Genome-wide simple sequence repeat markers in potato: abundance, distribution, composition, and polymorphism

Abstract

Simple sequence repeats (SSRs) are important sources of genetic diversity and are widely used as markers in genetics and molecular breeding. In this study, we examined four potato genomes of DM1-3 516 R44 (DM) from Solanum phureja, RH89039-16 (RH) from Solanum tuberosum, M6 from Solanum chacoense and Solanum commersonii to determine SSR abundance and distribution and develop a larger list of polymorphic markers for a potentially wide range of uses for the potato community. A total of 1,734,619 SSRs were identified across the four genomes with an average of 433,655 SSRs per genome and 2.31kb per SSR. The most abundant repeat units for mono-, di-, tri-, and tetra-nucleotide SSRs were (A/T)n, (AT/AT)n, (AAT/ATT)n, and (ATAT/ATAT)n, respectively. The SSRs were most abundant (78.79%) in intergenic regions and least abundant (3.68%) in untranslated regions. On average, 168,069 SSRs with unique flanking sequences were identified in the four genomes. Further, we identified 16,245 polymorphic SSR markers among the four genomes. Experimental validation confirmed 99.69% of tested markers could generate target bands. The high-density potato SSR markers developed in this study will undoubtedly facilitate the application of SSR markers for genetic research and marker-pyramiding in potato breeding.

Keywords: markers; polymorphism; potato; simple sequence repeat; whole-genome sequence.

Figure 1

Distributions of all 309,518 SSR loci (A), 228,033 SSR loci with unique flanking sequences (B), and 16,245 newly polymorphic SSR markers (C) across 12 chromosomes in the DM reference genome. Various densities are expressed in various colours. Centromeres are expressed in blue.

Figure 2

Characteristics of 16,245 polymorphic SSRs in potato: chromosome distribution (a) and genomic region (b).

Figure 3

PCR-validation of polymorphic SSRs. Lanes 1, 4, 7, and 10 are DM1-3 516 R44 (DM), RH89039-16 (RH), and CGN566744 in S. chacoense and CGN473412 in S. commersonii, respectively. Lanes 2–3 are randomly selected genotypes in S. phureja, 5–6 are randomly selected genotypes in S. tuberosome, 8–9 are randomly selected in S. chacoense while 11–12 are randomly selected in S. commersonii. SSR loci contain TNRs (CPSSR_6429 and CPSSR_7418) and DNRs (CPSSR_2046, CPSSR_7310, CPSSR_8720 and CPSSR_5141). M: marker.

Figure 4

Primers CPSSR_10194 (a) and CPSSR_6422 (b) can independently distinguish the four accessions. The first lane is a marker. Each accession was represented by nine genotypes.