EST-derived microsatellites from Actinidia species and their potential for mapping

Abstract

To increase the speed and reduce the cost of constructing a genetic map of Actinidia species (kiwifruit), for use in both breeding and functional genomics programmes, we sampled microsatellites from expressed sequence tags (ESTs) to evaluate their frequency of occurrence and level of polymorphism. Perfect dinucleotide repeats were the microsatellites selected, and these were found to be numerous in both the 5' and 3' ends of the genes represented. The microsatellites were of various lengths, the majority being repeats with the pattern (CT)(n)/(GA)(n). One hundred and fifty microsatellites, each with more than 10 dinucleotide repeat units, were chosen as possible markers, and when these were amplified, 93.5% were found to be polymorphic and segregating in a mapping population, with 22.6% amplifying more than one locus. Four marker categories were identified. Fully informative markers made up 27% of the total, 36.2% were female informative, 25.8% were male informative and 10% partly informative. The mapping population was an intraspecific cross in the diploid species Actinidia chinensis, with parents chosen for their diversity in fruit and plant characteristics, and for their geographical separation. Linkage was tested using the software 'Joinmap' and a LOD value of 3. The distribution of the EST-based markers over the linkage groups obtained appeared to be random, taking into consideration the small sample size, that the number of linkage groups (31) exceeded the chromosome number of n=29, and that a number of markers were not assigned to any group. Some microsatellite markers which amplified more than one locus mapped to separate linkage groups. According to our study in A. chinensis, EST-derived microsatellites give large numbers of possible markers very quickly and at reasonable cost. The markers are highly polymorphic, segregate in the mapping population, and increase the value of the genomic map by providing some functional information.

Rediscovering Medicinal Plants' Potential with OMICS: Microsatellite Survey in Expressed Sequence Tags of Eleven Traditional Plants with Potent Antidiabetic Properties

“…In Mangifera indica and Nelumbo nucifera, tetranucleotides and pentanucleotides were completely absent, whereas in Tinospora cordifolia, hexanucleotide was completely absent. The dinucleotide repeats (DNRs) are more frequent than the trinucleotide repeats (TNRs) in ESTs of Ananas comosus, Carica papaya, Catharanthus roseus, Jatropha curcas, Morus indica, and Nelumbo nucifera, similar to the previous reports in Actinidia (Fraser et al, 2004), Camellia (Sahu et al, 2012), and Picea species (Rungis et al, 2004). But the frequencies of TNRs were found to be more than DNRs in Citrus aurantium, Cynodon dactylon, Dioscorea alata, Mangifera indica, and Tinospora cordifolia, similar to most previous studies (Cordeiro et al, 2001;Kantety et al, 2002;Varshney et al, 2002;Thiel et al, 2003;Nicot et al, 2004).…”

Analysis of Genetic Diversity and SSR Allelic Variation in Rubber Tree (Hevea brasilensis)

“…As exactly as most crops (Fraser et al, 2004;Jung et al, 2005;Aggarwal et al, 2007), Feng et al (2009) reported that DNRs were the main repeat motif, and AG / TC were the predominant DNRs; In this study, 61 sequences were recovered from 5 loci, of which 44 sequences belonged to AG / TC repeats.…”

EST-SSRs as a resource for population genetic analyses

“…In fact, an estimated 2-5% of all plant-derived ESTs are thought to harbor SSRs (Kantety et al, 2002), although the actual frequency of SSR-bearing ESTs in any particular analysis is highly dependent on the search parameters (see below). Moreover, a large fraction of EST-SSRs (on the order of 80-90%) are typically found to be polymorphic (Bandopadhyay et al, 2004;Fraser et al, 2004;Pashley et al, 2006). Taking into account typical marker development attrition rates, it therefore seems likely that EST databases containing as few as 1000 sequences could provide enough markers to facilitate population genetic analyses.…”