Design and performance of a bovine 200 k SNP chip developed for endangered German Black Pied cattle (DSN)

Abstract Background German Black Pied cattle (DSN) are an endangered dual-purpose breed which was largely replaced by Holstein cattle due to their lower milk yield. DSN cattle are kept as a genetic reserve with a current herd size of around 2500 animals. The ability to track sequence variants specific to DSN could help to support the conservation of DSN’s genetic diversity and to provide avenues for genetic improvement. Results Whole-genome sequencing data of 304 DSN cattle were used to design a customized DSN200k SNP chip harboring 182,154 variants (173,569 SNPs and 8585 indels) based on ten selection categories. We included variants of interest to DSN such as DSN unique variants and variants from previous association studies in DSN, but also variants of general interest such as variants with predicted consequences of high, moderate, or low impact on the transcripts and SNPs from the Illumina BovineSNP50 BeadChip. Further, the selection of variants based on haplotype blocks ensured that the whole-genome was uniformly covered with an average variant distance of 14.4 kb on autosomes. Using 300 DSN and 162 animals from other cattle breeds including Holstein, endangered local cattle populations, and also a Bos indicus breed, performance of the SNP chip was evaluated. Altogether, 171,978 (94.31%) of the variants were successfully called in at least one of the analyzed breeds. In DSN, the number of successfully called variants was 166,563 (91.44%) while 156,684 (86.02%) were segregating at a minor allele frequency > 1%. The concordance rate between technical replicates was 99.83 ± 0.19%. Conclusion The DSN200k SNP chip was proved useful for DSN and other Bos taurus as well as one Bos indicus breed. It is suitable for genetic diversity management and marker-assisted selection of DSN animals. Moreover, variants that were segregating in other breeds can be used for the design of breed-specific customized SNP chips. This will be of great value in the application of conservation programs for endangered local populations in the future.

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Whole genome sequencing reveals high differentiation, low levels of genetic diversity and short runs of homozygosity among Swedish wels catfish

Heredity ◽

10.1038/s41437-021-00438-5 ◽

2021 ◽

Author(s):

Axel Jensen ◽

Mette Lillie ◽

Kristofer Bergström ◽

Per Larsson ◽

Jacob Höglund

Keyword(s):

Genetic Diversity ◽

Whole Genome Sequencing ◽

Genome Sequencing ◽

Whole Genome Sequencing Data ◽

Peripheral Populations ◽

Whole Genome ◽

Runs Of Homozygosity ◽

Sequencing Data ◽

Isolated Populations ◽

Native Populations

AbstractThe use of genetic markers in the context of conservation is largely being outcompeted by whole-genome data. Comparative studies between the two are sparse, and the knowledge about potential effects of this methodology shift is limited. Here, we used whole-genome sequencing data to assess the genetic status of peripheral populations of the wels catfish (Silurus glanis), and discuss the results in light of a recent microsatellite study of the same populations. The Swedish populations of the wels catfish have suffered from severe declines during the last centuries and persists in only a few isolated water systems. Fragmented populations generally are at greater risk of extinction, for example due to loss of genetic diversity, and may thus require conservation actions. We sequenced individuals from the three remaining native populations (Båven, Emån, and Möckeln) and one reintroduced population of admixed origin (Helge å), and found that genetic diversity was highest in Emån but low overall, with strong differentiation among the populations. No signature of recent inbreeding was found, but a considerable number of short runs of homozygosity were present in all populations, likely linked to historically small population sizes and bottleneck events. Genetic substructure within any of the native populations was at best weak. Individuals from the admixed population Helge å shared most genetic ancestry with the Båven population (72%). Our results are largely in agreement with the microsatellite study, and stresses the need to protect these isolated populations at the northern edge of the distribution of the species.

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Population Genomics of American Mink Using Whole Genome Sequencing Data

Genes ◽

10.3390/genes12020258 ◽

2021 ◽

Vol 12 (2) ◽

pp. 258

Author(s):

Karim Karimi ◽

Duy Ngoc Do ◽

Mehdi Sargolzaei ◽

Younes Miar

Keyword(s):

Population Genomics ◽

Association Studies ◽

American Mink ◽

Population History ◽

Whole Genome Sequencing Data ◽

Whole Genome ◽

Nucleotide Polymorphisms ◽

Sequencing Data ◽

Effective Population ◽

Cross Validation Error

Characterizing the genetic structure and population history can facilitate the development of genomic breeding strategies for the American mink. In this study, we used the whole genome sequences of 100 mink from the Canadian Centre for Fur Animal Research (CCFAR) at the Dalhousie Faculty of Agriculture (Truro, NS, Canada) and Millbank Fur Farm (Rockwood, ON, Canada) to investigate their population structure, genetic diversity and linkage disequilibrium (LD) patterns. Analysis of molecular variance (AMOVA) indicated that the variation among color-types was significant (p < 0.001) and accounted for 18% of the total variation. The admixture analysis revealed that assuming three ancestral populations (K = 3) provided the lowest cross-validation error (0.49). The effective population size (Ne) at five generations ago was estimated to be 99 and 50 for CCFAR and Millbank Fur Farm, respectively. The LD patterns revealed that the average r2 reduced to <0.2 at genomic distances of >20 kb and >100 kb in CCFAR and Millbank Fur Farm suggesting that the density of 120,000 and 24,000 single nucleotide polymorphisms (SNP) would provide the adequate accuracy of genomic evaluation in these populations, respectively. These results indicated that accounting for admixture is critical for designing the SNP panels for genotype-phenotype association studies of American mink.

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Quantifying the mapping precision of genome-wide association studies using whole-genome sequencing data

Genome Biology ◽

10.1186/s13059-017-1216-0 ◽

2017 ◽

Vol 18 (1) ◽

Cited By ~ 46

Author(s):

Yang Wu ◽

Zhili Zheng ◽

Peter M. Visscher ◽

Jian Yang

Keyword(s):

Whole Genome Sequencing ◽

Genome Sequencing ◽

Association Studies ◽

Genome Wide Association ◽

Whole Genome Sequencing Data ◽

Genome Wide Association Studies ◽

Whole Genome ◽

Sequencing Data ◽

Genome Wide

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Population-level genome-wide STR typing in Plasmodium species reveals higher resolution population structure and genetic diversity relative to SNP typing

10.1101/2021.05.19.444768 ◽

2021 ◽

Author(s):

Jiru Han ◽

Jacob E Munro ◽

Anthony Kocoski ◽

Alyssa E Barry ◽

Melanie Bahlo

Keyword(s):

Genetic Diversity ◽

Large Scale ◽

Tandem Repeats ◽

Plasmodium Species ◽

Whole Genome Sequence ◽

Whole Genome Sequencing Data ◽

Whole Genome ◽

Sequencing Data ◽

Genome Wide ◽

Field Samples

Short tandem repeats (STRs) are highly informative genetic markers that have been used extensively in population genetics analysis. They are an important source of genetic diversity and can also have functional impact. Despite the availability of bioinformatic methods that permit large-scale genome-wide genotyping of STRs from whole genome sequencing data, they have not previously been applied to sequencing data from large collections of malaria parasite field samples. Here, we have genotyped STRs using HipSTR in more than 3,000 Plasmodium falciparum and 174 Plasmodium vivax published whole-genome sequence data from samples collected across the globe. High levels of noise and variability in the resultant callset necessitated the development of a novel method for quality control of STR genotype calls. A set of high-quality STR loci (6,768 from P. falciparum and 3,496 from P. vivax) were used to study Plasmodium genetic diversity, population structures and genomic signatures of selection and these were compared to genome-wide single nucleotide polymorphism (SNP) genotyping data. In addition, the genome-wide information about genetic variation and other characteristics of STRs in P. falciparum and P. vivax have been made available in an interactive web-based R Shiny application PlasmoSTR (https://github.com/bahlolab/PlasmoSTR).

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Novel functional sequences uncovered through a bovine multiassembly graph

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.2101056118 ◽

2021 ◽

Vol 118 (20) ◽

pp. e2101056118

Author(s):

Danang Crysnanto ◽

Alexander S. Leonard ◽

Zih-Hua Fang ◽

Hubert Pausch

Keyword(s):

Genetic Diversity ◽

Reference Genome ◽

Bos Taurus ◽

Whole Genome Sequencing Data ◽

Whole Genome ◽

Sequencing Data ◽

Reference Allele ◽

Genomic Analyses ◽

Reference Quality ◽

Reference Genomes

Many genomic analyses start by aligning sequencing reads to a linear reference genome. However, linear reference genomes are imperfect, lacking millions of bases of unknown relevance and are unable to reflect the genetic diversity of populations. This makes reference-guided methods susceptible to reference-allele bias. To overcome such limitations, we build a pangenome from six reference-quality assemblies from taurine and indicine cattle as well as yak. The pangenome contains an additional 70,329,827 bases compared to the Bos taurus reference genome. Our multiassembly approach reveals 30 and 10.1 million bases private to yak and indicine cattle, respectively, and between 3.3 and 4.4 million bases unique to each taurine assembly. Utilizing transcriptomes from 56 cattle, we show that these nonreference sequences encode transcripts that hitherto remained undetected from the B. taurus reference genome. We uncover genes, primarily encoding proteins contributing to immune response and pathogen-mediated immunomodulation, differentially expressed between Mycobacterium bovis–infected and noninfected cattle that are also undetectable in the B. taurus reference genome. Using whole-genome sequencing data of cattle from five breeds, we show that reads which were previously misaligned against the Bos taurus reference genome now align accurately to the pangenome sequences. This enables us to discover 83,250 polymorphic sites that segregate within and between breeds of cattle and capture genetic differentiation across breeds. Our work makes a so-far unused source of variation amenable to genetic investigations and provides methods and a framework for establishing and exploiting a more diverse reference genome.

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Genetic Diversity of Meningococcal Serogroup B Vaccine Antigens among Carriage Isolates Collected from Students at Three Universities in the United States, 2015–2016

mBio ◽

10.1128/mbio.00855-21 ◽

2021 ◽

Vol 12 (3) ◽

Author(s):

Henju Marjuki ◽

How-Yi Chang ◽

Nadav Topaz ◽

Melissa J. Whaley ◽

Jeni Vuong ◽

...

Keyword(s):

Genetic Diversity ◽

Whole Genome Sequencing ◽

Genome Sequencing ◽

Disease Outbreaks ◽

Factor H ◽

Vaccine Antigen ◽

Whole Genome Sequencing Data ◽

Whole Genome ◽

Sequencing Data ◽

Vaccine Antigens

ABSTRACT Carriage evaluations were conducted during 2015 to 2016 at two U.S. universities in conjunction with the response to disease outbreaks caused by Neisseria meningitidis serogroup B and at a university where outbreak and response activities had not occurred. All eligible students at the two universities received the serogroup B meningococcal factor H binding protein vaccine (MenB-FHbp); 5.2% of students (181/3,509) at one university received MenB-4C. A total of 1,514 meningococcal carriage isolates were obtained from 8,905 oropharyngeal swabs from 7,001 unique participants. Whole-genome sequencing data were analyzed to understand MenB-FHbp’s impact on carriage and antigen genetic diversity and distribution. Of 1,422 isolates from carriers with known vaccination status (726 [51.0%] from MenB-FHbp-vaccinated, 42 [3.0%] from MenB-4C-vaccinated, and 654 [46.0%] from unvaccinated participants), 1,406 (98.9%) had intact fHbp alleles (716 from MenB-FHbp-vaccinated participants). Of 726 isolates from MenB-FHbp-vaccinated participants, 250 (34.4%) harbored FHbp peptides that may be covered by MenB-FHbp. Genogroup B was detected in 122/1,422 (8.6%) and 112/1,422 (7.9%) isolates from MenB-FHbp-vaccinated and unvaccinated participants, respectively. FHbp subfamily and peptide distributions between MenB-FHbp-vaccinated and unvaccinated participants were not statistically different. Eighteen of 161 MenB-FHbp-vaccinated repeat carriers (11.2%) acquired a new strain containing one or more new vaccine antigen peptides during multiple rounds of sample collection, which was not statistically different (P = 0.3176) from the unvaccinated repeat carriers (1/30; 3.3%). Our findings suggest that lack of MenB vaccine impact on carriage was not due to missing the intact fHbp gene; MenB-FHbp did not affect antigen genetic diversity and distribution during the study period. IMPORTANCE The impact of serogroup B meningococcal (MenB) vaccines on carriage is not completely understood. Using whole-genome sequencing data, we assessed the diversity and distribution of MenB vaccine antigens (particularly FHbp) among 1,514 meningococcal carriage isolates recovered from vaccinated and unvaccinated students at three U.S. universities, two of which underwent MenB-FHbp mass vaccination campaigns following meningococcal disease outbreaks. The majority of carriage isolates recovered from participants harbored intact fHbp genes, about half of which were recovered from MenB-FHbp-vaccinated participants. The distribution of vaccine antigen peptides was similar among carriage isolates recovered from vaccinated and unvaccinated participants, and almost all strains recovered from repeat carriers retained the same vaccine antigen profile, suggesting insignificant vaccine selective pressure on the carriage population in these universities.

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Detection of Autosomal Hemizygous Regions in the Fleckvieh Population Based on SNP-chip Data and Parent Offspring Pairs

Acta Universitatis Agriculturae et Silviculturae Mendelianae Brunensis ◽

10.11118/actaun201967061447 ◽

2019 ◽

Vol 67 (6) ◽

pp. 1447-1452

Author(s):

Judith Himmelbauer ◽

Gábor Mészáros ◽

Johann Sölkner

Keyword(s):

Dna Sequence ◽

Genome Sequencing ◽

Copy Number ◽

Population Based ◽

Whole Genome Sequencing Data ◽

Whole Genome ◽

Sequencing Data ◽

Chip Data ◽

Snp Chip ◽

Number Variation

A Copy Number Variation (CNV) is a loss or a gain in the DNA sequence, ranging from 50 basepairs to a few megabasepairs. Most studies use whole genome sequencing data to detect deletions. Due to the fact that SNP-chip data is more commonly used in livestock, especially in cattle, the detection of deletions based on SNP-chip data is of interest. In the present study an approach based on SNP chip data and the analysis of Mendelian mismatches in parent-offspring-pairs was developed. Use was made of the fact that deletions appear as homozygous after SNP Chip genotyping. For some SNPs with high number of mismatches, the inheritance of the mismatches could be traced back to one or a few bulls and thereby regions of possible deletions were defined. The study has shown that an approach based on Mendelian mismatches and SNP-chip data is a promising way of detecting deletions.

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Population-level genome-wide STR discovery and validation for population structure and genetic diversity assessment of Plasmodium species

PLoS Genetics ◽

10.1371/journal.pgen.1009604 ◽

2022 ◽

Vol 18 (1) ◽

pp. e1009604

Author(s):

Jiru Han ◽

Jacob E. Munro ◽

Anthony Kocoski ◽

Alyssa E. Barry ◽

Melanie Bahlo

Keyword(s):

Genetic Diversity ◽

Tandem Repeats ◽

Plasmodium Species ◽

Whole Genome Sequence ◽

Whole Genome Sequencing Data ◽

Whole Genome ◽

Sequencing Data ◽

Genome Wide ◽

Diversity Assessment ◽

Field Samples

Short tandem repeats (STRs) are highly informative genetic markers that have been used extensively in population genetics analysis. They are an important source of genetic diversity and can also have functional impact. Despite the availability of bioinformatic methods that permit large-scale genome-wide genotyping of STRs from whole genome sequencing data, they have not previously been applied to sequencing data from large collections of malaria parasite field samples. Here, we have genotyped STRs using HipSTR in more than 3,000 Plasmodium falciparum and 174 Plasmodium vivax published whole-genome sequence data from samples collected across the globe. High levels of noise and variability in the resultant callset necessitated the development of a novel method for quality control of STR genotype calls. A set of high-quality STR loci (6,768 from P. falciparum and 3,496 from P. vivax) were used to study Plasmodium genetic diversity, population structures and genomic signatures of selection and these were compared to genome-wide single nucleotide polymorphism (SNP) genotyping data. In addition, the genome-wide information about genetic variation and other characteristics of STRs in P. falciparum and P. vivax have been available in an interactive web-based R Shiny application PlasmoSTR (https://github.com/bahlolab/PlasmoSTR).

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