Article
Plant Sciences
Fatemeh Loni, Ahmad Ismaili, Babak Nakhoda, Hadi Darzi Ramandi, Zahra-Sadat Shobbar
Summary: This study used a meta-analysis approach to identify genomic regions and candidate genes associated with drought tolerance and yield-related traits in foxtail millet. The results provide valuable information for developing new high-yielding drought-tolerant genotypes.
PLANT GROWTH REGULATION
(2023)
Article
Biochemistry & Molecular Biology
Jingjuan Zhang, Maoyun She, Rongchang Yang, Yanjie Jiang, Yebo Qin, Shengnan Zhai, Sadegh Balotf, Yun Zhao, Masood Anwar, Zaid Alhabbar, Angela Juhasz, Jiansheng Chen, Hang Liu, Qier Liu, Ting Zheng, Fan Yang, Junkang Rong, Kefei Chen, Meiqin Lu, Shahidul Islam, Wujun Ma
Summary: In this study, large-scale field trials were conducted over two years using doubled haploid wheat populations, leading to the mapping of 227 QTL on 18 chromosomes, forming 35 QTL clusters. The variations in correlations within these clusters were shown to be important for wheat breeding. QTL clusters with positive correlations may be directly utilized for improving wheat yield, while those with negative correlations may have potential value for GPC or yield improvement in specific environments.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Plant Sciences
Hongchun Xiong, Yuting Li, Huijun Guo, Yongdun Xie, Linshu Zhao, Jiayu Gu, Shirong Zhao, Yuping Ding, Luxiang Liu
Summary: This study constructed a high-density genetic linkage map for wheat using the Wheat55K SNP Array and identified QTLs affecting heading date, plant height, thousand grain weight, and spike length in RILs. KASP markers were developed for validation of detected QTLs, and candidate genes affecting PH and TGW were identified, providing new insight into genetic study for wheat traits.
FRONTIERS IN PLANT SCIENCE
(2021)
Article
Plant Sciences
Giacomo Mangini, Antonio Blanco, Domenica Nigro, Massimo Antonio Signorile, Rosanna Simeone
Summary: The study identified QTL clusters for yield components in a durum wheat RIL population, with candidate genes affecting grain yield identified within these clusters.
Review
Biochemistry & Molecular Biology
Zhiqi Hao, Sai Ma, Lunping Liang, Ting Feng, Mengyuan Xiong, Shangshu Lian, Jingyan Zhu, Yanjun Chen, Lijun Meng, Min Li
Summary: This study explores the co-response mechanism of rice to drought and salt stress, identifying a set of co-responsive genes that are enriched in specific pathways. The haplotype network analysis of nine key genes reveals significant differences between different rice populations. Additionally, the collection of specific breeding varieties suggests the potential to improve drought and salt tolerance.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Nutrition & Dietetics
Karthik Kumar Manjunath, Hari Krishna, Narayana Bhat Devate, V. P. Sunilkumar, Divya Chauhan, Shweta Singh, C. N. Mishra, J. B. Singh, Nivedita Sinha, Neelu Jain, Gyanendra Pratap Singh, Pradeep Kumar Singh
Summary: Biofortification is an important approach globally to improve human nutrition by increasing the micronutrient content in staple food crops. In this study, chromosomal regions controlling grain iron concentration (GFeC), grain zinc concentration (GZnC), and thousand kernel weight (TKW) were identified in wheat using recombinant inbred lines (RILs). The results showed increased iron and zinc content under heat and combined stress conditions, while thousand kernel weight decreased. QTL analysis identified 32 chromosomal regions governing the traits, including a hotspot on chromosome 4B associated with grain iron, zinc, and thousand kernel weight. The identified markers can be used for marker-assisted selection (MAS) once validated.
FRONTIERS IN NUTRITION
(2023)
Article
Plant Sciences
Sina Nouraei, Md Sultan Mia, Hui Liu, Neil C. Turner, Guijun Yan
Summary: This study analyzed gene expression profiling in wheat to investigate the genetic control of drought tolerance. The researchers identified candidate genes and genetic markers associated with the qDSI.4B.1 locus, which can be used in breeding programs for drought tolerance. The study also revealed the biological processes involved in the response to drought stress.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Plant Sciences
Anuj Kumar, Dinesh Kumar Saini, Gautam Saripalli, P. K. Sharma, H. S. Balyan, P. K. Gupta
Summary: Meta-QTLs (MQTLs), ortho-MQTLs, and related candidate genes (CGs) for yield and its component traits were identified in wheat under water deficit conditions. A high density consensus map and known QTLs were used to identify 56 MQTLs, with narrower confidence intervals (CIs) compared to known QTLs. Marker trait associations were detected for 47 MQTLs, and 9 MQTLs were suggested for marker-assisted breeding (MAB). Furthermore, ortho-MQTLs and differentially expressed CGs (DECGs) were identified.
PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS
(2023)
Article
Plant Sciences
Yucui Han, Yue Zhao, Hairong Wang, Yiyang Zhang, Qin Ding, Lingjian Ma
Summary: This study investigated the mechanism of male sterility in YS3038 by mapping sterile genes and studying the expression of noncoding RNAs. Weighted gene coexpression network analysis and competitive endogenous RNA analysis identified key genes and interactions related to anther development and fertility conversion. Silencing candidate genes led to a decrease in seed setting rate, providing breeders with a new option for developing thermosensitive cytoplasmic male-sterile wheat lines.
PLANT PHYSIOLOGY AND BIOCHEMISTRY
(2021)
Article
Plant Sciences
Osvin Arriagada, Agata Gadaleta, Ilaria Marcotuli, Marco Maccaferri, Matteo Campana, Samantha Reveco, Christian Alfaro, Ivan Matus, Andres R. Schwember
Summary: In this study, a comprehensive MQTL analysis was conducted to identify genomic regions associated with grain-yield related traits in durum wheat. Candidate genes associated with MQTL were identified and their expression analysis under drought conditions was carried out. These results are important for increasing wheat grain yields under different water conditions and obtaining new genotypes adapted to climate change.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Biochemistry & Molecular Biology
Tanushree Halder, Hui Liu, Yinglong Chen, Guijun Yan, Kadambot H. M. Siddique
Summary: This study phenotyped root traits in wheat using 10 pairs of near-isogenic lines targeting four genomic regions (GRs) and identified 15 putative candidate genes associated with different root traits. Among the candidate genes, UDP-glycosyltransferase (UGT)-encoding genes and leucine-rich repeat receptor-like protein kinase (LRR-RLK)-encoding gene showed important functions for root trait control in other crops. Further confirmation and validation of these candidate genes are needed for marker-assisted wheat breeding.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Agronomy
Darshan Lal Sharma, Roopali Bhoite, Karyn Reeves, Kerrie Forrest, Rosemary Smith, Mirza A. N. N. U. Dowla
Summary: This study identified 39 SNPs and 18 haplotypes that confer tolerance to yield and yield traits in wheat grown on sodic-dispersive soils. These SNPs and haplotypes are associated with metal ion binding, photosynthesis genes, and transcription factors, which play important roles in different developmental stages of wheat. Furthermore, homozygous/biallelic SNPs related to yield and crop establishment were also identified on sodic-dispersive soils. These findings are valuable for haplotype-based breeding and genome editing to improve wheat yield potential on such challenging soils.
THEORETICAL AND APPLIED GENETICS
(2022)
Article
Agronomy
Min Wang, Renyu Zhang, Yangzi Zhao, Jieyuan Yao, Weiya Li, Zhixing Yang, Fei Sun, Xiaohong Yang
Summary: Prolificacy, the number of ears per plant, is an important trait in maize breeding and studying its genetic basis can contribute to the understanding of maize evolution. In this study, a stable quantitative trait locus, qEN7, was identified on chromosome 7, which explained a significant portion of phenotypic variation in ear number. The gene Zm00001d020683, encoding a putative INDERTERMINATE DOMAIN (IDD) transcription factor, was identified as the most likely candidate gene underlying qEN7. This discovery provides insights into the evolution of maize ear number and offers a valuable resource for breeding multi-ear maize cultivars. (reprinted from Crop Science Society of China and Institute of Crop Science, CAAS)
Article
Agronomy
Yunxiao Zhang, Hui Liu, Guijun Yan
Summary: The study assessed seven pairs of NILs targeting four QTL on wheat chromosome arms and found significant differences in PH and other traits among NIL pairs. SNP and candidate gene information can be useful for marker-assisted selection in breeding programs, and the four targeted QTL are crucial genomic regions controlling agronomic traits.
MOLECULAR BREEDING
(2021)
Article
Plant Sciences
Qing Meng, Zhiyuan Liu, Chunda Feng, Helong Zhang, Zhaosheng Xu, Xiaowu Wang, Jian Wu, Hongbing She, Wei Qian
Summary: In this study, a major quantitative trait locus (QTL) related to early bolting in spinach was identified, and two candidate genes associated with flowering regulatory pathways were proposed. This research provides a basis for understanding the molecular mechanisms of bolting in spinach.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Genetics & Heredity
H. Busra Cagirici, S. Galvez, Taner Z. Sen, Hikmet Budak
Summary: The critical roles of lncRNAs in biological processes have gained vast attention, and with the advancement of high-throughput sequencing technologies, high-quality data is now available for annotation. This study compares prediction accuracies of machine learning algorithms and presents a crop-specific coding potential prediction tool, LncMachine, with high accuracy when used with the Random Forest algorithm. LncMachine can be effortlessly applied to a wide range of studies by deploying user-provided algorithms in real time.
FUNCTIONAL & INTEGRATIVE GENOMICS
(2021)
Article
Biochemistry & Molecular Biology
Eugene Metakovsky, Laura Pascual, Patrizia Vaccino, Viktor Melnik, Marta Rodriguez-Quijano, Yulia Popovych, Sabina Chebotar, William John Rogers
Summary: The study compared the gamma-gliadins and non-coding DNA sequences of 15 different alleles of common wheat at the Gli-B1 locus using various tests, revealing at least seven independently originated variants. These variants may have originated from deeply diverged genotypes of the B genome donors in hexaploid wheat and contribute significantly to the current high genetic diversity in common wheat.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Genetics & Heredity
Sergio Galvez, Federico Agostini, Javier Caselli, Pilar Hernandez, Gabriel Dorado
Summary: The development of new high-performance computing architectures has not improved the execution time of widely used bioinformatics applications. Optimization of algorithms is necessary to take full advantage of new hardware, with BLVector showing significant reduction in execution time compared to BLAST+.
FRONTIERS IN GENETICS
(2021)
Article
Food Science & Technology
Eugene Metakovsky, Viktor Melnik, Laura Pascual, Colin W. Wrigley
Summary: Intra-varietal non-uniformity in wheat cultivars was observed due to spontaneous mutations at the Gli loci, leading to null alleles causing loss of gliadin electrophoretic bands. The null mutants were disproportional among different Gli loci, with some resulting in over-production of gliadins encoded by other loci. Additionally, mutations at Gli loci were found to result in loss of specific gliadins, alteration of electrophoretic mobility, and under-estimated occurrence rate of about 1%.
JOURNAL OF CEREAL SCIENCE
(2021)
Article
Plant Sciences
Matilde Lopez-Fernandez, Laura Pascual, Isabel Faci, Mario Fernandez, Magdalena Ruiz, Elena Benavente, Patricia Giraldo
Summary: Modern plant-breeding practices have narrowed the genetic base of wheat, highlighting the importance of introducing new germplasms with underexploited diversity. Wheat landraces from Spain exhibit a wide genetic diversity and quality-related traits, with specific alleles associated with high quality identified. Novel variability in high-molecular-weight glutenin and puroindolines within the landraces was also discovered, warranting further characterization for assessing its influence on wheat quality. Additionally, select landraces showing outstanding gluten quality and agronomic performance were identified for potential direct use in cropping systems.
Article
Plant Sciences
Estela Gimenez, Elena Benavente, Laura Pascual, Andres Garcia-Sampedro, Matilde Lopez-Fernandez, Jose Francisco Vazquez, Patricia Giraldo
Summary: In a genetics course, innovative teaching methods can enhance student motivation, while labs and practical classes are preferred academic activities. Designing lab practices focused on learning abstract concepts is complex, with an optimal F-2 population useful for teaching key genetic concepts and statistical analysis.
Review
Biochemistry & Molecular Biology
Gabriel Dorado, Sergio Galvez, Teresa E. Rosales, Victor F. Vasquez, Pilar Hernandez
Summary: Recent advancements in biomolecular research, including the development of molecular markers, nucleic acid amplification, and sequencing, are revolutionizing the field. These technologies are not only redefining the concept of genes and transcripts, but also making significant impacts in various areas such as medicine, agronomy, ecology, and biotechnology.
Article
Agronomy
Fernando Martinez-Moreno, Patricia Giraldo, Cristina Nieto, Magdalena Ruiz
Summary: A study evaluated the resistance of 84 bread wheat Spanish landraces to leaf rust and yellow rust. It was found that resistant landraces mostly originated from the north-west region with higher precipitation and more uniform temperatures.
Article
Plant Sciences
Maria Angeles Decena, Sergio Galvez-Rojas, Federico Agostini, Ruben Sancho, Bruno Contreras-Moreira, David L. Des Marais, Pilar Hernandez, Pilar Catalan
Summary: The study conducted a comparative genomics and evolution analysis of DHN genes in Brachypodium grass species, showing that key Bdhn genes are regulated by drought induction in different ecotypes, which may be a crucial factor in acquiring water-stress tolerance in plants.
Article
Biology
Etienne Paux, Stephane Lafarge, Francois Balfourier, Jeremy Derory, Gilles Charmet, Michael Alaux, Geoffrey Perchet, Marion Bondoux, Frederic Baret, Romain Barillot, Catherine Ravel, Pierre Sourdille, Jacques Le Gouis
Summary: The BREEDWHEAT project has provided new molecular tools for breeders to lay the foundation for future commercial wheat varieties. The project's outcomes will aid in the development of new and adapted wheat varieties that are more productive and sustainable. The project emphasizes the importance of using high-throughput genomic tools, genomic selection, and in silico modeling to improve wheat varieties.
Article
Agronomy
Laura Pascual, Aida Sole-Medina, Isabel Faci, Patricia Giraldo, Magdalena Ruiz, Elena Benavente
Summary: In this study, the wheat GS1 and GS2 genes were sequenced and analyzed in 15 bread wheat varieties, and significant effects on agronomic and grain quality traits were observed. Molecular markers were developed for genes GS1A, GS2A, and GS2D. Genetic interactions between GS1A and GS2A or GS2D were found to affect thousand-kernel weight and kernels per spike. The masking effect of alleles at one locus on positive alleles at hypostatic GS loci should be considered in gene pyramiding strategies.
MOLECULAR BREEDING
(2023)
Article
Agronomy
Matilde Lopez-Fernandez, Julian Garcia-Abadillo, Cristobal Uauy, Magdalena Ruiz, Patricia Giraldo, Laura Pascual
Summary: Association mapping in Spanish bread wheat landraces revealed six stable genomic regions associated with yield and identified 15 candidate genes. These regions have significant effects on grain traits and thousand kernel weight, making them potential targets for breeding.
THEORETICAL AND APPLIED GENETICS
(2023)
