Phenotypic and genotypic analysis of blotch/tiger stripe in Australian desi-type chickpea

Context The appearance of blotch/ tiger stripe on chickpea seeds is a genotype-specific seed marking which, although not considered a defect during seed inspection, is often rejected based on consumer trait preferences. Objective This study aimed to investigate the expression of blotch/tiger stripe, thousand grain weight (TGW) and days to podding in Australian desi-type chickpea. Methods A single seed-descent mapping population of 242 F7 derived progeny lines was selected from a controlled cross of two homozygous parent genotypes, PBA Slasher x Sonali. An independent set of nineteen cultivars/advanced genotypes was used to validate the results of the mapping population. Field trials were carried out over two years in Narrabri, north-western NSW, Australia. We phenotypically analysed the mapping population and validation set of cultivars/genotypes for the proportion of blotch/tiger stripe and then carried out composite interval mapping QTL analysis to identify genetic loci linked with the traits of interest. Significant markers that were identified in the mapping population were validated on the additional nineteen cultivars/genotypes. Results Significant phenotypic variation in the expression of blotch/tiger stripe was observed (P<0.001) and blotch/tiger stripe was found to be highly heritable (H2 = 0.98). TGW of seeds marked with blotch/tiger stripe (200.9 g) was significantly lower than that of unmarked seeds (208.2 g) (P<0.001). Five Quantitative Trait Loci (QTL) relating to blotch/tiger stripe were identified consistently across the two seasons. A major QTL linked with the reduced expression of blotch/tiger stripe was identified at QTL 1 which reduced the expression of the trait by up to 9.92%. KASP (Kompetitive Allele-specific PCR) markers were developed for this locus and validated in the set of nineteen cultivars/genotypes in which 13–19% of phenotypic variation was accounted for. Conclusions Significant phenotypic variation in the expression of blotch/tiger stripe was observed and the trait was found to be highly heritable. Five QTL relating to blotch/tiger stripe were identified and the region at QTL 1 was identified as a candidate for fine mapping to determine the genetic variant which is responsible for the trait. KASP markers developed in this study will be of value to breeders, allowing marker assisted selection (MAS) to screen for this trait in the absence of phenotypic symptoms. Implications & significance This study will benefit the chickpea industry by increasing industry awareness of the marking and reducing the prevalence of blotch/tiger stripe in breeding germplasm, therefore reducing seed rejection and protecting grower profits.