Comparison of the effectiveness of microsatellites and SNP panels for genetic identification, traceability and assessment of parentage in an inbred Angus herd

Development and evaluation of a novel single nucleotide polymorphism panel for North American bison

Genome-wide single nucleotide polymorphism (SNP) genotyping platforms have become increasingly popular in characterizing livestock and wildlife populations, replacing traditional methods such as microsatellite fragment analysis. Herein, we report the development and evaluation of a novel bison SNP panel for population management and conservation. Initially, 2474 autosomal SNPs were selected from existing bison whole-genome sequences and variable sites among bison on the GGSP bovine 50K Chip, based on minor allele frequency, data completeness, and chromosome location. Additionally, 20 mitochondrial SNPs were chosen to identify known mitochondrial haplotypes in bison according to previous research. The SNPs were further evaluated using genotyping-by-sequencing with 190 bison, representing the historical lineages that survived the major population crash of the late 1800s. Variants with high potential for genotyping error were filtered out, and the remaining SNPs were placed on a custom Illumina™ array. The final panel consisting of 798 autosomal and 13 mitochondrial SNPs was used to establish baseline genetic parameters, compare populations, and assign mitochondrial haplotypes in 995 bison across ten populations. These SNPs were also found to be highly informative for individual animal identification and parentage assignment. This SNP panel provides a powerful new method to establish a baseline for estimating genetic health of bison populations and a new tool for bison managers to make informed management decisions based on genetic information specific to their populations.

Comparative Analysis of Microsatellite and SNP Markers for Genetic Management of Red Deer

The analysis of population genetic structure and individual multilocus heterozygosity are crucial for wildlife management and conservation. Microsatellite markers have traditionally been used to assess these genetic parameters. However, single-nucleotide polymorphisms (SNPs) are becoming increasingly popular. Our goal here was to determine to what extent SNPs can provide better insights than microsatellites into the overall genetic status and population genetic processes in the species. To this end, we genotyped 210 red deer (Cervus elaphus) in the Spanish wild population with both 11 microsatellites and 31,712 SNPs. We compared parameters related to population genetic structure and individual multilocus heterozygosity obtained with both types of markers. Our results showed correlations between parameters measured using both microsatellites and SNPs, particularly those related to the level of genetic diversity and genetic differentiation. However, we found notably lower precision of microsatellites in measuring the distribution of genetic diversity among individuals. We conclude that microsatellites can be used to monitor the overall genetic status and detect broad patterns in red deer populations. Nevertheless, the greater precision of SNPs in inferring genetic structure and multilocus heterozygosity leads us to encourage scientists and wildlife managers to prioritize their use whenever possible.

Analysis of Doberman Pinscher and Toy Poodle samples with targeted next-generation sequencing

Next-generation sequencing (NGS) technologies have enabled the identification of many causal variants of genetic disorders, the development of parentage tests and the analysis of multiple traits in domestic animals. In this study, we evaluated the performance of a Canine Targeted Genotyping-by-Sequencing (GBS) custom panel (Thermo Fisher Scientific, Waltham, Ma, USA) in a cohort of 95 dog DNA samples, comprising 76 Doberman Pinschers and 19 Toy Poodles from Argentina. The used panel included 383 targets (228 parentage SNVs, 137 genetic disorder markers and 18 trait markers). While paternity analysis showed correct duo (97.4%; LOD > 2.98E⁺¹³) and trio (100%; LOD > 2.20E⁺¹⁵) parentage assignment, the panel resulted still insufficient for excluding close relatives in inbred populations. In this sense, close relatives were wrongly assigned as parents in 12.6% of duos and 0.3% of trios. We detected 17 polymorphic markers (genetic disorders, n = 4; hair type, n = 3; coat color, n = 10) and estimated their allele frequencies in the studied breeds. The accuracy of targeted GBS results were evaluated for three markers that were associated with Progressive rod-cone degeneration, von Willebrand disease type 1 and dilated cardiomyopathy by pyrosequencing and Sanger sequencing genotyping, showing 94-100% concordance among assays. The targeted GBS custom panel resulted cost-effective strategy to study the prevalence of genetic disorders and traits in a large number of samples and to analyze genetic interactions between previously reported variants. Once assays based on AgriSeq technology were standardized, their uses are a good strategy for large-scale routine genetic evaluation of animal populations.

A joint use of pooling and imputation for genotyping SNPs

Background

Despite continuing technological advances, the cost for large-scale genotyping of a high number of samples can be prohibitive. The purpose of this study is to design a cost-saving strategy for SNP genotyping. We suggest making use of pooling, a group testing technique, to drop the amount of SNP arrays needed. We believe that this will be of the greatest importance for non-model organisms with more limited resources in terms of cost-efficient large-scale chips and high-quality reference genomes, such as application in wildlife monitoring, plant and animal breeding, but it is in essence species-agnostic. The proposed approach consists in grouping and mixing individual DNA samples into pools before testing these pools on bead-chips, such that the number of pools is less than the number of individual samples. We present a statistical estimation algorithm, based on the pooling outcomes, for inferring marker-wise the most likely genotype of every sample in each pool. Finally, we input these estimated genotypes into existing imputation algorithms. We compare the imputation performance from pooled data with the Beagle algorithm, and a local likelihood-aware phasing algorithm closely modeled on MaCH that we implemented.

Results

We conduct simulations based on human data from the 1000 Genomes Project, to aid comparison with other imputation studies. Based on the simulated data, we find that pooling impacts the genotype frequencies of the directly identifiable markers, without imputation. We also demonstrate how a combinatorial estimation of the genotype probabilities from the pooling design can improve the prediction performance of imputation models. Our algorithm achieves 93% concordance in predicting unassayed markers from pooled data, thus it outperforms the Beagle imputation model which reaches 80% concordance. We observe that the pooling design gives higher concordance for the rare variants than traditional low-density to high-density imputation commonly used for cost-effective genotyping of large cohorts.

Conclusions

We present promising results for combining a pooling scheme for SNP genotyping with computational genotype imputation on human data. These results could find potential applications in any context where the genotyping costs form a limiting factor on the study size, such as in marker-assisted selection in plant breeding.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12859-022-04974-7.

Genome-Wide Association Study of Egg-Laying Traits and Egg Quality in LingKun Chickens

Egg production is the most important trait of laying hens. To identify molecular markers and candidate genes associated with egg production and quality, such as body weight at first oviposition (BWF), the number of eggs produced in 500 days (EN500), egg weight (EW), egg shell thickness (EST), egg shell strength (ESS), and Haugh unit (HU), a genome-wide analysis was performed in 266 LingKun Chickens. The results showed that thirty-seven single nucleotide polymorphisms (SNPs) were associated with all traits (p < 9.47 × 10⁻⁸, Bonferroni correction). These SNPs were located in close proximity to or within the sequence of the thirteen candidate genes, such as Galanin And GMAP Prepropeptide (GAL), Centromere Protein (CENPF), Glypican 2 (GPC2), Phosphatidylethanolamine N-Methyltransferase (PEMT), Transcription Factor AP-2 Delta (TFAP2D), and Carboxypeptidase Q (CPQ) gene related to egg-laying and Solute Carrier Family 5 Member 7 (SLC5A7), Neurocalcin Delta (NCALD), Proteasome 20S Subunit Beta 2 (PSMB2), Slit Guidance Ligand 3 (SLIT3), and Tubulin Tyrosine Ligase Like 7 (TTLL7) genes related to egg quality. Interestingly, one of the genes involved in bone formation (SLIT3) was identified as a candidate gene for ESS. Our candidate genes and SNPs associated with egg-laying traits were significant for molecular breeding of egg-laying traits and egg quality in LingKun chickens.

DNA fingerprinting reveals varietal composition of Vietnamese cassava germplasm (Manihot esculenta Crantz) from farmers' field and genebank collections

A molecular analysis using informative SNP markers in 1570 clones of cassava from Vietnam reveals varietal composition from farmers' field and genebank collections Cassava is the most important smallholder cash crops in Southeast Asia and is especially used in industrial products. Yet, systematic genetic studies on molecular markers from Vietnamese germplasm have not been considered for breeding and conservation programs. We conducted a molecular analysis of 1570 clones of cassava germplasm from farms across six agro-ecological zones using informative SNP markers. We unraveled the genetic diversity and population structure and provided insights into the value of breeding and conservation programs. Duplicated genotypes comprised 98% of the total sample of the Central Highlands region. Ninety-six SNPs were amplified Central Highlands and South East provinces had the highest allelic richness, covering up to 83% of alleles. The average observed heterozygosity (Ho = 0.43) was slightly higher than expected (He = 0.40) across SNP markers, suggesting an excess of heterozygotes plants. Diversity indexes indicated that cassava populations from North West and Eastern Vietnam are genetically diverse (mean He = 0.40). Genetic parentage tests identified 85 unique genetic groups within the varieties KM94, KM419, BRA1305, KM101, KM140, PER262, KM60, KM57 and two unidentified varieties, which accounted for 82% of the frequency distribution. KM94 is the most dominant variety in Vietnamese farms surveyed (38%), reflecting its superior quality and productivity. Discriminant analysis of principal components (DAPC) revealed four main subgroups, which were partially corroborated by neighbor joining (NJ) analyses. After removing duplicates, 31 unique genotypes were distributed across five of the agro-ecological zones. These were well distributed in the subgroups revealed via DAPC and NJ analyses. The genetic groups identified herein could be used to select unique accessions that should ideally conform with ex situ germplasm collections and identify areas where on-farm conservation programs should be targeted. Newly identified genotypes may also contribute as genetic breeding resources that could be used to adapt cassava to future changes and farmers' needs.

Genomic Population Structure of the Main Historical Genetic Lines of Spanish Merino Sheep

Simple Summary

Historical documentation shows that the Spanish Merino sheep was selected over many centuries due to the quality of wool, following which it was used to originate all other Merino breeds around the world, mainly by crossbreeding with local breeds. Today, the historical genetic lines that originated the Spanish Merino are still preserved in several closed herds in which they have been bred for nearly 200 years, maintaining their original genetic purity. Our study demonstrates, using a genomic approach, the exceptional genetic richness and variability of these lines, which are clearly differentiated from modern Merino breeds, and must therefore be protected to safeguard the large genetic pool they represent.

Abstract

According to historiographical documentation, the Romans first began to select Merino sheep in the Iberian Peninsula during the first century, with the aim of obtaining a breed appreciated for the quality of its wool. This process continued locally during the Middle Ages, when Spanish sheep were protected, and their export to foreign countries was banned. It was during the 16th century when individual Merino sheep were allowed to spread around the world to be used to improve the wool quality of local breeds. However, the wool crisis of the 1960s shifted the selection criteria of the Merino breed towards meat production at the expenses of wool. Consequently, individuals that display the genetic and phenotypic characteristics of those sheep originally bred in the kingdom of Spain in the Middle Ages are extremely difficult to find in commercial herds. In this study, we characterized the genetic basis of 403 individuals from the main historical Spanish Merino genetic lines (Granda, Hidalgo, Lopez-Montenegro, Maeso, Donoso and Egea), which were bred in isolation over the last 200 years, using a genomic approach based on genotyping data from the Axiom™ Ovine 50K SNP Genotyping Array. Our analysis included measuring population structure, genomic differentiation indexes, runs of homozygosity (ROH) patterns, and an analysis of molecular variance (AMOVA). The results showed large genetic differences between the historical lines, even though they belong to the same breed. In addition, ROH analysis showed differences due to increased inbreeding among the ancient generations compared with the modern Merino lines, confirming the breed’s ancestral and closed origin. However, our results also showed a high variability and richness within the Spanish historical Merino lines from a genetic viewpoint. This fact, together with their great ability to produce high-quality wool, suggests that ancestral Merino lines from Spain should be considered a valuable genetic population to be maintained as a resource for the improvement of wool-producing sheep breeds all around the world.

Development of 16 novel EST-SSR markers for species identification and cross-genus amplification in sambar, sika, and red deer

Deer genera around the globe are threatened by anthropogenic interference. The translocation of alien species and their subsequent genetic introgression into indigenous deer populations is particularly harmful to the species of greatest conservation concern. Products derived from deer, including venison and antler velvet, are also at risk of fraudulent labeling. The current molecular markers used to genetically identify deer species were developed from genome sequences and have limited applicability for cross-species amplification. The absence of efficacious diagnostic techniques for identifying deer species has hampered conservation and wildlife crime investigation efforts. Expressed sequence tag-simple sequence repeat (EST-SSR) markers are reliable tools for individual and species identification, especially in terms of cross-species genotyping. We conducted transcriptome sequencing of sambar (Rusa unicolor) antler velvet and acquired 11,190 EST-SSRs from 65,074 newly assembled unigenes. We identified a total of 55 unambiguous amplicons in sambar (n = 45), which were selected as markers to evaluate cross-species genotyping in sika deer (Cervus nippon, n = 30) and red deer (Cervus elaphus, n = 46), resulting in cross-species amplification rates of 94.5% and 89.1%, respectively. Based on polymorphic information content (>0.25) and genotyping fidelity, we selected 16 of these EST-SSRs for species identification. This marker set revealed significant genetic differentiation based on the fixation index and genetic distance values. Principal coordinate analysis and STRUCTURE analysis revealed distinct clusters of species and clearly identified red-sika hybrids. These markers showed applicability across different genera and proved suitable for identification and phylogenetic analyses across deer species.

Forensic DNA phenotyping: Canis familiaris breed classification and skeletal phenotype prediction using functionally significant skeletal SNPs and indels

This review highlights a novel application of breed identification and prediction of skeletal traits in forensic investigations using canine DNA evidence. Currently, genotyping methods used for canine breed classification involve the application of highly polymorphic short tandem repeats in addition to larger commercially available SNP arrays. Both applications face technical challenges. An additional approach to breed identification could be through genotyping SNPs and indels that characterise the array of skeletal differences displayed across domestic dog populations. Research has shown that a small number of genetic variants of large effect drive differences in skeletal phenotypes among domestic dog breeds. This feature makes functionally significant canine skeletal variants a cost-effective target for forensic investigators to classify individuals according to their breed. Further analysis of these skeletal variants would enable the prediction of external appearance. To date, functionally significant genes with genetic variants associated with differences in size, bulk, skull shape, ear shape, limb length, digit type, and tail morphology have been uncovered. Recommendations of a cost-effective genotyping method that can be readily designed and applied by forensic investigators have been given. Further advances to improve the field of canine skeletal forensic DNA phenotyping include the refinement of phenotyping methods, further biological validation of the skeletal genetic variants and establishing a publicly available database for storage of allele frequencies of the skeletal genetic variants in the wider domestic dog population.

Asymmetric allelic introgression across a hybrid zone of the coal tit (Periparus ater) in the central Himalayas

In the Himalayas, a number of secondary contact zones have been described for vicariant vertebrate taxa. However, analyses of genetic divergence and admixture are missing for most of these examples. In this study, we provide a population genetic analysis for the coal tit (Periparus ater) hybrid zone in Nepal. Intermediate phenotypes between the distinctive western "spot-winged tit" (P. a. melanolophus) and Eastern Himalayan coal tits (P. a. aemodius) occur across a narrow range of <100 km in western Nepal. As a peculiarity, another distinctive cinnamon-bellied form is known from a single population so far. Genetic admixture of western and eastern mitochondrial lineages was restricted to the narrow zone of phenotypically intermediate populations. The cline width was estimated 46 km only with a center close to the population of the cinnamon-bellied phenotype. In contrast, allelic introgression of microsatellite loci was asymmetrical from eastern P. a. aemodius into far western populations of phenotypic P. a. melanolophus but not vice versa. Accordingly, the microsatellite cline was about 3.7 times wider than the mitochondrial one.

Assessing the levels of intraspecific admixture and interspecific hybridization in Iberian wild goats (Capra pyrenaica)

Iberian wild goats (Capra pyrenaica, also known as Iberian ibex, Spanish ibex, and Spanish wild goat) underwent strong genetic bottlenecks during the 19th and 20th centuries due to overhunting and habitat destruction. From the 1970s to 1990s, augmentation translocations were frequently carried out to restock Iberian wild goat populations (very often with hunting purposes), but they were not systematically planned or recorded. On the other hand, recent data suggest the occurrence of hybridization events between Iberian wild goats and domestic goats (Capra hircus). Augmentation translocations and interspecific hybridization might have contributed to increase the diversity of Iberian wild goats. With the aim of investigating this issue, we have genotyped 118 Iberian wild goats from Tortosa-Beceite, Sierra Nevada, Muela de Cortes, Gredos, Batuecas, and Ordesa and Monte Perdido by using the Goat SNP50 BeadChip (Illumina). The analysis of genotypic data indicated that Iberian wild goat populations are strongly differentiated and display low diversity. Only three Iberian wild goats out from 118 show genomic signatures of mixed ancestry, a result consistent with a scenario in which past augmentation translocations have had a limited impact on the diversity of Iberian wild goats. Besides, we have detected eight Iberian wild goats from Tortosa-Beceite with signs of domestic goat introgression. Although rare, hybridization with domestic goats could become a potential threat to the genetic integrity of Iberian wild goats; hence, measures should be taken to avoid the presence of uncontrolled herds of domestic or feral goats in mountainous areas inhabited by this iconic wild ungulate.

A 2b-RAD parentage analysis pipeline for complex and mixed DNA samples

Next-generation sequencing technology has revolutionized genotyping in many fields of study, yet parentage analysis often still relies on microsatellite markers that are costly to generate and are currently available only for a limited number of species. 2b-RAD sequencing (2b-RAD) is a DNA sequencing technique developed for ecological population genomics that utilizes type IIB restriction enzymes to generate consistent, uniform fragments across samples. This technology is inexpensive, effective with low DNA inputs, and robust to DNA degradation. Here, we developed a probabilistic genotyping-by-sequencing genetic testing pipeline for parentage analysis by using 2b-RAD for inferring familial relationships from mixed DNA samples and populations. Our approach to partial paternity assignment utilizes a novel weighted outlier paternity index (WOPI) adapted for next-generation sequencing data and an identity-by-state (IBS) matrix-based clustering method for pedigree reconstruction. The combination of these two parentage assignment methods overcomes two major obstacles faced by other genetic testing methods: 1) It allows detection of parentage when closely related or inbred individuals are in the alleged parent population (e.g., in laboratory strains); and 2) it resolves mixed DNA samples. We successfully demonstrate this novel approach by correctly inferring paternity for samples pooled from multiple offspring (i.e., entire clutches) in a highly inbred population of an East African cichlid fish. The unique advantages of 2b-RAD in combination with our bioinformatics pipeline enable straightforward and cost-effective parentage analysis in any species regardless of genomic resources available.

Sex Reversal Syndrome in an Egyptian Arabian Horse Detected Using Genomic Data - A case report

A 4-year-old Straight Egyptian Arabian horse was evaluated in 2016 due to a malformation of external genitalia and male sexual behavior. On physical examination, small teats in the inguinal area and a rudimentary penis-like structure surrounded by a clitoral fossa could be seen. There was no evidence of vulva and vaginal canal. A stallion like behavior was observed, especially in the presence of mares in heat, when the animal was excited and aggressive and had erection of the penis-like structure. Blood samples were collected for two purposes: hormonal (testosterone and estradiol plasma concentration analyses) and genetic (cytogenetic and molecular analysis). The karyotype showed 32 pairs of chromosomes in all cells (2n = 64) including 14 and 18 pairs of metacentric and acrocentric chromosomes respectively, in agreement with a presumptive 64, XX complement. This result agree with STR and SNP molecular analysis, which also ruled out the possibility of hematopoietic chimerism. In addition, SNP genotyping showed no numerical chromosomal aberrations or large deletions or duplications, that can be linked to the phenotype in any autosome, nor numerical chromosomal abnormalities in the father and mother of the horse analyzed. In conclusion, we determined that the animal in the present study is a male pseudohermaphrodite.

Parentage Analysis in Giant Grouper (Epinephelus lanceolatus) Using Microsatellite and SNP Markers from Genotyping-by-Sequencing Data

Pedigree information is necessary for the maintenance of diversity for wild and captive populations. Accurate pedigree is determined by molecular marker-based parentage analysis, which may be influenced by the polymorphism and number of markers, integrity of samples, relatedness of parents, or different analysis programs. Here, we described the first development of 208 single nucleotide polymorphisms (SNPs) and 11 microsatellites for giant grouper (Epinephelus lanceolatus) taking advantage of Genotyping-by-sequencing (GBS), and compared the power of SNPs and microsatellites for parentage and relatedness analysis, based on a mixed family composed of 4 candidate females, 4 candidate males and 289 offspring. CERVUS, PAPA and COLONY were used for mutually verification. We found that SNPs had a better potential for relatedness estimation, exclusion of non-parentage and individual identification than microsatellites, and > 98% accuracy of parentage assignment could be achieved by 100 polymorphic SNPs (MAF cut-off < 0.4) or 10 polymorphic microsatellites (mean H_o = 0.821, mean PIC = 0.651). This study provides a reference for the development of molecular markers for parentage analysis taking advantage of next-generation sequencing, and contributes to the molecular breeding, fishery management and population conservation.

Ecology and population structure of some indigenous geese breeds and the impact of four GH and Pit-1 SNPs on their body weights

This study aims to determine the genetic correlation using nine microsatellite markers to reconstruct the history of some indigenous geese populations, along with the use of four single nucleotides polymorphisms (SNPs) to investigate their correlation with the geese body weight. Microsatellite markers are mainly used to provide updated information on changes in the population structure of geese breeds. The eight goose populations reported 24% private alleles specific for each population. Expected heterozygosity (He) ranged from 0.46 to 0.70. Three breeds were reported highly polymorphic. Inbreeding coefficient (Fis) revealed that three breeds were in a minimum level of extinction danger, while one breed was in a potential endangered situation. Phylogenetic tree, principal component analysis (PCA), and self-organizing map (SOM) were constructed using MATLAB to study the population distribution and relationship among these breeds. Four SNPs were detected, two SNPs at GH gene exon (C123T and C158T), and two SNPs at Pit-1 gene exons (G161A and T282G). Four SNP loci were reported to have a significant effect on geese body weight. They were CT genotype for C123T locus, TT genotype for C158T locus, GG genotype for G161A locus, and GG genotype for T282G locus.

Extent and direction of introgressive hybridization of mule and white-tailed deer in western Canada

Hybridization of mule deer (Odocoileus hemionus) and white-tailed deer (O. virginianus) appears to be a semi-regular occurrence in western North America. Previous studies confirmed the presence of hybrids in a variety of sympatric habitats, but their developing molecular resources limited identification to the earliest, most admixed generations. For this reason, estimates of hybrid production in wild populations often rely on anecdotal reports. As well, white-tailed deer populations' continued encroachment into historically mule deer-occupied habitats due to changes in land use, habitat homogenization, and a warming climate may increase opportunities for interspecific encounters. We sought to quantify the prevalence and extent of hybrid deer in the prairies of western Canada using a SNP assay with enhanced discriminating power. By updating the available molecular resources, we sought to identify and characterize previously cryptic introgression. We also investigated the influence of various parameters on hybridity by way of logistic regression. We observed overall hybridization rates of ~1.0%, slightly lower than that reported by previous studies, and found white-tailed-like hybrids to be more common than their mule deer-like counterparts. Here, we build upon past studies of hybridization in North American deer by increasing hybrid detection power, expanding sample sizes, demonstrating a new molecular resource applicable to future research and observing asymmetrical directionality of introgression.

Spontaneous hybridization and introgression between walleye (Sander vitreus) and sauger (Sander canadensis) in two large reservoirs: Insights from genotyping by sequencing

Anthropogenic activities may facilitate undesirable hybridization and genomic introgression between fish species. Walleye (Sander vitreus) and sauger (Sander canadensis) are economically valuable freshwater species that can spontaneously hybridize in areas of sympatry. Levels of genomic introgression between walleye and sauger may be increased by modifications to waterbodies (e.g., reservoir development) and inadvertent propagation of hybrids in stocking programs. We used genotyping by sequencing (GBS) to examine 217 fish from two large reservoirs with mixed populations of walleye and sauger in Saskatchewan, Canada (Lake Diefenbaker, Tobin Lake). Analyses with 20,038 (r90) and 478 (r100) single nucleotide polymorphisms clearly resolved walleye and sauger, and classified hybrids with high confidence. F1, F2, and multigeneration hybrids were detected in Lake Diefenbaker, indicating potentially high levels of genomic introgression. In contrast, only F1 hybrids were detected in Tobin Lake. Field classification of fish was unreliable; 7% of fish were misidentified based on broad species categories. Important for activities such as brood stock selection, 12 of 173 (7%) fish field identified as pure walleye, and one of 24 (4%) identified as pure sauger were actually hybrids. In addition, two of 15 (13%) field-identified hybrids were actually pure walleye or sauger. We conclude that hybridization and introgression are occurring in Saskatchewan reservoirs and that caution is warranted when using these populations in stocking programs. GBS offers a powerful and flexible tool for examining hybridization without preidentification of informative loci, eliminating some of the key challenges associated with other marker types.

Evaluation of the International Society for Animal Genetics bovine single nucleotide polymorphism parentage panel in South African Bonsmara and Drakensberger cattle

A panel of 200 single nucleotide polymorphisms (SNPs) have been recommended by the International Society for Animal Genetics (ISAG) for use in parentage verification of cattle. While the SNPs included on the ISAG panel are segregating in European Bos taurus and Bos indicus breeds, their applicability in South African (SA) Sanga cattle has never been evaluated. This study, therefore, assessed the usefulness of the ISAG panel in SA Bonsmara (BON) and Drakensberger (DRB) cattle. Genotypes of 185 ISAG SNPs from 64 BON and 97 DRB sire-offspring pairs were available, all of which were validated with 119,375 SNPs. Of the 185 ISAG SNPs, 14 and 18 in the BON and DRB, respectively (9 in common to both breeds), were either monomorphic, exhibited at least one discordance between validated sire-offspring pairs, or had poor call rate or clustering issue. The mean minor allele frequency of the 185 ISAG SNPs was 0.331 in the BON and 0.359 in the DRB. The combined probability of parentage exclusion (P_E) was the same (99.46%) for both breeds, while the probability of identity varied from 1.61 × 10^-48 (BON) to 1.11 × 10^-54 (DRB). Fifteen (23.4%) and 32 (33%) of the already validated sire-offspring pairs for the BON and DRB, respectively, were determined by the ISAG panel to be false-negatives based on a threshold of having at least two discordant SNPs. In comparison to sire discovery using the 119,375 SNPs, sire discovery using only the ISAG panel identified correctly 44 (out of 64 identified using the 119,375 SNPs) unique sire-offspring BON pairs and 62 (out of 97 identified using the 119,375 SNPs) unique sire-offspring DRB when all sires were masked. Five BON and three DRB offspring had > 1 sire nominated. This study demonstrated that the use of the ISAG panel may result in incorrect exclusions and multiple candidate sires for a given animal. Selection of more informative SNPs is, therefore, necessary in the pursuit of a low-cost and effective SNP panel for indigenous cattle breeds in SA.

The influence of anthropogenic habitat fragmentation on the genetic structure and diversity of the malaria vector Anopheles cruzii (Diptera: Culicidae)

Fragmentation of natural environments as a result of human interference has been associated with a decrease in species richness and increase in abundance of a few species that have adapted to these environments. The Brazilian Atlantic Forest, which has been undergoing an intense process of fragmentation and deforestation caused by human-made changes to the environment, is an important hotspot for malaria transmission. The main vector of simian and human malaria in this biome is the mosquito Anopheles cruzii. Anthropogenic processes reduce the availability of natural resources at the tree canopies, An. cruzii primary habitat. As a consequence, An. cruzii moves to the border of the Atlantic Forest nearing urban areas seeking resources, increasing their contact with humans in the process. We hypothesized that different levels of anthropogenic changes to the environment can be an important factor in driving the genetic structure and diversity in An. cruzii populations. Five different hypotheses using a cross-sectional and a longitudinal design were tested to assess genetic structure in sympatric An. cruzii populations and microevolutionary processes driving these populations. Single nucleotide polymorphisms were used to assess microgeographic genetic structure in An. cruzii populations in a low-endemicity area in the city of São Paulo, Brazil. Our results show an overall weak genetic structure among the populations, indicating a high gene flow system. However, our results also pointed to the presence of significant genetic structure between sympatric An. cruzii populations collected at ground and tree-canopy habitats in the urban environment and higher genetic variation in the ground-level population. This indicates that anthropogenic modifications leading to habitat fragmentation and a higher genetic diversity and structure in ground-level populations could be driving the behavior of An. cruzii, ultimately increasing its contact with humans. Understanding how anthropogenic changes in natural areas affect An. cruzii is essential for the development of more effective mosquito control strategies and, on a broader scale, for malaria-elimination efforts in the Brazilian Atlantic Forest.

Genetic Characterization of the Local Pirenaica Cattle for Parentage and Traceability Purposes

Pirenaica is the most important autochthonous cattle breed within the Protected Geographic Indication (PGI) beef quality label in the Basque region, in northern Spain. The short tandem repeats (STRs) are powerful markers to elucidate forensic cases and traceability across the agri-food sector. The main objective of the present work was to study the phylogenetic relationships of Pirenaica cattle and other breeds typically raised in the region and provide the minimum number of STR markers for parentage and traceability purposes. The 30-STR panel recommended by the International Society of Animal Genetics-Food and Agriculture Organization of the United Nations (ISAG-FAO) was compared against other commercial STR panels. The 30-STR panel showed a combined matching probability of 1.89 × 10-25 and a power of exclusion for duos of 0.99998. However, commercial STR panels showed a limited efficiency for a reliable parentage analysis in Pirenaica, and at least a 21-STR panel is needed to reach a power of exclusion of 0.9999. Machine-learning analysis also demonstrated a 95% accuracy in assignments selecting the markers with the highest FST in Pirenaica individuals. Overall, the present study shows the genetic characterization of Pirenaica and its phylogeny compared with other breeds typically raised in the Basque region. Finally, a 21-STR panel with the highest FST markers is proposed for a confident parentage analysis and high traceability.

Genotyping-free parentage assignment using RAD-seq reads

Parentage assignment is defined as the identification of the true parents of one focal offspring among a list of candidates and has been commonly used in zoological, ecological, and agricultural studies. Although likelihood-based parentage assignment is the preferred method in most cases, it requires genotyping a predefined set of DNA markers and providing their population allele frequencies. In the present study, we proposed an alternative method of parentage assignment that does not depend on genotype data and prior information of allele frequencies. Our method employs the restriction site-associated DNA sequencing (RAD-seq) reads for clustering into the overlapped RAD loci among the compared individuals, following which the likelihood ratio of parentage assignment could be directly calculated using two parameters-the genome heterozygosity and error rate of sequencing reads. This method was validated on one simulated and two real data sets with the accurate assignment of true parents to focal offspring. However, our method could not provide a statistical confidence to conclude that the first ranked candidate is a true parent.

Population Genomic Analyses of Wild and Farmed Striped Catfish Pangasianodon Hypophthalmus in the Lower Mekong River

The striped catfish Pangasianodon hypophthalmus is an important freshwater fish cultured in many countries where the collection of wild brooders is still widely practiced. Global farming development of this species makes use of significant natural resources that pose challenges for the genetic diversity of striped catfish. Hence, this study aims to conduct a systematic genetic diversity assessment of wild and farmed catfish stocks collected from four major pangasius-farming countries, using a new genotyping by sequencing platform known as DArT-seq technology. Our population genomic analyses using 7263 single-nucleotide polymorphisms (SNPs) after high-quality-control showed that there were two distinct populations of striped catfish in the lower Mekong river: (i) wild catfish from Thailand and (ii) catfish from Cambodia and Vietnam. The genetic diversity was greatest (0.363) in the wild stock from Thailand, but it was lower in farmed and wild stocks in other countries (0.049 to 0.088). The wild stocks were more genetically diverse than the farmed animals (0.103 vs. 0.064). The inbreeding coefficient ranged from 0.004 and 0.109, with the lowest value (−0.499) in the wild animals from Thailand. Molecular inference methods revealed high degree of historical effective population size (1043.9–1258.4), but there was considerable decline in the contemporary estimates in all populations (10.8 to 73.6). Our additional analyses calculating divergent times and migration patterns showed that the wild catfish from Thailand stand out as separate lineages, while those from Cambodia and Vietnam are genetically identical. Our results also indicated that the cultured stock in Bangladesh originated from the lower part of the Mekong river. These findings have significant practical implications in the context of genetic selection and conservation of striped catfish in the region. Collectively, they will contribute to the sustainable development of the striped catfish sector in these countries.

An empirical comparison of population genetic analyses using microsatellite and SNP data for a species of conservation concern

BACKGROUND

Use of genomic tools to characterize wildlife populations has increased in recent years. In the past, genetic characterization has been accomplished with more traditional genetic tools (e.g., microsatellites). The explosion of genomic methods and the subsequent creation of large SNP datasets has led to the promise of increased precision in population genetic parameter estimates and identification of demographically and evolutionarily independent groups, as well as questions about the future usefulness of the more traditional genetic tools. At present, few empirical comparisons of population genetic parameters and clustering analyses performed with microsatellites and SNPs have been conducted.

RESULTS

Here we used microsatellite and SNP data generated from Gunnison sage-grouse (Centrocercus minimus) samples to evaluate concordance of the results obtained from each dataset for common metrics of genetic diversity (HO, HE, FIS, AR) and differentiation (FST, GST, DJost). Additionally, we evaluated clustering of individuals using putatively neutral (SNPs and microsatellites), putatively adaptive, and a combined dataset of putatively neutral and adaptive loci. We took particular interest in the conservation implications of any differences. Generally, we found high concordance between microsatellites and SNPs for HE, FIS, AR, and all differentiation estimates. Although there was strong correlation between metrics from SNPs and microsatellites, the magnitude of the diversity and differentiation metrics were quite different in some cases. Clustering analyses also showed similar patterns, though SNP data was able to cluster individuals into more distinct groups. Importantly, clustering analyses with SNP data suggest strong demographic independence among the six distinct populations of Gunnison sage-grouse with some indication of evolutionary independence in two or three populations; a finding that was not revealed by microsatellite data.

CONCLUSION

We demonstrate that SNPs have three main advantages over microsatellites: more precise estimates of population-level diversity, higher power to identify groups in clustering methods, and the ability to consider local adaptation. This study adds to a growing body of work comparing the use of SNPs and microsatellites to evaluate genetic diversity and differentiation for a species of conservation concern with relatively high population structure and using the most common method of obtaining SNP genotypes for non-model organisms.

Symposium review: Advances in sequencing technology herald a new frontier in cattle genomics and genome-enabled selection

The cattle reference genome assembly has underpinned major innovations in beef and dairy genetics through genome-enabled selection, including removal of deleterious recessive variants and selection for favorable alleles affecting quantitative production traits. The initial reference assemblies, up to and including UMD3.1 and Btau4.1, were based on a combination of clone-by-clone sequencing of bacterial artificial chromosome clones generated from blood DNA of a Hereford bull and whole-genome shotgun sequencing of blood DNA from his inbred daughter/granddaughter named L1 Dominette 01449 (Dominette). The approach introduced assembly gaps, misassemblies, and errors, and it limited the ability to assemble regions that undergo rearrangement in blood cells, such as immune gene clusters. Nonetheless, the reference supported the creation of genotyping tools and provided a basis for many studies of gene expression. Recently, long-read sequencing technologies have emerged that facilitated a re-assembly of the reference genome, using lung tissue from Dominette to resolve many of the problems and providing a bridge to place historical studies in common context. The new reference, ARS-UCD1.2, successfully assembled germline immune gene clusters and improved overall continuity (i.e., reduction of gaps and inversions) by over 250-fold. This reference properly places nearly all of the legacy genetic markers used for over a decade in the industry. In this review, we discuss the improvements made to the cattle reference; remaining issues present in the assembly; tools developed to support genome-based studies in beef and dairy cattle; and the emergence of newer genome assembly methods that are producing even higher-quality assemblies for other breeds of cattle at a fraction of the cost. The new frontier for cattle genomics research will likely include a transition from the individual Hereford reference genome, to a "pan-genome" reference, representing all the DNA segments existing in commonly used cattle breeds, bringing the cattle reference into line with the current direction of human genome research.

In the surf zone: Reproductive strategy of the calico surfperch (Amphistichus koelzi) in a comparative context

We examined the reproductive life history of calico surfperch (Amphistichus koelzi), including mating season, pregnancy, gestation and multiple paternity utilizing restriction site-associated DNA sequencing. Furthermore, we compared the mating season of calico with barred (Amphistichus argenteus), walleye (Hyperprosopon argenteum) and silver (Hyperprosopon ellipticum) surfperches to determine if the timing of reproduction is divergent within and between the genera. In calico surfperch, the mating season occurs from October to November, and females gestate from December to May. All broods exhibit multiple paternity with a range of four to seven sires per brood. The mating season of calico overlaps completely with barred surfperch; however, barred surfperches have a protracted mating season which extends until the beginning of December, which may be due to differences in reproductive strategy such as size at first reproduction. In the genus, the Hyperprosopon mating season begins earlier than Amphistichus, with divergence in the onset of mating between Hyperprosopon congeners of approximately 1 month.

Development, characterization, and cross-amplification of polymorphic microsatellite markers for North American Trachymyrmex and Mycetomoellerius ants

Objective

The objective of this study is to develop and identify polymorphic microsatellite markers for fungus-gardening (attine) ants in the genus Trachymyrmex sensu lato. These ants are important ecosystem engineers and have been a model group for understanding complex symbiotic systems, but very little is understood about the intraspecific genetic patterns across most North American attine species. These microsatellite markers will help to better study intraspecific population genetic structure, gene flow, mating habits, and phylogeographic patterns in these species and potentially other congeners.

Results

Using next-generation sequencing techniques, we identified 17 and 12 polymorphic microsatellite markers from T. septentrionalis and Mycetomoellerius (formerly Trachymyrmex) turrifex, respectively, and assessed the genetic diversity of each marker. We also analyzed the cross-amplification success of the T. septentrionalis markers in two other closely related Trachymyrmex species, and identified 10 and 12 polymorphic markers for T. arizonensis and T. pomonae, respectively.

Inference of Breed Structure in Farm Animals: Empirical Comparison between SNP and Microsatellite Performance

Knowledge of population structure is essential to improve the management and conservation of farm animal genetic resources. Microsatellites, which have long been popular for this type of analysis, are more and more neglected in favor of whole-genome single nucleotide polymorphism (SNP) chips that are now available for the main farmed animal species. In this study, we compared genetic patterns derived from microsatellites to that inferred by SNPs, considering three pairs of datasets of sheep and cattle. Population genetic differentiation analyses (Fixation index, F_ST), as well as STRUCTURE analyses showed a very strong consistency between the two types of markers. Microsatellites gave pictures that were largely concordant with SNPs, although less accurate. The best concordance was found in the most complex dataset, which included 17 French sheep breeds (with a Pearson correlation coefficient of 0.95 considering the 136 values of pairwise F_ST, obtained with both types of markers). The use of microsatellites reduces the cost and the related analyses do not require specific computer equipment (i.e., information technology (IT) infrastructure able to provide adequate computing and storage capacity). Therefore, this tool may still be a very appropriate solution to evaluate, in a first stage, the general state of livestock at national scales. At a time when local breeds are disappearing at an alarming rate, it is urgent to improve our knowledge of them, in particular by promoting tools accessible to the greatest number.

Evidence for adaptive introgression of exons across a hybrid swarm in deer

Background

Secondary contact between closely related lineages can result in a variety of outcomes, including hybridization, depending upon the strength of reproductive barriers. By examining the extent to which different parts of the genome introgress, it is possible to infer the strength of selection and gain insight into the evolutionary trajectory of lineages. Following secondary contact approximately 8000 years ago in the Pacific Northwest, mule deer (Odocoileus hemionus hemionus) and black-tailed deer (O. h. columbianus) formed a hybrid swarm along the Cascade mountain range despite substantial differences in body size (up to two times) and habitat preference. In this study, we examined genetic population structure, extent of introgression, and selection pressures in freely interbreeding populations of mule deer and black-tailed deer using mitochondrial DNA sequences, 9 microsatellite loci, and 95 SNPs from protein-coding genes.

Results

We observed bi-directional hybridization and classified approximately one third of the 172 individuals as hybrids, almost all of which were beyond the F1 generation. High genetic differentiation between black-tailed deer and mule deer at protein-coding genes suggests that there is positive divergent selection, though selection on these loci is relatively weak. Contrary to predictions, there was not greater selection on protein-coding genes thought to be associated with immune function and mate choice. Geographic cline analyses were consistent across genetic markers, suggesting long-term stability (over hundreds of generations), and indicated that the center of the hybrid swarm is 20-30 km to the east of the Cascades ridgeline, where there is a steep ecological transition from wet, forested habitat to dry, scrub habitat.

Conclusions

Our data are consistent with a genetic boundary between mule deer and black-tailed deer that is porous but maintained by many loci under weak selection having a substantial cumulative effect. The absence of clear reproductive barriers and the consistent centering of geographic clines at a sharp ecotone suggests that ecology is a driver of hybrid swarm dynamics. Adaptive introgression in this study (and others) promotes gene flow and provides valuable insight into selection strength on specific genes and the evolutionary trajectory of hybridizing taxa.

Electronic supplementary material

The online version of this article (10.1186/s12862-019-1497-x) contains supplementary material, which is available to authorized users.

Genetic admixture despite ecological segregation in a North African sparrow hybrid zone (Aves, Passeriformes, Passer domesticus × Passer hispaniolensis)

Under different environmental conditions, hybridization between the same species might result in different patterns of genetic admixture. Particularly, species pairs with large distribution ranges and long evolutionary history may have experienced several independent hybridization events over time in different zones of overlap. In birds, the diverse hybrid populations of the house sparrow (Passer domesticus) and the Spanish sparrow (Passer hispaniolensis) provide a striking example. Throughout their range of sympatry, these two species do not regularly interbreed; however, a stabilized hybrid form (Passer italiae) exists on the Italian Peninsula and on several Mediterranean islands. The spatial distribution pattern on the Eurasian continent strongly contrasts the situation in North Africa, where house sparrows and Spanish sparrows occur in close vicinity of phenotypically intermediate populations across a broad mosaic hybrid zone. In this study, we investigate patterns of divergence and admixture among the two parental species, stabilized and nonstabilized hybrid populations in Italy and Algeria based on a mitochondrial marker, a sex chromosomal marker, and 12 microsatellite loci. In Algeria, despite strong spatial and temporal separation of urban early-breeding house sparrows and hybrids and rural late-breeding Spanish sparrows, we found strong genetic admixture of mitochondrial and nuclear markers across all study populations and phenotypes. That pattern of admixture in the North African hybrid zone is strikingly different from i) the Iberian area of sympatry where we observed only weak asymmetrical introgression of Spanish sparrow nuclear alleles into local house sparrow populations and ii) the very homogenous Italian sparrow population where the mitogenome of one parent (P. domesticus) and the Z-chromosomal marker of the other parent (P. hispaniolensis) are fixed. The North African sparrow hybrids provide a further example of enhanced hybridization along with recent urbanization and anthropogenic land-use changes in a mosaic landscape.

The Value of Reference Genomes in the Conservation of Threatened Species

Conservation initiatives are now more crucial than ever-over a million plant and animal species are at risk of extinction over the coming decades. The genetic management of threatened species held in insurance programs is recommended; however, few are taking advantage of the full range of genomic technologies available today. Less than 1% of the 13505 species currently listed as threated by the International Union for Conservation of Nature (IUCN) have a published genome. While there has been much discussion in the literature about the importance of genomics for conservation, there are limited examples of how having a reference genome has changed conservation management practice. The Tasmanian devil (Sarcophilus harrisii), is an endangered Australian marsupial, threatened by an infectious clonal cancer devil facial tumor disease (DFTD). Populations have declined by 80% since the disease was first recorded in 1996. A reference genome for this species was published in 2012 and has been crucial for understanding DFTD and the management of the species in the wild. Here we use the Tasmanian devil as an example of how a reference genome has influenced management actions in the conservation of a species.

Genome-wide association analysis of egg production performance in chickens across the whole laying period

BACKGROUND

Egg production is the most economically-important trait in layers as it directly influences benefits of the poultry industry. To better understand the genetic architecture of egg production, we measured traits including age at first egg (AFE), weekly egg number (EN) from onset of laying eggs to 80 weeks which was divided into five stage (EN1: from onset of laying eggs to 23 weeks, EN2: from 23 to 37 weeks, EN3: from 37 to 50 weeks, EN4: from 50 to 61 weeks, EN5: from 61 to 80 weeks) based on egg production curve and total egg number across the whole laying period (Total-EN). Then we performed genome-wide association studies (GWAS) in 1078 Rhode Island Red hens using a linear mixed model.

RESULTS

Estimates of pedigree and SNP-based genetic parameter showed that AFE and EN1 exhibited high heritability (0.51 ± 0.09, 0.53 ± 0.08), while the h2 for EN in other stages varied from low (0.07 ± 0.04) to moderate (0.24 ± 0.07) magnitude. Subsequently, seven univariate GWAS for AFE and ENs were carried out independently, from which a total of 161 candidate SNPs located on GGA1, GGA2, GGA5, GGA6, GGA9 and GGA24 were identified. Thirteen SNP located on GGA6 were associated with AFE and an interesting gene PRLHR that may affect AFE through regulating oxytocin secretion in chickens. Sixteen genome-wide significant SNPs associated with EN3 were in a strong linkage disequilibrium (LD) region spanning from 117.87 Mb to 118.36 Mb on GGA1 and the most significant SNP (rs315777735) accounted for 3.57% of phenotypic variance. Genes POLA1, PDK3, PRDX4 and APOO identified by annotating sixteen genome-wide significant SNPs can be considered as candidates associated with EN3. Unfortunately, our study did not find any candidate gene for the total egg number.

CONCLUSIONS

Findings in our study could provide promising genes and SNP markers to improve egg production performance based on marker-assisted breeding selection, while further functional validation is still needed in other populations.

Identification and evaluation of a core microsatellite panel for use in white-tailed deer (Odocoileus virginianus)

Background

Microsatellite loci have been used extensively over the past two decades to study the genetic characteristics of non-model species. The ease of microsatellite development and ability to adapt markers from related species has led to the proliferation of available markers for many commonly studied species. Because it is often infeasible to genotype individuals across all available loci, researchers generally rely on subsets of markers. Marker choice can bias inferences made using disparate suites of loci. This has been a primary motivation for efforts to identify uniform marker panels. Here, we use the geographic distribution of previous studies to identify microsatellite loci for white-tailed deer (Odocoileus virginianus) with the potential for widespread use, and we evaluate the effectiveness of this panel in a portion of the range where few previous studies have been conducted. The purpose was to consolidate the numerous genetic resources for this species into a manageable panel and to provide a uniform methodology that improves comparisons between past and future studies.

Results

We reviewed microsatellite panels from 58 previous or ongoing projects and identified 106 candidate loci. We developed a multiplex protocol and evaluated the efficacy of 17 of the most commonly used loci using 720 DNA samples collected from the Mid-Atlantic region of the United States of America. Amplification errors were detected in six of these loci. The 11 remaining loci were highly polymorphic, exhibited low frequencies of null alleles, and were easy to interpret with the aid of allele binning software.

Conclusions

The development of broadly-applicable, core microsatellite panels has the potential to improve repeatability and comparative ability for commonly studied species. The properties of the consolidated 11 microsatellite panel suggest that they are applicable for many common research objectives for white-tailed deer. The geographic distribution of previous studies using these markers provides a greater degree of confidence regarding the robustness to common sources of error related to amplification anomalies, such as null alleles, relative to loci with more limited use. While this does not replace further evaluation of genotyping errors, it does provide a common platform that benefits future research studies.

Electronic supplementary material

The online version of this article (10.1186/s12863-019-0750-z) contains supplementary material, which is available to authorized users.

Development of a Novel Mule Deer Genomic Assembly and Species-Diagnostic SNP Panel for Assessing Introgression in Mule Deer, White-Tailed Deer, and Their Interspecific Hybrids

Mule deer (Odocoileus hemionus) are endemic to a wide variety of habitats in western North America, many of which are shared in sympatry with their closely related sister-species white-tailed deer (Odocoileus virginianus), whom they hybridize with in wild populations. Although mule deer meet many ideal conditions for a molecular ecological research species, such as high abundance, ecological importance, and broad dispersal and gene flow, conservation genetic studies have been limited by a relative lack of existing genomic resources and inherent difficulties caused by introgression with white-tailed deer. Many molecular tools currently available for the study of cervids were designed using reference assemblies of divergent model species, specifically cattle (Bos taurus). Bovidae and Cervidae diverged approximately 28 million years ago, therefore, we sought to ameliorate the available resources by contributing the first mule deer whole genome sequence draft assembly with an average genome-wide read depth of 25X, using the white-tailed genome assembly (Ovir.te_1.0) as a reference. Comparing the two assemblies, we identified ∼33 million single nucleotide polymorphisms (SNPs) and insertion/deletion variants. We then verified fixed SNP differences between the two species and developed a 40-loci SNP assay capable of identifying pure mule deer, white-tailed deer, and interspecific hybrids. Assignment capacity of the panel, which was tested on simulated datasets, is reliable up to and including the third backcross hybrid generation. Identification of post-F1 hybrids will be necessary for hybrid zone population studies going forward, and the new mule deer assembly will be a valuable resource for genetic and comparative genomics studies.

Population genetics of Anopheles funestus, the African malaria vector, Kenya

Background

Anopheles funestus is among the major malaria vectors in Kenya and sub-Saharan Africa and has been recently implicated in persistent malaria transmission. However, its ecology and genetic diversity remain poorly understood in Kenya.

Methods

Using 16 microsatellite loci, we examined the genetic structure of An. funestus sampled from 11 locations (n = 426 individuals) across a wide geographical range in Kenya spanning coastal, western and Rift Valley areas.

Results

Kenyan An. funestus resolved as three genetically distinct clusters. The largest cluster (FUN1) broadly included samples from western and Rift Valley areas of Kenya with two clusters identified from coastal Kenya (FUN2 and FUN3), not previously reported. Geographical distance had no effect on population differentiation of An. funestus. We found a significant variation in the mean Plasmodium infectivity between the clusters (χ² = 12.1, df = 2, P = 0.002) and proportional to the malaria prevalence in the different risk zones of Kenya. Notably, there was variation in estimated effective population sizes between the clusters, suggesting possible differential impact of anti-vector interventions in represented areas.

Conclusions

Heterogeneity among Kenyan populations of An. funestus will impact malaria vector control with practical implications for the development of gene-drive technologies. The difference in Plasmodium infectivity and effective population size between the clusters could suggest potential variation in phenotypic characteristics relating to competence or insecticide resistance. This is worth examining in future studies.

Electronic supplementary material

The online version of this article (10.1186/s13071-018-3252-3) contains supplementary material, which is available to authorized users.

DNA-based Determination of Ancestry in Cynomolgus Macaques (Macaca fascicularis)

Interest in the genetic composition of cynomolgus macaques (Macaca fascicularis) has increased due to the rising demand for NHP models in human biomedical research. Significant genetic differences among regional populations of cynomolgus macaques can confound interpretations of research results because they do not solely reflect differences in experimental treatment effects. Therefore, the common origin of cynomolgus macaques used as research subjects should be verified by using region-specific genetic markers to minimize the influence of underlying genetic variation among animals selected as research subjects on phenotypes under study. We compared the effectiveness of 18 short tandem repeat (STR) markers with that of 83 single-nucleotide polymorphism (SNP) markers to differentiate the ancestry of cynomolgus macaques from 6 different populations (Cambodia, Sumatra, Mauritius, Singapore, and the islands of Luzon and Zamboanga in the Philippines). Genetic diversity indices such as allele numbers and expected heterozygosity based on SNP were lower and exhibited lower standard errors than those provided by STR, probably because, unlike STR, most SNP are biallelic and consequently exhibit maximal expected heterozygosity values of 0.50. However, the standard error of estimates of observed heterozygosity based on SNP was higher than that for STR, perhaps reflecting sampling errors. Only 27 SNP were required to match the resolving power of 17 STR to detect population structure, that is, 1.6 SNP:1 STR. Whereas STR only differentiated the Mauritian population from all other populations, SNP detected 4 genetically distinct groups (Cambodia, Singapore-Sumatra, Mauritius, and Zamboanga). SNP are poised to become as valuable as STR for understanding and detecting genetic structure among cynomolgus macaques. Although STR will remain an important tool for cynomolgus macaque population studies, SNP have the potential to become the mainstream marker type.

Genetic variations for egg quality of chickens at late laying period revealed by genome-wide association study

With the extension of the egg-laying cycle, the rapid decline in egg quality at late laying period has aroused great concern in the poultry industry. Herein, we performed a genome-wide association study (GWAS) to identify genomic variations associated with egg quality, employing chicken 600 K high-density SNP arrays in a population of 1078 hens at 72 and 80 weeks of age. The results indicated that a genomic region spanning from 8.95 to 9.31 Mb (~0.36 Mb) on GGA13 was significantly associated with the albumen height (AH) and the haugh unit (HU), and the two most significant SNPs accounted for 3.12 ~ 5.75% of the phenotypic variance. Two promising genes, MSX2 and DRD1, were mapped to the narrow significant region, which was involved in embryonic and ovary development and found to be related to egg production, respectively. Moreover, three interesting genes, RHOA, SDF4 and TNFRSF4, identified from three significant loci, were considered to be candidate genes for egg shell colour. Findings in our study could provide worthy theoretical basis and technological support to improve late-stage egg quality for breeders.

Accuracy of Imputation of Microsatellite Markers from BovineSNP50 and BovineHD BeadChip in Hanwoo Population of Korea

Until now microsatellite (MS) have been a popular choice of markers for parentage verification. Recently many countries have moved or are in process of moving from MS markers to single nucleotide polymorphism (SNP) markers for parentage testing. FAO-ISAG has also come up with a panel of 200 SNPs to replace the use of MS markers in parentage verification. However, in many countries most of the animals were genotyped by MS markers till now and the sudden shift to SNP markers will render the data of those animals useless. As National Institute of Animal Science in South Korea plans to move from standard ISAG recommended MS markers to SNPs, it faces the dilemma of exclusion of old animals that were genotyped by MS markers. Thus to facilitate this shift from MS to SNPs, such that the existing animals with MS data could still be used for parentage verification, this study was performed. In the current study we performed imputation of MS markers from the SNPs in the 500-kb region of the MS marker on either side. This method will provide an easy option for the labs to combine the data from the old and the current set of animals. It will be a cost efficient replacement of genotyping with the additional markers. We used 1,480 Hanwoo animals with both the MS data and SNP data to impute in the validation animals. We also compared the imputation accuracy between BovineSNP50 and BovineHD BeadChip. In our study the genotype concordance of 40% and 43% was observed in the BovineSNP50 and BovineHD BeadChip respectively.

Fresh is best: Accurate SNP genotyping from koala scats

Maintaining genetic diversity is a crucial component in conserving threatened species. For the iconic Australian koala, there is little genetic information on wild populations that is not either skewed by biased sampling methods (e.g., sampling effort skewed toward urban areas) or of limited usefulness due to low numbers of microsatellites used. The ability to genotype DNA extracted from koala scats using next‐generation sequencing technology will not only help resolve location sample bias but also improve the accuracy and scope of genetic analyses (e.g., neutral vs. adaptive genetic diversity, inbreeding, and effective population size). Here, we present the successful SNP genotyping (1272 SNP loci) of koala DNA extracted from scat, using a proprietary DArTseq^™ protocol. We compare genotype results from two‐day‐old scat DNA and 14‐day‐old scat DNA to a blood DNA template, to test accuracy of scat genotyping. We find that DNA from fresher scat results in fewer loci with missing information than DNA from older scat; however, 14‐day‐old scat can still provide useful genetic information, depending on the research question. We also find that a subset of 209 conserved loci can accurately identify individual koalas, even from older scat samples. In addition, we find that DNA sequences identified from scat samples through the DArTseq^™ process can provide genetic identification of koala diet species, bacterial and viral pathogens, and parasitic organisms.

Double-digest RAD sequencing outperforms microsatellite loci at assigning paternity and estimating relatedness: A proof of concept in a highly promiscuous bird

Information on genetic relationships among individuals is essential to many studies of the behaviour and ecology of wild organisms. Parentage and relatedness assays based on large numbers of single nucleotide polymorphism (SNP) loci hold substantial advantages over the microsatellite markers traditionally used for these purposes. We present a double-digest restriction site-associated DNA sequencing (ddRAD-seq) analysis pipeline that, as such, simultaneously achieves the SNP discovery and genotyping steps and which is optimized to return a statistically powerful set of SNP markers (typically 150-600 after stringent filtering) from large numbers of individuals (up to 240 per run). We explore the trade-offs inherent in this approach through a set of experiments in a species with a complex social system, the variegated fairy-wren (Malurus lamberti) and further validate it in a phylogenetically broad set of other bird species. Through direct comparisons with a parallel data set from a robust panel of highly variable microsatellite markers, we show that this ddRAD-seq approach results in substantially improved power to discriminate among potential relatives and considerably more precise estimates of relatedness coefficients. The pipeline is designed to be universally applicable to all bird species (and with minor modifications to many other taxa), to be cost- and time-efficient, and to be replicable across independent runs such that genotype data from different study periods can be combined and analysed as field samples are accumulated.