title: Estimation of pea (Pisum sativum L.) microsatellite mutation rate based on pedigree and single-seed descent analyses.
abstract: Microsatellites, or simple sequence repeats (SSRs) are widespread class of repetitive DNA sequences, used in population genetics, genetic diversity and mapping studies. In spite of the SSR utility, the genetic and evolutionary mechanisms are not fully understood. We have investigated three microsatellite loci with different position in the pea (Pisum sativum L.) genome, the A9 locus residing in LTR region of abundant retrotransposon, AD270 as intergenic and AF016458 located in 5'untranslated region of expressed gene. Comparative analysis of a 35 pair samples from seven pea varieties propagated by single-seed descent for ten generations, revealed single 4 bp mutation in 10th generation sample at AD270 locus corresponding to stepwise increase in one additional ATCT repeat unit. The estimated mutation rate was 4.76 × 10(-3) per locus per generation, with a 95% confidence interval of 1.2 × 10(-4) to 2.7 × 10(-2). The comparison of cv. Bohatýr accessions retrieved from different collections, showed intra-, inter-accession variation and differences in flanking and repeat sequences. Fragment size and sequence alternations were also found in long term in vitro organogenic culture, established at 1983, indicative of somatic mutation process. The evidence of homoplasy was detected across of unrelated pea genotypes, which adversaly affects the reliability of diversity estimates not only for diverse germplasm but also highly bred material. The findings of this study have important implications for Pisum phylogeny studies, variety identification and registration process in pea breeding where mutation rate influences the genetic diversity and the effective population size estimates.
authors.affiliation: Department of Plant Biology, Mendel University, Zemědělská, Brno, Czech Republic.
authors.forename: Jaroslava
authors.initials: J
authors.lastname: Cieslarová
authors.forename: Pavel
authors.initials: P
authors.lastname: Hanáček
authors.forename: Eva
authors.initials: E
authors.lastname: Fialová
authors.forename: Miroslav
authors.initials: M
authors.lastname: Hýbl
authors.forename: Petr
authors.initials: P
authors.lastname: Smýkal
mesh_terms: D020121:5' Untranslated Regions; D001947:Breeding; D021901:DNA, Intergenic; D018744:DNA, Plant / Q000235:genetics / Q000302:isolation & purification; D014644:Genetic Variation; D018745:Genome, Plant; D042822:Genomic Instability; D005838:Genotype; D018895:Microsatellite Repeats; D009154:Mutation; D018532:Pisum sativum / Q000235:genetics*; D010375:Pedigree; D018626:Retroelements; D012639:Seeds / Q000235:genetics*; D017422:Sequence Analysis, DNA; D020079:Terminal Repeat Sequences
chemical_list: D020121:5' Untranslated Regions; D021901:DNA, Intergenic; D018744:DNA, Plant; D018626:Retroelements