Biology subjects

Lim, F.-S.

Publications and source records attributed to Lim, F.-S..

3 recordsLinked to original sources

bioRxiv2026

QTL analysis of essential oil, seed shattering, thousand-grain weight and stalk attachment rate in Carum carvi

Caraway (Carum carvi L., 2n = 2x = 20) is a medicinal and aromatic plant of the Apiaceae family valued for its essential oil with the major terpenoids carvone and limonene. While the essential oil content represents an important quality trait, low seed shattering and high thousand-grain weight (TGW) are key determinants of seed yield. As molecular tools remain scarce within Apiaceae breeding beyond carrot, we conducted a QTL mapping for these seed-related traits using two previously established F2 populations (Effective N(P1) = 236; N(P2) = 266). In P1 with the non-shattering maternal parent Rekord, QTL mapping revealed at least one shattering locus on LG03 (PVE: 9.9%). In addition, loci associated with essential oil (LG08, 10.5% PVE) and TGW (LG09, 11.1% PVE) were detected. In P2, we identified six essential-oil loci (LG02-06, LG10; combined PVE: 49.2%), with five loci affecting both carvone and limonene, and one (LG03) exclusively limonene. Additionally, a major QTL for TGW mapped to LG02 (PVE: 15.6%). For stalk attachment rate one minor QTL was detected (LG07, 8.5% PVE), while no QTL co-localized with the major shattering locus. To pave the path towards fine-mapping, we designed and validated 26 diagnostic PACE markers covering five key QTLs.

genetics↗

bioRxiv2026

Analysis of SpCas9 on- and off-target effects in high efficiency multiplex editing in Arabidopsis

RNA-guided nucleases (RGNs), such as Cas9 from Streptococcus pyogenes (SpCas9), are widely used for plant genome editing. Previous surveys for off-targeting, the modification of unintended targets with similarity to the intended target, indicate high specificity of SpCas9 in plant cells. However, off-targeting has not been assessed for efficiency-optimized editing systems combined with extensive multiplexing, which might increase the likelihood of cleavage at unintended sites. We therefore analyzed Arabidopsis thaliana lines that had been extensively mutagenized using zCas9i and up to 29 gRNAs addressing >45 target sites over several rounds of editing. Genomes were sequenced by short- and long-read technologies, and genome-wide variants were catalogued. Our pipeline for variant calling reliably detected RGN-induced mutations at on-targets. When excluding these on-target modifications, variants were detected in edited lines at frequencies similar to those previously reported for spontaneous mutations. In further analyses, we did not find any evidence for an origin of these variants from RGN activity. Our data are thus consistent with high specificity of SpCas9. In contrast, we detected genomic reorganization events upon editing at two complex loci, RPP1 and RPP7, encompassing multiple homologous genes, and also identified an allele by WGS that had escaped detection by amplicon sequencing. We conclude that, while off-targets may efficiently be avoided by selection of specific gRNAs, on-target modifications may be more extensive than intended, especially at complex loci and/or during multiplexing.

plant biology↗

bioRxiv2025

High-quality haplotype-resolved genome assembly and annotation of Malus baccata 'Jackii'

Malus baccata Jackii has been observed to exhibit multiple disease resistances, thus rendering it a promising source for breeding new disease-resistant apple cultivars. Here, we present the first haplotype-resolved genome assembly and annotation of this genotype, achieved by integrating PacBio HiFi sequencing, Hi-C, and mRNA sequencing data with a range of bioinformatic tools and databases. The genome assembly comprises 17 pseudochromosomes with total scaffold lengths of 654.6 Mb and 637.5 Mb for the two haplotypes, respectively. Both haplotypes have scaffold N50 values exceeding 30 Mb, with 42,441 and 46,507 predicted genes, of which 99.9% were successfully annotated. The high quality of this genome is supported by BUSCO analysis values exceeding 97.5% for both haplotypes. This comprehensive dataset is well suited for a wide range of future genomic analyses and is anticipated to benefit apple breeding, particularly in the context of enhancing disease resistance.

genomics↗