Main content area

Molecular basis of off-type microsatellite markers in papaya

Fang, Jingping, Wood, Andrew, Chen, Rukai, Ming, Ray
Euphytica 2016 v.209 no.2 pp. 323-339
Carica papaya, DNA replication, alleles, genetic markers, genetic variation, meiosis, microsatellite repeats, molecular cloning, natural selection, papayas, parents, plant breeding, progeny, sequence analysis, sex chromosomes, single nucleotide polymorphism, tropics
Papaya (Carica papaya L.) is a major fruit crop in the tropics and is a model system for studying sex chromosome evolution in plants. From a simple sequence repeat (SSR) mapping project in papaya, 37 SSRs displayed non-parental alleles in the F₂ population, known as off-type markers. They all belong to Class I (≥20 bp, hypervariable markers). To investigate the molecular basis of these non-parental alleles, seven SSRs with off-type alleles were cloned and sequenced from two parents and selected F₂ individuals. SSR repeat motif variation was the major cause for the generation of off-type alleles and single nucleotide polymorphisms (SNPs) and Insertion/deletion also contributed to off-type polymorphism. Off-type SSRs arose after one meiosis at 3 % frequency. Two of the seven markers had no polymorphisms between the parents but non-parental alleles segregated among the F₂ individuals. Four of the seven markers exhibited SNPs between parents with transition and transversion at 2:1 ratio. Six markers showed additional SNPs between F₂ offspring and parents with transition and transversion at about 1:1 ratio, suggesting higher than expected level of transversion mutations at the F₂ population after one meiosis event between the parental genomes. These off-type SSRs were analyzed in a second F₂ population and 43 % of them were conserved. The major cause of off-type SSRs in papaya is the variation of repeat length in Type I SSRs, and the underlining mechanism might be DNA replication slippage of repeat motifs. The presence and high conservation of these off-type markers demonstrated that hypervariable class I SSRs could generate genetic variation in one generation and increase genetic diversity for natural selection to enhance fitness.