Development and Application of Microsatellites in Candidate Genes Related to Wood Properties in the Chinese White Poplar (Populus tomentosa Carr.)

Abstract

Gene-derived simple sequence repeats (genic SSRs), also known as functional markers, are often preferred over random genomic markers because they represent variation in gene coding and/or regulatory regions. We characterized 544 genic SSR loci derived from 138 candidate genes involved in wood formation, distributed throughout the genome of Populus tomentosa, a key ecological and cultivated wood production species. Of these SSRs, three-quarters were located in the promoter or intron regions, and dinucleotide (59.7%) and trinucleotide repeat motifs (26.5%) predominated. By screening 15 wild P. tomentosa ecotypes, we identified 188 polymorphic genic SSRs with 861 alleles, 2–7 alleles for each marker. Transferability analysis of 30 random genic SSRs, testing whether these SSRs work in 26 genotypes of five genus Populus sections (outgroup, Salix matsudana), showed that 72% of the SSRs could be amplified in Turanga and 100% could be amplified in Leuce. Based on genotyping of these 26 genotypes, a neighbour-joining analysis showed the expected six phylogenetic groupings. In silico analysis of SSR variation in 220 sequences that are homologous between P. tomentosa and Populus trichocarpa suggested that genic SSR variations between relatives were predominantly affected by repeat motif variations or flanking sequence mutations. Inheritance tests and single-marker associations demonstrated the power of genic SSRs in family-based linkage mapping and candidate gene-based association studies, as well as marker-assisted selection and comparative genomic studies of P. tomentosa and related species.

De Novo Assembly and Characterization of Bud, Leaf and Flowers Transcriptome from Juglans Regia L. for the Identification and Characterization of New EST-SSRs

“…capitata L.), sweet potato (Ipomoea batatas L.), and white poplar (Populus tomentosa Carr.) [9,13,14,48,49], but different from coconut tree (Cocos nucifera L.), field pea (Pisum sativum L.) and fava bean (Vicia faba L.), species in which tri-nucleotides were the most abundant EST-SSR markers [14,49,50].…”

Genetic architecture of growth traits in Populus revealed by integrated quantitative trait locus (QTL) analysis and association studies

“…tomentosa individuals in Guan Xian County, Shandong Province, China (36°23′N, 115°47′E). Phylogenetic analysis of 26 species from five subgenera (sections) of the genus Populus suggested that the parental species used to produce the linkage population here potentially possess the closest relationship of any Populus species (Du et al ., ), which probably reflects the fundamental similarity in the life histories of the two species, implying a possible shared genetic basis between intra‐ and interspecific variation. Integrated mapping in these populations might open up opportunities to simultaneously decipher the common genetic nature underlying growth traits in Populus .…”

Genome-Wide Microsatellite Characterization and Marker Development in the Sequenced Brassica Crop Species

“…Of these, only a small proportion (7.2, 6.1, 6.7% for B. rapa , B. oleracea and B. napus , respectively) was involved in the previously developed publicly available Brassica SSR markers (). This finding suggests that most of these newly developed Brassica genic SSR markers could represent the new ‘functional’ markers, which should be highly useful in evolutionary studies, 29 comparative mapping, 32 candidate gene association mapping 53 and molecular breeding.…”