Novel loci fsd6.1 and Csgl3 regulate ultra-high fruit spine density in cucumber
Quantitative Trait Loci (QTL) analysis of multiple populations in multiple environments revealed that the fsd6.2 locus, which includes the candidate gene Csgl3, controls high fruit spine density in natural cucumbers. GWAS identified a novel locus fsd6.1, which regulates ultra-high fruit spine density in combination with Csgl3, and evolved during cucumber domestication.
Fruit spine density, a domestication trait, largely influences the commercial value of cucumbers. However, the molecular basis of fruit spine density in cucumber remains unclear. In this study, four populations were derived from five materials, which included three with low fruit spine density, one with high fruit spine density, and one with ultra-high fruit spine density. Fruit spine densities were measured in 15 environments over a span of 6 years. The distributions were bimodal suggesting that fruit spine density is controlled by a major-effect QTL. QTL analysis determined that the same major-effect QTL, fsd6.2, is present in four populations. Fine mapping indicated that Csgl3 is the candidate gene at the fsd6.2 locus. Phylogenetic and geographical distribution analyses revealed that Csgl3 originated from China, which has the highest genetic diversity for fruit spine density. One novel minor-effect QTL, fsd6.1, was detected in the HR and HP populations derived from the cross between 65G and 02245. In addition, GWAS identified a novel locus that colocates with fsd6.1. Inspection of a candidate region of about 18 kb in size using pairwise LD correlations, combined with genetic diversity and phylogenetic analysis of fsd6.1 in natural populations, indicated that Csa6G421750 is the candidate gene responsible for ultra-high fruit spine density in cucumber. This study provides new insights into the origin of fruit spine density and the evolution of high/ultra-high fruit spine density during cucumber domestication.
We thank Dr. Graham Collins, formerly of the University of Adelaide, South Australia, for English editing of the manuscript. We thank LetPub for its linguistic assistance during the preparation of this manuscript. This work was supported by the National Key Research and Development Program of China [2016YFD0101705], the Earmarked Fund for Modern Agro-industry Technology Research System [CARS-25], Science and Technology Innovation Program of the Chinese Academy of Agricultural Science (CAAS-ASTIP-IVFCAAS), the National Natural Science Foundation of China (31572146), and the Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, China.
Author contribution statement
KB performed the experiments, analyzed experimental data, and wrote the paper. HM helped analyze data and collected the data for LM2012S and LM2012F. MW collected the data for LM2013S and LM2013F. XX collected the data for YR2014F, YR2015S, and YR2015F. ZS collected the data for CG lines. QX and LS collected the data for HR2016S, HR2016F, HP2016S, and HP2016F. WW and SW collected the data for HR2017S, HR2017F, HP2017S, and HP2017F. SZ and XG provided valuable research design. All authors read and approved the final manuscript.
Compliance with ethical standards
Conflict of interest
The authors declare that they have no conflict of interest.
The authors declare that this study complies with the current laws of the countries in which the experiments were performed.
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