Identification of a common major quantitative trait locus controlling onion bulb weight and development of molecular...

Bulb weight, crucial in onion breeding, is difficult to improve because of its low heritability and environmental variability, limiting phenotype-based selection. Previous studies have identified quantitative trait loci (QTL) for bulb shape; however, no significant QTLs have been detected for bulb weight. This study aimed to develop DNA markers for bulb weight selection through genetic analysis. A breeding line was evaluated in four environments (576 plants), each genotyped using 157 markers. Markers significantly associated with bulb weight were detected on chr8 using a genome-wide association study. An F2 population (245 plants) with a genetic background distinct from that of the breeding line was evaluated, and QTL for bulb weight were detected by composite interval mapping using 348 genome-wide marker genotypes. The position of a major QTL was identical to those of the associated markers detected in the breeding line, suggesting that the QTL is common and stable, regardless of genetic background. Three indel markers were designed near the QTL peak, and their combinations were used for haplotype definition. Eight plants per genetic resource line and commercial F1 cultivar were genotyped, and proportions of haplotypes within each line/cultivar were summarized. Almost all genetic resource lines contained at least two haplotypes, and haplotype pairs were unfixed in several F1 cultivars. Haplotype selection and fixation contribute to bulb weight stability and uniformity, making these DNA markers useful for efficient breeding. This study provides the first stable QTL for bulb weight, offering genetic insights that could facilitate marker-assisted selection and improve onion breeding efficiency.

The online version contains supplementary material available at 10.1007/s11032-025-01614-9.