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
Biotechnology & Applied Microbiology
Jose Marcelo Soriano Viana, Antonio Augusto Franco Garcia
Summary: Additive variance is generally the most important component of genotypic variance. LD and inbreeding have a significant effect on the magnitude of the genetic variances and covariances. In general, the additive x additive variance is the most important component of epistatic variance.
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
Genetics & Heredity
Cory A. Weller, Susanne Tilk, Subhash Rajpurohit, Alan O. Bergland
Summary: Genetic association studies using inbred reference panels may not reflect the genetic basis of natural populations. To address this issue, researchers developed a new approach called the Hybrid Swarm, which involves outbreeding inbred lines for a few generations to reduce sequencing costs and make fine-scale genetic mapping cost-effective. Comparative studies showed the Hybrid Swarm method outperforms inbred lines for quantitative traits but not for monogenic traits.
G3-GENES GENOMES GENETICS
(2021)
Article
Biochemical Research Methods
Alejandro Therese Navarro, Giorgio Tumino, Roeland E. Voorrips, Paul Arens, Marinus J. M. Smulders, Eric van de Weg, Chris Maliepaard
Summary: This study investigates the impact of genetic diversity on bi-allelic and multi-allelic models, and finds that using multi-allelic models can improve the detection power and accuracy of QTLs in populations with multiple functional QTL alleles.
BMC BIOINFORMATICS
(2022)
Article
Plant Sciences
Maria Jose Gonzalo, Luciano Carlos da Maia, Inmaculada Najera, Carlos Baixauli, Giovanni Giuliano, Paola Ferrante, Antonio Granell, Maria Jose Asins, Antonio Jose Monforte
Summary: This study investigated the genetic control of reproductive traits under heat stress conditions in two populations of inbred lines derived from crosses between two S. pimpinellifolium accessions and two tomato cultivars. The results identified the impact of heat stress on reproductive traits, detected QTL clusters, and revealed several epistatic interactions in one population.
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
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
J. Lucas Boatwright, Zachary W. Brenton, Richard E. Boyles, Sirjan Sapkota, Matthew T. Myers, Kathleen E. Jordan, Savanah M. Dale, Nadia Shakoor, Elizabeth A. Cooper, Geoffrey P. Morris, Stephen Kresovich
Summary: Studying carbon partitioning in sorghum can uncover genetic diversity among individuals and variants, aiding in understanding the genetic basis of carbon partitioning and enhancing our understanding of genetic determinants affecting unique phenotypes within Poaceae species.
G3-GENES GENOMES GENETICS
(2021)
Article
Genetics & Heredity
J. Lucas Boatwright, Zachary W. Brenton, Richard E. Boyles, Sirjan Sapkota, Matthew T. Myers, Kathleen E. Jordan, Savanah M. Dale, Nadia Shakoor, Elizabeth A. Cooper, Geoffrey P. Morris, Stephen Kresovich
Summary: Sorghum bicolor, a photosynthetically efficient C-4 grass, is a significant source of grain, forage, fermentable sugars, and cellulosic fibers. Its genetic diversity and carbon partitioning traits make it a preferred biomass crop for bioenergy and bioindustrial applications. The study aims to dissect the genetic basis of key traits in sorghum using a carbon-partitioning nested association mapping (NAM) population, which will facilitate the identification of biomass-related traits and improve our understanding of genetic determinants in Poaceae plants.
G3-GENES GENOMES GENETICS
(2021)
Article
Ecology
Xinyao He, Muhammad Rezaul Kabir, Krishna K. Roy, Felix Marza, Aakash Chawade, Etienne Duveiller, Carolina Saint Pierre, Pawan K. Singh
Summary: In this study, two recombinant inbred line populations were used to map QTL associated with head blast resistance in wheat. A major QTL was identified on the 2NS/2AS translocation region in both populations, along with several additional QTL on different chromosomes. The results confirmed the importance of the 2NS/2AS translocation in wheat blast resistance and identified some novel QTL for potential use in breeding programs, while also suggesting the need for further investigation into QTL with higher and more stable effects.
Review
Plant Sciences
Andrew D. Gloss, Margaret C. Steiner, John Novembre, Joy Bergelson
Summary: Genome-wide association studies (GWAS) have provided valuable insights into the genetic architecture of trait variation, but they have not identified all relevant loci. To address the limitations of GWAS, focusing on local populations and using mapping panels sampled from narrow geographic localities could offer additional insights. This review highlights the major complicating factors in GWAS and presents evidence for the power of GWAS in local populations.
CURRENT OPINION IN PLANT BIOLOGY
(2023)
Article
Biology
David McLeod, Sylvain Gandon
Summary: Studying the evolution of multidrug resistance (MDR) by focusing on the dynamical equations for linkage disequilibrium (LD) can simplify calculations, generate more insight, and provide a unified framework for understanding the role of population structure.
Article
Plant Sciences
Zhengjie Chen, Dengguo Tang, Kun Hu, Lei Zhang, Yong Yin, Jixing Ni, Peng Li, Le Wang, Tingzhao Rong, Jian Liu
Summary: Four genomic regions associated with the variation of single vs. paired spikelets in the maize x teosinte advanced mapping populations were identified, providing insights into the genetic basis of this trait and facilitating fine mapping of QTL.
Article
Genetics & Heredity
Asher Hudson, Sarah G. Odell, Pierre Dubreuil, Marie-Helene Tixier, Sebastien Praud, Daniel E. Runcie, Jeffrey Ross-Ibarra
Summary: Genotype-by-environment interactions are important for crop breeding and understanding environmental adaptation. This study found that genotype-by-environment interactions contributed as much as genotypic effects to the variation in important agronomic traits. Genetic correlations between traits also changed across environments, even among traits with low genotype-by-environment variance. A genome-wide association study identified only a small number of markers associated with genotype-by-environment interactions, possibly due to the polygenic nature of these interactions.
G3-GENES GENOMES GENETICS
(2022)
