Constructing <scp>STR</scp> Multiplexes for Individual Identification of Hungarian Red Deer

Szabolcsi, Zoltán; Egyed, Balázs; Zenke, Petra; Pádár, Zsolt; Borsy, Adrienn; Stéger, Viktor; Pasztor, Erzsebet; Csányi, Sándor; Buzás, Zsuzsanna; Orosz, László

doi:10.1111/1556-4029.12403

Cited by 22 publications

(33 citation statements)

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“…Being among the most important game animals for trophies, their populations have been managed, translocated and selectively hunted throughout their history and distribution area [26][27][28][29][30]. Recently a worldwide "deer industry" has been developed, whereby animals are farmed for venison and to some extent for antler products [31][32][33].…”

Section: Introductionmentioning

confidence: 99%

“…Genetic identification of red deer has become very important in forensic and population genetics as well as for wildlife conservation and parentage testing in animal breeding [25,31,34,35]. Although microsatellite markers have been used in red deer, genetic studies mostly rely on adopted STR markers originally developed in other cervids [31,35,36]. To date no reports on the development of microsatellite markers for red deer utilizing NGS technology and exploiting the sequence of the red deer genome have been published.…”

Section: Introductionmentioning

confidence: 99%

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Mining the red deer genome (CerEla1.0) to develop X-and Y-chromosome-linked STR markers

et al. 2020

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Microsatellites are widely applied in population and forensic genetics, wildlife studies and parentage testing in animal breeding, among others, and recently, high-throughput sequencing technologies have greatly facilitated the identification of microsatellite markers. In this study the genomic data of Cervus elaphus (CerEla1.0) was exploited, in order to identify microsatellite loci along the red deer genome and for designing the cognate primers. The bioinformatics pipeline identified 982,433 microsatellite motifs genome-wide, assorted along the chromosomes, from which 45,711 loci mapped to the X- and 1096 to the Y-chromosome. Primers were successfully designed for 170,873 loci, and validated with an independently developed autosomal tetranucleotide STR set. Ten X- and five Y-chromosome-linked microsatellites were selected and tested by two multiplex PCR setups on genomic DNA samples of 123 red deer stags. The average number of alleles per locus was 3.3, and the average gene diversity value of the markers was 0.270. The overall observed and expected heterozygosities were 0.755 and 0.832, respectively. Polymorphic Information Content (PIC) ranged between 0.469 and 0.909 per locus with a mean value of 0.813. Using the X- and Y-chromosome linked markers 19 different Y-chromosome and 72 X-chromosome lines were identified. Both the X- and the Y-haplotypes split to two distinct clades each. The Y-chromosome clades correlated strongly with the geographic origin of the haplotypes of the samples. Segregation and admixture of subpopulations were demonstrated by the use of the combination of nine autosomal and 16 sex chromosomal STRs concerning southwestern and northeastern Hungary. In conclusion, the approach demonstrated here is a very efficient method for developing microsatellite markers for species with available genomic sequence data, as well as for their use in individual identifications and in population genetics studies.

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Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Mining the red deer genome (CerEla1.0) to develop X-and Y-chromosome-linked STR markers

et al. 2020

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“…Other species groups may fulfill these criteria, for instance, marked salmonids (Gilbreath et al 1976); cetaceans individually recognized from scarring or coloration patterns (Constantine et al 2012, but see Carroll et al 2016 for a caveat of this technique for estimates including juvenile ageclasses); sea turtles, reptiles, and amphibians recognized by permanent marks (Spellerberg 1977, Balazs 1999, Waudby and Petit 2011; and any mammal species that may be tagged (Diefenbach and Alt 1998). Individual-precision genetic identification of individuals may allow this technique to be used without requiring the invasive marking of individuals (see Waits et al 2001, Banks et al 2003a, b, and Efford et al 2009), as genomic approaches can yield cost-effective, unambiguous recognition of individuals (Szabolcsi et al 2014, Ringler et al 2015, Woodruff et al 2015.…”

Section: Modelable Species Groupsmentioning

confidence: 99%

A model for first‐estimates of species‐specific, age‐specific mortality from centralized band‐recovery databases

2018

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Citation: Baylis, S. M., P. Sunnucks, and R. Clarke. 2018. A model for first-estimates of species-specific, age-specific mortality from centralized band-recovery databases. Ecosphere 9(4):e02136. 10.1002/ecs2.2136Abstract. Population mortality curves, otherwise known as lifetime distribution functions, can be indispensable in many areas of ecology and environmental management including population viability and stock management analyses, disaster-recovery monitoring, and fundamental evolutionary biology. Yet available modeling tools are often unable to estimate population mortality curves from commonly available datasets because these datasets fail to meet stringent experimental-design requirements. Here, we present a new method for estimating population mortality curves from records of marked individuals found dead. Such data are increasingly accessible in some of the largest biological datasets, such as continent-or nation-wide marking-and-recovery schemes for birds and other animals. The method accounts for known biases in availability by age class, variable monitoring effort through time, and mark loss. We show that our modeling approach generates accurate estimates of population mortality structure across a range of populations differing in marking histories, true mortality curves, monitoring regimes, and mark loss rates. Our approach can be applied to multiple species or groups at a time and can provide estimates of interannual adult, immature, and first-year survival rates, required by predictive modeling applications such as population viability analyses. Our approach is also capable of estimating apparent senescence rates for each population and facilitates evolutionary analyses of life-history traits. For example, our method is potentially useful for exploring the evolution of senescence or for inter-group comparisons of mortality rates where groups that differ by environment may be identified within mark-recovery records. To demonstrate the efficacy of this method, we present fitted population mortality curves for a suite of seabird species represented in a national mark-recapture database.

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“…Variation in the lengths of STRs can be detected using multiplex polymerase chain reaction (PCR) with fluorescently labelled primers that efficiently amplify polymorphic STRs. Multiplex STR typing systems have been established to identify individuals, and for paternity testing, in various mammals including horse , dog , boar , wolf , tiger and deer .…”

Section: Introductionmentioning

confidence: 99%

A novel 13‐plex STR typing system for individual identification and parentage testing of donkeys (Equus asinus)

Dang

Shang

Zhang

et al. 2019

Equine Veterinary Journal

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Summary Background Previous studies investigating donkey parentage and genetic diversity used horse‐specific multiplex systems. However, several mis‐allele and null‐allele issues were found with some of the horse primers when used in donkeys. In 2017, the International Society for Animal Genetics (ISAG) recommended 13 dinucleotide short tandem repeats (STRs) (AHT4, ASB23, HMS2, HMS3, HMS6, HMS7, HMS18, HTG7, HTG10, TKY297, TKY312, TKY337 and TKY343) as a core panel that should be used to identify individuals and to test for parentage in donkeys. To date, no single multiplex STR typing system containing all 13 donkey STRs recommended by the ISAG has been reported. Objectives To establish a novel and donkey‐specific multiplex STR typing system containing all 13 recommended STRs. Study design Assay development and validation in field population. Methods Primers for seven of the STRs were redesigned and conditions for polymerase chain reaction (PCR) were optimised. We analysed the allele sequences, sensitivity, species‐specificity and stutter ratios of this new system. Results A 13‐plex STR typing system for donkey was established. A full profile could be generated from a single PCR reaction using as little as 5 ng of DNA template with the 13 pairs of primers labelled with fluorescent dyes. An allele ladder, containing 101 alleles from the 13 STRs, was generated. No full genotype profile was generated with these primers if DNA from humans, or 11 other commonly encountered animals, was used. Genotypes could be generated for the horse and horse‐donkey hybrids (mule and hinny). Stutter ratios and population genetic parameters were calculated based on samples from 150 donkeys. The combined probabilities of paternity exclusion for this system were 0.988907326 (CPEduo) and 0.999665018 (CPEtrio). Main limitations This system cannot detect sex. Conclusions Our results indicate that our donkey‐specific 13‐plex STR typing system is sensitive, species‐specific and robust for individual identification, paternity testing and population genetic analysis in donkeys, and has potential forensic applications.

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Constructing STR Multiplexes for Individual Identification of Hungarian Red Deer

Cited by 22 publications

References 50 publications

Mining the red deer genome (CerEla1.0) to develop X-and Y-chromosome-linked STR markers

Mining the red deer genome (CerEla1.0) to develop X-and Y-chromosome-linked STR markers

A model for first‐estimates of species‐specific, age‐specific mortality from centralized band‐recovery databases

A novel 13‐plex STR typing system for individual identification and parentage testing of donkeys (Equus asinus)

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