Set Of Single Nucleotide Polymorphism Markers Research Articles

Genome-wide search for associations method for identification of molecular markers and candidate genes of breed affiliation of sheep of the North Caucasian meat and wool breed

To determine the loci associated with pedigree traits, a genome-wide search was conducted for associations of 275 heads of Russian sheep breeds genotyped using 600 thousand single nucleotide polymorphisms (SNPs). The studies were conducted according to the “case-control” type, where the “case” group is represented by animals of the North Caucasian meat and wool breed, the “control” included animals of other breeds (Karachay, Romanovskaya, Dzhalginsky merino and Russian meat merino). In this study, over 100 SNPs were identified with highly reliable differences in the frequency of occurrence in sheep of the North Caucasian meat and wool breed. For the subsequent analysis, 18 single nucleotides with the highest confidence indices localized on chromosomes were selected 1, 10, 11, 15, 17. As a result of a genome-wide study, significant SNP markers characteristic of the sheep breed under study, located directly in the genes or close to them, were determined. The conducted studies provide a set of new SNP markers and candidate genes associated with the breed characteristics of North Caucasian meat-wool sheep.

Construction of SNP fingerprints and genetic diversity analysis of radish (Raphanus sativus L.).

Radish (Raphanus sativus L.) is a vegetable crop with economic value and ecological significance in the genus Radish, family Brassicaceae. In recent years, developed countries have attached great importance to the collection and conservation of radish germplasm resources and their research and utilization, but the lack of population genetic information and molecular markers has hindered the development of the genetic breeding of radish. In this study, we integrated the radish genomic data published in databases for the development of single-nucleotide polymorphism (SNP) markers, and obtained a dataset of 308 high-quality SNPs under strict selection criteria. With the support of Kompetitive Allele-Specific PCR (KASP) technology, we screened a set of 32 candidate core SNP marker sets to analyse the genetic diversity of the collected 356 radish varieties. The results showed that the mean values of polymorphism information content (PIC), minor allele frequency (MAF), gene diversity and heterozygosity of the 32 candidate core SNP markers were 0.32, 0.30, 0.40 and 0.25, respectively. Population structural analysis, principal component analysis and genetic evolutionary tree analysis indicated that the 356 radish materials were best classified into two taxa, and that the two taxa of the material were closely genetically exchanged. Finally, on the basis of 32 candidate core SNP markers we calculated 15 core markers using a computer algorithm to construct a fingerprint map of 356 radish varieties. Furthermore, we constructed a core germplasm population consisting of 71 radish materials using 32 candidate core markers. In this study, we developed SNP markers for radish cultivar identification and genetic diversity analysis, and constructed DNA fingerprints, providing a basis for the identification of radish germplasm resources and molecular marker-assisted breeding as well as genetic research.

Development of an SNP marker set for marker-assisted backcrossing using genotyping-by-sequencing in tetraploid perilla.

High-quality molecular markers are essential for marker-assisted selection to accelerate breeding progress. Compared with diploid species, recently diverged polyploid crop species tend to have highly similar homeologous subgenomes, which is expected to limit the development of broadly applicable locus-specific single-nucleotide polymorphism (SNP) assays. Furthermore, it is particularly challenging to make genome-wide marker sets for species that lack a reference genome. Here, we report the development of a genome-wide set of kompetitive allele specific PCR (KASP) markers for marker-assisted recurrent selection (MARS) in the tetraploid minor crop perilla. To find locus-specific SNP markers across the perilla genome, we used genotyping-by-sequencing (GBS) to construct linkage maps of two F2 populations. The two resulting high-resolution linkage maps comprised 2326 and 2454 SNP markers that spanned a total genetic distance of 2133cM across 16 linkage groups and 2169cM across 21 linkage groups, respectively. We then obtained a final genetic map consisting of 22 linkage groups with 1123 common markers from the two genetic maps. We selected 96 genome-wide markers for MARS and confirmed the accuracy of markers in the two F2 populations using a high-throughput Fluidigm system. We confirmed that 91.8% of the SNP genotyping results from the Fluidigm assay were the same as the results obtained through GBS. These results provide a foundation for marker-assisted backcrossing and the development of new varieties of perilla.

Mapping the quantitative field resistance to stripe rust in a hard winter wheat population “Overley” × “Overland”

AbstractStripe (yellow) rust, caused by Puccinia striiformis f. sp. tritici, is a devastating disease of wheat (Triticum aestivum) worldwide. In commercial production, stripe rust reduces grain quality, grain yield, and forage yield. This study was conducted to identify quantitative trait locus (QTL) associated with field resistance to stripe rust in hard winter wheat. Stripe rust infection type and severity were rated in recombinant inbred lines (RILs, n = 204) derived from a cross between hard red winter wheat cultivars “Overley” and “Overland” in replicated field trials in the Great Plains and Pacific Northwest. RILs (n = 184) were genotyped with reduced representation sequencing to produce single nucleotide polymorphism (SNP) markers from alignment to the “Chinese Spring” reference sequence, IWGSC v2.1, and from alignment to the reference sequence for “Jagger,” which is a parent of Overley. Genetic linkage maps were developed independently from each set of SNP markers. QTL analysis identified genomic regions on chromosome arms 2AS, 2BS, 2BL, and 2DL that were associated with stripe rust resistance using multi‐environment best linear unbiased predictors for stripe rust infection type and severity. Results for the two linkage maps were very similar. PCR‐based SNP marker assays associated with the QTL regions were developed to efficiently identify these genomic regions in breeding populations.

SSR and SNP Marker-Based Investigation of Indian Rice Landraces in Relation to Their Genetic Diversity, Population Structure, and Geographical Isolation

India is blessed with an abundance of diverse rice landraces in its traditional cultivated areas. Two marker systems (simple sequence repeats (SSR) and single nucleotide polymorphism (SNP)) were used to study a set of 298 rice landrace accessions collected from six different regions of India (Andaman and Nicobar Islands, Chhattisgarh, Jharkhand, Uttar Pradesh, Uttarakhand, and West Bengal). Thirty hyper-variable simple sequence repeats (HvSSRs) and 32,782 single nucleotide polymorphisms (SNPs) were used in inferring genetic structure and geographical isolation. Rice landraces from Uttar Pradesh were the most diverse, with a gene diversity value of 0.42 and 0.49 with SSR and SNP markers, respectively. Neighbor-joining trees classified the rice landraces into two major groups with SSR and SNP markers, and complete geographical isolation was observed with SSR markers. Fast STRUCTURE analysis revealed four populations for SSR markers and three populations for SNP markers. The population structure with SSR markers showed that few individuals from Uttarakhand and Andaman and Nicobar Islands were grouped in small clusters. Population structure analysis with SNP markers showed not very distinct region-wise clustering among the rice landraces. Discriminant analysis of principal components (DAPC) and minimum spanning network (MSN) using SSR markers showed region-wise grouping of landraces with some intermixing, but DAPC and MSN with SNP markers showed very clear region-wise clustering. Genetic differentiation of rice landraces between the regions was significant with both SSR (Fst 0.094–0.487) and SNP markers (Fst 0.047–0.285). A Mantel test revealed a positive correlation between the genetic and geographic distance of rice landraces. The present study concludes that rice landraces investigated in this study were very diverse, and unlinked SSR markers show better geographical isolation than a large set of SNP markers.

Application of SolCAP Genotyping in Potato (Solanum tuberosum L.) Association Mapping.

Potato variety development entails a number of breeding steps, as well as testing and, finally, commercialization. Historically, phenotypic assesment were carried out to select and germplasm development. The US Department of Agriculture (USDA) funded the Solanaceae Coordinated Agricultural Project (SolCAP) to decode genomic resources into tools that breeders and geneticists can use. This project resulted in the creation of a genome-wide single-nucleotide polymorphism (SNP) array that can be used to evaluate elite potato-breeding germplasm. This array was used to genotype a diverse panel of Solanum species, as well as numerous biparental, diploid, and tetraploid populations. It has high marker density to generate genetic maps that can be used to identify numerous quantitative trait loci (QTLs) for agronomic, quality, biotic, and abiotic resistance traits. Up to now, numerous QTLs for important traits have been identified using new diploid and tetraploid genetic maps. SNP markers were used to assess germplasm relationships and fingerprint varieties and identify candidate genes. The Infinium 8303 SolCAP Potato array offers a common set of SNP markers that can be used for mapping, germplasm assessment, and fingerprinting with confidence. This array has also been helpful in furthering our understanding of the potato genome. Furthermore, some other Infinium potato arrays (i.e., 12K, 20K, and 25K) have been genotyped, and breeders can map quantitative trait loci (QTLs) across multiple populations to improve our understanding of economically important traits and lead to marker-assisted selection (MAS) and breeding and, ultimately, improved varieties.

Development of SNP Marker Sets for Marker-Assisted Background Selection in Cultivated Cucumber Varieties

Marker-assisted background selection is a powerful molecular tool that can enhance breeding efficiency through the analysis of a large number of markers representing the entire genomic background for precise selection. In the present study, the transcriptomes of 38 cucumber inbred lines with diverse traits were sequenced for single nucleotide polymorphism (SNP) mining for practical application to commercial cucumber breeding. A total of 62,378 high-quality SNPs were identified, of which 2462 SNPs were chosen based on the stringent filtering parameters. Finally, 363 evenly distributed common background selection markers (BMs) were developed and validated through polymorphism analysis and phylogenetic analysis using breeding materials with different genetic backgrounds; 327 out of 363 common BMs were useful for background selection. Moreover, the results of the phylogenetic analysis carried out using 50 selected core BMs were consistent with those for 327 common BMs. However, when the genotypes of breeding materials belonging to only the Baekdadagi-type were analyzed, the 327 common BMs showed a significant reduction in polymorphisms within the biased genomic locations. To address this issue, 59 highly polymorphic markers were selected as Baekdadagi BMs, as they showed better selection ability for the Baekdadagi-type. The 327 common BMs developed in the present study will enable efficient marker-assisted background selection in cucumber. Additionally, to reduce the genotyping cost, we suggested an alternative background selection strategy using both evenly distributed core BMs and biased Baekdadagi BMs for the improvement of commercial cucumber breeding programs.

Identification and Validation of a Core Single-Nucleotide Polymorphism Marker Set for Genetic Diversity Assessment, Fingerprinting Identification, and Core Collection Development in Bottle Gourd.

Germplasm collections are indispensable resources for the mining of important genes and variety improvement. To preserve and utilize germplasm collections in bottle gourd, we identified and validated a highly informative core single-nucleotide polymorphism (SNP) marker set from 1,100 SNPs. This marker set consisted of 22 uniformly distributed core SNPs with abundant polymorphisms, which were established to have strong representativeness and discriminatory power based on analyses of 206 bottle gourd germplasm collections and a multiparent advanced generation inter-cross (MAGIC) population. The core SNP markers were used to assess genetic diversity and population structure, and to fingerprint important accessions, which could provide an optimized procedure for seed authentication. Furthermore, using the core SNP marker set, we developed an accessible core population of 150 accessions that represents 100% of the genetic variation in bottle gourds. This core population will make an important contribution to the preservation and utilization of bottle gourd germplasm collections, cultivar identification, and marker-assisted breeding.

Metapopulation management of a critically endangered marsupial in the age of genomics

The value of genetic management is increasingly recognised in natural resource management particularly in relation to threatened species conservation and translocations. Technical advancements in methodologies available to conservation managers for genetic management present a challenge for long-running programs that monitor genetic diversity over time. Given that microsatellite and single nucleotide polymorphism (SNP) data are not interchangeable, conservation managers are faced with two options: continue using older techniques for consistency (limits genetic knowledge); or discard previous data and move to more precise modern genetic markers (wastes resources and prevents temporal monitoring). To achieve a balance, we should consider whether conservation recommendations made are broadly similar between interpretations of different marker sets, even if estimates are not directly comparable. Here we generated 13,194 SNPs for the woylie ( Bettongia penicillata ), an Australian marsupial, to provide conservation recommendations across their current range (N = 13 indigenous, reintroduced and haven populations) and provide guidance to conservation managers on how these recommendations align with those previously made using 12 microsatellite markers. Observed heterozygosity was significantly less than expected heterozygosity reflecting the historical bottleneck for the species. Only 4 of the 13 populations showed evidence of inbreeding, and effective population sizes ranged from 9.9 to 268.9. Trends in observed heterozygosity were broadly similar between microsatellite and SNP marker sets. Herein we provide advice for conservation managers undertaking translocations on using genetic data, highlight the benefits of moving to newer SNP based approaches for monitoring conservation actions over time, and show that historical management actions are supported by new technologies.

GWAS identifies an ortholog of the rice D11 gene as a candidate gene for grain size in an international collection of hexaploid wheat

Grain size is a key agronomic trait that contributes to grain yield in hexaploid wheat. Grain length and width were evaluated in an international collection of 157 wheat accessions. These accessions were genetically characterized using a genotyping-by-sequencing (GBS) protocol that produced 73,784 single nucleotide polymorphism (SNP) markers. GBS-derived genotype calls obtained on Chinese Spring proved extremely accurate when compared to the reference (> 99.9%) and showed > 95% agreement with calls made at SNP loci shared with the 90 K SNP array on a subset of 71 Canadian wheat accessions for which both types of data were available. This indicates that GBS can yield a large amount of highly accurate SNP data in hexaploid wheat. The genetic diversity analysis performed using this set of SNP markers revealed the presence of six distinct groups within this collection. A GWAS was conducted to uncover genomic regions controlling variation for grain length and width. In total, seven SNPs were found to be associated with one or both traits, identifying three quantitative trait loci (QTLs) located on chromosomes 1D, 2D and 4A. In the vicinity of the peak SNP on chromosome 2D, we found a promising candidate gene (TraesCS2D01G331100), whose rice ortholog (D11) had previously been reported to be involved in the regulation of grain size. These markers will be useful in breeding for enhanced wheat productivity.

Development and characterization of 56 SNP markers in Misgurnus anguillicaudatus

The dojo loach Misgurnus anguillicaudatus is an endemic freshwater species in Asia. The effective conservation and molecular-aided selection of M. anguillicaudatus were limited without sufficient molecular markers. In this study, 112 novel single nucleotide polymorphism (SNP) markers were screened based on 2b-RAD sequencing database, and 56 SNPs of them were developed and characterized by genotyping 40 individuals using SNaPshot method. The observed heterozygosity (Ho) ranged from 0.025 to 0.675, while the expected heterozygosity (He) varied from 0.025 to 0.500. The minor allele frequency (MAF) ranged from 0.013 to 0.500. Among these SNPs, 18 loci were found to deviate significantly from the Hardy–Weinberg equilibrium after Bonferroni correction (P < 0.05). The first set of SNP markers developed from M. anguillicaudatus will provide valuable information in further population genetic analysis and natural resource conservation.

DdRAD sequencing: an emerging technology added to the biosecurity toolbox for tracing the origin of brown marmorated stink bug, Halyomorpha halys (Hemiptera: Pentatomidae)

BackgroundBrown marmorated stink bug (BMSB), Halyomorpha halys (Hemiptera: Pentatomidae) is native to East Asia but has invaded many countries in the world. BMSB is a polyphagous insect pest and causes significant economic losses to agriculture worldwide. Knowledge on the genetic diversity among BMSB populations is scarce but is essential to understand the patterns of colonization and invasion history of local populations. Efforts have been made to assess the genetic diversity of BMSB using partial mitochondrial DNA sequences but genetic divergence on mitochondria is not high enough to precisely accurately identify and distinguish various BMSB populations. Therefore, in this study, we applied a ddRAD (double digest restriction-site associated DNA) sequencing approach to ascertain the genetic diversity of BMSB populations collected from 12 countries (2 native and 10 invaded) across four continents with the ultimate aim to trace the origin of BMSBs intercepted during border inspections and post-border surveillance.ResultA total of 1775 high confidence single nucleotide polymorphisms (SNPs) were identified from ddRAD sequencing data collected from 389 adult BMSB individuals. Principal component analysis (PCA) of the identified SNPs indicated the existence of two main distinct genetic clusters representing individuals sampled from regions where BMSB is native to, China and Japan, respectively, and one broad cluster comprised individuals sampled from countries which have been invaded by BMSB. The population genetic structure analysis further discriminated the genetic diversity among the BMSB populations at a higher resolution and distinguished them into five potential genetic clusters.ConclusionThe study revealed hidden genetic diversity among the studied BMSB populations across the continents. The BMSB populations from Japan were genetically distant from the other studied populations. Similarly, the BMSB populations from China were also genetically differentiated from the Japanese and other populations. Further genetic structure analysis revealed the presence of at least three genetic clusters of BMSB in the invaded countries, possibly originating via multiple invasions. Furthermore, this study has produced novel set of SNP markers to enhance the knowledge of genetic diversity among BMSB populations and demonstrates the potential to trace the origin of BMSB individuals for future invasion events.

Leveraging the 3000 Rice Genome Data for Computational Design of Polymorphic Markers in a Local Rice Variety Lacking Sequence Data

DNA markers can detect DNA sequence variations in the genome, and they are useful for genetic studies, DNA fingerprinting, and genotype-based selection in breeding programs. Rice, as one of the model plants for genetic and genomic studies, has abundant DNA markers stored in various online databases. Selecting markers in rice is not limited by marker availability but rather by their polymorphism in the target population. We developed a computational method to screen millions of single nucleotide polymorphism (SNP) markers listed in IRRI 3000 rice genome database in order to find a subset of markers that are polymorphic in an F2 mapping population created from a cross between a parental line with a known genome sequence and a local Indonesian variety with no genome sequence data. The parental lines were genotyped using an affordable medium-density SNP array. The genotype data was cross-referenced with the rice genome database to perform phylogenetic analysis and identify accessions clusters with the highest genetic similarities to each parental line. The cluster data was then used to identify monomorphic SNP candidates within the cluster but exhibit consistent polymorphism between the two clusters. Using this method, we obtained a SNP marker set for a segment in rice chromosome 8 with 76.19% polymorphism rate, which is much higher than the expected 1.06% polymorphism rate if the SNP markers were chosen randomly. The improved polymorphism rate was also observed when the method was applied to other random chromosome segments and randomly chosen parental candidates.

SNP marker assay and candidate gene identification for sex expression via genotyping-by-sequencing-based genome-wide associations (GWAS) analyses in Oriental melon (Cucumis melo L.var.makuwa)

The Oriental melon is an important delicious fruit crop across East Asia. Single-nucleotide polymorphisms (SNPs) are considered to be a useful genotyping tool both to detect genetic diversity and to protect breeder rights. This study used genotyping-by-sequencing (GBS) to detect genome-wide SNPs by analyzing 48 commercial Oriental melon varieties to generate 5640 filtered SNPs. Based on the high polymorphism information content (PIC), genetic and physical distances, a subset of 192 SNPs was selected as putative SNPs for validation via the Fluidigm JunoTM system. Of these, 164 SNPs were successfully validated in 87 Oriental melon varieties with a validation ratio of 85.41 %. Furthermore, these 87 Oriental melon varieties were classified into ten distinct groups, based on 164 SNP markers. Therefore, these large set of SNP markers detected here has several application, such as genetic diversity studies, varietal identification and marker-assisted selection (MAS) in the Oriental melon. Genome-wide associations (GWAS) analyses detected significant 18 SNPs associated with various morphological traits, including two novel SNPs for sex expression on chromosomes 1 and 8 that were not colocalized with previous studies. The four potential candidate genes such as MELO3C015898, MELO3C015904, MELO3C024563, and MELO3C024565 were predicted within the GWAS-SNPs regions for sex expression in the Oriental melon. Hence, identification of these candidate genes has provided the foundation to study the molecular genetic mechanism of sex expression trait in the Oriental melon.

Development of SNP markers for marker-assisted breeding in Chinese cabbage using Fluidigm genotyping assays

Traditional breeding methods usually involve field tests carried out by experienced breeders. However, such methods are costly and time-consuming. Recently, with the development of Next-Generation Sequencing (NGS) technology, molecular markers are being utilized for selection processes in breeding. To implement a high-throughput system using molecular markers in Chinese cabbage (Brassica rapa subsp. pekinensis) breeding, we developed single nucleotide polymorphism (SNP) marker sets for background selection and testing F1 purity using Fluidigm genotyping assays. SNPs were generated using NGS technology on 209 varieties of Chinese cabbage collected from around the world. Those with minor allele frequency ≥ 5% and polymorphism information content ≥ 0.3 were screened, and then based on the physical distribution among the 10 chromosomes, 177 SNPs were selected and synthesized for testing. To obtain marker sets with high selection efficiency, we tested 192 SNPs on 45 types of inbred lines and 29 types of F1 hybrids. Among the 192 SNPs, we selected 96 markers sets for background selection and 24 marker sets for F1 purity testing according to the following criteria; the genotype of the parents was homozygous, and the F1 follows the parents’ genotypes. These SNP sets are suitable for high-throughput systems using the 96.96 and 192.24 integrated fluidic circuit platforms of Fluidigm genotyping assays. These SNP marker sets are not only efficient for selecting of early fixed lines as background selection but are also useful for testing the purity of F1 hybrids.

Development of a set of SNP markers for population genetics of the red gorgonian (Paramuricea clavata), an emblematic species of the Mediterranean coralligenous

Transcriptome sequencing was used for the development of single nucleotide polymorphisms (SNP) for the red gorgonian (Paramuricea clavata). A total of 20,736 SNPs were identified, and 1718 had a coverage of over 100 reads. Of the 480 SNPs tested, 347 SNPs were successfully genotyped at 95 samples from the NW Mediterranean using a MassARRAY System. This set of markers will be of great value for population genetics and phylogeography.

Development of a New Am -Genome-Specific Single Nucleotide Polymorphism Marker Set for the Molecular Characterization of Wheat-Triticum monococcum Introgression Lines.

We identified 1247 polymorphic single nucleotide polymorphisms between Triticum monococcum and wheat. We identified 191 markers validated across all seven chromosomes of T. monococcum. Detected a T. monococcum introgression in leaf-rust-resistant lines. Cultivated einkorn wheat (Triticum monococcum L. subsp. monococcum, 2n = 2x = 14, Am Am ) and its wild relative T. monococcum subsp. aegilopoides are important sources of economically useful genes that can be exploited for wheat (Triticum aestivum L.) breeding. Einkorn has excellent resistance to fungal diseases and gene transfer is relatively simple via standard breeding methods. To fulfill the growing demand by modern prebreeding programs for a cost-effective high-throughput procedure for accurately detecting introgressed chromosomes or chromosome segments from T. monococcum into wheat, we used the Axiom Wheat-Relative Genotyping Array and developed a set of Am genome-specific exome-based single nucleotide polymorphism (SNP) markers suitable for rapid identification of T. monococcum chromatin in a wheat background. We identified 1247 polymorphic SNPs between T. monococcum and wheat. We identified 191 markers across all seven chromosomes of T. monococcum that are also present on an existing Triticum urartu Thum. ex Gandil. genetic map and potentially ordered them on the basis of the high macrocollinearity and conservation of marker order between T. monococcum and T. urartu. The marker set has been tested on leaf-rust-resistant BC3 F4 progenies of wheat-T. monococcum hybrids. Two markers (AX-94492165, AX-95073542) placed on the distal end of the chromosome arm 7AL detected a T. monococcum introgression into wheat. The SNP marker set thus proved highly effective in the identification of T. monococcum chromatin in a wheat background, offering a reliable method for screening and selecting wheat-T. monococcum introgression lines, a procedure that could significantly speed up prebreeding programs.

Identification and development of a core set of informative genic SNP markers for assaying genetic diversity in Chinese cabbage

Rapid, economical, and reliable genotyping is an important requirement for germplasm analysis and cultivar identification in crop species. Chinese cabbage (Brassica rapa L. subsp. pekinensis (Lour.) Hanelt) originated in China and is now an economically important vegetable crop worldwide, especially in East Asia. In this study, we evaluated 1167 single nucleotide polymorphisms (SNPs) among 166 representative Chinese cabbage inbred lines using a KASP genotyping assay. On the basis of polymorphisms and principal component analysis, we selected 60 core SNPs distributed on all Brassica rapa chromosomes with allele frequencies sufficiently balanced so as to provide adequate information for genetic identification. The core set of SNPs was used for construction of a neighbor-joining dendrogram, in which the 166 inbred lines were clustered into spring, summer, and autumn ecotype groups. Clustering of the ecotype groups was better resolved than that achieved with 1167 and 360 polymorphic SNP datasets. Stability and resolution of the core SNP markers were tested using 178 commercial hybrid Chinese cabbage cultivars to confirm their utility in genetic identification. The set of 60 informative and stable SNP markers showed high discriminatory power and relatively uniform genomic distribution (4–9 markers per chromosome). The SNPs represent a cost-efficient and accurate marker set for germplasm analysis and cultivar identification and are suitable for molecular marker-assisted breeding in Chinese cabbage.

Development and Application of Single‐Nucleotide Polymorphism (SNP) Genetic Markers for Conservation Monitoring of Burbot Populations

AbstractThe transboundary (Idaho, USA; and British Columbia, Canada) population of Burbot Lota lota native to the Kootenai River basin once provided a popular sport and commercial fishery and has been culturally significant to the Kootenai Tribe of Idaho for millennia. However, the population has experienced significant declines over the last 30 years, due primarily to habitat loss and alteration caused by water storage and diversion. By the late 1990s, the population was considered functionally extinct, with estimates of fewer than 50 Burbot in the wild and little to no recruitment, prompting an ongoing international recovery effort. As part of these recovery efforts, managers have been actively developing a hatchery supplementation program to rebuild the population and support future tribal subsistence harvest and recreational fisheries. Although supplementation breeding programs have the potential to rapidly rebuild depleted natural populations, careful genetic management is critical. To monitor genetic diversity and potential inbreeding in the broodstock and to provide parentage‐based tagging of supplementation offspring, we developed a set (N = 96) of highly variable single‐nucleotide polymorphism (SNP) genetic markers. The subset of 96 SNP markers was developed from a larger suite of 6,517 SNPs that were discovered by using restriction site‐associated DNA sequencing. This cost‐efficient technology allows for the rapid discovery of thousands of SNP markers in species that have not been extensively studied previously or for which there are little existing DNA sequence data. We demonstrated high accuracy (&gt;99%) of our SNP set for parentage and individual identification through simulated and empirical tests. The SNP marker set provides a powerful new tool for managing broodstock and for monitoring and genetically tagging Burbot to track the growth, survival, and movement of released individuals.

Development and validation of an exome-based SNP marker set for identification of the St, Jr and Jvs genomes of Thinopyrym intermedium in a wheat background

Key messageCytogenetic analysis and array-based SNP genotyping of wheat–Th. intermediumintrogression lines allowed identification of 634 chromosome-specific SNP markers across all twenty-one chromosomes ofTh. intermedium(StJrJvs, 2n = 6x = 42).Thinopyrum intermedium (2n = 6x = 42, StJrJvs) is one of the most promising reservoirs of useful genes including tolerance to abiotic stresses, perenniality and disease resistance not available in the cultivated bread wheat. The transfer of genetic diversity from wild species to wheat offers valuable responses to the effects of climate change. The new array-based single-nucleotide polymorphism (SNP) marker technology provides cheap and easy-to-use molecular markers for marker-assisted selection (MAS) in wheat breeding programmes. Here, we focus on the generation of a new chromosome-specific SNP marker set that can be used to characterize and identify the Th. intermedium chromosomes or chromosome segments transferred into wheat. A progressive investigation of marker development was conducted using 187 various newly developed wheat–Th. intermedium introgression lines and the Axiom® Wheat-Relative Genotyping array. We employed molecular cytogenetic techniques to clarify the genome constitution of the Th. intermedium parental lines and validated 634 chromosome-specific SNPs. Our data confirmed the allohexaploid nature of Th. intermedium and demonstrated that the St genome-specific GISH signal and markers are present at the centromeric regions of chromosomes 1Jvs, 2Jvs, 3Jvs and 7Jvs. The SNP markers presented here will be introduced into current wheat improvement programmes, offering a significant speed-up in wheat breeding and making it possible to deal with the transfer of the full genetic potential of Th. intermedium into wheat.