The Genotypes of Polymorphic Simple Sequence Repeat Loci Revealed by Whole-genome Resequencing Data of 30 Pyrus Accessions

Abstract

<jats:p>Simple sequence repeats (SSRs) are widely used in cultivar identification, genetic relationship analysis, and quantitative trait locus mapping. Currently, the selection of hybrid progeny plants in molecular marker-assisted breeding mostly relies on SSR markers because of their ease of operation. In <jats:italic>Pyrus</jats:italic>, a large number of SSR markers have been developed previously. The method to identify polymorphic SSRs quickly is still lacking in cultivated as well as wild pear species. We present a large number of polymorphic SSRs identified using a quick in silico approach applied across 30 cultivated and wild accessions from <jats:italic>Pyrus</jats:italic> species. A total of 49,147 SSR loci were identified in <jats:italic>Pyrus</jats:italic>, and their genotypes were evaluated by whole-genome resequencing data of 30 <jats:italic>Pyrus</jats:italic> accessions. The results show that most SSR loci were dinucleotide repeat motifs located in intergenic regions. The genotypes of all SSR loci were revealed in all accessions. A total of 23,209 loci were detected, with more than one genotype in all <jats:italic>Pyrus</jats:italic> accessions. We selected 702 highly polymorphic SSR loci to characterize the pear accessions with an average polymorphism information content value of 0.67, suggesting that these SSR loci were highly polymorphic. The genetic relationship of <jats:italic>Pyrus</jats:italic> species in the neighbor-joining (NJ) tree and population structure showed a clear division between the oriental and occidental accessions. The population structure split all oriental pears into two groups: cultivars and wild accessions. These new findings of the polymorphic SSR loci in this study are valuable for selecting appropriate markers in molecular marker-assisted breeding in <jats:italic>Pyrus</jats:italic>.</jats:p>

Chloroplast genome of the invasive Pyrus calleryana underscores the high molecular diversity of the species

“…phylogeny based on the plastidic sequences (trnL-F, accD-psaI) and the nuclear one LFY2int2-N (Zheng et al 2014), or the sequence data of 702 microsatellite loci across Pyrus spp. (Jiang et al 2019).…”

“…The original sample collectors deposited voucher specimens in their laboratory. This short-read archive was previously used to mine microsatellite markers for phylogenetic comparisons with other Pyrus species (Jiang et al 2019 ; CRR019697 of China National Center for Bioinformation; reads trimmed and filtered for high quality). The overall genome coverage was 13.8 × and all details pertaining to DNA isolation, sequencing, and quality assessment were published (Jiang et al 2019 ).…”

“…This short-read archive was previously used to mine microsatellite markers for phylogenetic comparisons with other Pyrus species (Jiang et al 2019 ; CRR019697 of China National Center for Bioinformation; reads trimmed and filtered for high quality). The overall genome coverage was 13.8 × and all details pertaining to DNA isolation, sequencing, and quality assessment were published (Jiang et al 2019 ). Other related datasets of P. calleryana were used for critical evaluation of our bioinformatics approach (SRR7135497; SRR7135498; SRR7135500).…”