Selection footprints reflect genomic changes associated with breeding efforts in 56 cucumber inbred lines

Bin Liu,Xingwang Liu,Sen Yang,Dailu Guan,Xuling Zhai,Huazhong Ren,Jing Huang,Shuying Chen,Shudan Xue

doi:10.1038/s41438-019-0209-4

Abstract

Cucumber selective breeding over recent decades has dramatically increased productivity and quality, but the genomic characterizations and changes associated with this breeding history remain unclear. Here, we analyzed the genome resequencing data of 56 artificially selected cucumber inbred lines that exhibit various phenotypes to detect trait-associated sequence variations that reflect breeding improvement. We found that the 56 cucumber lines could be assigned to group 1 and group 2, and the two groups formed a distinctive genetic structure due to the breeding history involving hybridization and selection. Differentially selected regions were identified between group 1 and group 2, with implications for genomic-selection breeding signatures. These regions included known quantitative trait loci or genes that were reported to be associated with agronomic traits. Our results advance knowledge of cucumber genomics, and the 56 selected inbred lines could be good germplasm resources for breeding.

Highlights

IntroductionThe breeding of cucumber germplasm was accomplished by selecting lines with desirable characteristics for propagation, while the new methodology has accompanied the development of high-volume parallel genotyping and sequencing technologies, for instance, genomic selection[6]
Cucumber (Cucumis sativus L.; 2n = 2x = 14) is generally considered to be an economically important vegetable crop worldwide[1], as well as a well-characterized model for studying fleshy fruit development[2]
According to our breeding aims, the 56 lines were assigned to group 1 (G1), which has a background similar to that of East Asian (EA) cucumber lines, and group 2 (G2), which has the Eurasian (EU) background (Supplementary Table 1; Supplementary Fig. 1)

Summary

Introduction

The breeding of cucumber germplasm was accomplished by selecting lines with desirable characteristics for propagation, while the new methodology has accompanied the development of high-volume parallel genotyping and sequencing technologies, for instance, genomic selection[6]. Artificial selection has greatly increased cucumber productivity and quality with expected improvements in traits, such as gynoecy, disease resistance, uniform ripening and bitterness[10,11,12,13], genetic gains in genomic selection are pending. Next-generation DNA sequencing technologies allow cost-effective genome sequencing at a population scale, which has led to the construction of variation maps for crop plants such as maize[14], rice[15], soybean[16], sorghum[17], apple[18], watermelon[19], pepper[20], and cucumber[3].

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