Quantitative trait locus analysis of cucumber fruit texture using double‐digest restriction‐site‐associated DNA sequencing

Koichiro Shimomura,Yosuke Yoshioka,Mitsuhiro Sugiyama,Yoichi Kawazu

doi:10.1007/s10681-021-02830-y

Abstract

Fruit firmness and crispness are important traits of cucumber because they directly affect its commercial value. We performed quantitative trait locus (QTL) analysis of these fruit texture traits with the double-digest restriction-site-associated DNA sequencing (ddRAD-Seq) technique and detected 31 QTLs for fruit firmness: 11 for placenta firmness, 12 for skin firmness, and 8 for flesh firmness; and 25 QTLs for crispness-related scores: 10 for flesh crispness index, 8 for flesh apparent fractal dimension by Richardson plot, and 7 for flesh apparent fractal dimension by box-counting (Kolmogorov’s dimension). Several QTLs associated with flesh firmness and crispness are located near regions for fruit length, diameter, and length-to-diameter ratio, and for resistance to powdery mildew and downy mildew, indicating that gene linkage is likely to limit breeding efficiency. Our results will contribute to the development of informative DNA markers closely linked to genes for desirable fruit texture traits that are required for effective selection of new cultivars.

Highlights

Fruit texture traits, such as firmness and crispness, are one of the most important characteristics in cucumber (Cucumis sativus L.), because these are directly related to consumer preference and demand
Several quantitative trait locus (QTL) associated with flesh firmness and crispness are located near regions for fruit length, diameter, and length-to-diameter ratio, and for resistance to powdery mildew and downy mildew, indicating that gene linkage is likely to limit breeding efficiency
DdRAD-Seq analysis returned an average of 0.5 million high-quality reads per sample with an average Q30 quality score of 94.38 at 279 out of 2664 single nucleotide polymorphism (SNP) sites in EC1, 1.7 million reads with Q30 = 90.26 at 607/3571 SNPs in EC2, and 1.3 million reads with Q30 = 94.54 at 496/2093 SNPs in EA

Summary

Introduction

Fruit texture traits, such as firmness and crispness, are one of the most important characteristics in cucumber (Cucumis sativus L.), because these are directly related to consumer preference and demand. Breeding efforts for many fruit vegetables have focused on improvement in texture, few advances have been made in identification of genetic mechanisms, because aspects of texture other than firmness are difficult to measure quantitatively. Cucumber fruit firmness has been quantified by scientific instruments for many years (Breene et al 1972; Jeon et al 1973; Kanno and Kamimura 1978; Thompson et al 1982). Improvements in computer and instrument performance have allowed researchers to develop new methods for the quantitative evaluation of fruit texture traits by mechanical (Horie et al 2004; Yoshioka et al 2009, 2010), acoustic (Sakurai et al 2005), and biorheological (Dan et al 2003; Kohyama et al 2009, 2013) measurements

Methods

Results

Conclusion