The SSR Null Allele Problem, and Its Consequences in Pedigree Reconstruction and Population Genetic Studies in Viticulture

Jahnke, Gizella; Smidla, József; Deák, Tamás; Oláh, Róbert; Szőke, Barna Árpád; Sárdy, Diána Ágnes Nyitrainé

doi:10.3390/horticulturae8070658

Horticulturae

2022

DOI: 10.3390/horticulturae8070658

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The SSR Null Allele Problem, and Its Consequences in Pedigree Reconstruction and Population Genetic Studies in Viticulture

Gizella Jahnke

József Smidla

Tamás Deák³

et al.

Abstract: Null alleles are alleles that are recessive to codominant markers without any effect on the phenotype. In SSR assays, there are several reasons for the lack of amplification at a locus: the primer does not bind well, longer fragments do not amplify due to imperfections in the PCR reaction, or the amount of DNA in the sample is insufficient. In microsatellite studies, null alleles are mostly used in pedigree analysis and population genetics calculations such as diversity estimation. Null alleles in pedigree ana… Show more

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Cited by 3 publications

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SSR marker-based individual identification system to trace illegal logging and geographic origin of teak (Tectona grandis L.f.) wood in India

Balakrishnan,

Unnikrishnan,

Ramasamy

et al. 2024

Forestry: An International Journal of Forest Research

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Illegal tree felling is one of the crucial problems in forestry worldwide. It is essential to develop adequate forensic techniques that can verify the origin of timber sourced at logging concessions. Teak wood—one of the most important timber species in India—is often illegally logged and also imported from other countries without certification. In our study, the best combination of Simple Sequence Repeat (SSR) markers identified was utilized for match testing the genetic profiles of seized and evidence woods. A genetic reference database was also developed to assign unknown wood samples to their source populations. Our results found a perfect match between the genetic profiles of seized wood and their respective evidence wood which ascertains the utility of genetic profiles as an efficient forensic tool. Further, efficiency of assignment tools based on different approaches such as distance-based, model-based and machine learning were tested. Mycorrhiza, a machine learning algorithm, was identified as the best assignment tool. However, only broad provenance-level assignment was possible due to the genetic admixture in a few natural teak populations. Mycorrhiza was then used to identify the origin of two plantations in India. The assignment test predicted that both the plantations had similar origin, having sourced seeds from multiple natural populations (through clonal seed orchards and seed production areas) and local populations in different ratio. The SSR markers and assignment tool from this study can be used as an effective forensic tool to curb illegal felling and to verify integrity of timber supply chains in India. Also, provenance-based assignment guarantees usage of these markers in a global scale. However, a collective global effort to develop and deposit a robust reference database in a common repository is a prerequisite to strengthen timber traceability worldwide.

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SSR marker-based individual identification system to trace illegal logging and geographic origin of teak (Tectona grandis L.f.) wood in India

Balakrishnan,

Unnikrishnan,

Ramasamy

et al. 2024

Forestry: An International Journal of Forest Research

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Morphological Traits Evaluated with Random Forest Method Explains Natural Classification of Grapevine (Vitis vinifera L.) Cultivars

Szűgyi-Reiczigel¹,

Ladányi²,

Bisztray

et al. 2022

Plants

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There are hundreds of morphologic and morphometric traits available to classify and identify grapevine (Vitis vinifera L.) genotypes, while statistical evaluation of those has certain limitations, especially when we have no information about the traits that are discriminative to a certain sample set. High numbers of investigated characters could cause redundancy, while reducing those numbers may result in data loss. Grapevine is one of the most important horticultural crops, with many cultivars in production. The characterization of the genotypes is of undeniably high importance. In this study, we analyzed a dataset of scientific and historical importance with 125 morphological traits of 97 grapevine cultivars described by Németh in 1966. However, the traits are not independent in a set of a large number of categorical traits with too few cultivars. Therefore, the number of traits was first reduced using a simple and effective algorithm to eliminate traits with redundant information content using the asymmetric measure of association Goodman and Kruskal’s λ. We reduced the number of traits from 125 to 59 without any information loss. For the classification, we applied a random forest (RF) method. In this way, 93% of the cultivars were correctly classified using only four traits of the data set. To our knowledge, only a few studies applied a trait elimination algorithm similar to ours in ampelography that can be used for other biological data sets of similar structure. The classification results give a morphological explanation to several cultivars from the Carpathian Basin, a territory where all three Vitis vinifera L. geographical groups, occidentalis, orientalis and pontica, are represented. We found that the information-loss-avoiding data reduction method we applied in our study solved the redundancy-caused interdependencies and provided a suitable dataset for classifying grapevine genotypes. For example, this method may successfully be applied in digital image analysis-based traditional morphometric investigations in ampelography.

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Cross species transferability of G-SSR and EST-SSR markers to Neltuma affinis Spreng.

Soldati,

Gavier-Pizarro,

Morales

et al. 2023

For. syst.

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Aim of study: To examine the transferability of G-SSR (genomic simple sequence repeats) and EST-SSR (expressed sequence tag simple sequence repeats) markers developed for several Neltuma species to N. affinis, a species with no genomic data. Area of study: West-Center of Entre Ríos province, Argentina. The set of molecular markers here proposed can be used to analyze samples from the entire species’ distribution range. Material and methods: Twenty-five genomic G-SSRs and eleven EST-SSRs from multiple species were amplified in thirty N. affinis genotypes. Polymorphism, discrimination power and possible deviations from Hardy-Weinberg equilibrium were assessed. Main results: Seventeen highly polymorphic G-SSRs were successfully transferred to N. affinis, with a PIC (polymorphic information content) average value of 0.811 and a He (expected heterozygosity) average value of 0.694; thirteen were validated, showing very low frequencies of null alleles and no linkage disequilibrium. Additionally, seven polymorphic EST-SSRs were transferred. As expected, PIC and He average values were low. Six out of seven markers were validated, and very low frequencies of null alleles and no linkage disequilibrium were observed. Research highlights: This work provides information on the levels of microsatellites’ cross transferability to N. affinis, and its polymorphism degree. Two sets of polymorphic SSRs (genomic and expressed) to study the genetic status of the species are proposed.

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The SSR Null Allele Problem, and Its Consequences in Pedigree Reconstruction and Population Genetic Studies in Viticulture

Cited by 3 publications

References 61 publications

SSR marker-based individual identification system to trace illegal logging and geographic origin of teak (Tectona grandis L.f.) wood in India

SSR marker-based individual identification system to trace illegal logging and geographic origin of teak (Tectona grandis L.f.) wood in India

Morphological Traits Evaluated with Random Forest Method Explains Natural Classification of Grapevine (Vitis vinifera L.) Cultivars

Cross species transferability of G-SSR and EST-SSR markers to Neltuma affinis Spreng.

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