Altering Plant Architecture to Improve Performance and Resistance

Genotype-Dependent Effect of Silencing of TaCKX1 and TaCKX2 on Phytohormone Crosstalk and Yield-Related Traits in Wheat

The influence of silenced TaCKX1 and TaCKX2 on coexpression of other TaCKX gene family members (GFMs), phytohormone regulation and yield-related traits was tested in awned-spike cultivar. We documented a strong feedback mechanism of regulation of TaCKX GFM expression in which silencing of TaCKX1 upregulated expression of TaCKX2 genes and vice versa. Additionally, downregulation of TaCKX2 highly upregulated the expression of TaCKX5 and TaNAC2-5A. In contrast, expression of these genes in silenced TaCKX1 was downregulated. Silenced TaCKX1 T₂ lines with expression decreased by 47% had significantly higher thousand grain weight (TGW) and seedling root mass. Silenced TaCKX2 T₂ lines with expression of TaCKX2.2.1 and TaCKX2.2.2 decreased by 33% and 30%, respectively, had significantly higher chlorophyll content in flag leaves. TaCKX GFM expression, phytohormone metabolism and phenotype were additionally modified by Agrobacterium-mediated transformation. Two novel phytohormones, phenylacetic acid (PAA) and topolins, lack of gibberellic acid (GA) and changed phytohormone contents in the 7 days after pollination (DAP) spikes of the awned-spike cultivar compared to a previously tested, awnless one, were detected. We documented that major mechanisms of coregulation of the expression of TaCKX GFMs were similar in different spring wheat cultivars, but, depending on content and composition of phytohormones, regulation of yield-related traits was variously impacted.

HEXOKINASE1 signalling promotes shoot branching and interacts with cytokinin and strigolactone pathways

Plant architecture is controlled by several endogenous signals including hormones and sugars. However, only little information is known about the nature and roles of the sugar signalling pathways in this process. Here we test whether the sugar signalling pathway mediated by HEXOKINASE1 (HXK1) is involved in the control of shoot branching. To test the involvement of HXK1 in shoot branching and in the hormonal network controlling this process, we modulated the HXK1 pathway using physiological and genetic approaches in rose, pea and arabidopsis. Mannose-induced HXK signalling triggered bud outgrowth in rose and pea. In arabidopsis, both HXK1 deficiency and defoliation led to decreased shoot branching and conferred hypersensitivity to auxin. Complementation of the HXK1 knockout mutant gin2 with a catalytically inactive HXK1, restored shoot branching to the wild-type level. HXK1-deficient plants displayed decreased cytokinin levels and increased expression of MAX2, which is required for strigolactone signalling. The branching phenotype of HXK1-deficient plants could be partly restored by cytokinin treatment and strigolactone deficiency could override the negative impact of HXK1 deficiency on shoot branching. Our observations demonstrate that HXK1 signalling contributes to the regulation of shoot branching and interacts with hormones to modulate plant architecture.

Cytokinin glucosyl transferases, key regulators of cytokinin homeostasis, have potential value for wheat improvement

The cytokinins, which are N⁶ -substituted adenine derivatives, control key aspects of crop productivity. Cytokinin levels are controlled via biosynthesis by isopentenyl transferase (IPT), destruction by cytokinin oxidase/dehydrogenase (CKX), and inactivation via glucosylation by cytokinin glucosyl transferases (CGTs). While both yield components and tolerance to drought and related abiotic stressors have been positively addressed via manipulation of IPT and/or CKX expression, much less attention has been paid to the CGTs. As naming of the CGTs has been unclear, we suggest COGT, CNGT, CONGT and CNOGT to describe the O-, N- and dual function CGTs. As specific CGT mutants of both rice and arabidopsis showed impacts on yield components, we interrogated the wheat genome database, IWGSC RefSeq v1.0 & v2.0, to investigate wheat CGTs. Besides providing unambiguous names for the 53 wheat CGTs, we show their expression patterns in 70 developmental tissues and their response characteristics to various stress conditions by reviewing more than 1000 RNA-seq data sets. These revealed various patterns of responses and showed expression generally being more limited in reproductive tissues than in vegetative tissues. Multiple cis-regulatory elements are present in the 3 kb upstream of the start codons of the 53 CGTs. Elements associated with abscisic acid, light and methyl jasmonate are particularly over-represented, indicative of the responsiveness of CGTs to the environment. These data sets indicate that CGTs have potential value for wheat improvement and that these could be targeted in TILLING or gene editing wheat breeding programmes.

Genomic mapping and identification of candidate genes encoding nulliplex-branch trait in sea-island cotton (Gossypium barbadense L.) by multi-omics analysis

Nulliplex branch is a key architectural trait in sea-island cotton (Gossypium barbadense L.), but its genetic basis is not well understood. Here we investigated the genetic basis of the nulliplex-branch trait in cotton by combining newly created bulked segregant analysis (BSA)-seq data, published RNA-seq data, and published whole-genome resequencing (WGR) data. We delimited the nulliplex-branch locus (qD07-NB) to D07, region 14.8-17.1 Mb, using various BSA methods and markers. We integrated our BSA data with WGR data of sea-island cotton varieties and detected a missense single-nucleotide polymorphism in the candidate gene (Gbar_D07G011870) of qD07-NB. This gene was under positive selection during sea-island cotton breeding in the Xinjiang Uygur Autonomous Region, China. Notably, the nulliplex-branch varieties possessed a better fiber quality than the long-branch varieties, and a set of high-quality molecular markers was identified for molecular breeding of the nulliplex-branch trait in cotton. We combined BSA-seq and RNA-seq data to compare gene expression profiles between two elite sea-island cotton varieties during three developmental stages. We identified eleven relevant candidate genes, five downregulated and six upregulated, in the qD07-NB locus. This research will expand our understanding of the genetic basis of the nulliplex-branch trait and provide guidance for architecture-focused breeding in cotton.

Supplementary Information

The online version contains supplementary material available at 10.1007/s11032-021-01229-w.

TaCKX2.2 Genes Coordinate Expression of Other TaCKX Family Members, Regulate Phytohormone Content and Yield-Related Traits of Wheat

TaCKX gene family members (GFMs) play essential roles in the regulation of cytokinin during wheat development and significantly influence yield-related traits. However, detailed function of most of them is not known. To characterize the role of TaCKX2.2 genes we silenced all homoeologous copies of both TaCKX2.2.1 and TaCKX2.2.2 by RNAi technology and observed the effect of silencing in 7 DAP spikes of T₁ and T₂ generations. The levels of gene silencing of these developmentally regulated genes were different in both generations, which variously determined particular phenotypes. High silencing of TaCKX2.2.2 in T₂ was accompanied by slight down-regulation of TaCKX2.2.1 and strong up-regulation of TaCKX5 and TaCKX11, and expression of TaCKX1, TaCKX2.1, and TaCKX9 was comparable to the non-silenced control. Co-ordinated expression of TaCKX2.2.2 with other TaCKX GFMs influenced phytohormonal homeostasis. Contents of isoprenoid, active cytokinins, their conjugates, and auxin in seven DAP spikes of silenced T₂ plants increased from 1.27 to 2.51 times. However, benzyladenine (BA) and abscisic acid (ABA) contents were significantly reduced and GA₃ was not detected. We documented a significant role of TaCKX2.2.2 in the regulation of thousand grain weight (TGW), grain number, and chlorophyll content, and demonstrated the formation of a homeostatic feedback loop between the transcription of tested genes and phytohormones. We also discuss the mechanism of regulation of yield-related traits.

Topological clustering of regulatory genes confers pathogenic tolerance to cassava brown streak virus (CBSV) in cassava

Robustness, a naïve property of biological systems, enables organisms to maintain functions during perturbation and is crucial for improving the resilience of crops to prevailing stress conditions and diseases, guaranteeing food security. Most studies of robustness in crops have focused on genetic superiority based upon individual genes, overlooking the collaborative actions of multiple responsive genes and the regulatory network topology. This research aims to uncover patterns of gene cooperation leading to organismal robustness by studying the topology of gene co-expression networks (GCNs) of both CBSV virus resistant and susceptible cassava cultivars. The resulting GCNs show higher topological clustering of cooperative genes in the resistant cultivar, suggesting that the network architecture is central to attaining robustness. Despite a reduction in the number of hub genes in the resistant cultivar following the perturbation, essential biological functions contained in the network were maintained through neighboring genes that withstood the shock. The susceptible cultivar seemingly coped by inducing more gene actions in the network but could not maintain the functions required for plant growth. These findings underscore the importance of regulatory network architecture in ensuring phenotypic robustness and deepen our understanding of transcriptional regulation.