Genetic Mapping of Quantitative Trait Loci for Fruit Mass, Total Soluble Solids and Susceptibility to Water Soaking in a Strawberry ( Fragaria spp.) Model Population

Integrated Genome-Wide Association and QTL Mapping Elucidate the Genetic Basis of Fruit Yield and Quality Traits in Pepper under Water Stress.

Water deficit is a major constraint on pepper (Capsicum annuum) yield, yet the genetic architecture of reproductive-stage drought tolerance remains poorly resolved. We phenotyped a Balkan C. annuum diversity panel (n = 133) and an interspecific backcross inbred line (BIL) population (n = 76) under well-watered (WW) and water-stress (WS) conditions. WS was applied from anthesis of the second truss as a stepwise reduction in irrigation volume relative to WW (30% for 7 days, then 60% thereafter), maintained for 90 days across the reproductive period. We assessed yield components, soluble solids, and stress-tolerance (STI) and stress-susceptibility (SSI) indices. Genome-wide association study (GWAS) identified 104 SNP-trait associations (P < 1×10-5), and QTL mapping detected 38 significant QTLs (1,000 permutations, α = 0.01), with the QTL intervals defined at LOD ≥ 8. Integrating GWAS and QTL mapping under WS revealed overlapping loci on chromosomes 5 and 6, harboring two consensus intergenic SNPs associated with yield components and soluble solids. Haplotype analysis linked chromosome 5 alleles to higher fruit number and soluble solids. At chromosome 6, the G allele at SNP 6_28348737 was enriched in tolerant lines for fruit number. These regions harbor candidate genes for reproductive development and stress response, including GREEN RIPE-LIKE1 (GRL1), CYP77A19, Endoglucanase-like, and FLOWERING PROMOTING FACTOR 1 (FPF1), possibly through cis-regulatory variation. Together, these results advance understanding of the genetic basis of pepper yield under drought and identify candidate breeding markers.

Genetic basis and breeding potential of fruit traits in interspecific F2 populations of watermelon (Citrullus lanatus [Thunb.] Matsum. & Nakai × Citrullus amarus Schrad.)

Watermelon is an economically important fruit crop cultivated worldwide for its nutritional value and commercial importance. However, yield stagnation and limited genetic diversity constrain further productivity gains. To address this constraint, the present study evaluates genetic variability, heritability and the breeding potential of key fruit traits in watermelon using two interspecific F2  populations developed from crosses between a wild Citrullus amarus Schrad. line and two elite Citrullus lanatus [Thunb.] Matsum. & Nakai lines, with the objective of harnessing untapped allelic diversity for crop improvement. Two F2 populations, CL 0732 × CL 0413 (Cross 1 (C1)) and CL 0732 × CL 0695 (Cross 2 (C2)), were evaluated for fruit length, fruit width, rind thickness, total soluble solids (TSS) and fruit weight using standard statistical parameters, including genotypic and phenotypic coefficients of variation, heritability, genetic advance and transgressive segregation index (TSI). Results revealed substantial genetic variability, with high GCV (18.09–85.71 %) and heritability (70.43–97.67 %) across traits, indicating strong additive gene action. While the C2 population exhibited higher trait means, C1 demonstrated superior breeding potential based on standardised range, TSI and usefulness index, suggesting a greater likelihood of recovering superior recombinant inbred lines. Strong positive correlations between fruit weight and fruit length, fruit width and TSS support indirect selection strategies. The findings underscore the value of wild × cultivated crosses for broadening the genetic base of cultivated watermelon. Overall, this research provides a robust framework for identifying promising breeding populations and implementing targeted selection strategies to improve watermelon yield and quality.

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.

Trait Associations and Path Analysis for Green Fruit Yield in Elite Selections from Multi-parent Derived Populations of Chilli (Capsicum annuum L.)

Green fruit yield is a complex quantitative trait influenced by several yield-related components, and understanding the relative contribution of these traits is essential for effective selection in chilli breeding. The present study was undertaken to assess the association of green fruit yield with yield-related traits among elite selections derived from five superior eight-parent multi-parent (MP) populations of chilli. The selected MP-derived populations comprised D4 × D3, D4 × D2, D5 × D2, D6 × D2 and D7 × D2. Elite progenies derived from superior plants within these populations were evaluated during the 2020 rainy season at the experimental farm of the University of Agricultural Sciences, Bengaluru. Observations were recorded for average fruit weight, average fruit number plant-1, average fruit length, average fruit width and green fruit yield per plant. Phenotypic correlation coefficients were estimated separately for each MP-derived population, while path coefficient analysis was performed using the pooled dataset to partition the correlations into direct and indirect effects. Average fruit number plant-1 exhibited a strong and positive association with green fruit yield across all five populations. Average fruit length showed significant positive associations with green fruit yield. Path analysis revealed the highest positive direct effect for average fruit number plant-1, followed by average fruit width and average fruit weight. The findings suggest that fruit number plant-1 may serve as an important selection criterion for improving green fruit yield, with fruit length and fruit width serving as complementary traits depending on the genetic background of the population.

Dissection of genetic architecture for tiller and yield - related traits in sugarcane (Saccharum spontaneum L.) by genome - wide association study.

Sugarcane (Saccharum spp.) is an important crop for food and energy security. Identifying SNPs and genes associated with sugarcane yield and related traits is crucial for developing high - yielding sugarcane cultivars through molecular breeding. Here, we measured nine phenotypic traits across 160 sugarcane genotypes and employed multiple statistical models (namely MLM, CMLM, MLMM, FarmCPU and SUPER) in GWAS to identify stable and pleiotropic loci. A total of 200 SNPs corresponding to 137 QTLs were detected to be significantly associated with nine traits using multiple statistical models, among which 18 QTLs were consistently identified by two or more models. Notably, the SNP S9A_47793177 on chromosome 9A showed the strongest association with phenotypic variation in aboveground biomass, with a phenotypic explanation rate of 70.54%. Additionally, several QTLs significantly associated with tillering - related traits were identified, suggesting that these QTLs may play crucial roles in the regulation of tillering. The QTLs and SNPs identified in this study provide a significant foundation for molecular marker - assisted breeding in sugarcane. This advancement can significantly enhance the efficiency of genetic improvement for sugarcane yield and tillering - related traits.

Mapping quantitative trait loci (QTLs) for plant architecture traits using a high-density genetic linkage map in diploid potato (Solanum chacoense)