Biology subjects

Rathjen, T.

Publications and source records attributed to Rathjen, T..

3 recordsLinked to original sources

bioRxiv2024

Deciphering transcriptional programming during lupin (Lupinus angustifolius) seed development using RNA-seq

Lupin (Lupinus spp.) seeds are valued for their high protein content (35-40%) for both human and animal consumption. Seed development in crop plants is a critical factor influencing both seed fate and yield, hence, understanding the molecular mechanisms of seed development is essential. This study conducted a transcriptome analysis of Narrow Leaf Lupin (NLL) during seed development stages (3, 6, 9, 12, 15, 18, and 21 days after flowering) to investigate transcriptional dynamics and identify key candidate genes that control seed development. Approximately 357 million sequencing reads were generated from nine samples from leave, flower and seed tissues, enabling the identification of 34,769 expressed genes. The analysis revealed dynamic gene expression, with early stages marked by high metabolic activity and later stages focusing on storage protein synthesis and nutrient reservoir formation. The differential expression patterns of seed storage protein genes, including cupin groups (, {beta}, {gamma}, and {delta} conglutins), were notable. The expression of and {beta} conglutins increased at later stages (15-21 days after flowering), supporting their role in grain filling and nutrient storage. Genes related to quinolizidine alkaloid biosynthesis, such as lysine/ornithine decarboxylase and purine permease transporter 1, showed late expression patterns suggesting alkaloid synthesis and transport during later stages. Many of the well-established transcription factors (TFs) known for their roles in seed development (bHLH, AP2, MYB, ERF, C2H2, NAC, WRKY, and C3H zinc finger families) showed differential expression, thus reinforcing the validity of our findings. These findings lay the groundwork for understanding the genetic and molecular mechanisms of seed development in lupin, contributing to enhanced crop management and breeding programs.

plant biology↗

bioRxiv2024

OzWheat: a genome-to-phenome platform to resolve complex traits for wheat pre-breeding and research.

For over a century, Australian wheat breeders have successfully adapted wheat to a broad range of climatic conditions and crop management practices. The OzWheat genome-to-phenome (G2P) platform was established to capture this breeding history and explore traits, genes, and their interactions with the environment to enable ongoing research and deliver targets for wheat improvement. A panel of 285 cultivars and landraces were chosen through knowledge of breeding pedigrees to represent both global diversity and the historic flow of genetic variation over more than 100 years of selective breeding in Australia. Genetic characterisation of the panel included identification of genome-wide sequence variants and gene expression profiling across environments. Important traits for adaptation (flowering time and plant height) were assayed in controlled environments and at multiple field sites and years, with genome-wide association analyses (GWAS) using linear mixed models detecting both known and novel loci. Here, we report establishment of the OzWheat G2P platform as a powerful tool to integrate wheat genomes and phenomes and demonstrate its use to identify candidate genes and understand gene by environment interactions. This provides the wheat research and breeding community a new resource to support future cultivar development.

genomics↗

bioRxiv2024

Twisted Sister1: an agravitropic mutant of bread wheat (Triticum aestivum) with altered root and shoot architectures.

We identified a mutant of hexaploid wheat (Triticum aestivum) with impaired responses to gravity. The mutant named Twisted Sister1 (TS1) had agravitropic roots that were often twisted along with altered shoot phenotypes. Roots of TS1 were insensitive of externally applied auxin with the genetics and physiology suggestive of a mutated AUX/IAA transcription factor gene. Hexaploid wheat possesses over eighty AUX/IAA genes and sequence information did not identify an obvious candidate. Bulked segregant analysis of an F2 population mapped the mutation to chromosome 5A and subsequent mapping located the mutation to a 41 Mbp region. RNA-seq identified the TraesCS5A03G0149800 gene encoding a TaAUX/IAA protein to be mutated in the highly conserved domain II motif. We confirmed TraesCS5A03G0149800 as underlying the mutant phenotype by generating transgenic Arabidopsis thaliana. Analysis of RNA-seq data suggested broad similarities between Arabidopsis and wheat for the role of AUX/IAA genes in gravity responses. Here we show that the sequenced wheat genome along with previous knowledge largely from the model species Arabidopsis, gene mapping, RNA-seq and expression in Arabidopsis have enabled cloning of a key wheat gene defining plant architecture.

plant biology↗