Biology subjects

Kiesbauer, J.

Publications and source records attributed to Kiesbauer, J..

4 recordsLinked to original sources

bioRxiv2025

Candidate genes for stem rust resistance in Italian ryegrass revealed by nested association mapping

Stem rust, caused by Puccinia graminis ssp. graminicola, is a major disease affecting the outcrossing species Italian ryegrass (Lolium multiflorum Lam.), leading to substantial reductions in seed yield. Until now, knowledge on the genetic control of stem rust resistance in Italian ryegrass has been limited to a few quantitative trait loci identified in bi-parental mapping populations. To discover novel resistance sources for use in breeding programs, appropriate plant populations, reliable phenotyping methods and advanced genomic tools are essential. In this study, we utilized a previously established F2 nested association mapping (NAM) population comprising 708 individuals derived from 24 founder plants exhibiting high variation in stem rust resistance. Phenotypic evaluation was conducted under natural inoculation in three location-by-year combinations. By integrating reduced-representation sequencing of the NAM population with whole-genome sequencing of the founder plants, we identified 3,199,253 SNP markers for association mapping. The high SNP marker density, together with the strong detection power of the NAM population, enabled the identification of four novel candidate genes. Two of these genes, located on chromosomes 6 and 7, encode receptor-like serine/threonine kinases that are known to play a role in stem rust resistance in other crops. Within the serine/threonine kinase gene Chr7.32208, two superior haplotypes were identified that can be directly implemented as selection criteria in breeding programs. The novel stem rust resistance candidate genes reported here provide promising targets for functional validation and the improvement of stem rust resistance in Italian ryegrass breeding. Key messageField phenotyping of a previously established NAM population for stem rust resistance, combined with high-density genotyping, enabled the identification of novel sources of stem rust resistance in Italian ryegrass.

plant biology↗

bioRxiv2025

The first nested association mapping (NAM) population for outbreeding Italian ryegrass reveals candidate genes for seed shattering and related traits

Nested association mapping (NAM) populations are a powerful tool for investigating the genetic control of agronomically important traits and have been successfully used in many inbreeding crops. Here, we present the first NAM population established in an outcrossing forage grass species, Italian ryegrass (Lolium multiflorum Lam.), to dissect the genetic control of seed shattering. The NAM population was based on 23 diverse and one common founder plants and consisted of 708 F2 individuals. Reduced-representation sequencing (ddRAD) of the 708 F2 individuals, combined with whole genome sequencing data of the 24 founder plants, yielded a total of 3,199,253 SNPs that were used for population structure analysis, parentship analysis and genome-wide association studies. Phenotypic data for seed shattering and seed yield-related traits, collected in three year x location environments, showed high phenotypic variance within the NAM population. A total of seven QTL were identified for seed shattering, seed yield, spike length, flag leaf length and flowering time. Within these QTL regions, one candidate gene for seed shattering and three candidate genes for flowering time were identified. For seed shattering, the significant SNP association within the gene chr7.26897, known to be in involved in ripening-related pathways, explained 10.03% of the phenotypic variance. These candidate genes identified provide valuable targets for functional validation and demonstrate the effectiveness of NAM populations for elucidating the genetic architecture of complex traits in outcrossing forage grasses.

plant biology↗

bioRxiv2024

Chromosome-level haplotype-resolved genome assembly provides insights into the highly heterozygous genome of Italian ryegrass (Lolium multiflorum Lam.)

Italian ryegrass (Lolium multiflorum Lam.) is an important forage grass, providing a major source of feed for ruminants in temperate regions. Due to its highly heterozygous and repeat-rich genome, high-quality chromosome-level genome assemblies are scarce for Italian ryegrass. Here, we sequenced the genome of a genotype from the Italian ryegrass cultivar Rabiosa (hereafter referred to as Rabiosa), and we obtained Oxford Nanopore Technologies long reads ([~]60-fold coverage), Illumina short reads ([~]85-fold coverage) and high-throughput chromosome conformation capture data ([~]60-fold coverage). With Rabiosa as the parent, we constructed an F1 population consisting of 305 individuals, which were genotyped by reduced representation sequencing for linkage map construction and quantitative trait loci (QTL) analysis. Using whole-genome sequencing data of Rabiosa and the genetic linkage map, we first generated a chromosome-level unphased haploid assembly (scaffold N50 of 338.75 Mb, total BUSCO score of 94.60%). Then, based on the unphased assembly and a reference-based phasing approach, we generated a chromosome-level haplotype-resolved assembly containing both haplotypes (scaffold N50 of [~]250 Mb and total BUSCO score of [~]90% for each haplotype). Between the two haplotypes of Rabiosa, we observed a highly collinear gene order at chromosome level and a high sequence variation at local level. With a graph-based reference built from the unphased and the haplotype-resolved assemblies of Rabiosa, we conducted a QTL analysis, and two QTL significantly associated with stem rust resistance were detected. The genome assemblies of Rabiosa will serve as invaluable genomic resources to facilitate genomic applications in forage grass research and breeding.

genomics↗

bioRxiv2023

Higher seed yield through selection for reduced seed shattering in Italian ryegrass (Lolium multiflorum Lam.)

Seed shattering, i.e., the loss of seeds at ripening stage shortly before or during seed harvest, is strongly reducing seed yield in Italian ryegrass (Lolium multiflorum Lam.). The aim of this study was to evaluate the possibility to reduce seed shattering within breeding germplasm via recurrent phenotypic selection on spaced plants. Starting from a founder population of 300 plants serving as F0 population, two cycles of phenotypic selection for high and low seed shattering were applied and compared to randomly selected individuals on spaced plant level and in plot trials. Comparison of the five resulting populations in a spaced plant trial revealed a significant effect of selection, with lowest seed shattering (15.3%) observed in the population selected twice for decreased shattering (15.3%) and highest seed shattering (47.9%) for the population selected twice for increased shattering. The same ranking of the five F2 populations was observed in a subsequent trial with sown plots. Thus, using the method presented here, recurrent selection on single spaced plants allows to efficiently reduce seed shattering and, therefore, to increase seed yield in swards.

plant biology↗