Comparison of AFLP and SSR for Genetic Diversity Analysis of Brassica napus Hybrids

Li, Li; Wanapu, Chokchai; Huang, X. Q.; Huang, Tuan; Li, Qiyi; Yi, Peng; GuiMin, Huang

doi:10.5539/jas.v3n3p101

Cited by 13 publications

(13 citation statements)

References 27 publications

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“…Lower polymorphism of dominant markers in comparison with codominant markers was confirmed before in other studies (Garcia et al, 2004; van Treuren & van Hintum, 2009; Li et al, 2011; Hamza et al, 2013). Lower variation of ISJ markers can also result from their conserved sequences.…”

Section: Discussionsupporting

confidence: 77%

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

Bilska

Szczecińska

2016

PeerJ

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BackgroundResearch into the protection of rare and endangered plant species involves genetic analyses to determine their genetic variation and genetic structure. Various categories of genetic markers are used for this purpose. Microsatellites, also known as simple sequence repeats (SSR), are the most popular category of markers in population genetics research. In most cases, microsatellites account for a large part of the noncoding DNA and exert a neutral effect on the genome. Neutrality is a desirable feature in evaluations of genetic differences between populations, but it does not support analyses of a population’s ability to adapt to a given environment or its evolutionary potential. Despite the numerous advantages of microsatellites, non-neutral markers may supply important information in conservation genetics research. They are used to evaluate adaptation to specific environmental conditions and a population’s adaptive potential. The aim of this study was to compare the level of genetic variation in Pulsatilla patens populations revealed by neutral SSR markers and putatively adaptive ISJ markers (intron-exon splice junction).MethodsThe experiment was conducted on 14 Polish populations of P. patens and three P. patens populations from the nearby region of Vitebsk in Belarus. A total of 345 individuals were examined. Analyses were performed with the use of eight SSR primers specific to P. patens and three ISJ primers.ResultsSSR markers revealed a higher level of genetic variation than ISJ markers (He = 0.609, He = 0.145, respectively). An analysis of molecular variance (AMOVA) revealed that, the overall genetic diversity between the analyzed populations defined by parameters FST and ΦPT for SSR (20%) and ΦPT for ISJ (21%) markers was similar. Analysis conducted in the Structure program divided analyzed populations into two groups (SSR loci) and three groups (ISJ markers). Mantel test revealed correlations between the geographic distance and genetic diversity of Polish populations of P. patens for ISJ markers, but not for SSR markers.ConclusionsThe results of the present study suggest that ISJ markers can complement the analyses based on SSRs. However, neutral and adaptive markers should not be alternatively applied. Neutral microsatellite markers cannot depict the full range of genetic variation in a population because they do not enable to analyze functional variation. Although ISJ markers are less polymorphic, they can contribute to the reliability of analyses based on SSRs.

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Section: Discussionsupporting

confidence: 77%

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

Bilska

Szczecińska

2016

PeerJ

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“…These findings are consistent with other studies comparing the level of polymorphism detected with SSR and AFLP markers [11, 16], and can be explained by the fact that SSR markers detect multiple alleles at a given locus, usually pre-selected for its high variability, whereas AFLP assays mainly detect single alleles at multiple loci randomly distributed in the genome.…”

Section: Resultssupporting

confidence: 92%

Assessment of diversity and genetic relationships of Neonectria ditissima: the causal agent of fruit tree canker

et al. 2016

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Background Neonectria ditissima is one of the most important fungal pathogens of apple trees, where it causes fruit tree canker. Information about the amount and partitioning of genetic variation of this fungus could be helpful for improving orchard management strategies and for breeding apple cultivars with high levels of genetically determined resistance. In this study single-spore Neonectria isolates originating from both the same and from different perithecia, apple cultivars and apple orchards in Sweden and Belgium, were evaluated for AFLP- and SSR-based genetic similarity and for mating system.ResultsSeven SSR loci produced a total of 31 alleles with an average of 4 alleles per locus, while 11 AFLP primer combinations produced an average of 35 fragments per primer combination and 71 % polymorphic fragments. An AFLP-based analysis of molecular variance (AMOVA) revealed that 89 % of the variation was found within orchards and 11 % between orchards. Genetic similarity among the studied isolates was illustrated with a principal coordinate analyseis (PCoA) and a dendrogram. AFLP-based Jaccard’s similarity coefficients were the highest when single-ascospore isolates obtained from the same perithecium were compared, medium-high for isolates from different perithecia on the same tree, and lowest when isolates from different trees were compared.ConclusionsBased on the results of PCoA and AMOVA analysis, isolates from the same or geographically close orchards did not group together. Since AFLP profiles differed also when single-ascospore isolates from the same perithecium were compared, the mating system of N. ditissima is most likely heterothallic.

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“…In oilseed rape, unlike several other important crops, we cannot use sources of genetic variation from natural populations (Prakash & Hinata 1980) and therefore techniques and approaches recognizing the extent of genetic variability are very beneficial. Molecular markers used in this study have also been used as effective tools to provide molecular data and evaluate genetic relationships in other studies although they did not include such diverse genetic resources (Sobotka et al 2004;Li et al 2011;Abdelmigid 2012). The importance and benefit of this study lies in the direct comparison of all accessions tested by three molecular techniques and their genetic diversity evaluation for the purposes of combinational crossing of distant genotypes in line and hybrid breeding.…”

Section: Discussionmentioning

confidence: 99%

Genetic diversity assessment in winter oilseed rape (Brassica napus L.) collection using AFLP, ISSR and SSR markers

Havlíčková¹,

Jozová²,

Rychla³

et al. 2014

Czech J. Genet. Plant Breed.

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Havlíčková L., Jozová E., Rychlá A., Klíma M., Kučera V., Čurn V. (2014): Genetic diversity assessment in winter oilseed rape (Brassica napus L.) collection using AFLP, ISSR and SSR markers. Czech J. Genet. Plant Breed., 50: 216-225.The genetic diversity of 94 accessions of winter oilseed rape (Brassica napus L.), representing past and contemporary material utilized in the Czech breeding programmes, was determined using microsatellites (SSRs), ISSRs and AFLPs. All three kinds of markers differed in the range of observed polymorphism and differentiated clearly each accession. Altogether 89 SSR, 1003 AFLP and 53 ISSR markers were evaluated. Their average rates of polymorphic bands were 100%, 53.9% and 90.6%, respectively, indicating high genetic diversity among the accessions. The greatest genetic distance was found by ISSRs (62.3%) whereas significantly lower distances of 49.4% in SSRs and 35.5% in AFLPs were observed. The genetic similarity matrix clearly distinguished all accessions. A set of the most distinct varieties was established. The analysis of the genetic pattern of the accessions indicated two groups comprising most of the modern Czech breeding materials, revealing a distinct shift in breeding. Surprisingly, molecular analyses did not support breeders' views about a narrow genetic base of the Czech breeding materials. The choice of appropriate technology for different aspects of germplasm evaluation is also discussed.

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Comparison of AFLP and SSR for Genetic Diversity Analysis of Brassica napus Hybrids

Cited by 13 publications

References 27 publications

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

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

Assessment of diversity and genetic relationships of Neonectria ditissima: the causal agent of fruit tree canker

Genetic diversity assessment in winter oilseed rape (Brassica napus L.) collection using AFLP, ISSR and SSR markers

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