Review
Plant Sciences
Muhammad Yasir, Hafiza Hamrah Kanwal, Quaid Hussain, Muhammad Waheed Riaz, Muhammad Sajjad, Junkang Rong, Yurong Jiang
Summary: Over the past two decades, high-density SNP arrays and DNA sequencing technology have been widely used in crop research, particularly in cotton crops. Genome-wide association studies (GWAS) have provided an important tool for uncovering the relationship between crop phenotypes and underlying genetics, helping to advance crop breeding and improvement.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Biochemical Research Methods
Dat Thanh Nguyen, Quan Hoang Nguyen, Nguyen Thuy Duong, Nam S. Vo
Summary: Despite the advancement of sequencing technology, SNP arrays remain the most cost-effective genotyping solution for large-scale genomic research. This study introduces a novel method called LmTag for tag SNP selection, which improves imputation performance and prioritizes highly functional SNP markers. It is particularly suitable for under-represented populations and non-model species in developing countries.
BRIEFINGS IN BIOINFORMATICS
(2022)
Review
Biology
Javaid Akhter Bhat, Deyue Yu, Abhishek Bohra, Showkat Ahmad Ganie, Rajeev K. Varshney
Summary: The review discusses mining crop haplotypes for dissecting complex traits and enhancing genomics-assisted breeding, providing avenues for faster breeding of high-yielding cultivars to adapt to future climates. It highlights the vital role of genomics-assisted breeding in improving crop breeding efficiency and delivering better varieties.
COMMUNICATIONS BIOLOGY
(2021)
Review
Plant Sciences
Jagesh Kumar Tiwari, Suresh Reddy Yerasu, Nagendra Rai, Dhananjaya P. Singh, Achuit K. Singh, Suhas G. Karkute, Prabhakar M. Singh, Tusar K. Behera
Summary: Tomatoes are important vegetable crops, and genomics-assisted breeding shows great potential in this field. With the rapid development and cost reduction of sequencing technologies, as well as the use of high-throughput genotyping platforms and bioinformatics tools, the tomato genome has been decoded and extensively studied, providing valuable information for breeding programs. Genomics-assisted breeding has made progress in identifying genes and SNP markers associated with agronomic traits, and the genomic selection method is expected to improve breeding efficiency and genetic gain.
CRITICAL REVIEWS IN PLANT SCIENCES
(2022)
Article
Genetics & Heredity
Haoqiang Ye, Zipeng Zhang, Duanyang Ren, Xiaodian Cai, Qianghui Zhu, Xiangdong Ding, Hao Zhang, Zhe Zhang, Jiaqi Li
Summary: The size of reference population is important for genomic prediction. This study used WGS data to construct LD-based haplotypes and explored the impact of different SNP densities, variant representation, and reference population size on prediction accuracy. The results showed that GBLUP using WGS data improved prediction accuracy in multi-population and haplotype method had better performance in multi-population genomic evaluation.
FRONTIERS IN GENETICS
(2022)
Article
Genetics & Heredity
Simone Rubinacci, Diogo M. Ribeiro, Robin J. Hofmeister, Olivier Delaneau
Summary: GLIMPSE is a new method for haplotype phasing and genotype imputation of low-coverage sequencing datasets, showing remarkable performance across different coverages and human populations. This method achieves genome imputation at a cost lower than US$1, outperforming other methods and improving imputation accuracy over the full allele frequency range. The study indicates the promising potential of low-coverage imputation and suggests a paradigm shift in the design of future genomic studies.
Article
Biochemistry & Molecular Biology
Zachariah Gompert, Jeffrey L. Feder, Patrik Nosil
Summary: Understanding the impact of selection on the genome is crucial in biology. Indirect selection can affect functionally neutral genetic regions through statistical associations with genes under direct selection, leading to widespread genetic loci being impacted across the genome. This process, including unknown causal variants and genetic associations, makes aspects of evolution more predictable and has implications for evolutionary principles in both basic and applied science.
Article
Plant Sciences
Muluken Enyew, Tileye Feyissa, Anders S. Carlsson, Kassahun Tesfaye, Cecilia Hammenhag, Amare Seyoum, Mulatu Geleta
Summary: This study conducted a genome-wide association study (GWAS) using sorghum genetic resources in Ethiopia to identify genomic regions and candidate genes associated with major agronomic traits in sorghum. The study revealed the genetic variation in sorghum traits and identified several novel and previously known quantitative trait loci. The major findings of this study were the significant association of major effect SNP loci with traits such as panicle width, days to flowering, grain yield, and panicle length.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Behavioral Sciences
Konstantinos Voskarides, Nefeli Giannopoulou, Rasha Eid, Konstantinos Parperis, Andreas Chatzittofis
Summary: Several studies have confirmed the association between autoimmune diseases and psychiatric disorders, with genetic evidence supporting this link. This study aimed to investigate the genetic linkage between genetic variants predisposing to autoimmune diseases and psychiatric disorders by constructing common haplotypes. The results showed multiple chromosomal regions containing genetic variants associated with both diseases, and specific genetic haplotypes were identified. Notably, six autoimmune diseases shared a common haplotype with psychiatric diseases at the HLA locus 6p21-22.
BRAIN AND BEHAVIOR
(2023)
Editorial Material
Biochemistry & Molecular Biology
Zachariah Gompert, Jeffrey L. Feder, Patrik Nosil
Summary: This paper quantifies the genome-wide consequences of natural selection and addresses the effects of indirect selection due to the correlation of genetic regions. The critiques on the paper do not substantially affect the findings of the study.
Article
Multidisciplinary Sciences
Adriano De Marino, Abdallah Amr Mahmoud, Madhuchanda Bose, Karatug Ozan Bircan, Andrew Terpolovsky, Varuna Bamunusinghe, Sandra Bohn, Umar Khan, Biljana Novkovic, Puya G. Yazdi
Summary: This study compared the latest versions of popular HMM-based tools for phasing and imputation, evaluated them using multiple metrics, and determined the best combinations for different situations and analysis needs. An automated pipeline was also created to optimize imputation results.
Article
Biochemistry & Molecular Biology
Michael A. Hardigan, Anne Lorant, Dominique D. A. Pincot, Mitchell J. Feldmann, Randi A. Famula, Charlotte B. Acharya, Seonghee Lee, Sujeet Verma, Vance M. Whitaker, Nahla Bassil, Jason Zurn, Glenn S. Cole, Kevin Bird, Patrick P. Edger, Steven J. Knapp
Summary: The cultivated strawberry, originating from early 18th-century Europe, has undergone significant genomic changes over 300 years of breeding history, leading to global expansion in production. Research shows increased heterozygosity in interspecific hybrids, selective sweeps across the genome, and substantial allelic diversity in octoploid species. Despite genetic gains in modern cultivars, nucleotide diversity and heterozygosity are lower, suggesting potential trade-offs in agricultural selection.
MOLECULAR BIOLOGY AND EVOLUTION
(2021)
Article
Plant Sciences
Catja Selga, Alexander Koc, Aakash Chawade, Rodomiro Ortiz
Summary: The study introduces a pipeline to reduce genotyping costs by decreasing the number of SNPs and individuals, as well as pruning for linkage disequilibrium. Both GWAS and GS analyses can be performed without loss of information, making them applicable to large potato breeding populations.
Article
Genetics & Heredity
Guangliang Gao, Dengfeng Gao, Xianzhi Zhao, Songsong Xu, Keshan Zhang, Rui Wu, Chunhui Yin, Jing Li, Youhui Xie, Silu Hu, Qigui Wang
Summary: Through a genome-wide association study (GWAS), researchers identified genetic markers associated with goose reproductive performance and egg quality traits, providing new insights for marker-assisted selection.
FRONTIERS IN GENETICS
(2021)
Article
Plant Sciences
Kyu-Won Kim, Bhagwat Nawade, Jungrye Nam, Sang-Ho Chu, Jungmin Ha, Yong-Jin Park
Summary: This study presents an integrated SNP array system for rice breeding research, which combines SNPs from eight different data resources. The developed 580 K Axiom Rice Genotyping Chip demonstrates robust and highly efficient genotyping in various studies, including GWAS and GS. This cost-effective genotyping platform will accelerate rice breeding research.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Agronomy
Nicholas Garst, Vikas Belamkar, Amanda Easterly, Mary J. J. Guttieri, Hannah Stoll, Amir M. H. Ibrahim, P. Stephen Baenziger
Summary: Hybrid wheat has the potential to yield more than conventional inbred cultivars, but the production cost of hybrid seed needs to be minimized for commercial success. This research identified anther extrusion, pollen 50 date, plant height, and pollination duration as the most important traits for hybrid seed production. These traits varied among genotypes and showed significant differences among years, but consistent performance patterns were observed.
Article
Agronomy
P. S. Baenziger, K. A. Frels, J. Boehm, V. Belamkar, D. J. Rose, L. Xu, S. M. Finnie, S. N. Wegulo, T. Regassa, A. C. Easterly, C. F. Creech, D. K. Santra, R. N. Klein, Y. Jin, J. Kolmer, M. -S. Chen, R. L. Bowden, M. J. Guttieri, G. Bai, I. El-Basyoni Salah, S. D. Masterson, J. Poland
Summary: A new hard white winter wheat variety, NW13493, was developed for the Great Plains region. It has white kernels, good agronomic performance, disease resistance, and suitable quality for making bread. NW13493 was licensed to Bay State Milling Company and released in February 2021. It shows excellent winter survival, agronomic performance, disease resistance, and end-use quality for bread making.
JOURNAL OF PLANT REGISTRATIONS
(2023)
Article
Agronomy
P. S. Baenziger, S. D. Masterson, J. D. Boehm, V Belamkar, M. D. Barnett, D. J. Rose, L. Xu, S. N. Wegulo, T. Regassa, A. C. Easterly, C. F. Creech, D. K. Santra, G. R. Kruger, G. W. Hergert, R. N. Klein, Y. Jin, J. Kolmer, M. -S Chen, G. L. Hein, R. L. Bowden, M. J. Guttieri, G. Bai, I. El-Basyoni Salah, J. Poland
Summary: LCS Valiant is a wheat cultivar developed by the University of Nebraska-Lincoln and USDA-ARS, known for its early maturity, strong adaptability, disease resistance, and good quality for making bread.
JOURNAL OF PLANT REGISTRATIONS
(2023)
Article
Agronomy
Amira M. Mourad, Shamseldeen Eltaher, Andreas Boerner, Ahmed Sallam
Summary: This study provides insights into the genetic control of kernel yield under controlled and heavy metals conditions, which is crucial for breeding wheat varieties tolerant to lead and tin.
Article
Plant Sciences
Samar M. Esmail, Ghady E. Omar, Amira M. I. Mourad
Summary: Wheat stripe rust, a global cause of yield losses, has overcome resistance in most highly resistant wheat genotypes. The study focuses on testing the effectiveness of Trichoderma asperellum strain T34, a naturally occurring bioagent in Egyptian fields, against the disease. Significant differences were found between T34 and stripe rust, indicating the effectiveness of T34 in resisting stripe rust. A genome-wide association study identified gene models controlling resistance under normal conditions and T34-induced resistance, with only one common gene model found, suggesting two different genetic systems controlling resistance under each condition. Investigation of biological processes sheds light on the genetic control of stripe rust resistance. The study provides valuable insights for future wheat breeding programs.
Article
Genetics & Heredity
Elsayed A. Mohamed, Asmaa A. M. Ahmed, Matias Schierenbeck, Mohamed Y. Hussein, P. Stephen Baenziger, Andreas Boerner, Ahmed Sallam
Summary: In this study, the tolerance of 41 spring wheat genotypes to drought stress at the germination stage was tested. The Citr15314 genotype showed the best performance under both PEG concentrations. Furthermore, the effect of two genes, TaDreb-B1 and Fehw3, on drought tolerance at the germination stage was studied.
Editorial Material
Genetics & Heredity
Ahmed Sallam, Ahmad M. Alqudah, P. Stephen Baenziger, Awais Rasheed
FRONTIERS IN GENETICS
(2023)
Article
Plant Sciences
Amira M. I. Mourad, Alexey Morgounov, P. Stephen Baenziger, Samar M. Esmail
Summary: Common bunt is a major wheat disease that causes significant damage to grain yield and quality in the USA and Turkey. Although seed treatment with fungicides is an effective control method, it is forbidden in organic and low-income fields, leading to a preference for planting resistant cultivars. The use of fungicides has resulted in limited efforts to breed resistant genotypes, and the genetic diversity for this trait is low in modern wheat germplasm. However, synthetic wheat genotypes have been found to be an effective source of increasing diversity in wheat germplasm.
Article
Biochemistry & Molecular Biology
Shamseldeen Eltaher, Mostafa Hashem, Asmaa A. M. Ahmed, P. Stephen Baenziger, Andreas Boerner, Ahmed Sallam
Summary: With the advances in DNA markers, KASP markers have the potential to accelerate breeding programs and improve drought tolerance. In this study, two previously reported KASP markers, TaDreb-B1 and 1-FEH w3, were investigated for marker-assisted selection of drought tolerance. The results showed that TaDreb-B1 marker provided better consistency in improving drought tolerance than 1-FEH w3.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Microbiology
Nashwa M. A. Sallam, Heba-Alla S. AbdElfatah, Hadeel M. M. Khalil Bagy, Ameer Elfarash, Kamal A. M. Abo-Elyousr, Edward J. Sikora, Ahmed Sallam
Summary: Controlling early blight of tomatoes using endophytic bacteria is an eco-friendly and sustainable approach. Three endophytic bacterial isolates, namely Enterobacter cloacae HS-6 (B4), Pseudomonas gessardii HS-5 (B7), and Pseudomonas mediterranea HS-4 (B17), were found to be effective against the growth of pathogenic fungal isolates. The expression of the defense response gene beta-1.3 glucanase increased significantly after inoculation with the efficient biocontrol agent E. cloacae.
FRONTIERS IN MICROBIOLOGY
(2023)
Letter
Food Science & Technology
P. Stephen Baenziger, Katherine Frels, Steve Greenspan, Julie Jones, Alison Lovegrove, Devin Rose, Peter Shewry, Rod Wallace