A gene-based capture assay for surveying patterns of genetic diversity and insecticide resistance in a worldwide group of invasive mosquitoes

AbstractUnderstanding patterns of diversification, genetic exchange, and pesticide resistance in insect species of human health concern is necessary for effective population reduction and management. With the broad availability of next-generation sequencing technologies, one of the best approaches for surveying such patterns involves the simultaneous genotyping of many samples for large numbers of genetic markers from across the known genome. To this end, the targeting of gene sequences of known function or inheritance can be a cost-effective strategy. One insect group of substantial health concern are the mosquito taxa that make up the Culex pipiens complex. Members of this complex transmit damaging arboviruses and filariae worms to humans, as well as other pathogens that are detrimental to endangered vertebrate species such as bird malaria. Here we describe our development of a targeted gene-based assay for surveying genetic diversity and population structure in this mosquito complex. To test the utility of this assay, we examined taxonomic divergence among samples from several members of the complex, as well as distinct populations of the relatively under-studied Culex quinquefasciatus, an urban pantropical species. We also examined the presence of known insecticide-resistance conferring alleles. Broadly, our developed gene-based assay proved effective for examining patterns of taxonomic and geographic clustering within the species complex, as well as for surveying genetic variants that have been associated with insecticide resistance. This assay will be useful for future studies that aim to understand the genetic mechanisms underlying the evolution of ubiquitous and increasingly damaging disease vectors.

Download Full-text

Characterization of a haplotype- reference panel for genotyping by low-pass sequencing in Swiss Large White pigs

10.21203/rs.3.rs-318745/v1 ◽

2021 ◽

Author(s):

Adéla Nosková ◽

Meenu Bhati ◽

Naveen Kumar Kadri ◽

Danang Crysnanto ◽

Stefan Neuenschwander ◽

...

Keyword(s):

Genetic Diversity ◽

Principal Component ◽

Cost Effective ◽

Reference Panel ◽

Effective Population ◽

Large White ◽

Breeding Populations ◽

Low Pass ◽

Signatures Of Selection ◽

Genomic Inbreeding

Abstract Background The key-ancestor approach has been frequently applied to prioritize individuals for whole-genome sequencing based on their marginal genetic contribution to current populations. Using this approach, we selected 70 key ancestors from two lines of the Swiss Large White breed that have been selected divergently for fertility and fattening traits and sequenced their genomes with short paired-end reads. Results Using pedigree records, we estimated the effective population size of the dam and sire line to 72 and 44, respectively. In order to assess sequence variation in both lines, we sequenced the genomes of 70 boars at an average coverage of 16.69-fold. The boars explained 87.95 and 95.35% of the genetic diversity of the breeding populations of the dam and sire line, respectively. Reference-guided variant discovery using the GATK revealed 26,862,369 polymorphic sites. Principal component, admixture and FST analyses indicated considerable genetic differentiation between the lines. Genomic inbreeding quantified using runs of homozygosity was higher in the sire than dam line (0.28 vs 0.26). Using two complementary approaches (CLR and iHS), we detected 51 signatures of selection. However, only six signatures of selection overlapped between both lines. We used the sequenced haplotypes of the 70 key ancestors as a reference panel to call 22,618,811 genotypes in 175 pigs that had been sequenced at very low coverage (1.11-fold) using GLIMPSE. The genotype concordance, non-reference sensitivity and non-reference discrepancy between thus inferred and Illumina PorcineSNP60 BeadChip-called genotypes was 97.60, 98.73 and 3.24%, respectively. The low-pass sequencing-derived genomic relationship coefficients were highly correlated (r > 0.99) with those obtained from microarray genotyping. Conclusions We assessed genetic diversity within and between two lines of the Swiss Large White pig breed. Our analyses revealed considerable differentiation, even though the split into two populations occurred only few generations ago. The sequenced haplotypes of the key ancestor animals enabled us to implement genotyping by low-pass sequencing which offers an intriguing cost-effective approach to increase the variant density over current array-based genotyping by more than 350-fold.

Download Full-text

An enzyme-linked immunosorbent assay for the detection of Rathayibacter toxicus, the bacterium involved in annual ryegrass toxicity, in hay

Australian Journal of Agricultural Research ◽

10.1071/ar03125 ◽

2006 ◽

Vol 57 (7) ◽

pp. 731 ◽

Cited By ~ 6

Author(s):

A. M. Masters ◽

A. R. Gregory ◽

R. J. Evans ◽

J. E. Speijers ◽

S. S. Sutherland

Keyword(s):

Monoclonal Antibody ◽

Immunosorbent Assay ◽

Specific Antigen ◽

Cost Effective ◽

Enzyme Linked Immunosorbent Assay ◽

Annual Ryegrass ◽

Capture Assay ◽

Large Numbers ◽

Soluble Polysaccharide ◽

Annual Ryegrass Toxicity

An enzyme-linked immunosorbent assay (ELISA) for Rathayibacter toxicus is described. The development of a monoclonal antibody for a specific antigen from R. toxicus and a polyclonal antibody raised against the same R. toxicus preparation enabled a capture assay format. The assay is specific for a soluble polysaccharide produced by the bacterium and was found to be sensitive enough to detect antigen equivalent to less than one gall per kilogram of hay. The applicability of the assay to samples of pasture or hay is demonstrated. Cost-effective testing of large numbers of samples for the presence of R. toxicus is possible with the ELISA. This will assist stockowners, hay producers, and hay exporters in the management of the risk of annual ryegrass toxicity.

Download Full-text

Genetic Resilience of a Once Endangered Species, Tibetan Antelope (Pantholops hodgsonii)

10.1101/628727 ◽

2019 ◽

Author(s):

Yue Shi ◽

Jiarui Chen ◽

Jianping Su ◽

Tongzuo Zhang ◽

Samuel K. Wasser

Keyword(s):

Genetic Diversity ◽

Gene Flow ◽

Population Size ◽

Effective Population Size ◽

Genetic Bottleneck ◽

Migration Routes ◽

Effective Population ◽

Human Disturbances ◽

Population Reduction ◽

Tibetan Antelope

AbstractPopulation reduction is generally assumed to reduce the population’s genetic diversity and hence its ability to adapt to environmental change. However, if life history traits that promote gene flow buffer populations from such impacts, conservation efforts should aim to maintain those traits in vulnerable species. Tibetan antelope (Pantholops hodgsonii) has experienced population reduction by 95% due to poaching during the 20th century. We hypothesize that opportunities for gene flow provided by their sex-specific migration buffered their genetic diversity from the poaching impacts. We measured the mtDNA (control region, CR) and nuDNA (microsatellites or STRs) diversity, population differentiation, along with the change in effective population size (pre-poaching era vs. post-poaching era) and tested for a genetic bottleneck. Our results showed that Tibetan antelope maintained considerable genetic diversity in both mtDNA CR and STR markers (Hd = 0.9970 and Hobs = 0.8446, respectively), despite a marked reduction in post-poaching effective population size 368.9 (95% CI of 249.3 - 660.6) compared to the pre-poaching average (4.93×103 - 4.17×104). Post-poached populations also had low population structure and showed no evidence of a genetic bottleneck. Pairwise Fst values using CR haplotype frequencies were higher than those using STR allele frequencies, suggesting different degrees of gene flow mediated by females and males. This study suggests that the Tibetan antelope’s sex-specific migration buffered their loss of genetic diversity in the face of severe demographic decline. These findings highlight the importance of recognizing the traits likely to maintain genetic diversity and promoting conservation efforts that allow them to be exercised. For Tibetan antelope, this requires assuring that their migration routes remain unobstructed by growing human disturbances while continuing to enforce anti-poaching law enforcement efforts.

Download Full-text

Characterization of a haplotype-reference panel for genotyping by low-pass sequencing in Swiss Large White pigs

10.1101/2021.03.11.434987 ◽

2021 ◽

Author(s):

Adéla Nosková ◽

Meenu Bhati ◽

Naveen Kumar Kadri ◽

Danang Crysnanto ◽

Stefan Neuenschwander ◽

...

Keyword(s):

Genetic Diversity ◽

Principal Component ◽

Cost Effective ◽

Reference Panel ◽

Effective Population ◽

Large White ◽

Breeding Populations ◽

Low Pass ◽

Signatures Of Selection ◽

Genomic Inbreeding

AbstractBackgroundThe key-ancestor approach has been frequently applied to prioritize individuals for whole-genome sequencing based on their marginal genetic contribution to current populations. Using this approach, we selected 70 key ancestors from two lines of the Swiss Large White breed that have been selected divergently for fertility and fattening traits and sequenced their genomes with short paired-end reads.ResultsUsing pedigree records, we estimated the effective population size of the dam and sire line to 72 and 44, respectively. In order to assess sequence variation in both lines, we sequenced the genomes of 70 boars at an average coverage of 16.69-fold. The boars explained 87.95 and 95.35% of the genetic diversity of the breeding populations of the dam and sire line, respectively. Reference-guided variant discovery using the GATK revealed 26,862,369 polymorphic sites. Principal component, admixture and FSTanalyses indicated considerable genetic differentiation between the lines. Genomic inbreeding quantified using runs of homozygosity was higher in the sire than dam line (0.28 vs 0.26). Using two complementary approaches (CLR and iHS), we detected 51 signatures of selection. However, only six signatures of selection overlapped between both lines. We used the sequenced haplotypes of the 70 key ancestors as a reference panel to call 22,618,811 genotypes in 175 pigs that had been sequenced at very low coverage (1.11-fold) using GLIMPSE. The genotype concordance, non-reference sensitivity and non-reference discrepancy between thus inferred and Illumina PorcineSNP60 BeadChip-called genotypes was 97.60, 98.73 and 3.24%, respectively. The low-pass sequencing-derived genomic relationship coefficients were highly correlated (r > 0.99) with those obtained from microarray genotyping.ConclusionsWe assessed genetic diversity within and between two lines of the Swiss Large White pig breed. Our analyses revealed considerable differentiation, even though the split into two populations occurred only few generations ago. The sequenced haplotypes of the key ancestor animals enabled us to implement genotyping by low-pass sequencing which offers an intriguing cost-effective approach to increase the variant density over current array-based genotyping by more than 350-fold.

Download Full-text

Characterization of a haplotype-reference panel for genotyping by low-pass sequencing in Swiss Large White pigs

BMC Genomics ◽

10.1186/s12864-021-07610-5 ◽

2021 ◽

Vol 22 (1) ◽

Author(s):

Adéla Nosková ◽

Meenu Bhati ◽

Naveen Kumar Kadri ◽

Danang Crysnanto ◽

Stefan Neuenschwander ◽

...

Keyword(s):

Genetic Diversity ◽

Principal Component ◽

Cost Effective ◽

Reference Panel ◽

Fixation Index ◽

Effective Population ◽

Large White ◽

Breeding Populations ◽

Low Pass ◽

Signatures Of Selection

AbstractBackgroundThe key-ancestor approach has been frequently applied to prioritize individuals for whole-genome sequencing based on their marginal genetic contribution to current populations. Using this approach, we selected 70 key ancestors from two lines of the Swiss Large White breed that have been selected divergently for fertility and fattening traits and sequenced their genomes with short paired-end reads.ResultsUsing pedigree records, we estimated the effective population size of the dam and sire line to 72 and 44, respectively. In order to assess sequence variation in both lines, we sequenced the genomes of 70 boars at an average coverage of 16.69-fold. The boars explained 87.95 and 95.35% of the genetic diversity of the breeding populations of the dam and sire line, respectively. Reference-guided variant discovery using the GATK revealed 26,862,369 polymorphic sites. Principal component, admixture and fixation index (FST) analyses indicated considerable genetic differentiation between the lines. Genomic inbreeding quantified using runs of homozygosity was higher in the sire than dam line (0.28 vs 0.26). Using two complementary approaches, we detected 51 signatures of selection. However, only six signatures of selection overlapped between both lines. We used the sequenced haplotypes of the 70 key ancestors as a reference panel to call 22,618,811 genotypes in 175 pigs that had been sequenced at very low coverage (1.11-fold) using the GLIMPSE software. The genotype concordance, non-reference sensitivity and non-reference discrepancy between thus inferred and Illumina PorcineSNP60 BeadChip-called genotypes was 97.60, 98.73 and 3.24%, respectively. The low-pass sequencing-derived genomic relationship coefficients were highly correlated (r > 0.99) with those obtained from microarray genotyping.ConclusionsWe assessed genetic diversity within and between two lines of the Swiss Large White pig breed. Our analyses revealed considerable differentiation, even though the split into two populations occurred only few generations ago. The sequenced haplotypes of the key ancestor animals enabled us to implement genotyping by low-pass sequencing which offers an intriguing cost-effective approach to increase the variant density over current array-based genotyping by more than 350-fold.

Download Full-text

Genetic Diversity at Resistance Gene Clusters in Wild Populations of Lactuca

10.32747/2000.7573075.bard ◽

2000 ◽

Author(s):

Richard Michelmore ◽

Eviatar Nevo ◽

Abraham Korol ◽

Tzion Fahima

Keyword(s):

Genetic Diversity ◽

Molecular Markers ◽

Disease Control ◽

Resistance Gene ◽

Resistance Genes ◽

Research Work ◽

Ex Situ ◽

Large Numbers ◽

Major Cluster ◽

Genetic Mechanisms

Genetic resistance is often the least expensive, most effective, and ecologically-sound method of disease control. It is becoming apparent that plant genomes contain large numbers of disease resistance genes. However, the numbers of different resistance specificities within a genepool and the genetic mechanisms generating diversity are poorly understood. Our objectives were to characterize diversity in clusters of resistance genes in wild progenitors of cultivated lettuce in Israel and California in comparison to diversity within cultivated lettuce, and to determine the extent of gene flow, recombination, and genetic instability in generating variation within clusters of resistance genes. Genetic diversity of resistance genes was analyzed in wild and cultivated germplasm using molecular markers derived from lettuce resistance gene sequences of the NBS-LRR type that mapped to the major cluster if resistance genes in lettuce (Sicard et al. 1999). Three molecular markers, one microsatellite marker and two SCAR markers that amplified LRR- encoding regions, were developed from sequences of resistance gene homologs at the Dm3 cluster (RGC2s) in lettuce. Variation for these markers was assessed in germplasm including 74 genotypes of cultivated lettuce, L. saliva and 71 accessions of the three wild Lactuca spp., L. serriola, L. saligna and L. virosa that represent the major species in the sexually accessible genepool for lettuce. Diversity was also studied within and between natural populations of L. serriola from Israel and California. Large numbers of haplotypes were detected indicating the presence of numerous resistance genes in wild species. We documented a variety of genetic events occurring at clusters of resistance genes for the second objective (Sicard et al., 1999; Woo el al., in prep; Kuang et al., in prepb). The diversity of resistance genes in haplotypes provided evidence for gene duplication and unequal crossing over during the evolution of this cluster of resistance genes. Comparison of nine resistance genes in cv. Diana identified 22 gene conversion and five intergenic recombinations. We cloned and sequenced a 700 bp region from the middle of RGC2 genes from six genotypes, two each from L. saliva, L. serriola, and L. saligna . We have identified over 60 unique RGC2 sequences. Phylogenetic analysis surprisingly demonstrated much greater similarity between than within genotypes. This led to the realization that resistance genes are evolving much slower than had previously been assumed and to a new model as to how resistance genes are evolving (Michelmore and Meyers, 1998). The genetic structure of L. serriola was studied using 319 AFLP markers (Kuang et al., in prepa). Forty-one populations from Turkey, Armenia, Israel, and California as well as seven European countries were examined. AFLP marker data showed that the Turkish and Armenian populations were the most polymorphic populations and the European populations were the least. The Davis, CA population, a recent post-Columbian colonization, showed medium genetic diversity and was genetically close to the Turkish populations. Our results suggest that Turkey - Armenia may be the center of origin and diversity of L. serriola and may therefore have the greatest diversity of resistance genes. Our characterization of the diversity of resistance genes and the genetic mechanisms generating it will allow informed exploration, in situ and ex situ conservation, and utilization of germplasm resources for disease control. The results of this project provide the basis for our future research work, which will lead to a detailed understanding of the evolution of resistance genes in plants.

Download Full-text

Evolutionary genetics of small populations

10.1093/oso/9780198783398.003.0002 ◽

2017 ◽

Author(s):

Richard Frankham ◽

Jonathan D. Ballou ◽

Katherine Ralls ◽

Mark D. B. Eldridge ◽

Michele R. Dudash ◽

...

Keyword(s):

Genetic Diversity ◽

Population Size ◽

Evolutionary Genetics ◽

Small Population ◽

Small Populations ◽

Effective Population ◽

Genetic Management ◽

Evolutionary Genetic ◽

Loss Of Genetic Diversity ◽

Number Of Individuals

Genetic management of fragmented populations involves the application of evolutionary genetic theory and knowledge to alleviate problems due to inbreeding and loss of genetic diversity in small population fragments. Populations evolve through the effects of mutation, natural selection, chance (genetic drift) and gene flow (migration). Large outbreeding, sexually reproducing populations typically contain substantial genetic diversity, while small populations typically contain reduced levels. Genetic impacts of small population size on inbreeding, loss of genetic diversity and population differentiation are determined by the genetically effective population size, which is usually much smaller than the number of individuals.

Download Full-text

Trends in genetic diversity and the effect of inbreeding in American Angus cattle under genomic selection

Genetics Selection Evolution ◽

10.1186/s12711-021-00644-z ◽

2021 ◽

Vol 53 (1) ◽

Author(s):

Emmanuel A. Lozada-Soto ◽

Christian Maltecca ◽

Duc Lu ◽

Stephen Miller ◽

John B. Cole ◽

...

Keyword(s):

Genetic Diversity ◽

Beef Cattle ◽

Genomic Selection ◽

Inbreeding Depression ◽

Growth Traits ◽

Effective Population ◽

Angus Cattle ◽

Genomic Inbreeding ◽

Chromosome Segments ◽

The Impact

Abstract Background While the adoption of genomic evaluations in livestock has increased genetic gain rates, its effects on genetic diversity and accumulation of inbreeding have raised concerns in cattle populations. Increased inbreeding may affect fitness and decrease the mean performance for economically important traits, such as fertility and growth in beef cattle, with the age of inbreeding having a possible effect on the magnitude of inbreeding depression. The purpose of this study was to determine changes in genetic diversity as a result of the implementation of genomic selection in Angus cattle and quantify potential inbreeding depression effects of total pedigree and genomic inbreeding, and also to investigate the impact of recent and ancient inbreeding. Results We found that the yearly rate of inbreeding accumulation remained similar in sires and decreased significantly in dams since the implementation of genomic selection. Other measures such as effective population size and the effective number of chromosome segments show little evidence of a detrimental effect of using genomic selection strategies on the genetic diversity of beef cattle. We also quantified pedigree and genomic inbreeding depression for fertility and growth. While inbreeding did not affect fertility, an increase in pedigree or genomic inbreeding was associated with decreased birth weight, weaning weight, and post-weaning gain in both sexes. We also measured the impact of the age of inbreeding and found that recent inbreeding had a larger depressive effect on growth than ancient inbreeding. Conclusions In this study, we sought to quantify and understand the possible consequences of genomic selection on the genetic diversity of American Angus cattle. In both sires and dams, we found that, generally, genomic selection resulted in decreased rates of pedigree and genomic inbreeding accumulation and increased or sustained effective population sizes and number of independently segregating chromosome segments. We also found significant depressive effects of inbreeding accumulation on economically important growth traits, particularly with genomic and recent inbreeding.

Download Full-text

Genotyping Strategies Using ddRAD Sequencing in Farmed Arctic Charr (Salvelinus alpinus)

Animals ◽

10.3390/ani11030899 ◽

2021 ◽

Vol 11 (3) ◽

pp. 899

Author(s):

Fotis Pappas ◽

Christos Palaiokostas

Keyword(s):

Genetic Diversity ◽

Salvelinus Alpinus ◽

Arctic Charr ◽

Cost Effective ◽

Limiting Factors ◽

Phenotypic Traits ◽

Production Volume ◽

High Coverage ◽

Genomic Relationships ◽

Low Coverage

Incorporation of genomic technologies into fish breeding programs is a modern reality, promising substantial advances regarding the accuracy of selection, monitoring the genetic diversity and pedigree record verification. Single nucleotide polymorphism (SNP) arrays are the most commonly used genomic tool, but the investments required make them unsustainable for emerging species, such as Arctic charr (Salvelinus alpinus), where production volume is low. The requirement to genotype a large number of animals for breeding practices necessitates cost effective genotyping approaches. In the current study, we used double digest restriction site-associated DNA (ddRAD) sequencing of either high or low coverage to genotype Arctic charr from the Swedish national breeding program and performed analytical procedures to assess their utility in a range of tasks. SNPs were identified and used for deciphering the genetic structure of the studied population, estimating genomic relationships and implementing an association study for growth-related traits. Missing information and underestimation of heterozygosity in the low coverage set were limiting factors in genetic diversity and genomic relationship analyses, where high coverage performed notably better. On the other hand, the high coverage dataset proved to be valuable when it comes to identifying loci that are associated with phenotypic traits of interest. In general, both genotyping strategies offer sustainable alternatives to hybridization-based genotyping platforms and show potential for applications in aquaculture selective breeding.

Download Full-text

Population structure and genetic diversity of non-native aoudad populations

Scientific Reports ◽

10.1038/s41598-021-91678-2 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Sunčica Stipoljev ◽

Toni Safner ◽

Pavao Gančević ◽

Ana Galov ◽

Tina Stuhne ◽

...

Keyword(s):

Genetic Diversity ◽

Control Region ◽

Effective Population ◽

The Czech Republic ◽

Mitochondrial Dna Control Region ◽

Mountain Ranges ◽

Spanish Populations ◽

Microsatellite Alleles ◽

Shared Alleles ◽

Number Of Individuals

AbstractThe aoudad (Ammotragus lervia Pallas 1777) is an ungulate species, native to the mountain ranges of North Africa. In the second half of the twentieth century, it was successfully introduced in some European countries, mainly for hunting purposes, i.e. in Croatia, the Czech Republic, Italy, and Spain. We used neutral genetic markers, the mitochondrial DNA control region sequence and microsatellite loci, to characterize and compare genetic diversity and spatial pattern of genetic structure on different timeframes among all European aoudad populations. Four distinct control region haplotypes found in European aoudad populations indicate that the aoudad has been introduced in Europe from multiple genetic sources, with the population in the Sierra Espuña as the only population in which more than one haplotype was detected. The number of detected microsatellite alleles within all populations (< 3.61) and mean proportion of shared alleles within all analysed populations (< 0.55) indicates relatively low genetic variability, as expected for new populations funded by a small number of individuals. In STRUCTURE results with K = 2–4, Croatian and Czech populations cluster in the same genetic cluster, indicating joined origin. Among three populations from Spain, Almeria population shows as genetically distinct from others in results, while other Spanish populations diverge at K = 4. Maintenance of genetic diversity should be included in the management of populations to sustain their viability, specially for small Czech population with high proportion of shared alleles (0.85) and Croatian population that had the smallest estimated effective population size (Ne = 5.4).

Download Full-text