Abstract
BackgroundThe identification and characterisation of quantitative trait loci (QTL) is an important step towards identifying functional sequences underpinning important crop traits and for developing accurate markers for selective breeding strategies. In this study, a genotyping-by-sequencing (GBS) approach detected QTL conditioning desirable fruit quality traits in papaya.ResultsFor this, a linkage map was constructed comprising 219 single nucleotide polymorphism (SNP) loci across 10 linkage groups and covering 509 centiMorgan (cM). In total, 21 QTLs were identified for seven key fruit quality traits, including flesh sweetness, fruit weight, fruit length, fruit width skin freckle, flesh thickness and fruit firmness. Several QTL for flesh sweetness, fruit weight, length, width and firmness were stable across harvest years and individually explained up to 19.8% of the phenotypic variance of a particular trait. Where possible, candidate genes were proposed and explored further for their application to marker-assisted breeding.ConclusionsThis study has extended knowledge on the inheritance and genetic control for key papaya physiological and fruit quality traits. Candidate genes together with associated SNP markers represent a valuable resource for the future of strategic selective breeding of elite Australian papaya cultivars.
Highlights
The identification and characterisation of quantitative trait loci (QTL) is an important step towards identifying functional sequences underpinning important crop traits and for developing accurate markers for selective breeding strategies
This study focused on linkage mapping and QTL analysis for fruit quality traits in a papaya F2 population developed from the cross ‘RB2’ x ‘Sunrise Solo’
The remaining 597 distorted markers were skewed towards an heterozygous genotype (Additional file 5: Table S4)
Summary
The identification and characterisation of quantitative trait loci (QTL) is an important step towards identifying functional sequences underpinning important crop traits and for developing accurate markers for selective breeding strategies. A genotyping-by-sequencing (GBS) approach detected QTL conditioning desirable fruit quality traits in papaya. In Australia, papaya is an important domestic fresh fruit crop with just 6.5 thousand tons grown annually [24]. Marker-assisted selection (MAS) has been introduced in papaya breeding programs elsewhere to efficiently develop superior varieties with desired traits [6, 64, 66]. The ‘AU9’ x ‘Sunup’ map of Chen et al [15] comprised 706 simple sequence repeat (SSR) markers in 12 LG over 1070 cM, within which elongated fruit shape was associated with a QTL in LG1.
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