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Article|15 Nov 2019|OPEN
Selection footprints reflect genomic changes associated with breeding efforts in 56 cucumber inbred lines
Bin Liu1 , Dailu Guan2 , Xuling Zhai1 , Sen Yang1 , Shudan Xue1 , Shuying Chen1 , Jing Huang3 , Huazhong Ren1 , and Xingwang Liu,1 ,
1Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, College of Horticulture, China Agricultural University, Beijing 100193, P. R. China
2Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus Universitat Autònoma de Barcelona, Bellaterra 08193, Spain
3Department of Agronomy, College of Agriculture, Purdue University, West Lafayette, IN 47907, USA
*Corresponding author. E-mail: renhuazhong@cau.edu.cn,Liuxw01@cau.edu.cn

Horticulture Research 6,
Article number: 127 (2019)
doi: https://doi.org/10.1038/s41438-019-0209-4
Views: 1084

Received: 02 Jun 2019
Revised: 01 Sep 2019
Accepted: 13 Oct 2019
Published online: 15 Nov 2019

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.