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R. Kölliker

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Open access Sep 2026

The first Nested Association Mapping (NAM) population for Italian ryegrass reveals genomic regions associated with seed shattering

Nested association mapping (NAM) populations are a powerful tool for investigating the genetic control of agronomically important traits and have been successfully used in self-pollinating crop species. Here, we present the first NAM population established in the outcrossing forage grass species Italian ryegrass ( Lolium multiflorum Lam.), to dissect the genetic control of seed shattering. High and stable seed yields are essential for the commercial success of new cultivars. Seed shattering strongly reduces seed yield in Italian ryegrass, but has so far not been targeted in Italian ryegrass breeding programs. The NAM population was based on one common and 23 diverse founder plants and consisted of 708 F 2 individuals. Reduced-representation sequencing (ddRAD) of the 708 F 2 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 field trials, showed high phenotypic variance within the NAM population. A total of seven quantitative trait loci (QTL) were identified for seed shattering, seed yield, spike length, flag leaf length and flowering time. Within these QTL regions, one putative candidate gene for seed shattering and three putative candidate genes for flowering time were identified. For seed shattering, the significantly associated SNP within the gene chr7.26897 , known to be involved in ripening-related pathways, explained 10.03% of the phenotypic variance. The identified loci provide valuable resources for breeding. The QTL regions containing putative candidate genes identified within these loci offer promising targets for functional validation and demonstrate the effectiveness of NAM populations for elucidating the genetic architecture of complex traits in outcrossing forage grasses.

Jenny Kiesbauer, C. Grieder, Meril Sindelar et al. · BMC Plant Biology · 0 citations

Open access Sep 2026

Chromosome-level, haplotype-resolved genome assembly of the tanniferous forage legume big trefoil (Lotus pedunculatus Cav.) using CiFi

Big trefoil (Lotus pedunculatus Cav.) is a perennial forage legume that thrives on acidic, low-fertility soils and produces condensed tannins that reduce enteric methanogenesis in ruminants. Despite this agronomic potential, genomic resources for the species remain scarce, and the existing haploid assembly does not resolve the two haplotypes of this outcrossing diploid species. Here we present a haplotype-resolved, chromosome-level reference genome for L. pedunculatus genotype Lusitano29 – the first plant genome assembled using CiFi, a long-read chromosome conformation capture method. We combined PacBio HiFi long reads with CiFi concatemers produced from DpnII and Hind III libraries; in silico digestion and combinatorial pairing of the resulting monomers yielded 790.3 M and 10.3 M pseudo-paired contacts, respectively, enabling scaffolding and manual curation to chromosome level. The 991.1 Mb assembly resolves two phased haplotypes of 500 and 491 Mb, with 96.6% of the sequence anchored in twelve pseudo-chromosomes (six per haplotype). Telomeric repeats were detected at 19 of 24 pseudo-chromosome ends, and no structural errors were detected (scaffold N50 73.8 Mb; consensus QV 64.7; k-mer completeness 99.4%; genome-mode BUSCO completeness 97.0%; CRAQ S-AQI 100.0). Annotation supported by PacBio Iso-Seq full-length transcripts predicted 38,069 and 36,484 protein-coding genes in haplotypes 1 and 2, respectively (protein-mode BUSCO completeness 96.5%), indicating a high completeness of annotated genes. This genome assembly provides a foundation for allele-aware trait dissection of proanthocyanidin biosynthesis, comparative genomics in Lotus, and population genomics and genomics-assisted breeding in L. pedunculatus.

Alexander T. Pettersson, Yu-Tang Chen, Tim Davalan et al. · bioRxiv · 0 citations