Abstract
Chinese cherry (Cerasus pseudocerasus (Lindl.) G.Don) is an economically important tetraploid fruiting cherry species native to China. Simple sequence repeats (SSRs)—due to their codominance, polymorphism, and stability—have been widely applied in genetic identification and trait-association analysis. In this study, using comparative genomics strategy and the data of one high-quality whole genome and seven preliminarily assembled genome sequences, we constructed a database containing 25,779 polymorphic SSR loci to efficiently develop novel markers. Sixty-four SSR loci covering eight linkage groups were selected to design primer pairs. Sixty (93.75%) primer pairs yielded specific bands and 32 (50.00%) exhibited moderate-to-high levels of informativeness (PIC ranging from 0.264 to 0.728) in 94 Chinese cherry accessions. A total of 38 primer pairs exhibited high transferability across 13 Cerasus taxa. The marker SAUCps203 was species-specific in C. pseudocerasus by checking with 114 accessions from Cerasus and 16 relatives, suggesting its potential application in accurate identification of Chinese cherry or its interspecific hybrid. Moreover, 1081 out of 1122 individuals from three cross F1 populations of Chinese cherry were identified as true hybrid offspring by using only five SSR markers. Trait association analysis suggested that 20 SSR loci were significantly associated with soluble solids and fruit size, with explained phenotypic variance ranging from 9.02% to 26.35%. This study will provide a basis for SSR-based germplasm identification and further marker-assisted selection (MAS) of Chinese cherry.
Highlights
Chinese cherry (Cerasus pseudocerasus), belonging to the genus Cerasus of the familyRosaceae, is an important tetraploid fresh fruit crop (2n = 4x = 32) [1,2]
The effective strategy used in this study is advantageous for screening informative Simple sequence repeats (SSRs) markers from large-scale markers by assessing their potential to detect fragment length polymorphism among different cultivated and wild Chinese cherry accessions
This study constructed a database containing 25,779 polymorphic SSR loci of Chinese cherry based on comparative genomic analyses
Summary
Chinese cherry (Cerasus pseudocerasus), belonging to the genus Cerasus of the family. Rosaceae, is an important tetraploid fresh fruit crop (2n = 4x = 32) [1,2]. It originates in Southwest China and is widely distributed in the North and East China Plain, Qinling. Its cultivation history dates back to 3000 years ago in China [4]. Chinese cherry is characterized by early bloom and maturity, and is full flavored, with rich nutritional ingredients and trace elements, wide adaptability, and intensive disease/pest resistance [5]. The cherry industry is developing rapidly and has increasingly contributed to the rural vitalization of China. We have carried out field investigation and assessment of cherry resources across its locality in China [5,6].
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