Using Mendelian Inheritance To Improve High-Throughput SNP Discovery

Chen, Nancy; Hout, Cristopher V. Van; Gottipati, Srikanth; Clark, Andrew G.

doi:10.1534/genetics.114.169052

Cited by 35 publications

(36 citation statements)

References 50 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…To investigate the genomic contributions of immigrants to the study population, we genotyped 3,583 individuals at 15,416 single nucleotide polymorphisms (SNPs; see Supplemental Experimental Procedures) [13]. Here, autosomal SNPs were thinned to retain 7,834 SNPs in approximate linkage equilibrium.…”

Section: Resultsmentioning

confidence: 99%

See 1 more Smart Citation

Genomic Consequences of Population Decline in the Endangered Florida Scrub-Jay

et al. 2016

Self Cite

View full text Add to dashboard Cite

Summary Understanding the population genetic consequences of declining population size is important for conserving the many species worldwide facing severe decline [1]. Thorough empirical studies on the impacts of population reduction at a genome-wide scale in the wild are scarce because they demand huge field and laboratory investments [1, 2]. Previous studies have demonstrated the importance of gene flow in introducing genetic variation to small populations [3], but few have documented both genetic and fitness consequences of decreased immigration through time in a natural population [4-6]. Here we assess temporal variation in gene flow, inbreeding, and fitness using longitudinal genomic, demographic, and phenotypic data from a long-studied population of federally Threatened Florida Scrub-Jays (Aphelocoma coerulescens; hereafter FSJ). We exhaustively sampled and genotyped the study population over two decades, providing one of the most detailed longitudinal investigations of genetics in a wild animal population to date. Immigrants were less heterozygous than residents but still introduced genetic variation into our study population. Owing to regional population declines, immigration into the study population declined from 1995-2013, resulting in increased levels of inbreeding and reduced fitness via inbreeding depression, even as the population remained demographically stable. Our results show that, contrary to conventional wisdom, small peripheral populations that already have undergone a genetic bottleneck may play a vital role in preserving genetic diversity of larger and seemingly stable populations. These findings underscore the importance of investing in the persistence of small populations and maintaining population connectivity in conservation of fragmented species.

show abstract

Section: Resultsmentioning

confidence: 99%

“…We used genotypingby-sequencing of immigrants and residents from 1978–2008 to discover SNPs [13], then designed custom Illumina iSelect BeadChips for 15,416 genome-wide SNPs (Figure S1). We genotyped 4,032 samples at Geneseek, Inc. (Lincoln, NE).…”

Section: Methodsmentioning

confidence: 99%

Genomic Consequences of Population Decline in the Endangered Florida Scrub-Jay

et al. 2016

Self Cite

View full text Add to dashboard Cite

show abstract

“…; Chen et al . ). To generate a SNP genotyping panel like the one described here, SNPs of interest must be surrounded by adequate flanking sequence for primer or probe design; such sequence is usually not generated by RAD‐seq or GBS unless paired‐end sequencing is conducted.…”

Section: Discussionmentioning

confidence: 97%

A comparative assessment ofSNPand microsatellite markers for assigning parentage in a socially monogamous bird

Kaiser

Taylor

Chen

et al. 2016

Molecular Ecology Resources

Self Cite

View full text Add to dashboard Cite

Single-nucleotide polymorphisms (SNPs) are preferred over microsatellite markers in many evolutionary studies, but have only recently been applied to studies of parentage. Evaluations of SNPs and microsatellites for assigning parentage have mostly focused on special cases that require a relatively large number of heterozygous loci, such as species with low genetic diversity or with complex social structures. We developed 120 SNP markers from a transcriptome assembled using RNA-sequencing of a songbird with the most common avian mating system-social monogamy. We compared the effectiveness of 97 novel SNPs and six previously described microsatellites for assigning paternity in the black-throated blue warbler, Setophaga caerulescens. We show that the full panel of 97 SNPs (mean H = 0.19) was as powerful for assigning paternity as the panel of multiallelic microsatellites (mean H = 0.86). Paternity assignments using the two marker types were in agreement for 92% of the offspring. Filtering individual samples by a 50% call rate and SNPs by a 75% call rate maximized the number of offspring assigned with 95% confidence using SNPs. We also found that the 40 most heterozygous SNPs (mean H = 0.37) had similar power to assign paternity as the full panel of 97 SNPs. These findings demonstrate that a relatively small number of variable SNPs can be effective for parentage analyses in a socially monogamous species. We suggest that the development of SNP markers is advantageous for studies that require high-throughput genotyping or that plan to address a range of ecological and evolutionary questions.

show abstract

“…; Haaland & Skaug ; Chen et al . ) provides a cost–effective alternative to sequencing the same individuals multiple times (He et al . ; Mastretta‐Yanes et al .…”

Section: Introductionmentioning

confidence: 99%

Finding the right coverage: the impact of coverage and sequence quality on single nucleotide polymorphism genotyping error rates

Fountain

Pauli

Reid

et al. 2016

Molecular Ecology Resources

View full text Add to dashboard Cite

Restriction-enzyme-based sequencing methods enable the genotyping of thousands of single nucleotide polymorphism (SNP) loci in nonmodel organisms. However, in contrast to traditional genetic markers, genotyping error rates in SNPs derived from restriction-enzyme-based methods remain largely unknown. Here, we estimated genotyping error rates in SNPs genotyped with double digest RAD sequencing from Mendelian incompatibilities in known mother-offspring dyads of Hoffman's two-toed sloth (Choloepus hoffmanni) across a range of coverage and sequence quality criteria, for both reference-aligned and de novo-assembled data sets. Genotyping error rates were more sensitive to coverage than sequence quality and low coverage yielded high error rates, particularly in de novo-assembled data sets. For example, coverage ≥5 yielded median genotyping error rates of ≥0.03 and ≥0.11 in reference-aligned and de novo-assembled data sets, respectively. Genotyping error rates declined to ≤0.01 in reference-aligned data sets with a coverage ≥30, but remained ≥0.04 in the de novo-assembled data sets. We observed approximately 10- and 13-fold declines in the number of loci sampled in the reference-aligned and de novo-assembled data sets when coverage was increased from ≥5 to ≥30 at quality score ≥30, respectively. Finally, we assessed the effects of genotyping coverage on a common population genetic application, parentage assignments, and showed that the proportion of incorrectly assigned maternities was relatively high at low coverage. Overall, our results suggest that the trade-off between sample size and genotyping error rates be considered prior to building sequencing libraries, reporting genotyping error rates become standard practice, and that effects of genotyping errors on inference be evaluated in restriction-enzyme-based SNP studies.

show abstract

Using Mendelian Inheritance To Improve High-Throughput SNP Discovery

Cited by 35 publications

References 50 publications

Genomic Consequences of Population Decline in the Endangered Florida Scrub-Jay

Genomic Consequences of Population Decline in the Endangered Florida Scrub-Jay

A comparative assessment ofSNPand microsatellite markers for assigning parentage in a socially monogamous bird

Finding the right coverage: the impact of coverage and sequence quality on single nucleotide polymorphism genotyping error rates

Contact Info

Product

Resources

About