Development and validation of a low-density KASP marker panel for parentage verification and early vigor classification in cashew (Anacardium occidentale L.)
摘要
Cashew (Anacardium occidentale L.) breeding is constrained by a long reproductive cycle and the high cost of field evaluation, making early, marker-assisted selection of hybrids highly desirable. In this study, 119 F1 hybrids and their five parents, derived from a diallel mating design, were characterised by combining juvenile morphological evaluation with KASP-SNP genotyping. Nine vegetative traits linked to seedling vigor were recorded six months after planting. The hybrids exhibited considerable phenotypic diversity, with very high coefficients of variation for the number of branches (181%) and the length of branches (161%), indicating substantial variability among hybrids and suggesting a possible influence of heterosis. Hierarchical clustering and principal component analysis separated the genotypes into a vigorous group (parents TPTO2 and N1) and a less vigorous group (parent YKKF1), reflecting parental origin. Concurrently, 150 yield-associated SNPs identified by genome-wide association were converted to KASP assays; 57 robust, polymorphic markers (mean call rate 99.3%) were retained and anchored on the chromosome-scale cashew reference genome. The Bayesian and elbow clustering methods both resolved two genetic sub-populations, in accordance with the phenotypic structure and declared pedigree. Parent-offspring compatibility analysis revealed that most apparent incompatibilities resulted from parental allele dropout heterozygous parents mis-scored as homozygous confirmed by inspection of raw fluorescence clusters, leaving only five hybrids as genuine candidate off-types. A compact KASP panel combined with juvenile vigor assessment enables efficient hybrid selection and pedigree validation. This approach offers a practical, cost-effective tool to accelerate genetic gain in cashew improvement programmes.