Genome-wide characterization of microsatellites and genetic diversity assessment of spinach in the Chinese germplasm collection

Abstract

Spinach is a nutritional leafy green vegetable, and it also serves as a model species for studying sex chromosome evolution. Genetic marker development and genome structure analysis are important in breeding practice and theoretical evolution studies of spinach. In this study, the frequency and distribution of different microsatellites in the recently released draft spinach genome were characterized. A total of 261,002 perfect microsatellites were identified (estimated frequency: ~262.1 loci/Mbp). The most abundant microsatellites were tetranucleotide and trinucleotide, accounting for 33.2% and 27.7% of the total number of microsatellites, respectively. A total of 105 primer pairs were designed and screened, and 34 were polymorphic among the detected spinach cultivars. Combined with seven primer sets developed previously, 41 primer pairs were used to investigate genetic diversity among 43 spinach cultivars in China. The average polymorphism information content value of the 41 markers was 0.43, representing an intermediate level. The spinach cultivars had a low genetic diversity, and no detectable common factors were shared by each group in the UPGMA dendrogram. This study’s findings facilitate further investigations on the organization of the microsatellites in spinach genome and provide clues for future breeding applications of spinach in China.

Genome-wide simple sequence repeats (SSR) markers discovered from whole-genome sequence comparisons of multiple spinach accessions

“…The relatively lower number of alleles (range of 2–5 with an average of 2.9 alleles/locus) reported in this study is due to a careful and strict allele scoring employed here. The average PIC value of the markers in this study was 0.25, which is slightly lower than the previous report in spinach (average PIC 0.43) 20 and is explained by the low number of alleles reported in this study. The use of fluorescently labeled primers in the multiplex set and fragment analysis in capillary electrophoresis can increase allele calling at high precision with clearer results and eliminate the difficulties with scoring bands in the agarose and polyacrylamide gel electrophoresis method.…”

“…The SSR distribution in the Sp75 genome was previously reported 20 and is not described in detail here. This study aimed to generate a large set of polymorphic SSR loci to extend their use in future genetic studies in spinach.…”

“…Another study reported a set of 85 polymorphic SSR markers mined from genome sequences of a spinach cultivar, and the loci were genotyped in a set of 48 worldwide spinach accessions and found clustering of spinach accessions based on geographical origin 19 . Recently, 34 new polymorphic SSR markers were developed from the spinach reference genome of Xu et al 27 and were used to assess the genetic diversity of Chinese spinach germplasm collection 20 . A fewer number of SSR markers have been reported in spinach; thus, the availability of a large number of useful SSR markers will facilitate spinach genetics and breeding.…”

The Landscape of Genome-Wide and Gender-Specific Microsatellites in Indo-Pacific Humpback Dolphin and Potential Applications in Cetacean Resource Investigation

“…In addition, microsatellites are valuable tools for population genetic analyses since they are a rich source of hypervariable codominant markers [3,4]. They are currently the most important codominant markers and have been extensively used in quantitative trait loci (QTL) mapping, genetic diversity studies, marker-assisted selective breeding, and evolutionary studies [1,[5][6][7]. However, the development of novel markers is still a labor-intensive and time-consuming process.…”

Genetic Diversity, Structure, and Selective Sweeps in Spinacia turkestanica Associated With the Domestication of Cultivated Spinach

“…Few genetic diversity studies have been performed on spinach. Diversity analyses were first carried out for spinach accessions using polymerase chain reaction (PCR) assays based on simple sequence repeat (SSR) and target region amplification polymorphism (TRAP) markers to generate genetic fingerprint data ( Hu et al, 2007 ; Khattak et al, 2007 ; Kuwahara et al, 2014 ; Göl et al, 2017 ; Li et al, 2018 ; Bhattarai et al, 2021 ). These studies found spinach accessions to be clustered based on their geographic origin, with separation of accessions into two to three major groups.…”