Parentage assignment using microsatellite DNA typing for the endangered numbat (Myrmecobius fasciatus)

The numbat (Myrmecobius fasciatus) is an endangered and peculiar marsupial with a diet that consists almost exclusively of termites. This study developed a parentage-testing system for numbats using microsatellite markers. Nineteen loci detected 143 alleles, with 4–13 alleles/locus and average expected heterozygosity of 77% (range 0.665–0.855). The total parentage exclusion probability was >0.9999 (given only the genotype of the offspring), >0.9999 for excluding a candidate parent from the parentage of an arbitrary offspring (given the genotype of the offspring and parent) and the probability of identity for full-sibs was 4.6×10–9. Overall, these microsatellites offer a simple and highly informative marker-set for parentage identification in numbats.

Fifteen novel microsatellites for the Louisiana Waterthrush (Aves: Parulidae: Parkesia motacilla) using MiSeq sequencing

The Louisiana Waterthrush (Parkesia motacilla) breeds along wooded streams throughout much of eastern North America, and winters in the Caribbean and Central America. Because of its dependence on stream macroinvertebrates—which are themselves dependent on high water quality—the Louisiana Waterthrush may serve as a useful bioindicator of both stream and landscape integrity. Perhaps unique among eastern North American songbirds, the Louisiana Waterthrush often maintains essentially linear territories along streams, and this provides a unique context in which to ask questions about the genetic (as opposed to social) mating system of this species. We developed 15 microsatellite loci for Louisiana Waterthrush using MiSeq sequencing. All loci presented here are polymorphic, with 3-15 alleles detected in a reference sample of 35-43 individuals. For parentage analyses, these loci have a combined non-exclusion probability of 0.0011 if neither parent is known a priori, and a non-exclusion probability of < 0.0001 if one parent is known. These 15 loci thus provide high discriminatory power to assign parentage to nestlings, and can also be used to examine population genetic structure within the species.

Fifteen novel microsatellites for the Louisiana Waterthrush (Aves: Parulidae: Parkesia motacilla) using MiSeq sequencing

The Louisiana Waterthrush (Parkesia motacilla) breeds along wooded streams throughout much of eastern North America, and winters in the Caribbean and Central America. Because of its dependence on stream macroinvertebrates—which are themselves dependent on high water quality—the Louisiana Waterthrush may serve as a useful bioindicator of both stream and landscape integrity. Perhaps unique among eastern North American songbirds, the Louisiana Waterthrush often maintains essentially linear territories along streams, and this provides a unique context in which to ask questions about the genetic (as opposed to social) mating system of this species. We developed 15 microsatellite loci for Louisiana Waterthrush using MiSeq sequencing. All loci presented here are polymorphic, with 3-15 alleles detected in a reference sample of 35-43 individuals. For parentage analyses, these loci have a combined non-exclusion probability of 0.0011 if neither parent is known a priori, and a non-exclusion probability of < 0.0001 if one parent is known. These 15 loci thus provide high discriminatory power to assign parentage to nestlings, and can also be used to examine population genetic structure within the species.

Looking for breed differentiating SNP loci and for a SNP set for parentage testing in Mangalica

The whole genome of Mangalica animals has been screened on the Illumina porcine chip giving the possibility (1) to replace the previously applied ten microsatellite markers by nine SNP loci to classify the Blond, Swallow-Belly and Red Mangalica individuals into three different breed groups (P>0.95); (2) to propose 54 SNP loci for parentage testing in Mangalica pigs where the exclusion probability is 0.999115 if one parent is known and the probability of identity is 1.54×10-23.

Evaluation of parentage testing in the Czech population of Holsteincattle

A set of 233 Holstein calves, their 233 dams and 44 sires from 4 large-sized herds was genotyped for 10 microsatellites recommended by ISAG for paternity/parentage testing. Heterozygosity of microsatellites ranged from 0.607 (SPS115) to 0.835 (TGLA227), and PIC from 0.575 (SPS115) to 0.816 (TGLA227) confirming a high polymorphism of each analysed locus. Their combined exclusion probability reached 0.999, which made them suitable and sufficiently accurate for parentage testing. A conflict between putative parents and calf in at least 2 markers with combined exclusion probability &gt; 0.9 was required to reject parentage. The pedigree was considered incorrect in 25 (10.73%) out of the evaluated progeny/parent trios, of which in 10 samples the genotype of both parents did not match their offspring, and in 2 samples the putative dam was in conflict with the calf genotype. This result shows that the interchange of calves on farms with large-sized herds plays the role as important as the errors in sire identification, or recording mistakes. &nbsp;

Microsatellite panels suggested for parentage testing in cattle: informativeness revealed in Finnish Ayrshire and Holstein-Friesian populations (Research Note)

Informativeness of eleven microsatellite markers suggested for parentage control in cattle by the International Society for Animal Genetics (ISAG) was studied in Finnish Ayrshire and Holstein-Friesian populations. Calculations were based on a sample of 100 non-sib artificial insemination bulls. Assuming one known parent the nine loci suggested for routine testing exhibited exclusion probabilities of 99.84% in the Ayrshires and 99.91% in the Holstein-Friesians. The addition of markers INRA23 and TGLA53, recommended for further investigations, increased the attained values to 99.94% in Ayrshires and to 99.98% in Holstein-Friesians. The recommended core set of six microsatellites provided a combined exclusion probability of 98.25% in Ayrshires and 99.32% in Holstein-Friesians. Although the combined values were high in general, a relatively low level of polymorphism was detected in some instances.;

Paternity Analysis in Higher Polyploids

The breeding of new sweetpotato varieties is a highly inefficient process, confounded by incompatibility, poor fertility, open-pollination, and its hexaploid nature. Upwards of 12 to 20 lines are currently combined in open-pollinated nurseries based on good horticultural characteristics. Most progeny after several years of selection can be traced back to just three or four maternal lines. A method that would identify the paternal parent of superior progeny would enable breeders the ability to combine parents that exhibit superior combining ability in more-efficient, smaller nurseries. The objective of this work is to explore by means of computer simulation the application of genealogy reconstruction techniques on hexaploid individuals with PCR-based data. The progeny obtained on each female parent is fractionally assigned to each male with non zero exclusion probability proportional to its paternity likelihood. Computer simulations show that at least five different alleles per loci are needed to reach a reasonable discriminatory level. Also, the number of loci scored should not be less than 20. An increment in the number of alleles or loci increases the discriminatory power; but, the number of alleles produces a far more important effect than the number of loci.