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Abstract
Marker-assisted background selection is a powerful molecular tool that can enhance breeding efficiency through the analysis of a large number of markers representing the entire genomic background for precise selection. In the present study, the transcriptomes of 38 cucumber inbred lines with diverse traits were sequenced for single nucleotide polymorphism (SNP) mining for practical application to commercial cucumber breeding. A total of 62,378 high-quality SNPs were identified, of which 2462 SNPs were chosen based on the stringent filtering parameters. Finally, 363 evenly distributed common background selection markers (BMs) were developed and validated through polymorphism analysis and phylogenetic analysis using breeding materials with different genetic backgrounds; 327 out of 363 common BMs were useful for background selection. Moreover, the results of the phylogenetic analysis carried out using 50 selected core BMs were consistent with those for 327 common BMs. However, when the genotypes of breeding materials belonging to only the Baekdadagi-type were analyzed, the 327 common BMs showed a significant reduction in polymorphisms within the biased genomic locations. To address this issue, 59 highly polymorphic markers were selected as Baekdadagi BMs, as they showed better selection ability for the Baekdadagi-type. The 327 common BMs developed in the present study will enable efficient marker-assisted background selection in cucumber. Additionally, to reduce the genotyping cost, we suggested an alternative background selection strategy using both evenly distributed core BMs and biased Baekdadagi BMs for the improvement of commercial cucumber breeding programs.
Highlights
Cucumber, Cucumis sativus L. (2n = 2x = 14), an important cucurbitaceous crop, is one of the ten major vegetables in the world
Transcriptome sequencing of 38 inbred group A individuals was performed for the identification of single nucleotide polymorphism (SNP)
The background selection technique using a large set of molecular markers covering the whole genome is a very useful tool for the quick development inbred lines in commercial seed companies
Summary
Four major types of cucumber, the Huánan-type (southern China), Huábei-type (northern China), European-type, and a Huánan × Huábei-type, are consumed worldwide [2]. Among these types, the Baekdadagitype and Chwicheong-type belong to the Huábei group, and the Gasi-type belongs to the Huánan group [2]. The Baekdadagi-type cucumber is cultivated mostly in northeastern Asian countries, including Korea, China, and Japan. It is a popular cucumber variety on the Korean market and is consumed as a preparation in various side dishes [2]. The upper part of the stalk region and the lower part of the blossom region of the fruit of the Baekdadagi-type cucumbers have a green skin color, which gradually turns into white-green as it moves down to the center of the fruit
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