Dissecting the role of MADS-box genes in monocot floral development and diversity

Many monocot plants have high social and economic value. These include grasses such as rice (Oryza sativa), wheat (Triticum aestivum) and barley (Hordeum vulgare), which produce soft commodities for many food and beverage industries, and ornamental flowers like lily (Lilium longiflorum) and orchid (Oncidium Gower Ramsey), which represent an important component of international flower markets. There is constant pressure to improve the development and diversity of these species with a significant emphasis on flower development, and this is particularly relevant considering the impact of changing environments on reproduction and thus yield. MADS-box proteins are a family of transcription factors that contain a conserved 56 amino acid MADS-box motif. In plants, attention has been devoted to characterisation of this family due to their roles in inflorescence and flower development, which holds promise for the modification of floral architecture for plant breeding. This has been explored in diverse angiosperms, but particularly the dicot model Arabidopsis thaliana. The focus of this review is on the less-well characterised roles of the MADS-box proteins in monocot flower development and how changes in MADS-box proteins throughout evolution may have contributed to creating a diverse range of flowers. Examining these changes within the monocots can identify the importance of certain genes and pinpoint those which might be useful in future crop improvement and breeding strategies

Analysis of MADS-box genes and heat stress in barley (Hordeum vulgare)

Barley is a widely grown, economically important cereal crop used for stock feed, malting and brewing. Fundamental understanding of the underlying genetic network controlling floral organ development is essential for potential modification of floral architecture for plant breeding. ABCDE-model MADS-box proteins are a type of MADS-box family transcription factors that contain a conserved 60 amino acid MADS-box motif and that are involved in inflorescence and flower development. In the dicot model Arabidopsis thaliana and in crops like rice (Oryza sativa), maize (Zea mays) and wheat (Triticum aestivum) most of the ABCDE-model MADS-box flowering genes have been identified. In barley (Hordeum vulgare) however, only a select number of MADS-box flowering genes have been investigated. Identifying the role and structure of the ABCDE-model MADS-box genes in barley floral development could shed a light on the evolutionary differences between barley and closely related crops and the development of their inflorescences and flower morphogenesis. In this thesis I aimed to identify the expression patterns of the ABCDE-model MADS-box genes in barley by qRT-PCR and in situ hybridization. To investigate the function of the B-class genes in barley the CRES-T dominant repression system, also known as SRDX, was used. Results showed that the expression patterns of the ABCDE MADS-box genes are conserved in barley and that the B-class genes have a redundant function in stamens and lodicule development. MADS-box transcription factors have been shown to be involved in abiotic stress tolerance in several different species like tomato, rice and sheepgrass. Abiotic stresses, particularly global warming, are the major causes of crop yield losses by affecting fertility and seed set. Prior to analysis of the specific impact of abiotic stress on the MADS-box genes, it is important to understand the effects of abiotic stress on barley per se. Effects of heat stress on reproductive structures and fertility in barley have not been extensively investigated. In this thesis the effect of high temperature conditions on floral development in three commercial European spring barley varieties during two vulnerable reproductive stages, meiosis and mitosis, was examined by using fertility assays, 3-dimensional modelling, cytology and immunolabelling. Results showed that male reproductive organs are more vulnerable to heat stress than female reproductive organs and that certain varieties are more tolerant to heat stress

Analysis of MADS-box genes and heat stress in barley (Hordeum vulgare)

Barley is a widely grown, economically important cereal crop used for stock feed, malting and brewing. Fundamental understanding of the underlying genetic network controlling floral organ development is essential for potential modification of floral architecture for plant breeding. ABCDE-model MADS-box proteins are a type of MADS-box family transcription factors that contain a conserved 60 amino acid MADS-box motif and that are involved in inflorescence and flower development. In the dicot model Arabidopsis thaliana and in crops like rice (Oryza sativa), maize (Zea mays) and wheat (Triticum aestivum) most of the ABCDE-model MADS-box flowering genes have been identified. In barley (Hordeum vulgare) however, only a select number of MADS-box flowering genes have been investigated. Identifying the role and structure of the ABCDE-model MADS-box genes in barley floral development could shed a light on the evolutionary differences between barley and closely related crops and the development of their inflorescences and flower morphogenesis. In this thesis I aimed to identify the expression patterns of the ABCDE-model MADS-box genes in barley by qRT-PCR and in situ hybridization. To investigate the function of the B-class genes in barley the CRES-T dominant repression system, also known as SRDX, was used. Results showed that the expression patterns of the ABCDE MADS-box genes are conserved in barley and that the B-class genes have a redundant function in stamens and lodicule development. MADS-box transcription factors have been shown to be involved in abiotic stress tolerance in several different species like tomato, rice and sheepgrass. Abiotic stresses, particularly global warming, are the major causes of crop yield losses by affecting fertility and seed set. Prior to analysis of the specific impact of abiotic stress on the MADS-box genes, it is important to understand the effects of abiotic stress on barley per se. Effects of heat stress on reproductive structures and fertility in barley have not been extensively investigated. In this thesis the effect of high temperature conditions on floral development in three commercial European spring barley varieties during two vulnerable reproductive stages, meiosis and mitosis, was examined by using fertility assays, 3-dimensional modelling, cytology and immunolabelling. Results showed that male reproductive organs are more vulnerable to heat stress than female reproductive organs and that certain varieties are more tolerant to heat stress

Tumor mutational burden assessment and standardized bioinformatics approach using custom NGS panels in clinical routine

International audienceBackground: High tumor mutational burden (TMB) was reported to predict the efficacy of immune checkpoint inhibitors (ICIs). Pembrolizumab, an anti-PD-1, received FDA-approval for the treatment of unresectable/metastatic tumors with high TMB as determined by the FoundationOne®CDx test. It remains to be determined how TMB can also be calculated using other tests. Results: FFPE/frozen tumor samples from various origins were sequenced in the frame of the Institut Curie (IC) Molecular Tumor Board using an in-house next-generation sequencing (NGS) panel. A TMB calculation method was developed at IC (IC algorithm) and compared to the FoundationOne® (FO) algorithm. Using IC algorithm, an optimal 10% variant allele frequency (VAF) cut-off was established for TMB evaluation on FFPE samples, compared to 5% on frozen samples. The median TMB score for MSS/POLE WT tumors was 8.8 mut/Mb versus 45 mut/Mb for MSI/POLE-mutated tumors. When focusing on MSS/POLE WT tumor samples, the highest median TMB scores were observed in lymphoma, lung, endometrial, and cervical cancers. After biological manual curation of these cases, 21% of them could be reclassified as MSI/POLE tumors and considered as “true TMB high.” Higher TMB values were obtained using FO algorithm on FFPE samples compared to IC algorithm (40 mut/Mb [10–3927] versus 8.2 mut/Mb [2.5–897], p Conclusions: We herein propose a TMB calculation method and a bioinformatics tool that is customizable to different NGS panels and sample types. We were not able to retrieve TMB values from FO algorithm using our own algorithm and NGS panel