Application of single nucleotide polymorphisms to non‐model species: a technical review

Garvin, Michael R.; Saitoh, Kenji; Gharrett, Anthony J.

doi:10.1111/j.1755-0998.2010.02891.x

Cited by 188 publications

(188 citation statements)

References 196 publications

(306 reference statements)

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“…Whether, or not, NKCC is regulated by MF is also well worth to further study. This study shows that SNPs are suitable markers for candidate gene association studies because they possess important traits (Garvin et al 2010;Seeb et al 2011). Indeed, the SNP variants present in gene coding regions make it possible to identify candidate genotypes for genetic selection programs in economic species (Bester-van der Merwe et al 2011;Garvin et al 2010).…”

Section: Discussionmentioning

confidence: 81%

Effects of salinity acclimation and eyestalk ablation on Na+, K+, 2Cl− cotransporter gene expression in the gill of Portunus trituberculatus:a molecular correlate for salt-tolerant trait

Zhang

Ping

et al. 2016

Cell Stress and Chaperones

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The Na− cotransporter (NKCC) is an important gene in ion transport. In order to elucidate its function, and regulatory mechanisms, in salinity acclimation, the complete cDNA sequence of NKCC (4218 bp) from Portunus trituberculatus (PtNKCC) was first cloned and characterized. It was found to encode 1055 amino acids containing conserved AA-permease and SLC12 motifs. Results show that PtNKCC is expressed to the greatest extent in gills. High salinity stress exposure led to significant increases (9.6-fold) of PtNKCC mRNA expression in the gills 12 h after treatment, declining to less than the levels seen in the control group between 48 and 72 h. During low salinity stress, expression levels of PtNKCC in gills were found to be upregulated at each sampling time, reaching their peak after 6 h (a 12.4-fold increase). Eyestalk ablation also triggered an 11.3-fold increase in PtNKCC mRNA, while re-injection with eyestalk homogenates significantly reduced the expression of PtNKCC mRNA. Four single nucleotide polymorphisms (SNPs) were detected in the PtNKCC open reading frame, and one SNP was associated with salt tolerance. Our results indicate that PtNKCC plays an important role in the salinity acclimation of P. trituberculatus, while there may be a compound present in the XOSG that inhibits the expression of PtNKCC.

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Section: Discussionmentioning

confidence: 81%

Effects of salinity acclimation and eyestalk ablation on Na+, K+, 2Cl− cotransporter gene expression in the gill of Portunus trituberculatus:a molecular correlate for salt-tolerant trait

Zhang

Ping

et al. 2016

Cell Stress and Chaperones

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“…Moreover the MAF value can be affected in the application of cross-species genotyping arrays by ascertainment bias, the systematic deviations from the expected allele frequency distribution leading to downstream biases in the evaluation of many indices (Satkoski Trask et al, 2011). Probability that a SNP is identified in ascertainment panel with small size compared to the population is a function of its MAF and the SNP discovery process, favours the most variable sites and eliminates rare SNPs (Garvin et al, 2010;Helyar et al, 2011). The evaluation of population genetic parameters such as diversity can be biased mainly because the SNPs on the chip optimized for model species are not completely representative for nonmodel animals.…”

Section: Resultsmentioning

confidence: 99%

Investigation of the genetic distances of bovids and cervids using BovineSNP50k BeadChip

et al. 2015

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Abstract. This study presents the application of BovineSNP50 BeadChip for genome-wide screening of two taurine breeds (Bos primigenius taurus) and Zebu (Bos primigenius indicus), and two species from the family Cervidae: red deer (Cervus elaphus) and fallow deer (Dama dama). The aim of the paper was to evaluate the use of bovine array for cross-species genotyping and analyse single nucleotide polymorphism (SNP) distribution, diversity within groups of animals and genetic distance among analysed species. The number of polymorphic SNPs decreased with the increase of phylogenetic distance between species, which also reflected a decrease in call rate (from 99.54 to 61.19 %). The minor allele frequency (MAF) values were significantly different between species and ranged from 0.18 ± 15 (Zebu) to 0.26 ± 0.14 (Pinzgau). The subsequent analyses of genetic diversity were based on the polymorphic loci detected in cervids. Differences in the expected heterozygosity was low (0.06), on average 0.34. In analysed groups the F IS values were close to zero, which suggested low SNP variance within them. The value of F IT indicated homozygote excess in evaluated individuals. Analysis of molecular variance revealed that most of the variability was distributed within all individuals. Observed genetic distances within and across groups of animals suggested that taurine cattle and cervids were more distant. The study results showed that genotyping array prepared for model species can be applied not only to organisms for which was developed, but can be also successfully used in closely related and more phylogenetically divergent species.

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“…Other applications of the analysis of SNPs are, for example, population genetic studies concerning the history, structure and demography of populations or molecular systematic studies and parentage analyses (Garvin et al 2010;Morin et al 2004). The SNPs identified in this study are suitable for population genetic investigations complementing other frequently used markers such as microsatellites and AFLPs.…”

Section: Introductionmentioning

confidence: 99%

DNA sequence variation and development of SNP markers in beech (Fagus sylvatica L.)

Seifert¹,

Vornam²,

Finkeldey³

2012

Eur J Forest Res

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European beech (Fagus sylvatica L.) is one of the most important deciduous tree species in Central Europe. The potential of beech to adapt to climate change, higher temperatures, and less precipitation in the summer months is still unknown. Most studies in beech used microsatellite, AFLP (amplified fragment length polymorphism), or isozyme markers, which have only a restricted potential to analyze adaptation. Only few studies investigated genes probably involved in the adaptation to drought stress and bud phenology in beech. In this study, SNP (single nucleotide polymorphisms) markers were developed in order to analyze adaptation and their technical advantages compared to microsatellites and AFLPs were discussed. Partial sequences of ten candidate genes probably involved in drought stress and/or bud phenology were identified at the genomic level, and SNPs and indels (insertions/deletions) in coding and non-coding regions were analyzed. Plant material was sampled along a precipitation gradient in Germany. In total, 8,145 bp were sequenced and analyzed, 4,038 bp were located in exon and 4,107 bp in intron regions. 63 SNPs and 11 indels were detected, which are differently distributed over the studied gene regions. The nucleotide diversity ranged from 0 to 6.62 (p 9 10 -3 ) and is comparable to other tree species, whereas the mean nucleotide diversity (2.64) for F. sylvatica is comparatively low. These results will help to investigate the genetic basis of drought stress and bud burst and to conduct association mapping in natural populations. Furthermore, the detected SNPs can also be used for population genetic studies.

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Application of single nucleotide polymorphisms to non‐model species: a technical review

Cited by 188 publications

References 196 publications

Effects of salinity acclimation and eyestalk ablation on Na+, K+, 2Cl− cotransporter gene expression in the gill of Portunus trituberculatus:a molecular correlate for salt-tolerant trait

Effects of salinity acclimation and eyestalk ablation on Na+, K+, 2Cl− cotransporter gene expression in the gill of Portunus trituberculatus:a molecular correlate for salt-tolerant trait

Investigation of the genetic distances of bovids and cervids using BovineSNP50k BeadChip

DNA sequence variation and development of SNP markers in beech (Fagus sylvatica L.)

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