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Glison N, Gaiero P, Monteverde E, Speranza PR. Breeding for reduced seed dormancy to domesticate new grass species. Genet Mol Biol 2024; 47Suppl 1:e20230262. [PMID: 38666746 PMCID: PMC11046443 DOI: 10.1590/1678-4685-gmb-2023-0262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Accepted: 03/01/2024] [Indexed: 04/29/2024] Open
Abstract
Introducing new grass species into cultivation has long been proposed as beneficial to increase the sustainability and diversity of productive systems. However, wild species with potential tend to show high seed dormancy, causing slow, poor, and unsynchronized seedling emergence. Meanwhile, domesticated species, such as cereals, show lower seed dormancy, facilitating their successful establishment. In this work, we conduct a review of phenotypic variation on seed dormancy and its genetic and molecular basis. This quantitative and highly heritable trait shows phenotype plasticity which is modulated by environmental factors. The level of dormancy depends on the expression of genes associated with the metabolism and sensitivity to the hormones abscisic acid (ABA) and gibberellins (GA), along with other dormancy-specific genes. The genetic regulation of these traits is highly conserved across species. The low seed dormancy observed in cereals and some temperate forages was mostly unconsciously selected during various domestication processes. Emphasis is placed on selecting materials with low seed dormancy for warm-season forage grasses to improve their establishment and adoption. Finally, we review advances in the domestication of dallisgrass, where seed dormancy was considered a focus trait throughout the process.
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Affiliation(s)
- Nicolás Glison
- Universidad de la República, Facultad de Agronomía, Departamento de Biología Vegetal, Montevideo, Uruguay
| | - Paola Gaiero
- Universidad de la República, Facultad de Agronomía, Departamento de Biología Vegetal, Montevideo, Uruguay
| | - Eliana Monteverde
- Universidad de la República, Facultad de Agronomía, Departamento de Biología Vegetal, Montevideo, Uruguay
- University of Illinois, Department of Crop Sciences, Urbana, IL, USA
| | - Pablo R. Speranza
- Universidad de la República, Facultad de Agronomía, Departamento de Biología Vegetal, Montevideo, Uruguay
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Melandri G, Monteverde E, Riewe D, AbdElgawad H, McCouch SR, Bouwmeester H. Can biochemical traits bridge the gap between genomics and plant performance? A study in rice under drought. Plant Physiol 2022; 189:1139-1152. [PMID: 35166848 PMCID: PMC9157150 DOI: 10.1093/plphys/kiac053] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Accepted: 01/17/2022] [Indexed: 05/13/2023]
Abstract
The possibility of introducing metabolic/biochemical phenotyping to complement genomics-based predictions in breeding pipelines has been considered for years. Here we examine to what extent and under what environmental conditions metabolic/biochemical traits can effectively contribute to understanding and predicting plant performance. In this study, multivariable statistical models based on flag leaf central metabolism and oxidative stress status were used to predict grain yield (GY) performance for 271 indica rice (Oryza sativa) accessions grown in the field under well-watered and reproductive stage drought conditions. The resulting models displayed significantly higher predictability than multivariable models based on genomic data for the prediction of GY under drought (Q2 = 0.54-0.56 versus 0.35) and for stress-induced GY loss (Q2 = 0.59-0.64 versus 0.03-0.06). Models based on the combined datasets showed predictabilities similar to metabolic/biochemical-based models alone. In contrast to genetic markers, models with enzyme activities and metabolite values also quantitatively integrated the effect of physiological differences such as plant height on GY. The models highlighted antioxidant enzymes of the ascorbate-glutathione cycle and a lipid oxidation stress marker as important predictors of rice GY stability under drought at the reproductive stage, and these stress-related variables were more predictive than leaf central metabolites. These findings provide evidence that metabolic/biochemical traits can integrate dynamic cellular and physiological responses to the environment and can help bridge the gap between the genome and the phenome of crops as predictors of GY performance under drought.
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Affiliation(s)
- Giovanni Melandri
- Laboratory of Plant Physiology, Wageningen University and Research, Wageningen, the Netherlands
- School of Integrative Plant Sciences, Plant Breeding and Genetics Section, Cornell University, Ithaca, New York, USA
| | - Eliana Monteverde
- School of Integrative Plant Sciences, Plant Breeding and Genetics Section, Cornell University, Ithaca, New York, USA
- Departamento de Biología Vegetal, Facultad de Agronomía, Laboratorio de Evolución y Domesticación de las Plantas, Universidad de La República, Montevideo, Uruguay
| | - David Riewe
- Julius Kühn-Institute (JKI), Federal Research Centre for Cultivated Plants, Institute for Ecological Chemistry, Plant Analysis and Stored Product Protection, Berlin, Germany
- Department of Molecular Genetics, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Seeland, Germany
| | - Hamada AbdElgawad
- Laboratory for Integrated Molecular Plant Physiology Research, University of Antwerp, Antwerp, Belgium
- Department of Botany, Faculty of Science, Beni-Suef University, Beni Suef, Egypt
| | - Susan R McCouch
- School of Integrative Plant Sciences, Plant Breeding and Genetics Section, Cornell University, Ithaca, New York, USA
| | - Harro Bouwmeester
- Laboratory of Plant Physiology, Wageningen University and Research, Wageningen, the Netherlands
- Plant Hormone Biology group, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, the Netherlands
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Monteverde E, Gutierrez L, Blanco P, Pérez de Vida F, Rosas JE, Bonnecarrère V, Quero G, McCouch S. Integrating Molecular Markers and Environmental Covariates To Interpret Genotype by Environment Interaction in Rice ( Oryza sativa L.) Grown in Subtropical Areas. G3 (Bethesda) 2019; 9:1519-1531. [PMID: 30877079 PMCID: PMC6505146 DOI: 10.1534/g3.119.400064] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Accepted: 03/05/2019] [Indexed: 01/11/2023]
Abstract
Understanding the genetic and environmental basis of genotype × environment interaction (G×E) is of fundamental importance in plant breeding. If we consider G×E in the context of genotype × year interactions (G×Y), predicting which lines will have stable and superior performance across years is an important challenge for breeders. A better understanding of the factors that contribute to the overall grain yield and quality of rice (Oryza sativa L.) will lay the foundation for developing new breeding and selection strategies for combining high quality, with high yield. In this study, we used molecular marker data and environmental covariates (EC) simultaneously to predict rice yield, milling quality traits and plant height in untested environments (years), using both reaction norm models and partial least squares (PLS), in two rice breeding populations (indica and tropical japonica). We also sought to explain G×E by differential quantitative trait loci (QTL) expression in relation to EC. Our results showed that PLS models trained with both molecular markers and EC gave better prediction accuracies than reaction norm models when predicting future years. We also detected milling quality QTL that showed a differential expression conditional on humidity and solar radiation, providing insight for the main environmental factors affecting milling quality in subtropical and temperate rice growing areas.
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Affiliation(s)
- Eliana Monteverde
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca NY 14853
| | - Lucía Gutierrez
- Department of Agronomy, University of Wisconsin - Madison WI 53706
| | - Pedro Blanco
- Programa Nacional de Investigación en arroz, Instituto Nacional de Investigación Agropecuaria (INIA), INIA Treinta y Tres 33000, Uruguay
| | - Fernando Pérez de Vida
- Programa Nacional de Investigación en arroz, Instituto Nacional de Investigación Agropecuaria (INIA), INIA Treinta y Tres 33000, Uruguay
| | - Juan E Rosas
- Programa Nacional de Investigación en arroz, Instituto Nacional de Investigación Agropecuaria (INIA), INIA Treinta y Tres 33000, Uruguay
- Unidad de Biotecnología, Instituto Nacional de Investigación Agropecuaria (INIA), Estación Experimental Wilson Ferreira Aldunate 90200, Uruguay
| | - Victoria Bonnecarrère
- Unidad de Biotecnología, Instituto Nacional de Investigación Agropecuaria (INIA), Estación Experimental Wilson Ferreira Aldunate 90200, Uruguay
| | - Gastón Quero
- Department of Plant Biology, College of Agriculture, Universidad de la República, Montevideo, Uruguay
| | - Susan McCouch
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca NY 14853
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Quero G, Gutiérrez L, Monteverde E, Blanco P, Pérez de Vida F, Rosas J, Fernández S, Garaycochea S, McCouch S, Berberian N, Simondi S, Bonnecarrère V. Genome-Wide Association Study Using Historical Breeding Populations Discovers Genomic Regions Involved in High-Quality Rice. Plant Genome 2018; 11:170076. [PMID: 30512035 DOI: 10.3835/plantgenome2017.08.0076] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Rice ( L.) is one of the most important staple food crops in the world; however, there has recently been a shift in consumer demand for higher grain quality. Therefore, understanding the genetic architecture of grain quality has become a key objective of rice breeding programs. Genome-wide association studies (GWAS) using large diversity panels have successfully identified genomic regions associated with complex traits in diverse crop species. Our main objective was to identify genomic regions associated with grain quality and to identify and characterize favorable haplotypes for selection. We used two locally adapted rice breeding populations and historical phenotypic data for three rice quality traits: yield after milling, percentage of head rice recovery, and percentage of chalky grain. We detected 22 putative quantitative trait loci (QTL) in the same genomic regions as starch synthesis, starch metabolism, and cell wall synthesis-related genes are found. Additionally, we found a genomic region on chromosome 6 in the population that was associated with all quality traits and we identified favorable haplotypes. Furthermore, this region is linked to the gene that codes for a starch branching enzyme I, which is implicated in starch granule formation. In , we also found two putative QTL linked to , , and . Our study provides an insight into the genetic basis of rice grain chalkiness, yield after milling, and head rice, identifying favorable haplotypes and molecular markers for selection in breeding programs.
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Rosas JE, Martínez S, Blanco P, Pérez de Vida F, Bonnecarrère V, Mosquera G, Cruz M, Garaycochea S, Monteverde E, McCouch S, Germán S, Jannink JL, Gutiérrez L. Resistance to Multiple Temperate and Tropical Stem and Sheath Diseases of Rice. Plant Genome 2018; 11:170029. [PMID: 29505639 DOI: 10.3835/plantgenome2017.03.0029] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Stem rot and aggregated sheath spot are the two major stem and sheath diseases affecting rice (Oryza sativa L.) in temperate areas. A third fungal disease, sheath blight, is a major disease in tropical areas. Resistance to these diseases is a key objective in rice breeding programs but phenotyping is challenged by the confounding effects of phenological and morphological traits such as flowering time (FT) and plant height (PH). This study sought to identify quantitative trait loci (QTL) for resistance to these three diseases after removing the confounding effects of FT and PH. Two populations of advanced breeding germplasm, one with 316 tropical japonica and the other with 325 indica genotypes, were evaluated in field and greenhouse trials for resistance to the diseases. Phenotypic means for field and greenhouse disease resistance, adjusted by FT and PH, were analyzed for associations with 29,000 single nucleotide polymorphisms (SNPs) in tropical japonica and 50,000 SNPs in indica. A total of 29 QTL were found for resistance that were not associated with FT or PH. Multilocus models with selected resistance-associated SNPs were fitted for each disease to estimate their effects on the other diseases. A QTL on chromosome 9 accounted for more than 15% of the phenotypic variance for the three diseases. When resistance-associated SNPs at this locus from both the tropical japonica and indica populations were incorporated into the model, resistance was improved for all three diseases with little impact on FT and PH.
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Garber HJ, McGonigle JJ, Slomka GT, Monteverde E. Clomipramine treatment of stereotypic behaviors and self-injury in patients with developmental disabilities. J Am Acad Child Adolesc Psychiatry 1992; 31:1157-60. [PMID: 1429420 DOI: 10.1097/00004583-199211000-00027] [Citation(s) in RCA: 48] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The authors report an open clinical trial of clomipramine for chronic stereotypic and self-injurious behaviors in 11 consecutive patients with concomitant developmental disorders. Ten patients (91%) had marked decreases in rates of target behaviors. No seizures occurred despite the inclusion of six patients with previous histories of epileptic events, and improvement was evident regardless of level of mental retardation. These findings support both the clinical use of serotonergic medications in this population and the need for further research.
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Affiliation(s)
- H J Garber
- Allegheny Neuropsychiatric Institute, Oakdale, Pennsylvania
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