Article
Plant Sciences
Mark J. Miller, Qijian Song, Benjamin Fallen, Zenglu Li
Summary: Improving yield is crucial in soybean breeding for profitability. Cross prediction allows breeders to identify the best parental combinations, enhancing genetic gain and efficiency. This study developed optimal cross selection methods for soybean breeding and validated them using historical data, marker evaluations, and genomic selection models.
FRONTIERS IN PLANT SCIENCE
(2023)
Article
Biotechnology & Applied Microbiology
Carolina P. Moraleda, Diego Robledo, Alejandro P. Gutierrez, Jorge del-Pozo, Jose M. Yanez, Ross D. Houston
Summary: The resistance to SRS is a polygenic trait, and this study has identified relevant genes and pathways that are likely to play a role in mediating genetic resistance through genome-wide association analysis and RNA-sequencing.
Article
Biochemistry & Molecular Biology
Christen M. Bossu, Marina Rodriguez, Christine Rayne, Debra A. Chromczak, Philip G. Higgins, Lynne A. Trulio, Kristen C. Ruegg
Summary: The accelerating loss of global biodiversity is worsened by habitat fragmentation and inbreeding in small populations. To address this issue, conservation practitioners often use assisted breeding programs to increase genetic diversity in declining populations. This study demonstrates the value of genomic approaches in enhancing genetic diversity through assisted breeding efforts, focusing on a highly inbred population of Western burrowing owls. The findings highlight the importance of genomic tools in preserving the adaptive potential of small, inbred populations at risk of further decline.
Review
Biotechnology & Applied Microbiology
Gopalareddy Krishnappa, Siddanna Savadi, Bhudeva Singh Tyagi, Sanjay Kumar Singh, Harohalli Masthigowda Mamrutha, Satish Kumar, Chandra Nath Mishra, Hanif Khan, Krishnappa Gangadhara, Govindareddy Uday, Gyanendra Singh, Gyanendra Pratap Singh
Summary: Increasing the rate of crop improvement is crucial for sustained food production and meeting the needs of a growing population. Genomic selection offers accelerated breeding cycles through the rapid selection of superior genotypes, with advantages in prediction accuracy and efficiency over other breeding methods. Integrating novel technologies into GS can further enhance efficiency and speed, facilitating the development of new varieties.
Article
Fisheries
Serap Gonen, Tillmann J. Benfey, Amber F. Garber
Summary: The yield from fisheries and aquaculture production has increased due to the growing world population and increased seafood consumption. Aquaculture production has surpassed wild fisheries, including species such as Atlantic salmon. However, the challenge of rising seawater temperatures due to climate change poses a concern for Atlantic salmon aquaculture. This study focused on determining the genomic heritability of seawater temperature tolerance in Atlantic salmon and its genetic architecture for effective broodstock management.
Review
Plant Sciences
Changrong Ye, Zhilong He, Jiayu Peng, Rui Wang, Xiangnan Wang, Mengjiao Fu, Ying Zhang, Ai Wang, Zhixian Liu, Gaofeng Jia, Yongzhong Chen, Bingchuan Tian
Summary: This review summarizes the assembly of the reference genomes of oiltea-camellia, genes related to economic traits, disease resistance, and environmental stress tolerances, discusses future directions of integrating multiple omics for evaluating genetic resources and mining key genes, and explores the application of new molecular breeding and gene editing technologies to accelerate the breeding process of oiltea-camellia.
FRONTIERS IN PLANT SCIENCE
(2023)
Article
Evolutionary Biology
Klara L. Verbyla, Peter D. Kube, Bradley S. Evans
Summary: The Australian Salmon Enterprises of Tasmania implemented genomic information into the prediction of breeding values for Atlantic salmon in 2016, with the program finalized and fully implemented in 2018. By utilizing efficient genotyping platforms, genetic gains were accelerated significantly and the ability to select parents improved. The economic impacts for the industry were considerable, with substantial improvements observed in genetic gains and the use of genomic selection for commercial production.
EVOLUTIONARY APPLICATIONS
(2022)
Review
Plant Sciences
Jakob Petereit, Jacob Marsh, Philipp E. Bayer, Monica F. Danilevicz, William J. W. Thomas, Jacqueline Batley, David Edwards
Summary: Soybean, a legume of economic and nutritional value, has seen increasing yields due to the breeding of improved varieties and the application of genetic and genomic approaches. With advancements in genome technologies, studying variations between individuals and populations has become more accessible. The development of soybean pangenomes has revealed significant structural variations between individuals and provided valuable information for breeding improved cultivars.
Review
Fisheries
Kunyin Jiang, Chen Chen, Gaowei Jiang, Yong Chi, Chengxun Xu, Lingfeng Kong, Hong Yu, Shikai Liu, Qi Li
Summary: Oysters are an important shellfish species that have been cultured for thousands of years. The oyster aquaculture industry has rapidly developed over the past few decades, with researchers making efforts to improve commercially important traits through selective breeding and other techniques. Advances in oyster breeding have resulted in the development of strains with desirable characteristics, such as fast growth and disease resistance, and have contributed to the sustainability and economic benefits of oyster production. However, challenges such as infectious diseases, environmental concerns, and climate change remain.
REVIEWS IN AQUACULTURE
(2023)
Article
Biochemistry & Molecular Biology
Di Cui, Han Zhou, Xiaoding Ma, Zechuan Lin, Linhua Sun, Bing Han, Maomao Li, Jianchang Sun, Jin Liu, Guixiu Jin, Xianju Wang, Guilan Cao, Xing Wang Deng, Hang He, Longzhi Han
Summary: A large-scale genomic analysis reveals that introgressions from Xian/indica (XI) rice have contributed to yield improvements and disease resistance in Geng/japonica (GJ) rice. Key gene haplotypes controlling plant architecture, yield components, and pest and disease resistance were introduced from XI to GJ rice through introgression. In particular, the GN-related gene Gnd5 has consistently introgressed into GJ cultivars since the 1980s.
PLANT COMMUNICATIONS
(2022)
Review
Plant Sciences
Gayle M. Volk, Patrick F. Byrne, Clarice J. Coyne, Sherry Flint-Garcia, Patrick A. Reeves, Chris Richards
Summary: Plant genebanks provide genetic resources for breeding and research programs, with access to high-quality, standardized data being crucial. Advances in technology allow for collection of phenomic and genomic data, which can directly inform breeding programs. Consideration of homogeneity and heterogeneity in genebank collections during data collection and documentation is important for meeting the needs of plant genetic resource managers and users.
Review
Food Science & Technology
Nurul Huda, Xiangdong Li, Tanzim Jahan, Yuqi He, Chaonan Guan, Kaixuan Zhang, Ainong Gao, Milen I. Georgiev, Meiliang Zhou
Summary: Coix is a minor cereal crop with diverse bioactive compounds and significant therapeutic effects, but there is insufficient attention on breeding and genomic studies of Coix.
FOOD REVIEWS INTERNATIONAL
(2023)
Article
Plant Sciences
Iago Hale, Xiao Ma, Arthur T. O. Melo, Francis Kwame Padi, Prasad S. Hendre, Sarah B. Kingan, Shawn T. Sullivan, Shiyu Chen, Jean-Marc Boffa, Alice Muchugi, Agyemang Danquah, Michael Teye Barnor, Ramni Jamnadass, Yves Van de Peer, Allen Van Deynze
Summary: The shea tree is a defining component of agroforestry parklands in Sahelo-Sudanian Africa, playing a central role in sustaining local livelihoods and farming environments. Despite its economic, cultural, and ecological importance, shea remains semi-domesticated with no history of systematic genetic improvement. Researchers have successfully developed and released a chromosome-scale reference genome for shea, along with resources for potential genome-assisted breeding and conservation efforts across the shea belt in SSA.
FRONTIERS IN PLANT SCIENCE
(2021)
Article
Agronomy
Shengxue Liu, Hongwei Wang, Feng Qin
Summary: Reliance on agriculture for food security is a constant in modern societies, but global climate change and population growth have increased pressure on sustainable agriculture, specifically due to drought stress which threatens crop growth and yield. Recent research has made progress in identifying genetic variations that affect drought-resistance traits, which can potentially be engineered to develop stress-resistant crop cultivars. Molecular-breeding technologies are being employed to develop drought-resistant germplasm in various crops.
Review
Plant Sciences
Ning Yang, Jianbing Yan
Summary: Maize is one of the most widely grown crops globally, with genomics approaches considered the best solution for accelerating yield improvement. Current research focuses on exploring genetic variation, genomes, DNA modifications, and transcription levels in different maize varieties, while also discussing the application of genetic engineering for yield improvement and future directions for maize genomics studies.
CURRENT OPINION IN PLANT BIOLOGY
(2021)
Article
Evolutionary Biology
Maria E. Lopez, Laura Benestan, Jean-Sebastien Moore, Charles Perrier, John Gilbey, Alex Di Genova, Alejandro Maass, Diego Diaz, Jean-Paul Lhorente, Katharina Correa, Roberto Neira, Louis Bernatchez, Jose M. Yanez
EVOLUTIONARY APPLICATIONS
(2019)
Article
Biochemistry & Molecular Biology
Rafael Vilhena Reis Neto, Grazyella Massako Yoshida, Jean Paul Lhorente, Jose Manuel Yanez
MOLECULAR GENETICS AND GENOMICS
(2019)
Article
Fisheries
Liane N. Bassini, Jean P. Lhorente, Marcela Oyarzun, Rama Bangera, Jose M. Yanez, Roberto Neira
Article
Fisheries
David Tapia, Agustin Barria, Juan Kuznar, Jose M. Yanez
JOURNAL OF FISH DISEASES
(2020)
Article
Genetics & Heredity
Agustin Barria, Rodrigo Marin-Nahuelpi, Pablo Caceres, Maria E. Lopez, Liane N. Bassini, Jean P. Lhorente, Jose M. Yanez
G3-GENES GENOMES GENETICS
(2019)
Review
Agriculture, Dairy & Animal Science
J. M. Yanez, R. Joshi, G. M. Yoshida
Article
Multidisciplinary Sciences
Maria Cadiz, Maria E. Lopez, Diego Diaz-Dominguez, Giovanna Caceres, Grazyella M. Yoshida, Daniel Gomez-Uchida, Jose M. Yanez
SCIENTIFIC REPORTS
(2020)
Article
Biotechnology & Applied Microbiology
Grazyella M. Yoshida, Jose M. Yanez
Summary: The study utilized a multi-trait genome-wide association approach to identify quantitative trait loci (QTL) and genes associated with body traits in Nile tilapia. By combining summary statistics from single-trait genome-wide association studies, the study increased the statistical power for detecting genetic associations with body traits. The high-resolution mtGWAS allowed the detection of significant SNPs linked to functional candidate genes, providing further insights into genetic variants underlying body trait variation in cichlid fish.
Article
Evolutionary Biology
Grazyella M. Yoshida, Jose M. Yanez
Summary: Utilizing imputation of genotypes and whole-genome sequencing data, this study investigated the genetic architecture of growth traits in rainbow trout under chronic heat stress, revealing the polygenic nature of these traits. GWAS identified important functional candidate genes associated with growth traits, and using preselected SNPs based on GWAS hits improved the accuracy of genomic prediction. The use of WGS slightly increased prediction accuracy, supporting the evidence of the polygenic nature of growth traits measured under heat stress.
EVOLUTIONARY APPLICATIONS
(2022)
Article
Fisheries
Baltasar F. Garcia, Alvaro Bonaguro, Carolina Araya, Roberto Carvalheiro, Jose M. Yanez
Summary: The inclusion of genomic information has accelerated genetic gain in shrimp breeding. Evaluating LD decay is crucial for assessing the feasibility of genomic selection. A study using a 50K SNP array tool characterized genomic diversity and LD in a farmed shrimp population.
AQUACULTURE REPORTS
(2021)
Review
Fisheries
David Tapia, Yoanna Eissler, Felipe E. Reyes-Lopez, Juan Kuznar, Jose Manuel Yanez
Summary: IPNV is a major pathogen in global aquaculture, causing highly contagious diseases in salmonids and research focusing on molecular characterisation and selective breeding. Recent studies have concentrated on IPNV classification, molecular epidemiology and global distribution, as well as genetic improvements for IPNV resistance and immune responses in salmonids.
REVIEWS IN AQUACULTURE
(2022)
Review
Evolutionary Biology
Jose M. Yanez, Peng Xu, Roberto Carvalheiro, Ben Hayes
Summary: The increasing global demand for food and the challenges facing animal farming require improvements in efficiency and sustainable practices. Genomic technologies can accelerate genetic progress in animal breeding and help meet the protein needs of future human consumption.
EVOLUTIONARY APPLICATIONS
(2022)
Review
Fisheries
Jose M. Yanez, Agustin Barria, Maria E. Lopez, Thomas Moen, Baltasar F. Garcia, Grazyella M. Yoshida, Peng Xu
Summary: Advancements in genomic technologies have played a crucial role in the genetic improvement of aquaculture species through the discovery and application of DNA-markers, such as SNPs. Specific genomic regions associated with economically important traits have been identified using GWAS, allowing the incorporation of markers linked to QTL into aquaculture breeding programs through MAS. However, most economically relevant traits are controlled by multiple QTLs, each explaining only a small portion of the genetic variation.
REVIEWS IN AQUACULTURE
(2023)
Article
Genetics & Heredity
Charles Sanchez-Roncancio, Baltasar Garcia, Jousepth Gallardo-Hidalgo, Jose M. Yanez
Summary: This study conducted GWAS using imputed genotypes at the sequence level and identified candidate genes associated with resistance to Piscirickettsia salmonis in rainbow trout. A total of 24 candidate genes were identified, which were mainly related to phagocytosis, innate immune response, inflammation, oxidative response, lipid metabolism, and apoptotic process.