Development and Cross-Species Transferability of Novel Genomic-SSR Markers and Their Utility in Hybrid Identification and Trait Association Analysis in Chinese Cherry

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.

Haplotype-resolved genome assembly for tetraploid Chinese cherry (Prunus pseudocerasus) offers insights into fruit firmness

“…S2 ; Supplementary Data Table S3 ). The P. pseudocerasus genome was twice the size of the diploid P. avium genome (2 n = 2 x ), suggesting that P. pseudocerasus is a tetraploid species, which is consistent with previous reports [ 35 , 36 ]. After obtaining the draft genome (824.19 Mb) ( Supplementary Data Table S4 ), we conducted a chromosome-level assembly using 176.35 Gb of Hi-C reads.…”

Genome-Wide Identification of the WD40 Gene Family in Tomato (Solanum lycopersicum L.)

“…A large number of SSRs are distributed across eukaryotic genomes, and the use of SSR markers plays an important role in genetic diversity studies [ 68 ], comparative genomics [ 69 ], trait association analysis [ 70 ] and linkage mapping [ 71 ]. The development of SSR technology has facilitated the identification of functional genes in horticultural crops such as grapes [ 72 ], strawberries [ 73 ] and melons [ 74 ], which has accelerated the progress of genetic improvement and improved the selection and breeding of new cultivars.…”

Assessment of Simple Sequence Repeat (SSR) Markers Derived from Whole-Genome Sequence (WGS) of Mungbean (Vigna radiata L. Wilczek): Cross-Species Transferability and Population Genetic Studies in Vigna Species

“…In another study, 120 Nicotiana multiple (X) genome (NIX) SSR markers developed from seven genomes were tested on five Nicotiana accessions, i.e., N. syl, N. tom, N. tab K326, N. ben, and unknown genomic sequence, and 100% amplification was recorded in four accessions [70]. Similarly, using Chinese cherry, which is a fruiting cherry species, Liu et al [71] applied 39 genomic SSR markers derived from the whole genome and seven preliminary assembled genome sequences from 94 Chinese cherry accessions and 13 Cerasus taxa. Of these 39 SSRs, 19 SSRs have 100% transferability in all 94 cherry accessions.…”