations. The results show the presence of nonadditive genetic effects in hybrid potato yield, with general combining ability effects being greater than specific combining ability effects. Tuber number is highly correlated with the genetic components of total yield. Tuber volume has the largest proportion of additive and nonadditive genetic variation.
G3-GENES GENOMES GENETICS
(2022)
Article
Biochemical Research Methods
Wenhao Li, Martin P. Boer, Bart-Jan van Rossum, Chaozhi Zheng, Ronny V. L. Joosen, Fred A. van Eeuwijk
Summary: In this study, we developed an R package called statgenMPP for QTL analysis in multi-parent populations (MPPs). The package provides easy-to-use functionalities including IBD calculations, mixed model solutions, and visualizations for QTL mapping in various MPP designs.
Article
Agronomy
Daniela Bustos-Korts, Martin P. Boer, Karine Chenu, Bangyou Zheng, Scott Chapman, Fred A. van Eeuwijk
Summary: This paper explores the impact of environmental quality and genotype sensitivity on crop yield through crop simulation and statistical modeling. The study reveals an increasing frequency of severe water and temperature stress in recent years in the NE Australian wheat-belt, highlighting the need for future varieties to adapt to more challenging conditions. By fitting response surfaces, predicted yields demonstrate changes in relative genotype performance with location and year type, providing insights into genotype by environment interactions.
