Multi-allelic gene editing in an apomictic, tetraploid turf and forage grass (Paspalum notatum Flüggé) using CRISPR/Cas9

Comparison of genotyping assays for detection of targeted CRISPR/Cas mutagenesis in highly polyploid sugarcane

Sugarcane (Saccharum spp.) is an important biofuel feedstock and a leading source of global table sugar. Saccharum hybrid cultivars are highly polyploid (2n = 100-130), containing large numbers of functionally redundant hom(e)ologs in their genomes. Genome editing with sequence-specific nucleases holds tremendous promise for sugarcane breeding. However, identification of plants with the desired level of co-editing within a pool of primary transformants can be difficult. While DNA sequencing provides direct evidence of targeted mutagenesis, it is cost-prohibitive as a primary screening method in sugarcane and most other methods of identifying mutant lines have not been optimized for use in highly polyploid species. In this study, non-sequencing methods of mutant screening, including capillary electrophoresis (CE), Cas9 RNP assay, and high-resolution melt analysis (HRMA), were compared to assess their potential for CRISPR/Cas9-mediated mutant screening in sugarcane. These assays were used to analyze sugarcane lines containing mutations at one or more of six sgRNA target sites. All three methods distinguished edited lines from wild type, with co-mutation frequencies ranging from 2% to 100%. Cas9 RNP assays were able to identify mutant sugarcane lines with as low as 3.2% co-mutation frequency, and samples could be scored based on undigested band intensity. CE was highlighted as the most comprehensive assay, delivering precise information on both mutagenesis frequency and indel size to a 1 bp resolution across all six targets. This represents an economical and comprehensive alternative to sequencing-based genotyping methods which could be applied in other polyploid species.

Transcriptome-guided breeding for Paspalum notatum: producing apomictic hybrids with enhanced omega-3 content

KEY MESSAGE

Transcriptomics- and FAME-GC-MS-assisted apomixis breeding generated Paspalum notatum hybrids with clonal reproduction and increased α-linolenic acid content, offering the potential to enhance livestock product's nutritional quality and reduce methane emissions A low omega-6:omega-3 fatty acid ratio is considered an indicator of the nutritional impact of milk fat on human health. In ruminants, major long-chain fatty acids, such as linoleic acid (18:2, omega-6) and α-linolenic acid (18:3, omega-3), originate from dietary sources and reach the milk via the bloodstream. Since forages are the primary source of long-chain fatty acids for such animals, they are potential targets for improving milk lipid composition. Moreover, a high 18:3 content in their diet is associated with reduced methane emissions during grazing. This work aimed to develop genotypes of the forage grass Paspalum notatum with high leaf 18:3 content and the ability for clonal reproduction via seeds (apomixis). We assembled diploid and polyploid Paspalum notatum leaf transcriptomes and recovered sequences of two metabolism genes associated with the establishment of lipid profiles, namely SUGAR-DEPENDENT 1 (SDP1) and PEROXISOMAL ABC TRANSPORTER 1 (PXA1). Primers were designed to amplify all expressed paralogs in leaves. qPCR was used to analyse SDP1 and PXA1 expression in seven divergent genotypes. Reduced levels of SDP1 and PXA1 were found in the polyploid sexual genotype Q4188. Fatty acid methyl esters/gas chromatography/mass spectrometry (FAME/GC/MS) assays confirmed an increased percentage of 18:3 in this genotype. Crosses between Q4188 and the obligate apomictic pollen donor Q4117 resulted in two apomictic F1 hybrids (JS9 and JS71) with reduced SDP1 and PXA1 levels, increased 18:3 content, and clonal maternal reproduction. These materials could enhance milk and meat quality while reducing greenhouse gas emissions during grazing.

Chromosome-scale genome assembly and annotation of Paspalum notatum Flüggé var. saurae

Paspalum notatum Flüggé is an economically important subtropical fodder grass that is widely used in the Americas. Here, we report a new chromosome-scale genome assembly and annotation of a diploid biotype collected in the center of origin of the species. Using Oxford Nanopore long reads, we generated a 557.81 Mb genome assembly (N50 = 56.1 Mb) with high gene completeness (BUSCO = 98.73%). Genome annotation identified 320 Mb (57.86%) of repetitive elements and 45,074 gene models, of which 36,079 have a high level of confidence. Further characterisation included the identification of 59 miRNA precursors together with their putative targets. The present work provides a comprehensive genomic resource for P. notatum improvement and a reference frame for functional and evolutionary research within the genus.

CRISPR/Cas9-mediated knockout of NYC1 gene enhances chlorophyll retention and reduces tillering in Zoysia matrella (L.) Merrill

KEY MESSAGE

Genome editing by CRISPR/Cas9 can be applied to Z. matrella 'Wakaba', and knockout mutants of ZmNYC1 gene exhibited stay-green phenotype and reduced tillering. Zoysia matrella is a widely used C4 warm-season turfgrass for landscaping, golf courses, and sports fields. Here, we used the CRISPR/Cas9 system to target the Non-Yellow Coloring1 (ZmNYC1) gene in the highly heterozygous allotetraploid Z. matrella 'Wakaba', aiming to generate a novel stay-green variety. Of 441 Agrobacterium-infected calli, 22 (5.0%) were transformed, and 14 of these (63.6%) showed targeted mutations through cleaved amplified polymorphic sequences analysis. Sequencing analysis revealed mutations mostly consisting of 1 or 2 bp indels, occurring 2 to 4 bp upstream of the PAM sequence. Regenerated plants exhibited five ZmNYC1 target locus genotypes, including homozygous mutants with a complete knockout of all four alleles in the T0 generation. Under dark treatment, ZmNYC1-mutated plants displayed suppressed chlorophyll b (Chl b) degradation, leading to higher chlorophyll content and Chl b, with a lower chlorophyll a/chlorophyll b ratio compared to the wild type (WT). However, the ZmNYC1 mutation also inhibited plant growth in homozygous mutant genotypes, exhibiting reduced tillering compared to WT. Additionally, during winter simulation, mutant with a complete knockout retained greenness longer than the WT. This is the first successful use of CRISPR/Cas9 genome editing in zoysiagrass. The mutants of the ZmNYC1 gene would serve as valuable breeding material for developing improved zoysiagrass varieties that can maintain their green color for longer periods, even during winter dormancy.