QTL mapping of melon fruit quality traits using a high-density GBS-based genetic map

Abstract

BackgroundMelon shows a broad diversity in fruit morphology and quality, which is still underexploited in breeding programs. The knowledge of the genetic basis of fruit quality traits is important for identifying new alleles that may be introduced in elite material by highly efficient molecular breeding tools.ResultsIn order to identify QTLs controlling fruit quality, a recombinant inbred line population was developed using two commercial cultivars as parental lines: “Védrantais”, from the cantalupensis group, and “Piel de Sapo”, from the inodorus group. Both have desirable quality traits for the market, but their fruits differ in traits such as rind and flesh color, sugar content, ripening behavior, size and shape. We used a genotyping-by-sequencing strategy to construct a dense genetic map, which included around five thousand variants distributed in 824 bins. The RIL population was phenotyped for quality and morphology traits, and we mapped 33 stable QTLs involved in sugar and carotenoid content, fruit and seed morphology and major loci controlling external color of immature fruit and mottled rind. The median confidence interval of the QTLs was 942 kb, suggesting that the high density of the genetic map helped in increasing the mapping resolution. Some of these intervals contained less than a hundred annotated genes, and an integrative strategy combining gene expression and resequencing data enabled identification of candidate genes for some of these traits.ConclusionSeveral QTLs controlling fruit quality traits in melon were identified and delimited to narrow genomic intervals, using a RIL population and a GBS-based genetic map.Electronic supplementary materialThe online version of this article (10.1186/s12870-018-1537-5) contains supplementary material, which is available to authorized users.

Identification of fruit size associated quantitative trait loci featuring SLAF based high-density linkage map of goji berry (Lycium spp.)

“…At last, we followed strict principles of filtering to get high-quality SLAFs (detail in methods). Totally, 214,961 polymorphic SLAFs were obtained with a polymorphism rate of 43.47%, higher than the previously identified [41,42,22]. In the current study, 8 segregation types were obtained with 24,329 maximum number of markers accounting for (aa×bb) homozygous group, which was greater than the previous reports [22,24].…”

“…(2018) [41]; investigated QTLs regarding fruit morphological traits in Cucumis melo L. and found Among the leaf related traits, qLL10-2.1 stable QTL corresponding to leaf length was spanned on…”

Multi-allelic APRR2 Gene is Associated with Fruit Pigment Accumulation in Melon and Watermelon

“…Burger et al , (2006 a ) described a recessive gene for light immature exterior color in a cross between an American muskmelon ( Reticulatus group) and an American honeydew-type melon, ( Inodorous group). Recently, a major gene for external color of immature fruit was mapped in a cross between “Védrantais”, a Charentais line from the Cantalupensis group, and “Piel de Sapo”, from the Inodorous group (Pereira et al , 2018). The dominant light rind from the “Védrantais” parent, that most likely correspond to the Wi gene, was mapped to ∼1.6 Mb interval on chromosome 7 (Pereira et al , 2018).…”

“…Recently, a major gene for external color of immature fruit was mapped in a cross between “Védrantais”, a Charentais line from the Cantalupensis group, and “Piel de Sapo”, from the Inodorous group (Pereira et al , 2018). The dominant light rind from the “Védrantais” parent, that most likely correspond to the Wi gene, was mapped to ∼1.6 Mb interval on chromosome 7 (Pereira et al , 2018). These results confirm our observation that the dominant light grayish rind of Charentais accessions is phenotypically and genetically distinct and controlled by a different gene from the one we identified in the current study, which correspond to the recessive gene described by Burger et al , (2006 a ).…”

“…This complexity is also expressed by the independent genetic control of flesh and rind colors in melon as best demonstrated by the ability to combine different rind and flesh colors through classical breeding. Rind and flesh color QTLs were mapped in multiple melon populations (Monforte et al , 2004; Cuevas et al , 2008, 2009; Harel-Beja et al , 2010; Galpaz et al , 2018; Pereira et al , 2018) and a few causative color genes were identified (Feder et al , 2015; Tzuri et al , 2015). However, so far, a common regulator that affects pigmentation throughout the different developmental stages and fruit tissues (rind and flesh) has not been described in melon.…”