TB1: from domestication gene to tool for many trades

Igartua, Ernesto; Contreras‐Moreira, Bruno; Casas, Ana M.

doi:10.1093/jxb/eraa308

Cited by 12 publications

(13 citation statements)

References 25 publications

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“…The first one translates CDS to genomic coordinates, the second one retrieves the predicted consequences of the SNP in the coding sequence. This recipe can be used to annotate genomic variants in a given gene across germplasm panels, as done in [ 48 ]:…”

Section: Methodsmentioning

confidence: 99%

Scripting Analyses of Genomes in Ensembl Plants

Contreras‐Moreira

Naamati

Rosello

et al. 2022

Plant Bioinformatics

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Ensembl Plants (http://plants.ensembl.org) offers genome-scale information for plants, with four releases per year. As of release 47 (April 2020) it features 79 species and includes genome sequence, gene models, and functional annotation. Comparative analyses help reconstruct the evolutionary history of gene families, genomes, and components of polyploid genomes. Some species have gene expression baseline reports or variation across genotypes. While the data can be accessed through the Ensembl genome browser, here we review specifically how our plant genomes can be interrogated programmatically and the data downloaded in bulk. These access routes are generally consistent across Ensembl for other non-plant species, including plant pathogens, pests, and pollinators.

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Section: Methodsmentioning

confidence: 99%

Scripting Analyses of Genomes in Ensembl Plants

Contreras‐Moreira

Naamati

Rosello

et al. 2022

Plant Bioinformatics

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“…Although complete sequences of the genomes of higher plants are not well studied in comparison with the genomes of humans and animals, there has been rapid progress in this field from a highly fragmented genome assembly with incomplete gene models to a full “pseudomolecule” reference sequence along with detailed gene model annotation. Reference sequence allows the physical anchoring of genes in complete chromosomal order and provides improved gene models that facilitate the design of transgenic constructs and primers [ 172 , 173 ].…”

Section: Reference Genomes and Assessment Of Genomic Variationmentioning

confidence: 99%

“…Several other challenges remain, with the most common for crop species being polyploidy, which is particularly evident in wheat. Due to functional redundancy, it will be necessary to knock out all homoeologs of a gene to determine its phenotypic impact [ 172 , 173 , 192 ]. In wheat, over 98% of the genome is non-coding; therefore, it is necessary to identify open chromatin regions to define non-coding but functionally important regions.…”

Section: The Research Bottleneck In Plant Sciences Is Shifting From Genotyping To Phenotypingmentioning

confidence: 99%

Will Plant Genome Editing Play a Decisive Role in “Quantum-Leap” Improvements in Crop Yield to Feed an Increasing Global Human Population?

Buzdin

Патрушев

2021

Plants

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Growing scientific evidence demonstrates unprecedented planetary-scale human impacts on the Earth’s system with a predicted threat to the existence of the terrestrial biosphere due to population increase, resource depletion, and pollution. Food systems account for 21–34% of global carbon dioxide (CO2) emissions. Over the past half-century, water and land-use changes have significantly impacted ecosystems, biogeochemical cycles, biodiversity, and climate. At the same time, food production is falling behind consumption, and global grain reserves are shrinking. Some predictions suggest that crop yields must approximately double by 2050 to adequately feed an increasing global population without a large expansion of crop area. To achieve this, “quantum-leap” improvements in crop cultivar productivity are needed within very narrow planetary boundaries of permissible environmental perturbations. Strategies for such a “quantum-leap” include mutation breeding and genetic engineering of known crop genome sequences. Synthetic biology makes it possible to synthesize DNA fragments of any desired sequence, and modern bioinformatics tools may hopefully provide an efficient way to identify targets for directed modification of selected genes responsible for known important agronomic traits. CRISPR/Cas9 is a new technology for incorporating seamless directed modifications into genomes; it is being widely investigated for its potential to enhance the efficiency of crop production. We consider the optimism associated with the new genetic technologies in terms of the complexity of most agronomic traits, especially crop yield potential (Yp) limits. We also discuss the possible directions of overcoming these limits and alternative ways of providing humanity with food without transgressing planetary boundaries. In conclusion, we support the long-debated idea that new technologies are unlikely to provide a rapidly growing population with significantly increased crop yield. Instead, we suggest that delicately balanced humane measures to limit its growth and the amount of food consumed per capita are highly desirable for the foreseeable future.

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“…However, the green revolution genes Rht-B1b and Rht-D1b also decreased KNS and TKW while reduce PH [ 9 ]. To date, the number of major genes which affect PH in wheat and without causing substantial deleterious agronomic effects, is not large [ 10 ]. Therefore, the exploration and utilization of new dwarfing QTL/genes have been a major focus in wheat research.…”

Section: Introductionmentioning

confidence: 99%

“…Among them, Rht12 encodes a gibberellin (GA) 2-β-dioxygenase [ 15 ], Rht23 likely encodes an AP2 transcription factor [ 16 ], Rht24b encodes a GA 2-oxidase [ 17 ], and Rht8 encodes a ribonuclease H-like protein [ 18 , 19 ]. Additionally, several other genes regulating PH have been cloned using comparative genomics and genome wide association study approaches, including TaDEP1 [ 20 ], TaCOLD1 [ 21 ], TaTB1 [ 10 , 22 ], and TaARF12 [ 23 ].…”

Section: Introductionmentioning

confidence: 99%

Identification and validation of plant height, spike length and spike compactness loci in common wheat (Triticum aestivum L.)

Liu

Shi

et al. 2022

BMC Plant Biol

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Background Plant height (PH), spike length (SL) and spike compactness (SCN) are important agronomic traits in wheat due to their strong correlations with lodging and yield. Thus, dissection of their genetic basis is essential for the improvement of plant architecture and yield potential in wheat breeding. The objective of this study was to map quantitative trait loci (QTL) for PH, SL and SCN in a recombinant inbred line (RIL) population derived from the cross ‘PuBing3228 × Gao8901’ (PG-RIL) and to evaluate the potential values of these QTL to improve yield. Results In the current study, Five, six and ten stable QTL for PH, SL, and SCN, respectively, were identified in at least two individual environments. Five major QTL QPh.cas-5A.3, QPh.cas-6A, QSl.cas-6B.2, QScn.cas-2B.2 and QScn.cas-6B explained 5.58–25.68% of the phenotypic variation. Notably, two, three and three novel stable QTL for PH, SL and SCN were identified in this study, which could provide further insights into the genetic factors that shape PH and spike morphology in wheat. Conditional QTL analysis revealed that QTL for SCN were mainly affected by SL. Moreover, a Kompetitive Allele Specific PCR (KASP) marker tightly linked to stable major QTL QPh.cas-5A.3 was developed and verified using the PG-RIL population and a natural population. Conclusions Twenty-one stable QTL related to PH, SL, and SCN were identified. These stable QTL and the user-friendly marker KASP8750 will facilitate future studies involving positional cloning and marker-assisted selection in breeding.

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TB1: from domestication gene to tool for many trades

Abstract: This article comments on: Dixon LE, Pasquariello M, Boden SA. 2020. TEOSINTE BRANCHED1 regulates height and stem internode length in bread wheat. Journal of Experimental Botany 71, 4742–4750.

Cited by 12 publications

References 25 publications

Scripting Analyses of Genomes in Ensembl Plants

Scripting Analyses of Genomes in Ensembl Plants

Will Plant Genome Editing Play a Decisive Role in “Quantum-Leap” Improvements in Crop Yield to Feed an Increasing Global Human Population?

Identification and validation of plant height, spike length and spike compactness loci in common wheat (Triticum aestivum L.)

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