Microhaplotype genotyping-by-sequencing of 98 highly polymorphic markers in three chestnut tree species

Laurent, Benoit; Larue, Clément; Chancerel, Émilie; Guichoux, Erwan; Petit, Rémy J.; Barreneche, Teresa; Robin, Cécile; Lepais, Olivier

doi:10.1007/s12686-020-01157-5

Cited by 5 publications

(4 citation statements)

References 16 publications

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“…The mean ampli cation rate was 99.9% (97.8-100%) per SNP locus and 99.9% (98.7-100%) per sample. By contrast, the mean ampli cation rate was 92.2% (76.9-100%) per SSR locus and 91.7% (41.5-100%) per sample (Laurent et al 2020).…”

Section: Introductionmentioning

confidence: 85%

“…A number of molecular markers have been previously developed in chestnuts, especially SSRs (e.g. Buck et al 2003;Marinoni et al 2003;Durand et al 2010;Fernández-Cruz and Fernández-López 2012;Pereira-Lorenzo et al 2017;Bouffartigue et al 2020;Laurent et al 2020;Nishio et al 2021). However, SNPs have some important advantages over SSRs (Guichoux et al 2011).…”

Section: Introductionmentioning

confidence: 99%

“…To evaluate the utility of these markers for species and hybrid identi cation, we used the Bayesian clustering analysis software Structure (Pritchard et al 2000) and compared the results with those obtained with SSRs (Laurent et al 2020). A total of 91 unique genotypes were characterized with both types of markers and used for the comparison (Larue 2021, Files 3 and 4; Supplementary 3).…”

Section: Introductionmentioning

confidence: 99%

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Development of Highly Validated SNP Markers for Genetics Analyses of Chestnut Species.

Larue

Guichoux

Laurent

et al. 2021

Preprint

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To better study and manage chestnut trees and species, we identified nuclear single nucleotide polymorphism (SNP) markers using restriction-associated DNA sequencing. Out of 343 loci tested, 68 SNP markers were selected that withhold stringent quality criteria such as quasi-systematic amplification across species and Mendelian segregation in both purebred and hybrid individuals. They provide sufficient power for species, hybrids and backcross characterization as well as for clonal identification, as shown by a comparison with single sequenced repeat (SSR) loci.

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Section: Introductionmentioning

confidence: 85%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Development of Highly Validated SNP Markers for Genetics Analyses of Chestnut Species.

Larue

Guichoux

Laurent

et al. 2021

Preprint

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“…So, the microhaplotype loci established on the basis of nonbinary SNP and piSNP may be very useful forensic multifunctional markers. However, most other previously published microhaplotype panels were focused on the flanking region variations of the ancestry-informative SNP (aiSNP) and binary iiSNP [15][16][17][18][19][20][21][22][23][24][25][26][27][28][29][30]. So, the increased polymorphism and forensic applications of microhaplotype loci based on nonbinary SNP and piSNP should be further investigated.…”

Section: Introductionmentioning

confidence: 99%

Considering the flanking region variants of nonbinary SNP and phenotype‐informative SNP to constitute 30 microhaplotype loci for increasing the discriminative ability of forensic applications

et al. 2021

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The flanking region variants of nonbinary SNPs and phenotype-informative SNPs (piS-NPs) have been observed, which may greatly improve the discriminative ability after constituting microhaplotype. In this study, 30 microhaplotype loci based on the nonbinary SNPs and piSNPs (shown to be related to phenotypes such as hair and eye color) were selected. Genotyping were conducted on 100 unrelated northern Han Chinese, and the 26 populations from the 1000 Genome Project were also included for comparison of populations differentiation. The simulated study was conducted for evaluating the efficiency of kinship testing. These 30 microhaplotype loci we selected had good polymorphism, with a mean effective number of alleles (Ae) of 3.46. The average Ae increase was 1.27 compared with the target SNPs. The populations from the five regions worldwide could also be distinguished using these loci. The results of kinship testing showed that these microhaplotype loci had the similar ability as 15 STR loci of AmpFlSTR R Identifiler R PCR Amplification Kit to identify the biological parent and a stronger ability to exclude the nonbiological parents. So, these 30 microhaplotype loci may be multifunctional for forensic application, including the ability of personal identification and kinship testing equivalent to 15 STR loci, and the power of ancestry inference for distinguishing the main intercontinental population. Moreover, our selected phenotypic microhaplotype loci may theoretically have phenotype prediction capabilities. But the phenotype prediction efficiency of these phenotypic microhaplotype loci may be worse than that of piSNPs and the detailed prediction accuracy of different populations needs to be further studied.

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Development of highly validated SNP markers for genetic analyses of chestnut species

Larue

Guichoux

Laurent

et al. 2021

Conservation Genet Resour

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Microhaplotype genotyping-by-sequencing of 98 highly polymorphic markers in three chestnut tree species

Cited by 5 publications

References 16 publications

Development of Highly Validated SNP Markers for Genetics Analyses of Chestnut Species.

Development of Highly Validated SNP Markers for Genetics Analyses of Chestnut Species.

Considering the flanking region variants of nonbinary SNP and phenotype‐informative SNP to constitute 30 microhaplotype loci for increasing the discriminative ability of forensic applications

Development of highly validated SNP markers for genetic analyses of chestnut species

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