Linkage Mapping Study Reveals Conservative QTL and Candidate Genes for Fusarium Ear Rot Resistance in Maize

QTL detection for fruit commercial quality traits in diploid and triploid banana populations

Desert bananas (Musa spp.) are a major fruit crop worldwide for which postharvest quality traits are major determinants for consumer acceptance and adoption of new cultivars. They are thus important targeted traits in breeding yet their genetic basis remains poorly characterized. We report the first QTL mapping study of two of these quality traits, finger drop resistance and bruising susceptibility, using two biparental populations sharing the same genetic background but differing in ploidy level: a diploid Pisang Madu × Galéo population and a triploid Pisang Madu T × Galéo population. For finger drop, heritability reached 0.47 in diploids and 0.38 in triploids. Two significant QTLs, q1_FD_M7-1 and q2_FD_M11, were detected in the diploid population and together explained 28.12% of the phenotypic variance. q1_FD_M7-1 was located in a non-recombining chromosomal region associated with a reciprocal translocation in Pisang Madu. Candidate genes co-localizing with finger drop QTLs included expansins, xyloglucan endotransglucosylases, and pectin methylesterases involved in cell wall remodeling. For bruising susceptibility, heritability was higher in triploids (0.57) than in diploids (0.48). One QTL and one putative QTL detected in the triploid population together explained 28.78% of the phenotypic variance. Cross-ploidy validation showed moderate predictive ability of QTL-based models between populations, with prediction accuracies of 0.52 for finger drop and 0.42 for bruising susceptibility. These QTLs are promising targets for marker-assisted selection to accelerate the development of new desert banana cultivars which are urgently needed to diversify the current production mainly based on monoculture of Cavendish.

QTL Mapping for Leaf Rust Resistance in a Wheat Recombinant Inbred Line Population of Liang66-S/Hengmai28

Leaf rust (LR), caused by Puccinia triticina, is a major constraint to global wheat production. Identifying quantitative trait loci (QTLs), conferring adult-plant resistance (APR), and developing breeder-friendly markers are essential for durable disease control. In this study, a recombinant inbred line (RIL) population derived from Liang66-S × Hengmai28 was evaluated for leaf rust severity across four environments. Maximum disease severity (MDS) showed continuous variation and moderate to high correlations among environments, indicating polygenic inheritance. Five APR QTLs were mapped on chromosomes 2BL, 3BS, 3BL, 7BL and 7DL, explaining 4.5–9.8% of the phenotypic variance (PVE) with LOD scores of 2.9–7.9. Among these, QLr.DFI-2BL, QLr.DFI-3BS, and QLr.DFI-7BL correspond to previously reported APR loci, whereas QLr.DFI-3BL and QLr.DFI-7DL represent potentially novel loci. QLr.DFI-3BL was detected across all four environments, while QLr.DFI-3BS and QLr.DFI-7BL showed the highest R2 (7.7–8.5% and 8.4–9.8%). Multiple defense-related genes within the QTL intervals for LR were identified, including the putative NBS-LRR, the putative BTB/POZ-MATH, F-box, receptor-like kinase, polyphenol oxidase, calcium-dependent protein kinase, peroxidase, and ethylene-responsive transcription factors. Based on the flanking markers, five KASP markers were developed. K-LR-3BS (for QLr.DFI-3BS) and K-LR-7BL (for QLr.DFI-7BL) successfully genotyped a natural population with 120 accessions, with call rates of 100% and 94.2%, and showed significant association with reduced leaf rust severity. However, further validation in diverse genetic backgrounds and populations is required before they can be considered for routine marker-assisted selection. These results provide two KASP markers as promising markers that require further validation in diverse backgrounds and highlight QLr.DFI-3BS and QLr.DFI-7BL as promising targets for fine mapping and eventual cloning of APR genes in wheat.

Exploring the Diversity of Blast Resistance Genes in Rice Lines Using PCR-Based Functional STS Markers

Rice blast, caused by Pyricularia oryzae (syn. Magnaporthe oryzae), remains one of the most destructive diseases of rice worldwide. Developing resistant varieties is a sustainable strategy for disease management, and information on the diversity of blast resistance genes is important for selecting breeding parents. This study evaluated the effectiveness of functional sequence-tagged site (STS) markers for resolving genetic diversity among advanced rice lines derived from multiple-cross populations. A total of 104 genotypes, comprising 100 advanced lines and four parental varieties (Ciherang, Inpari 13, Inpari 10, and Situ Bagendit), were analyzed using eight gene-specific STS markers associated with four blast resistance genes (Pii, Pia, Pikp, and Pita). Polymorphism information content (PIC) values ranged from 0.80 to 0.96, with a mean of 0.89. UPGMA cluster analysis separated the genotypes into two major groups at a similarity coefficient of 0.90, although most lines occurred in one group and lines with the same parental background were distributed among different subgroups. Observed heterozygosity was low (Ho = 0.09), indicating limited resolution for distinguishing closely related lines despite the high PIC values. Functional STS markers were informative for detecting allelic variation but were insufficient for resolving fine-scale relationships within this genetically narrow breeding population. Combining marker analysis with phenotypic evaluation and higher-resolution markers is therefore recommended to improve selection for blast resistance.

Genetic mapping identifies QTL and candidate genes including Mendel's A gene controlling high levels of partial resistance to Fusarium avenaceum in Pea

Fav-Ps2.1 is the first major QTL reported for Fusarium avenaceum resistance in pea and co-localizes with Mendel’s A gene and putative resistance genes. A novel moderate-effect QTL Fav-Ps5.1 and one epistatic locus, independent of the A gene, were also reported. Flavonoid compounds associated with resistance to this pathogen were identified. Fusarium avenaceum, a necrotrophic soil-borne pathogen, is a member of the root rot pathogen complex posing a major threat to pea yield and quality worldwide. Strong resistance to Fusarium root rot (FRR) in pea is associated with seed coat and flower pigmentation, controlled by Mendel’s A locus regulating anthocyanin biosynthesis. It is not clear whether the A locus is acting alongside resistance genes to confer high levels of resistance or whether alternative genetic pathways exist in pea cultivars. In this study, a pea recombinant inbred line population of 160 lines called PR-20 (AA×aa), polyphenolic profiles, and the pea reference genome were leveraged to understand the genetic control of Fusarium avenaceum resistance. Two novel quantitative trait loci (QTLs) including a major QTL Fav-Ps2.1 (41–42.2 cM) on chromosome 6 with 95% phenotypic variance explained (PVE), a moderate-effect QTL Fav-Ps5.1 (126–134 cM) on chromosome 3 with 9% PVE, and a putative epistatic interaction with 15% PVE, associated with resistance to F. avenaceum were identified. Both the epistatic region and Fav-Ps5.1 are anthocyanin pigment-independent. Fav-Ps5.1 is co-localized with many defense-response and flavonoid-related genes including NDR1/HIN1-like protein, WDR, MYB111, WRKY, Chitinase, PAL1, F-box/LRR-repeat protein, E3 ubiquitin–protein ligase PUB22, ABC transporters, and probable ethylene response sensor 1. Fav-Ps2.1 is co-localized with 35 disease resistance-related genes and overlaps with the A locus, which may explain the high PVE. A ‘pea tobacco mosaic virus (TMV) resistance N-like protein’ gene, encoding TIR-LRR domains, marks the peak of Fav-Ps2.1 at ~ 0.12 cM upstream of the A locus. Regression analysis with whole seed polyphenolic compounds in randomly selected 14 PR-20 lines including the parents showed that some colorless flavonoids (anthocyanin precursors), encoded by genes other than A, explained more variation in disease resistance (R2 = 87–99%; P ≤ 0.001), compared to the A gene-encoding anthocyanin compounds (R2 = 38–86%; P ≤ 0.018). Our results demonstrate that high FRR resistance is not determined only by the A locus but emerges from multiple coordinated resistance loci. These findings provide new insights into the genetic basis of F. avenaceum resistance for breeding FRR resistance in white-flowered pea varieties.

Identification of stripe rust resistance loci in Gansu wheat landraces using genome-wide association analysis

Association Mapping of Seedling Resistance to Fusarium graminearum Root Rot and Development of KASP Assays in Soybean

Findings identify useful genetic targets and molecular markers for improving soybean resistance to root rot caused by F. graminearum.