MutMap Reveals a Structural Deletion at the Chalcone Synthase Locus Controlling Black Seed Coat in a Gamma-Irradiated Vietnamese Soybean Mutant

Development of KASP marker to enhance breeding efficiency for phytophthora blight resistance in sesame through QTL analysis.

BACKGROUND Phytophthora blight, caused by Phytophthora nicotianae, is a destructive disease that severely affects sesame (Sesamum indicum L.). Developing resistant cultivars remains the most effective management strategy. This study aimed to identify genomic regions associated with Phytophthora blight resistance and to develop molecular markers for use in sesame breeding. RESULTS Whole-genome resequencing (WGS) was performed for the resistant cultivar Geonbaek, the susceptible cultivar Milsung, and 99 recombinant inbred lines (RILs). Using a high-density genetic map, we identified a major resistance locus on chromosome 10, designated qPB10. The IM-ADD analysis defined a 0.51-Mb marker interval with an LOD score of 25.67, and a complementary binary-trait analysis independently detected the same locus at 75.10 cM. Genomic analysis of the target region revealed several immune-related genes, including clusters encoding nucleotide-binding leucine-rich repeat (NLR) proteins and other defense-associated factors. To utilize these findings in breeding, kompetitive allele-specific PCR (KASP) markers were developed based on sequence polymorphisms within the qPB10 interval. Validation using the RIL population and a diverse panel of sesame cultivars identified a robust marker that reliably discriminates resistant genotypes. CONCLUSION These findings establish qPB10 as the primary locus governing Phytophthora blight resistance in sesame. The KASP markers developed in this study enable efficient marker-assisted selection without the need for extensive disease phenotyping. These results provide a practical genomic resource for accelerated breeding of resistant cultivars and establish a foundation for future functional characterization of resistance mechanisms.

Molecular Mapping and CRISPR/Cas9 Validation Reveal That SlVQ10 Regulates Seed Size in Tomato

Together, the genetic and genome–editing data support SlVQ10 as the gene underlying ssm and indicate that it promotes seed size in tomato.

Fine Mapping and Candidate Gene Analysis of a Major Locus Controlling Black Seed Coat Color in Mung Bean (Vigna radiata L.)

Seed coat color is an important quality trait in mung bean (Vigna radiata) and is closely associated with seed appearance, commercial value, and phytochemical composition. To investigate the genetic basis of black seed coat formation, six F2 populations were derived from reciprocal crosses between the black-seeded accession LZL115 and the green-seeded accession LZL156. Among 755 F2 plants, 559 produced black-coated seeds and 196 produced green-coated seeds, conforming to a 3:1 segregation ratio (χ2 = 0.37, p = 0.54). These results indicated that black seed coat color was dominant and consistent with the control by a single dominant locus, designated VrScL115, in the LZL115 × LZL156 genetic background. Bulked segregant analysis sequencing (BSA-seq) initially mapped VrScL115 to an approximately 2.90 Mb region on chromosome 4. Using newly developed KASP markers and recombinant screening in expanded F2 populations, the locus was further delimited to a 121.79 kb interval between markers LS_K3333 and LS_K3379. Of the 11 annotated genes within this interval, LOC106758748 was the only gene containing high-confidence coding-sequence variants between the parents. This gene encodes a putative R2R3-MYB transcription factor homologous to MYB90. Comparative sequence analysis identified several allelic variants potentially associated with black seed coat color, and protein structure prediction indicated local structural differences between the parental proteins. LOC106758748 showed consistently higher expression in the developing seed coats of LZL115 than in those of LZL156 at 10, 15, and 20 days after pollination, with expression peaking at 15 days. Haplotype analysis of 246 mung bean accessions showed that the LZL115-associated allele combination at LS_K3352, LS_K3365, LS_K3367, and LS_K3370 was present in 21 of 27 black-seeded accessions (77.8%) and absent from all 219 non-black accessions, corresponding to a specificity of 100% and a false-negative rate of 22.2%. These findings support LOC106758748 as the leading candidate gene for VrScL115; however, direct in vivo functional validation is still required to confirm its causal role in black seed coat formation. The four-marker combination may be useful for identifying germplasm carrying the LZL115-associated allele, although further validation in independent germplasm populations is required.

Fine mapping and candidate gene analysis of qPH19.1, a locus for soybean (Glycine max L.) plant height

Characterisation and Fine Mapping of a Dwarf Locus BnDF3 Encoding a GSK3 Kinase in Brassica napus

Results demonstrated that BnDF3 is a gain‐of‐function allele functioning as the gain‐of‐function BIN2 gene in brassinosteroid (BR) signalling pathway, which may provide both a functional marker and a novel genetic resource useful in variety breeding targeted to strong lodging resistance.

A telomere-to-telomere Brassica napus genome identifies BnaWRKY44 regulation of seed coat color and oil.

A T2T rapeseed resource and a BnaWRKY44-BnaVPT1 module for breeding high-oil, yellow-seeded rapeseed are provided for breeding high-oil, yellow-seeded rapeseed.