Article
Agronomy
Yong Jia, Sharon Westcott, Tianhua He, Lee Anne McFawn, Tefera Angessa, Camila Hill, Cong Tan, Xiaoqi Zhang, Gaofeng Zhou, Chengdao Li
Summary: This study identified 37 QTL loci related to grain kernel discoloration through genome-wide association studies in a diverse barley germplasm, including two major QTL hotspots. There is a genetic correlation between grain brightness and black point traits, with black point traits being more susceptible to environmental influence and grain brightness traits having higher heritability.
Article
Fisheries
Xin He, Yushan Liao, Zexin Yang, Hongxing Liu, Shi Wang, Yongbo Bao
Summary: The blood clam Tegillarca granosa is a commercially important bivalve species. This study conducted genome-wide association studies and identified 39 SNP markers associated with the growth traits of T. granosa. Additionally, 27 candidate genes potentially involved in T. granosa growth were identified. Enrichment analysis highlighted the role of transmembrane transport, immune system function, protein family metabolism, and JAK-STAT signaling pathways in T. granosa growth.
Article
Fisheries
Baohua Duan, Tongxu Kang, Haifu Wan, Shumei Mu, Yueqiang Guan, Weibiao Liu, Zejian Li, Yang Tian, Yuqin Ren, Xianjiang Kang
Summary: The SIF gene in the swimming crab (Portunus trituberculatus) was investigated to understand its biological function. The study found that the SIF gene had higher expression in the fast-growing group compared to the slow-growing group, and it was ubiquitously expressed in various tissues, with the highest expression in the heart. Additionally, four SNPs in the SIF gene were found to be significantly associated with growth traits in the swimming crab.
AQUACULTURE REPORTS
(2023)
Article
Plant Sciences
Gianluca Bretani, Salar Shaaf, Alessandro Tondelli, Luigi Cattivelli, Stefano Delbono, Robbie Waugh, William Thomas, Joanne Russell, Hazel Bull, Ernesto Igartua, Ana M. M. Casas, Pilar Gracia, Roberta Rossi, Alan H. H. Schulman, Laura Rossini
Summary: In this study, a total of 261 barley accessions were phenotyped for culm diameter and culm wall thickness using an image analysis-based protocol. Genome-wide association studies revealed 192 quantitative trait loci (QTLs) associated with these traits, including 21 loci that impact lodging without affecting plant height. This research provides insights into the genetic control of culm morphology in barley and highlights the potential for improving lodging resistance and yield stability.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Biochemistry & Molecular Biology
Seong-Hoon Kim, Rupesh Tayade, Byeong-Hee Kang, Bum-Soo Hahn, Bo-Keun Ha, Yoon-Ha Kim
Summary: This study conducted a genome-wide association study (GWAS) on 357 soybean landraces to analyze root traits. It identified 112 significant SNP loci and 55 putative candidate genes. These findings suggest that the combined approach of SNP array and GWAS can be used to understand the genetic basis of soybean root traits and improve soybean breeding.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Irina V. Rozanova, Yuriy N. Grigoriev, Vadim M. Efimov, Alexander V. Igoshin, Elena K. Khlestkina
Summary: This study conducted a genome-wide association study on 94 barley varieties and identified 64 SNP markers significantly associated with spike productivity traits. Among them, 23 SNP markers were validated and 14 markers on chromosomes 2H, 4H and 5H were suggested for marker-assisted breeding programs.
Article
Plant Sciences
Liqiang He, Yao Sui, Yanru Che, Huixian Wang, Khalid Y. Rashid, Sylvie Cloutier, Frank M. You
Summary: This study evaluated the resistance of 445 flax accessions to pasmo, a disease caused by the fungus Septoria linicola. Genetic analysis identified numerous QTNs associated with pasmo resistance, providing potential targets for improving resistance in flax breeding programs. Additionally, the study discovered candidate genes and gene-environment interactions that contribute to pasmo resistance in flax.
FRONTIERS IN PLANT SCIENCE
(2023)
Article
Agronomy
Prabin Bajgain, James A. Anderson
Summary: The study genetically mapped six domestication traits of intermediate wheatgrass and identified markers and haplotype blocks significantly associated with these traits. Results suggest that increasing the frequency of favorable alleles in IWG populations via marker-assisted selection and genomic selection is an effective approach to improve IWG's domestication traits.
Article
Plant Sciences
M. Q. U. Farooqi, David Moody, Guihua Bai, Amy Bernardo, Paul St. Amand, Art J. Diggle, Zed Rengel
Summary: This study identified 1199 potential QTLs associated with root traits in barley through phenotypic and genotypic analysis of 191 barley accessions. Furthermore, it identified important genomic regions related to root traits.
FRONTIERS IN PLANT SCIENCE
(2023)
Article
Plant Sciences
Cassia da Silva Linge, Lichun Cai, Wanfang Fu, John Clark, Margaret Worthington, Zena Rawandoozi, David H. Byrne, Ksenija Gasic
Summary: The research team conducted a multi-locus genome wide association study on 620 individuals from three public fresh market peach breeding programs, revealing 967 quantitative trait nucleotides (QTNs) associated with fruit quality traits.
FRONTIERS IN PLANT SCIENCE
(2021)
Article
Genetics & Heredity
Yang Da, Zuoxiang Liang, Dzianis Prakapenka
Summary: The rapid growth in genomic selection data presents unprecedented opportunities to discover and utilize complex genetic effects for improving phenotypes, but there is a lack of methodology. This study developed multifactorial methods to investigate the contributions of global low-order and local high-order epistasis effects to phenotypic variance and the accuracy of genomic prediction of quantitative traits. These methods provide a capability to evaluate the contributions of complex genetic effects to phenotypic variance and prediction accuracy and discover and utilize complex genetic effects for improving quantitative trait phenotypes.
FRONTIERS IN GENETICS
(2022)
Article
Agriculture, Dairy & Animal Science
Yang Li, Lei Pu, Liangyu Shi, Hongding Gao, Pengfei Zhang, Lixian Wang, Fuping Zhao
Summary: Number of teats is crucial for lactating sows. Genome-wide association studies identified significant SNPs related to teat number traits, providing new insights into the genetic mechanism of these traits in pigs.
Article
Plant Sciences
Hua Zhong, Shuai Liu, Tong Sun, Weilong Kong, Xiaoxiao Deng, Zhaohua Peng, Yangsheng Li
Summary: By conducting single-locus and multi-locus genome-wide association studies on a panel of 529 rice core varieties, a total of 152, 106, 12, 111, and 64 SNPs associated with various yield-related traits were detected. Furthermore, 74 significant quantitative trait nucleotides were identified across different multi-locus GWAS methods, and 20 common QTNs were discovered by both single-locus and multi-locus methods. Two candidate key genes (LOC_Os09g02830 and LOC_Os07g31450) were found to affect grain width and thousand-grain weight, respectively.
Article
Agriculture, Dairy & Animal Science
Jianmei Chen, Ziyi Wu, Ruxue Chen, Zhihui Huang, Xuelei Han, Ruimin Qiao, Kejun Wang, Feng Yang, Xin-Jian Li, Xiu-Ling Li
Summary: In this study, genome-wide association analyses were performed to explore genes related to sow reproductive traits in French White sows. A notable region and four promising genes were detected, providing a theoretical basis for subsequent molecular breeding. The findings of this study are of great importance for improving the economic benefits of the pig industry.
Article
Cardiac & Cardiovascular Systems
Jairo Lumpuy-Castillo, Claudia Vales-Villamarin, Ignacio Mahillo-Fernandez, Iris Perez-Nadador, Leandro Soriano-Guillen, Oscar Lorenzo, Carmen Garces
Summary: This study analyzed the relationship between ACE2 polymorphisms and cardiovascular risk factors in children, and found that certain ACE2 mutations are associated with obesity and hyperlipidemia in females.
FRONTIERS IN CARDIOVASCULAR MEDICINE
(2022)
Article
Biotechnology & Applied Microbiology
Davoud Torkamaneh, Jerome Laroche, Babu Valliyodan, Louise O'Donoughue, Elroy Cober, Istvan Rajcan, Ricardo Vilela Abdelnoor, Avinash Sreedasyam, Jeremy Schmutz, Henry T. Nguyen, Francois Belzile
Summary: The GmHapMap is a worldwide haplotype map for soybean that covers extensive diversity and can be applied in soybean genomics and breeding. Genetic data analysis can help identify candidate causal SNPs and alleles that contribute to phenotypic differences. Additionally, predicting loss-of-function mutations allows for exploration of gene function.
PLANT BIOTECHNOLOGY JOURNAL
(2021)
Letter
Biotechnology & Applied Microbiology
Davoud Torkamaneh, Jerome Laroche, Brian Boyle, David L. Hyten, Francois Belzile
PLANT BIOTECHNOLOGY JOURNAL
(2021)
Article
Agronomy
Jean Carlos Alekcevetch, Andre Luiz de Lima Passianotto, Everton Geraldo Capote Ferreira, Adriana Brombini dos Santos, Danielle Cristina Gregorio da Silva, Waldir Pereira Dias, Francois Belzile, Ricardo Vilela Abdelnoor, Francismar Correa Marcelino-Guimaraes
Summary: A locus on chromosome 13 associated with resistance to M. javanica was identified by combining GWAS, resequencing, genetic mapping, and expression profiling. SNPs in this region were able to distinguish between susceptible and resistant soybean accessions, with 25 accessions sharing the resistance haplotype. Additionally, two SNP-based TaqMan (R) assays were developed and validated as important tools for marker-assisted selection in soybean breeding programs to introduce resistance to root-knot nematodes.
THEORETICAL AND APPLIED GENETICS
(2021)
Article
Genetics & Heredity
Wayne Xu, James R. Tucker, Wubishet A. Bekele, Frank M. You, Yong-Bi Fu, Raja Khanal, Zhen Yao, Jaswinder Singh, Brian Boyle, Aaron D. Beattie, Francois Belzile, Martin Mascher, Nicholas A. Tinker, Ana Badea
Summary: The genome sequence of Canadian two-row malting barley cultivar AAC Synergy was assembled for the first time using a combination of sequencing technologies, resulting in a contiguous assembly with high gene completeness. This represents an important genomic resource for barley research in Canada.
G3-GENES GENOMES GENETICS
(2021)
Article
Biotechnology & Applied Microbiology
Davoud Torkamaneh, Marc-Andre Lemay, Francois Belzile
Summary: The construction of a pan-genome for cultivated soybean reveals a significant amount of novel genes, with over 90.6% of genes in the core genome shared by 99% of accessions. The PanSoy represents a major advancement in capturing the extent of genetic variation in cultivated soybean, serving as a valuable resource for soybean genomics research and breeding.
PLANT BIOTECHNOLOGY JOURNAL
(2021)
Article
Agronomy
Martine Jean, Elroy Cober, Louise O'Donoughue, Istvan Rajcan, Francois Belzile
Summary: Genomic predictions of cross performance can help breeders improve multiple key traits simultaneously, leading to greater genetic gains with fewer resources.
Article
Agronomy
T. D. Vuong, H. Sonah, G. Patil, C. Meinhardt, M. Usovsky, K. S. Kim, F. Belzile, Z. Li, R. Robbins, J. G. Shannon, H. T. Nguyen
Summary: Genetic analysis identified a unique combination of major QTL for resistance to important soybean nematodes in one soybean accession, providing comprehensive insights for researchers to choose a cost-effective and efficient platform for QTL mapping.
THEORETICAL AND APPLIED GENETICS
(2021)
Article
Biology
Marc-Andre Lemay, Jonas A. Sibbesen, Davoud Torkamaneh, Jeremie Hamel, Roger C. Levesque, Francois Belzile
Summary: Structural variants (SVs) are relatively long genomic variations implicated in various processes. Discovering SVs based on short reads is challenging, but the increasing availability of long-read technologies has facilitated SV discovery. Results show that long-read and short-read sequencing technologies can be efficiently combined to enhance SV analysis.
Article
Biotechnology & Applied Microbiology
Amina Abed, Ana Badea, Aaron Beattie, Raja Khanal, James Tucker, Francois Belzile
Summary: This study developed a high-resolution consensus linkage map based on GBS-derived SNPs for barley genetic studies, providing useful information for genomic research and genotyping tools.
Article
Plant Sciences
Genevieve Arsenault-Labrecque, Parthasarathy Santhanam, Yanick Asselin, Benjamin Cinget, Amandine Lebreton, Caroline Labbe, Francois Belzile, Mark Gijzen, Richard R. Belanger
Summary: In this study, a specific Avr gene interacting with the soybean resistance gene Rps8 was identified using genotyping-by-sequencing approach. The interaction between Rps8 and Avr3a was confirmed through functional analyses. This study also revealed a clear distinction between Rps3a and Rps8, which has not been previously reported.
MOLECULAR PLANT PATHOLOGY
(2022)
Article
Multidisciplinary Sciences
Honore Tekeu, Eddy L. M. Ngonkeu, Sebastien Belanger, Pierre F. Djocgoue, Amina Abed, Davoud Torkamaneh, Brian Boyle, Patrick M. Tsimi, Wuletaw Tadesse, Martine Jean, Francois Belzile
Summary: This study demonstrated that GBS can provide highly accurate SNP data in hexaploid wheat to analyze genetic characteristics related to grain length and width, as well as to study the genomic regions controlling these traits. Seven SNPs associated with grain size were identified, revealing three QTLs and a potential candidate gene located on chromosome 2D. These findings have implications for enhancing wheat productivity through breeding.
SCIENTIFIC REPORTS
(2021)
Article
Plant Sciences
Maxime de Ronne, Parthasarathy Santhanam, Benjamin Cinget, Caroline Labbe, Amandine Lebreton, Heng Ye, Tri D. Vuong, Haifei Hu, Babu Valliyodan, David Edwards, Henry T. Nguyen, Francois Belzile, Richard Belanger
Summary: A new P. sojae resistance QTL with a relatively major effect was identified in this study, spanning a region of about 500 kb on chromosome 15. Plants carrying the favorable allele at this QTL showed a 60% increase in resistance. This offers new opportunities for developing improved soybean cultivars with broad resistance to P. sojae through marker-assisted selection.
Review
Plant Sciences
Francois Belzile, Martine Jean, Davoud Torkamaneh, Aurelie Tardivel, Marc-Andre Lemay, Chiheb Boudhrioua, Genevieve Arsenault-Labrecque, Chloe Dussault-Benoit, Amandine Lebreton, Maxime de Ronne, Vanessa Tremblay, Caroline Labbe, Louise O'Donoughue, Vincent-Thomas Boucher St-Amour, Tanya Copley, Eric Fortier, Dave T. Ste-Croix, Benjamin Mimee, Elroy Cober, Istvan Rajcan, Tom Warkentin, Eric Gagnon, Sylvain Legay, Jerome Auclair, Richard Belanger
Summary: The SoyaGen project aims to develop genomics-derived solutions to challenges faced by soybean breeders. As a result of collaborative efforts, the project has delivered SNP datasets, SNP markers, diagnostic tools, and a genomic prediction approach for soybean molecular breeding. These tools and approaches have broad applicability to soybean breeding efforts worldwide.
FRONTIERS IN PLANT SCIENCE
(2022)
Review
Plant Sciences
Mohsen Niazian, Francois Belzile, Davoud Torkamaneh
Summary: Sequence and expression data obtained by next-generation sequencing (NGS)-based forward genetics methods allow the identification of candidate causal genes. Reverse genetics techniques, such as CRISPR/Cas9, are valuable for providing experimental evidence of a gene's function.
Article
Biotechnology & Applied Microbiology
Manel Fallah, Martine Jean, Vincent-Thomas Boucher St-Amour, Louise O'Donoughue, Francois Belzile
Summary: Genetic linkage maps are used to localize markers on the genome, but individual maps have limitations in resolution and coverage. Consensus genetic maps overcome these limitations by merging information from multiple populations, providing a more extensive and uniform coverage.