Genome Wide Characterization of Short Tandem Repeat Markers in Sweet Orange (Citrus sinensis)

Abstract

Sweet orange (Citrus sinensis) is one of the major cultivated and most-consumed citrus species. With the goal of enhancing the genomic resources in citrus, we surveyed, developed and characterized microsatellite markers in the ≈347 Mb sequence assembly of the sweet orange genome. A total of 50,846 SSRs were identified with a frequency of 146.4 SSRs/Mbp. Dinucleotide repeats are the most frequent repeat class and the highest density of SSRs was found in chromosome 4. SSRs are non-randomly distributed in the genome and most of the SSRs (62.02%) are located in the intergenic regions. We found that AT-rich SSRs are more frequent than GC-rich SSRs. A total number of 21,248 SSR primers were successfully developed, which represents 89 SSR markers per Mb of the genome. A subset of 950 developed SSR primer pairs were synthesized and tested by wet lab experiments on a set of 16 citrus accessions. In total we identified 534 (56.21%) polymorphic SSR markers that will be useful in citrus improvement. The number of amplified alleles ranges from 2 to 12 with an average of 4 alleles per marker and an average PIC value of 0.75. The newly developed sweet orange primer sequences, their in silico PCR products, exact position in the genome assembly and putative function are made publicly available. We present the largest number of SSR markers ever developed for a citrus species. Almost two thirds of the markers are transferable to 16 citrus relatives and may be used for constructing a high density linkage map. In addition, they are valuable for marker-assisted selection studies, population structure analyses and comparative genomic studies of C. sinensis with other citrus related species. Altogether, these markers provide a significant contribution to the citrus research community.

Novel polymorphic EST-based microsatellite marker isolation and characterization from Poncirus trifoliata (Rutaceae)

“…Direct comparison of the frequency of occurrence of SSRs in different reports is difficult given that estimates are dependent on the SSR mining tools, search criteria, size of the data set and the redundancy of EST sequences. Dinucleotide repeats were the most frequent motif types in the transcribed region of the P. trifoliata genome, as has often been observed in other plant species [21] . In addition, the frequency of motif types varies greatly according to the SSR search criteria and search tools.…”

A comparative genomics approach revealed evolutionary dynamics of microsatellite imperfection and conservation in genus Gossypium

“…Many researchers have reported 3-nt repeats’ abundance as characteristics in monocots [42, 43]. Similarly, predominate abundance of 2-nt repeats has been reported in dicots [44, 45], but paramount abundance of other motifs is not out of the scope. The resultant fluctuations might be owed to variations in search parameters.…”

Identification of genetic diversity among mutant lemon and mandarin varieties using different molecular markers

“…SSR based molecular typing is one of the most widely used marker system in genetic relationship studies because SSR markers are transferable, highly polymorphic, useful, codominant, reproducible, effective, randomly and widelydistributed along the genome (Hussein et al, 2003;Biswas et al, 2011;Carrillo-Medrano et al, 2018). SSR markers have been the most commonly preferred markers in molecular biology for mapping (Chen et al, 2008;Gulsen et al, 2010) and genetic diversity analyses in citrus (Barkley et al, 2006;Barkley et al, 2009;Uzun et al, 2011;Kacar et al, 2013;Biswas et al, 2014;Polat, 2015;Carrillo-Medrano et al, 2018).ISSR based molecularcharacterization is carried out using a single marker (Capparelli et al, 2004) allowing a cost-effective mapping (Sankar and Moore, 2001), and it was successfully used to determine genetic diversity in citrus (Capparelli et al, 2004;Shahsavar et al, 2007;Uzun et al, 2010).…”