TB1: from domestication gene to tool for many trades

PEP-ASSOCIATED PROTEIN 3 regulates rice tiller formation and grain yield by controlling chloroplast biogenesis

Plastid-encoded RNA polymerase (PEP) plays a pivotal role in chloroplast development by governing the transcription of chloroplast genes, and PEP-associated proteins (PAPs) modulate PEP transcriptional activity. Therefore, PAPs provide an intriguing target for those efforts to improve yield, by enhancing chloroplast development. In this study, we identified the rice (Oryza sativa) OsPAP3 gene and characterized its function in chloroplast development. OsPAP3 expression was light-dependent and leaf-specific, similar to the PEP-dependent chloroplast gene RUBISCO LARGE SUBUNIT (OsRbcL), and OsPAP3 protein localized to chloroplast nucleoids where PEP functions. Analysis of loss-of-function and gain-of-function mutants showed that the expression of OsPAP3 is tightly linked to chloroplast gene expression and chloroplast biogenesis in rice. Homozygous knockout mutants of OsPAP3 had fewer chloroplasts than wild type, whereas plants overexpressing OsPAP3 had more chloroplasts. Also, OsPAP3 knockout suppressed the PEP-dependent expression of chloroplast genes, but OsPAP3 overexpression increased their expression. These findings indicate that OsPAP3 regulates chloroplast biogenesis in rice by controlling the PEP-dependent expression of chloroplast genes. More importantly, data from 3 seasons of field cultivation revealed that the overexpression of OsPAP3 improves rice grain yield by approximately 25%, largely due to increased tiller formation. Collectively, these observations suggest that OsPAP3 regulates rice growth and productivity by promoting chloroplast development.

Advances in Research on the Regulation of Floral Development by CYC-like Genes

CYCLOIDEA (CYC)-like genes belong to the TCP transcription factor family and play important roles associated with flower development. The CYC-like genes in the CYC1, CYC2, and CYC3 clades resulted from gene duplication events. The CYC2 clade includes the largest number of members that are crucial regulators of floral symmetry. To date, studies on CYC-like genes have mainly focused on plants with actinomorphic and zygomorphic flowers, including Fabaceae, Asteraceae, Scrophulariaceae, and Gesneriaceae species and the effects of CYC-like gene duplication events and diverse spatiotemporal expression patterns on flower development. The CYC-like genes generally affect petal morphological characteristics and stamen development, as well as stem and leaf growth, flower differentiation and development, and branching in most angiosperms. As the relevant research scope has expanded, studies have increasingly focused on the molecular mechanisms regulating CYC-like genes with different functions related to flower development and the phylogenetic relationships among these genes. We summarize the status of research on the CYC-like genes in angiosperms, such as the limited research conducted on CYC1 and CYC3 clade members, the necessity to functionally characterize the CYC-like genes in more plant groups, the need for investigation of the regulatory elements upstream of CYC-like genes, and exploration of the phylogenetic relationships and expression of CYC-like genes with new techniques and methods. This review provides theoretical guidance and ideas for future research on CYC-like genes.

Differential chromatin binding preference is the result of the neo-functionalization of the TB1 clade of TCP transcription factors in grasses

The understanding of neo-functionalization of plant transcription factors (TFs) after gene duplication has been extensively focused on changes in protein-protein interactions, the expression pattern of TFs, or the variation of cis-elements bound by TFs. Yet, the main molecular role of a TF, that is, its specific chromatin binding for the direct regulation of target gene expression, continues to be mostly overlooked. Here, we studied the TB1 clade of the TEOSINTE BRANCHED 1, CYCLOIDEA, PROLIFERATING CELL FACTORS (TCP) TF family within the grasses (Poaceae). We identified an Asp/Gly amino acid replacement within the TCP domain, originated within a paralog TIG1 clade exclusive for grasses. The heterologous expression of Zea mays TB1 and its two paralogs BAD1 and TIG1 in Arabidopsis mutant plants lacking the TB1 ortholog BRC1 revealed distinct functions in plant development. Notably, the Gly acquired in the TIG1 clade does not impair TF homodimerization and heterodimerization, while it modulates chromatin binding preferences. We found that in vivo TF recognition of target promoters depends on this Asp/Gly mutation and directly impacts downstream gene expression and subsequent plant development. These results provided new insights into how natural selection fine-tunes gene expression regulation after duplication of TFs to define plant architecture.

Tiller Number1 encodes an ankyrin repeat protein that controls tillering in bread wheat

Wheat (Triticum aestivum L.) is a major staple food for more than one-third of the world's population. Tiller number is an important agronomic trait in wheat, but only few related genes have been cloned. Here, we isolate a wheat mutant, tiller number1 (tn1), with much fewer tillers. We clone the TN1 gene via map-based cloning: TN1 encodes an ankyrin repeat protein with a transmembrane domain (ANK-TM). We show that a single amino acid substitution in the third conserved ankyrin repeat domain causes the decreased tiller number of tn1 mutant plants. Resequencing and haplotype analysis indicate that TN1 is conserved in wheat landraces and modern cultivars. Further, we reveal that the expression level of the abscisic acid (ABA) biosynthetic gene TaNCED3 and ABA content are significantly increased in the shoot base and tiller bud of the tn1 mutants; TN1 but not tn1 could inhibit the binding of TaPYL to TaPP2C via direct interaction with TaPYL. Taken together, we clone a key wheat tiller number regulatory gene TN1, which promotes tiller bud outgrowth probably through inhibiting ABA biosynthesis and signaling.

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

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.

Scripting Analyses of Genomes in Ensembl Plants

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.

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

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.