Fine-mapping and comparative genomic analysis reveal the gene composition at the S and Z self-incompatibility loci in grasses

Self-incompatibility (SI) is a genetic mechanism of hermaphroditic plants to prevent inbreeding after self-pollination. Allogamous Poaceae species exhibit a unique gametophytic SI system controlled by two multi-allelic and independent loci, S and Z. Despite intense research efforts in the last decades, the genes that determine the initial recognition mechanism are yet to be identified. Here, we report the fine-mapping of the Z-locus in perennial ryegrass (Lolium perenne L.) and provide evidence that the pollen and stigma components are determined by two genes encoding DUF247 domain proteins (ZDUF247-I and ZDUF247-II) and the gene sZ, respectively. The pollen and stigma determinants are located side-by-side and were genetically linked in 10,245 individuals of two independent mapping populations segregating for Z. Moreover, they exhibited high allelic diversity as well as tissue-specific gene expression, matching the expected characteristics of SI determinants known from other systems. Revisiting the S-locus using the latest high-quality whole-genome assemblies revealed a similar gene composition and structure as found for Z, supporting the hypothesis of a duplicated origin of the two-locus SI system of grasses. Ultimately, comparative genomic analyses across a wide range of self-compatible and self-incompatible Poaceae species revealed that the absence of a functional copy of at least one of the six putative SI determinants is accompanied by a self-compatible phenotype. Our study provides new insights into the origin and evolution of the unique gametophytic SI system in one of the largest and economically most important plant families.Open access articleThis item from the UA Faculty Publications collection is made available by the University of Arizona with support from the University of Arizona Libraries. If you have questions, please contact us at [email protected]

Callus Induction from Diverse Explants and Genotypes Enables Robust Transformation of Perennial Ryegrass (Lolium perenne L.)

Genetic transformation of perennial ryegrass (Lolium perenne L.) is critical for fundamental and translational research in this important grass species. It often relies on Agrobacterium-mediated transformation of callus tissue. However, callus induction is restricted to a few genotypes that respond well to tissue culture. Here, we report callus induction from different perennial ryegrass genotypes and explants, such as shoot tips, seeds, and anthers, which were transformed with several plasmids for functional genomics. β-glucuronidase (GUS) histochemical staining showed the LmdsRNAbp promoter sequence was active in stigmas, spikelets, anthers, and leaves. We also transformed calli with plasmids allowing gene silencing and gene knock-out using RNA interference and CRISPR/Cas9, respectively, for which genotypic and phenotypic investigations are ongoing. Using 19 different constructs, 262 transgenic events were regenerated. Moreover, the protocol regenerated a doubled haploid transgenic event from anther-derived calli. This work provides a proof-of-concept method for expanding the range of genotypes amenable to transformation, thus, serving research and breeding initiatives to improve this important grass crop for forage and recreation

Wide-area analysis-ready radar backscatter composites

The benefits of composite products are well known to users of data from optical sensors: cloud-cleared composite reflectance or index products are commonly used as an analysis-ready data (ARD) layer. No analogous composite products are currently in widespread use that is based on spaceborne radar satellite backscatter signals. Here, we present a methodology to produce wide-area ARD composite backscatter images. They build on the existing heritage of geometrically and radiometrically terrain corrected level 1 products. By combining backscatter measurements of a single region seen from multiple satellite tracks (incl. ascending and descending), they are able to provide wide-area coverage with low latency. The analysis-ready composite backscatter maps provide flattened backscatter estimates that are geometrically and radiometrically corrected for slope effects. A mask layer annotating the local quality of the composite resolution is introduced. Multiple tracks are combined by weighting each observation by its local resolution, generating seamless wide-area backscatter maps suitable for applications ranging from wet snow monitoring to land cover classification or short-term change detection

Understanding forage grass genomes beyond single nucleotide variation - an example on self-incompatibility

The genera Lolium and Festuca comprise the most important forage and turf grass species of temperate regions worldwide. Despite tremendous advancements in DNA sequencing technologies and genome assembly methods, genome sequences of highest quality in terms of completeness, correctness and contiguity are yet to be established for the Lolium-Festuca species complex. The International Lolium-Festuca Pangenome Consortium (ILFPC) has set out to fill this gap and aims at establishing multiple high-quality genome sequences to advance forage and turf grass research and breeding. Here we report about first results of the joint efforts within ILFPC and, more importantly, how the established genomic resources can help answering biological questions. Using self-incompatibility (SI) as an example, we present how whole genome assemblies can be used to resolve the gene content and order at one SI locus, previously identified by fine-mapping. The multiple genomes obtained through ILFPC also enabled us to compare the gene constitution of different genotypes within and across species and link this information to SI functionality. The availability of multiple high-quality genome assemblies constitutes a milestone for genetic studies, functional biology and genomics-assisted breeding. Moreover, comparing genomes and moving towards pangenomics opens new opportunities to describe structural genome variation and unlock genetic diversity in the Lolium-Festuca species complex

Fine-Mapping and Comparative Genomic Analysis Reveal the Gene Composition at the S and Z Self-incompatibility Loci in Grasses

Self-incompatibility (SI) is a genetic mechanism of hermaphroditic plants to prevent inbreeding after self-pollination. Allogamous Poaceae species exhibit a unique gametophytic SI system controlled by two multi-allelic and independent loci, S and Z. Despite intense research efforts in the last decades, the genes that determine the initial recognition mechanism are yet to be identified. Here, we report the fine-mapping of the Z-locus in perennial ryegrass (Lolium perenne L.) and provide evidence that the pollen and stigma components are determined by two genes encoding DUF247 domain proteins (ZDUF247-I and ZDUF247-II) and the gene sZ, respectively. The pollen and stigma determinants are located side-by-side and were genetically linked in 10,245 individuals of two independent mapping populations segregating for Z. Moreover, they exhibited high allelic diversity as well as tissue-specific gene expression, matching the expected characteristics of SI determinants known from other systems. Revisiting the S-locus using the latest high-quality whole-genome assemblies revealed a similar gene composition and structure as found for Z, supporting the hypothesis of a duplicated origin of the two-locus SI system of grasses. Ultimately, comparative genomic analyses across a wide range of self-compatible and self-incompatible Poaceae species revealed that the absence of a functional copy of at least one of the six putative SI determinants is accompanied by a self-compatible phenotype. Our study provides new insights into the origin and evolution of the unique gametophytic SI system in one of the largest and economically most important plant families.Open access articleThis item from the UA Faculty Publications collection is made available by the University of Arizona with support from the University of Arizona Libraries. If you have questions, please contact us at [email protected]