Molecular Markers for Genetic Diversity

Burg, K.

doi:10.1007/124_2017_9

Cited by 3 publications

(2 citation statements)

References 47 publications

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“…SNPs are usually biallelic as co-dominant markers, and less informative compared with that of highly polymorphic microsatellites, but this can be compensated for by employing large numbers of markers (e.g., SNP chips) or WGS [74,75]. Microsatellite markers are co-dominant, multi-allelic, highly polymorphic, relatively evenly spaced throughout genomes, and require low quality template DNA input (10-100 ng); but they are time-consuming and expensive to develop, and require technical expertise or uorescently labelled primers for simple sequence repeats (SSR) analysis and high-resolution agarose or polyacrylamide gel separation [76][77][78][79][80][81]. By contrast, SINE RIPs are biallelic, co-dominant, highly polymorphic, give accurate and reproducible results, and exhibit high coverage and an even distribution among mammal genomes, suggesting great potential as genetic markers.…”

Section: Application Of Sine Rips In Population Genetic Analysismentioning

confidence: 99%

SINE jumping contributes to large-scale polymorphisms in the pig genomes

D’Alessandro

Muráni

Zheng

et al. 2021

Preprint

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Background: Molecular markers based on retrotransposon insertion polymorphisms (RIPs) have been developed and are widely used in plants and animals. Short interspersed nuclear elements (SINEs) exert wide impacts on gene activity and even on phenotypes. However, SINE RIP profiles in livestock remain largely unknown, and not be revealed in pigs. Results: Our data revealed that SINEA1 displayed the most polymorphic insertions (22.5% intragenic and 26.5% intergenic), followed by SINEA2 (10.5% intragenic and 9% intergenic) and SINEA3 (12.5% intragenic and 5.0% intergenic). We developed a genome-wide SINE RIP mining protocol and obtained a large number of SINE RIPs (36,284), with over 80% accuracy and an even distribution in chromosomes (14.5/Mb), and 74.34% of SINE RIPs generated by SINEA1 element. Over 65% of pig SINE RIPs overlap with genes, with significant enrichment in the first and second introns of protein-coding and long non-coding RNA genes. Nearly half of the RIPs are common in these pig breeds. Sixteen SINE RIPs were applied for population genetic analysis in 23 pig breeds, the phylogeny tree and cluster analysis were generally consistent with the geographical distributions of native pig breeds in China. Conclusions: Our analysis revealed that SINEA1–3 elements, particularly SINEA1, are high polymorphic across different pig breeds, and generate large-scale structural variations in the pig genomes. And over 35, 000 SINE RIP markers were obtained. These data indicate that young SINE elements play important roles in creating new genetic variations and shaping the evolution of pig genome, and also provide strong evidences to support the great potential of SINE RIPs as genetic markers, which can be used for population genetic analysis and quantitative trait locus (QTL) mapping in pig.

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Section: Application Of Sine Rips In Population Genetic Analysismentioning

confidence: 99%

SINE jumping contributes to large-scale polymorphisms in the pig genomes

D’Alessandro

Muráni

Zheng

et al. 2021

Preprint

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“…The chloroplast genome is highly conserved throughout all plant species due to the absence of recombination. Several sequences will act as "repetitive" DNA in whole DNA preparations because the cpDNA in the cell has a high copy number and makes up between 10% and 15% of the total DNA [14]. Chloroplast DNA is commonly used for molecular identification today.…”

Section: Introductionmentioning

confidence: 99%

Biochemical and molecular identification of ten plum (Prunus salicina L.) cultivars in Egypt based on their physiological traits, chloroplast and mitochondrial DNA markers

Al-Agwany,

Said,

Mohamed

et al. 2023

Journal of Scientific Research in Science

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Plum (Prunus salicina L.) includes more than 20 species with morphological variations, a wide genetic variety and nutrient qualities that are beneficial to human health. The properties of plum fruit cultivars that are influenced by their genetic profile can be used for effective evaluation. In order to identify chemical constituents and genetic relations among ten plum cultivars grown in Egypt, studies were carried out on the chlorophyll in leaves, some physiological characteristics of fruits, chloroplast (cpDNA) and mitochondrial DNA (mtDNA). Significant differences were observed in chlorophyll a, chlorophyll b and carotenoids in plum leaves, as well as total sugar, total soluble solids (TSS), pH and titratable acidity (TA) among plum cultivars. Five cpDNA regions (trnL, trnL-trnF, trnH-psbA, matK and rbcL) and two mtDNA regions (nad4 and nad9) were amplified. Among the loci, the PCR success rate varied greatly; the locus nad4 in the mitochondria had the greatest success rate 100 % followed by the chloroplast loci rbcL and matK 60%, then (trn L, trnL-trnF, trnH-psbA and nad9) with a success amplified rate of 50%. This study supports the applicability of the cpDNA and mtDNA markers to detect and identify the cytoplasmic variation in plum trees. The study will contribute to the knowledge about Prunus salicina cultivars and will be helpful in expanding the plum gene pool, which can be utilized in future plant breeding programs for the improvement of existing plum cultivars.

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SINE jumping contributes to large-scale polymorphisms in the pig genomes

et al. 2021

View full text Add to dashboard Cite

Background Molecular markers based on retrotransposon insertion polymorphisms (RIPs) have been developed and are widely used in plants and animals. Short interspersed nuclear elements (SINEs) exert wide impacts on gene activity and even on phenotypes. However, SINE RIP profiles in livestock remain largely unknown, and not be revealed in pigs. Results Our data revealed that SINEA1 displayed the most polymorphic insertions (22.5 % intragenic and 26.5 % intergenic), followed by SINEA2 (10.5 % intragenic and 9 % intergenic) and SINEA3 (12.5 % intragenic and 5.0 % intergenic). We developed a genome-wide SINE RIP mining protocol and obtained a large number of SINE RIPs (36,284), with over 80 % accuracy and an even distribution in chromosomes (14.5/Mb), and 74.34 % of SINE RIPs generated by SINEA1 element. Over 65 % of pig SINE RIPs overlap with genes, most of them (> 95 %) are in introns. Overall, about one forth (23.09 %) of the total genes contain SINE RIPs. Significant biases of SINE RIPs in the transcripts of protein coding genes were observed. Nearly half of the RIPs are common in these pig breeds. Sixteen SINE RIPs were applied for population genetic analysis in 23 pig breeds, the phylogeny tree and cluster analysis were generally consistent with the geographical distributions of native pig breeds in China. Conclusions Our analysis revealed that SINEA1–3 elements, particularly SINEA1, are high polymorphic across different pig breeds, and generate large-scale structural variations in the pig genomes. And over 35,000 SINE RIP markers were obtained. These data indicate that young SINE elements play important roles in creating new genetic variations and shaping the evolution of pig genome, and also provide strong evidences to support the great potential of SINE RIPs as genetic markers, which can be used for population genetic analysis and quantitative trait locus (QTL) mapping in pig.

show abstract

Molecular Markers for Genetic Diversity

Cited by 3 publications

References 47 publications

SINE jumping contributes to large-scale polymorphisms in the pig genomes

SINE jumping contributes to large-scale polymorphisms in the pig genomes

Biochemical and molecular identification of ten plum (Prunus salicina L.) cultivars in Egypt based on their physiological traits, chloroplast and mitochondrial DNA markers

SINE jumping contributes to large-scale polymorphisms in the pig genomes

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