Efficiency of different PCR-based marker systems for assessment of Iris pumila genetic diversity

Abstract

Abstract:We investigated informativeness and effectiveness of different marker types (ISSR, IRAP, REMAP, RGAP and LP-PCR that employ primers based on the conservative sequences of abiotic stress response genes) to study genetic diversity of Iris pumila L. By the number of amplicons per primer, number of polymorphic amplicons per primer and resolving power index (Rp), ISSR-markers were the most efficient followed by LP-PCR-markers. In order of decreasing value of indicators of genetic diversity "the percentage of polymorphic bands", and "the average Jaccard's genetic distance between plants", marker systems may be arranged as follows: ISSR > RAPD > LP-PC > RGAP ≈ IRAP. For ISSR-markers, the percentage of polymorphic bands was 1.3-1.7 times higher than for the others, and the average genetic distance was 1.2-1.3 times higher. Different marker systems were ranked by the value of Nei's gene diversity and the Shannon's index as follows: ISSR > RAPD ≈ LP-PCR > RGAP ≈ IRAP, with the highest and the lowest values differing 1.4 times. Genetic population structure was investigated with program Structure 2.3. The data of all marker systems suggest that all genomes under study belonged to one population. The PCoA and cluster analyses based on genetic distances showed distinctions in clustering generated from different markers data and summarized data, as well as the lack of strong clusters. Mantel test revealed significant positive correlation between the matrices of genetic distances generated by the data of almost all marker systems. The strongest correlation was found between RGAP-and IRAP-markers (r = 0.452, p = 0.01) and between RGAP and ISSR (r = 0.430, p = 0.01). ISSR, RAPD and LP-PCR proved to be more effective for the study of I. pumila genetic diversity, nevertheless, joint use of different marker systems will provide a more comprehensive assessment of variation in different genomic regions.

Comparison of the effectiveness of ISJ and SSR markers and detection of outlier loci in conservation genetics ofPulsatilla patenspopulations

“…This observation is consistent with the increasingly popular trend where both neutral variation and adaptive variation are analyzed (Woodhead et al, 2005; Kirk & Freeland, 2011; Coscia et al, 2012; Bublyk et al, 2013). A reliable estimation of genetic variation plays a key role in conservation genetics because it supports evaluations of the present and future populations’ conditions (Kirk & Freeland, 2011).…”

“…Furthermore, in a Structure analysis performed by Singh et al (2013), the values of K were determined by the applied markers (K = 5 for SSRs, K = 15 for SNPs). Bublyk et al (2013), however, analyzed three types of markers amplifying non-coding sequences (RAPD, ISSR, inter-retrotransposon amplified polymorphism (IRAP)) and two types of markers based on conserved gene sequences: disease resistance (resistance gene analog polymorphism (RGAP)) and abiotic stress response (long primer polymerase chain reaction (LP-PCR)), and found different grouping patterns of Iris pumila individuals in PCoA diagrams for each marker. An analysis of I. pumila populations in the Structure program also produced ambiguous results (Bublyk et al, 2013).…”

“…Bublyk et al (2013), however, analyzed three types of markers amplifying non-coding sequences (RAPD, ISSR, inter-retrotransposon amplified polymorphism (IRAP)) and two types of markers based on conserved gene sequences: disease resistance (resistance gene analog polymorphism (RGAP)) and abiotic stress response (long primer polymerase chain reaction (LP-PCR)), and found different grouping patterns of Iris pumila individuals in PCoA diagrams for each marker. An analysis of I. pumila populations in the Structure program also produced ambiguous results (Bublyk et al, 2013). A single genetic group was identified by RAPD, ISSR and LP-PCR markers, and two genetic groups were distinguished by IRAP and RGAP markers.…”

Discrimination of common Iris species from Egypt based on their genetic and metabolic profiling

“…Previous data determined the genetic diversity among several Iris species collected from different localities used RAPD (rapid amplified polymorphic DNA) and/or ISSR 41–47 . Different genetic markers [ISSR, inter‐retrotransposon amplified polymorphism (IRAP), retrotransposon‐microsatellite amplified polymorphism (REMAP), resistance gene analogue polymorphism (RGAP) and long primer (LP)‐PCR] were also used to study the genetic diversity of some Iris species, where the ISSR‐markers were found to be the most efficient 48 . Amplified fragment length polymorphisms (AFLPs) was used to determine diversity among I. pseudacorus population and other 14 Iris species 6,49 .…”

Inter-Simple Sequence Repeat Data Reveals High Genetic Diversity in Wild Populations of the Narrowly Distributed Endemic Lilium regale in the Minjiang River Valley of China

“…ISSR markers represent mostly noncoding regions of the genome flanked by SSRs. Several genetic studies of natural populations using ISSR markers have demonstrated their high variability, reproducibility [ 16 , 34 , 35 , 36 ] and relative ease of use in population-level studies in a variety of organisms [ 36 , 37 , 38 ] including plants [ 15 , 22 , 39 , 40 , 41 ]. ISSR markers are particularly useful for population genetic studies of rare species for which no previously characterized molecular markers are available [ 21 , 22 , 40 , 41 ].…”