Genome-wide Single Nucleotide Polymorphism Markers Research Articles

Review of sheep breeding and genetic research in Türkiye

The livestock industry in Türkiye is vital to the country’s agricultural sector and economy. In particular, sheep products are an important source of income and livelihood for many Turkish smallholder farmers in semi-arid and highland areas. Türkiye is one of the largest sheep producers in the world and its sheep production system is heavily dependent on indigenous breeds. Given the importance of the sheep industry in Türkiye, a systematic literature review on sheep breeding and genetic improvement in the country is needed for the development and optimization of sheep breeding programs using modern approaches, such as genomic selection. Therefore, we conducted a comprehensive literature review on the current characteristics of sheep populations and farms based on the most up-to-date census data and breeding and genetic studies obtained from scientific articles. The number of sheep has increased in recent years, mainly due to the state’s policy of supporting livestock farming and the increase in consumer demand for sheep dairy products with high nutritional and health benefits. Most of the genetic studies on indigenous Turkish sheep have been limited to specific traits and breeds. The use of genomics was found to be incipient, with genomic analysis applied to only two major breeds for heritability or genome-wide association studies. The scope of heritability and genome-wide association studies should be expanded to include traits and breeds that have received little or no attention. It is also worth revisiting genetic diversity studies using genome-wide single nucleotide polymorphism markers. Although there was no report of genomic selection in Turkish sheep to date, genomics could contribute to overcoming the difficulties of implementing traditional pedigree-based breeding programs that require accurate pedigree recording. As indigenous sheep breeds are better adapted to the local environmental conditions, the proper use of breeding strategies will contribute to increased income, food security, and reduced environmental footprint in a sustainable manner.

Genome-wide association study of soluble solids content, flesh color, and fruit shape in citron watermelon.

Fruit quality traits are crucial determinants of consumers' willingness to purchase watermelon produce, making them major goals for breeding programs. There is limited information on the genetic underpinnings of fruit quality traits in watermelon. A total of 125 citron watermelon (Citrullus amarus) accessions were genotyped using single nucleotide polymorphisms (SNPs) molecular markers generated via whole-genome resequencing. A total of 2,126,759 genome-wide SNP markers were used to uncover marker-trait associations using single and multi-locus GWAS models. High broad-sense heritability for fruit quality traits was detected. Correlation analysis among traits revealed positive relationships, with the exception of fruit diameter and fruit shape index (ratio of fruit length to fruit diameter), which was negative. A total of 37 significant SNP markers associated with soluble solids content, flesh color, fruit length, fruit diameter, and fruit shape index traits were uncovered. These peak SNPs accounted for 2.1%-23.4% of the phenotypic variation explained showing the quantitative inheritance nature of the evaluated traits. Candidate genes relevant to fruit quality traits were uncovered on chromosomes Ca01, Ca03, Ca06, and Ca07. These significant molecular markers and candidate genes will be useful in marker-assisted breeding of fruit quality traits in watermelon.

Predicting phenotypes from novel genomic markers using deep learning.

Genomic selection (GS) models use single nucleotide polymorphism (SNP) markers to predict phenotypes. However, these predictive models face challenges due to the high dimensionality of genome-wide SNP marker data. Thanks to recent breakthroughs in DNA sequencing and decreased sequencing cost, the study of novel genomic variants such as structural variations (SVs) and transposable elements (TEs) become increasingly prevalent. In this article, we develop a deep convolutional neural network model, NovGMDeep, to predict phenotypes using SVs and TEs markers for GS. The proposed model is trained and tested on samples of Arabidopsis thaliana and Oryza sativa using k-fold cross-validation. The prediction accuracy is evaluated using Pearson's Correlation Coefficient (PCC), mean absolute error (MAE) and SD of MAE. The predicted results showed higher correlation when the model is trained with SVs and TEs than with SNPs. NovGMDeep also has higher prediction accuracy when comparing with conventional statistical models. This work sheds light on the unappreciated function of SVs and TEs in genotype-to-phenotype associations, as well as their extensive significance and value in crop development.

V-primer: software for the efficient design of genome-wide InDel and SNP markers from multi-sample variant call format (VCF) genotyping data.

DNA markers are indispensable tools in genetics and genomics research as well as in crop breeding, particularly for marker-assisted selection. Recent advances in next-generation sequencing technology have made it easier to obtain genome sequences for various crop species, enabling the large-scale identification of DNA polymorphisms among varieties, which in turn has made DNA marker design more accessible. However, existing primer design software is not suitable for designing many types of genome-wide DNA markers from next-generation sequencing data. Here, we describe the development of V-primer, high-throughput software for designing insertion/deletion, cleaved amplified polymorphic sequence, and single-nucleotide polymorphism (SNP) markers. We validated the applicability of these markers in different crops. In addition, we performed multiplex PCR targeted amplicon sequencing using SNP markers designed with V-primer. Our results demonstrate that V-primer facilitates the efficient and accurate design of primers and is thus a useful tool for genetics, genomics, and crop breeding. V-primer is freely available at https://github.com/ncod3/vprimer.

Population structure of Caspian Kutum (Rutilus frisii, Nordmann, 1840) in the southern coast of Caspian Sea using Genome-wide single nucleotide polymorphism markers

The Caspian kutum (Rutilus frisii, Nordmann, 1840) is one of the most important semi-anadromous endemic fish species in the southern part of the Caspian Sea. The fisheries from wild populations of R. frisii are declined drastically due to variability of sea levels, overfishing, and illegal fishing. For this regard, genetic studies is very noticed to maintain of remained this endangered species. Here, we used restriction site-associated DNA sequencing (RAD-seq) approach to explore population structure, genetic variability, and single nucleotide polymorphisms (SNPs) from 146 individuals from eight rivers in Iran. In total 86,274 SNP loci were determined, and after filtering, 16,193 high-quality SNP markers were applied in statistical analyses. Twenty-eight percent of selected SNPs were located in genic regions and about 65% of these SNPs were in the coding sequence. Of the 102 SNP loci, 42 loci were found to be polymorphic and bi-allelic. The minor allele frequency (MAF) of these SNPs varied from 0.156 to 0.471. The observed heterozygosity (Ho) per locus ranged from 0.119 to 0.864, while the expected heterozygosity (He) per locus was from 0.142 to 0.569. Among these SNP loci, 22 SNP loci were significantly deviated from the Hardy–Weinberg equilibrium (P < 0.01) after Bonferroni correction. Both Principal coordinate analysis (PCA) and Bayesian clustering satisfyingly showed population genomic structure in Caspian kutum populations, indicating the description of distinct population segments. The first development of SNP markers in this study provides the better monitoring of population genetic variation in Caspian kutum at a more detailed level and in the scarce of genetic information about this species.

Conservation status and historical relatedness of South African communal indigenous goat populations using a genome-wide single-nucleotide polymorphism marker.

Indigenous goats form the majority of populations in smallholder, low input, low output production systems and are considered an important genetic resource due to their adaptability to different production environments and support of communal farming. Effective population size (N e ), inbreeding levels, and the runs of homozygosity (ROHs) are effective tools for exploring the genetic diversity and understanding the demographic history in efforts to support breeding strategies to use and conserve genetic resources. Across populations, the current N e of Gauteng was the lowest at 371 animals, while the historical N e across populations suggests that the ancestor N e has decreased by 53.86%, 44.58%, 42.16%, and 41.16% in Free State (FS), North West (NW), Limpopo (LP), and Gauteng (GP), respectively, over the last 971 generations. Genomic inbreeding levels related to ancient kinship (F ROH > 5 Mb) were highest in FS (0.08 ± 0.09) and lowest in the Eastern Cape (EC) (0.02 ± 0.02). A total of 871 ROH island regions which include important environmental adaptation and hermo-tolerance genes such as IL10RB, IL23A, FGF9, IGF1, EGR1, MTOR, and MAPK3 were identified (occurring in over 20% of the samples) in FS (n = 37), GP (n = 42), and NW (n = 2) populations only. The mean length of ROH across populations was 7.76 Mb and ranged from 1.61 Mb in KwaZulu-Natal (KZN) to 98.05 Mb (GP and NW). The distribution of ROH according to their size showed that the majority (n = 1949) of the detected ROH were > 5 Mb in length compared to the other categories. Assuming two hypothetical ancestral populations, the populations from KZN and LP are revealed, supporting PC 1. The genomes of KZN and LP share a common origin but have substantial admixture from the EC and NW populations. The findings revealed that the occurrence of high N e and autozygosity varied largely across breeds in communal indigenous goat populations at recent and ancient events when a genome-wide single-nucleotide polymorphism (SNP) marker was used. The use of Illumina goat SNP50K BeadChip shows that there was a migration route of communal indigenous goat populations from the northern part (LP) of South Africa to the eastern areas of the KZN that confirmed their historical relatedness and coincides with the migration periods of the Bantu nation.

Genomics-Assisted Improvement of Super High-Yield Hybrid Rice Variety "Super 1000" for Resistance to Bacterial Blight and Blast Diseases.

The two-line rice hybrid “Super 1000” (GX24S × R900) represents a major landmark achievement of breeding for super-hybrid rice in China. However, both male parent R900 and hybrid “Super 1000” have an obvious defect of high susceptibility to rice bacterial blight (BB) and blast. Thus, improving disease resistance and maintaining the original high-yield capacity are essential for the sustainable application of “Super 1000.” In this study, the application of closely linked single-nucleotide polymorphism (SNP) markers for foreground selection of dominant resistance gene loci together with genome-wide SNP markers for the background selection rapidly improved the disease resistance of R900 without disturbing its high-yield capacity. A series of improved R900 lines (iR900, in BC2Fn and BC3Fn generations) were developed to stack resistance genes (Xa23+Pi9, Xa23+Pi1+Pi2/9) by marker-assisted backcrossing and field selection for phenotypes, and further crossed with the female line GX24S to obtain improved hybrid variety Super 1000 (iS1000). The genetic backgrounds of iS1000 and “Super 1000” were profiled by using a 56 K SNP-Chip, and results showed that they shared 98.76% of similarity. Meanwhile, evaluation of the field disease resistance showed that the iR900 lines and iS1000 hybrids possess significantly enhanced resistance to both BB and rice blast. Resistance spectrum assays revealed that the iR900 lines and their derived hybrids exhibited high-level resistance to 28 Xoo strains tested, and enhanced resistance to leaf blast at the seedling stage when infected with 38 Magnaporthe oryzae isolates. Between 2019 and 2020, the multi-location field trials across the middle and lower reaches of the Yangtze River were launched and showed that the iS1000 slightly out-yielded than the original variety. In a large-scale demonstration site (6.73 ha, Yunnan, China), the iS1000 achieved 17.06 t/hm2 of yield in 2019. Moreover, the high similarity was observed in main agronomic traits and grain quality when comparing the improved lines/hybrids to original ones (iR900 vs. R900, iS1000 vs. S1000). This work presented a typical genomics-assisted breeding strategy and practice, which involves in directional introgression and rapid stack of multiple disease resistance genes, endowing the super-high-yield hybrid rice variety with holistic disease resistance but without yield penalty.

How methodological changes have influenced our understanding of population structure in threatened species: insights from tiger populations across India.

Unprecedented advances in sequencing technology in the past decade allow a better understanding of genetic variation and its partitioning in natural populations. Such inference is critical to conservation: to understand species biology and identify isolated populations. We review empirical population genetics studies of Endangered Bengal tigers within India, where 60–70% of wild tigers live. We assess how changes in marker type and sampling strategy have impacted inferences by reviewing past studies, and presenting three novel analyses including a single-nucleotide polymorphism (SNP) panel, genome-wide SNP markers, and a whole-mitochondrial genome network. At a broad spatial scale, less than 100 SNPs revealed the same patterns of population clustering as whole genomes (with the exception of one additional population sampled only in the SNP panel). Mitochondrial DNA indicates a strong structure between the northeast and other regions. Two studies with more populations sampled revealed further substructure within Central India. Overall, the comparison of studies with varied marker types and sample sets allows more rigorous inference of population structure. Yet sampling of some populations is limited across all studies, and these should be the focus of future sampling efforts. We discuss challenges in our understanding of population structure, and how to further address relevant questions in conservation genetics.This article is part of the theme issue ‘Celebrating 50 years since Lewontin's apportionment of human diversity’.

Genetic diversity and signatures of selection in the mito-gynogenetic olive flounder Paralichthys olivaceus revealed by genome-wide SNP markers

The artificial gynogenesis technique has been proven to be an effective genetic tool and has been widely used in fish breeding. The evaluation of the genetic basis of the artificial gynogenetic population is essential for breeding and farming, and the detection of the signatures of selection is potential to elucidate genes and mutations associated with important phenotypic traits. Olive flounder Paralichthys olivaceus is a commercially important flatfish species cultured in China, Japan, and Korea, and artificial gynogenesis has been used for its genetic breeding. In this study, the genetic variation of the artificial mito-gynogenetic population and common population of the flounder were analyzed using SNP markers with 2b-RAD genotyping technique. A total of 162 mito-gynogenetic and 90 common flounders were used, and 39,018 high-quality genome-wide single nucleotide polymorphisms (SNPs) were identified across two populations. The average observed heterozygosity (Ho) and average expected heterozygosity (He) of SNP were 0.1895 and 0.2413, and 0.0222 and 0.2974 in the common and mito-gynogenetic populations, respectively. Most loci significantly deviated from Hardy-Weinberg equilibrium (HWE) after Bonferroni correction in the former population. However, the genetic distance between the two populations suggested no significant genetic differentiation. Furthermore, analysis of run of homozygosity (ROH) showed low level of genomic inbreeding in the common population (inbreed coefficient was 0.2171) compared to higher inbreeding in the mito-gynogenetic population (inbreed coefficient was 0.9227). Short ROHs were more frequent in the common population, while long ROHs were more frequent in the mito-gynogenetic population, providing insight in the developmental history of the flounder. A total of 580 genes with putative selection signatures were identified across the two populations based on selective sweeps. These genes were involved in 39 KEGG pathways associated with some important traits, such as reproduction (e.g., sox8 and sox9) and immune response (e.g., dctn5 and socs-1). These results would be helpful for molecular marker-assisted breeding and conservation of genetic resources in the olive flounder and other marine culture fish.

Heterotic prediction of hybrid performance based on genome-wide SNP markers and the phenotype of parental inbred lines in heading Chinese cabbage (Brassica rapa L. ssp. pekinensis)

Chinese cabbage (Brassica rapa L. ssp. Pekinensis) is the most widely consumed leafy vegetable in Asia. Most commercial cultivars are F1 hybrids with high yield and good quality. To increase the breeding efficiency, heterotic prediction of hybrid performance was studied. Fourteen parental lines of Chinese cabbage were studied in a half-diallel cross to produce 91 hybrids. The average mid-parent heterosis (MPH) for 14 agronomic traits ranged from −5.07% to 106.76%, while the average high-parent heterosis (HPH) ranged from −109.90% to 80.56%. Significant HPH was observed in the growth period (−109.90%), biomass (80.56%), and plant weight (15.20%), which exhibited comprehensive advantages in breeding. Two methods were used to calculate the genetic distance (GD) between the parents based on 2,444,676 single nucleotide polymorphisms (SNPs): total SNPs (GDtotal) and homozygous differential SNPs (GDhomo). Parental clustering based on total SNPs divided the parents into three major types, namely “flat-topped”, “ovate”, and “cylindrical”. These types were more suitable for their traditional pedigree relationships. The correlation between the GD, mean parental phenotype, and heterosis indicated that the phenotype of the parental inbred lines may be useful for predicting heterosis because it is rapid and simple, whereas GD calculated using SNP markers led to a moderate improvement in heterotic prediction. GDhomo was a better predictor of heterosis and F1 performance than GDtotal. These results confirmed that whole-genome SNP markers are an effective tool for evaluating GD in Chinese cabbage and are useful for parent selection in breeding.

Genomic selection with fixed-effect markers improves the prediction accuracy for Capsaicinoid contents in Capsicum annuum.

Capsaicinoids provide chili peppers (Capsicum spp.) with their characteristic pungency. Several structural and transcription factor genes are known to control capsaicinoid contents in pepper. However, many other genes also regulating capsaicinoid contents remain unknown, making it difficult to develop pepper cultivars with different levels of capsaicinoids. Genomic selection (GS) uses genome-wide random markers (including many in undiscovered genes) for a trait to improve selection efficiency. In this study, we predicted the capsaicinoid contents of pepper breeding lines using several GS models trained with genotypic and phenotypic data from a training population. We used a core collection of 351 Capsicum accessions and 96 breeding lines as training and testing populations, respectively. To obtain the optimal number of single nucleotide polymorphism (SNP) markers for GS, we tested various numbers of genome-wide SNP markers based on linkage disequilibrium. We obtained the highest mean prediction accuracy (0.550) for different models using 3294 SNP markers. Using this marker set, we conducted GWAS and selected 25 markers that were associated with capsaicinoid biosynthesis genes and quantitative trait loci for capsaicinoid contents. Finally, to develop more accurate prediction models, we obtained SNP markers from GWAS as fixed-effect markers for GS, where 3294 genome-wide SNPs were employed. When four to five fixed-effect markers from GWAS were used as fixed effects, the RKHS and RR-BLUP models showed accuracies of 0.696 and 0.689, respectively. Our results lay the foundation for developing pepper cultivars with various capsaicinoid levels using GS for capsaicinoid contents.

Inferring genetic characteristics of Japanese Black cattle populations using genome-wide single nucleotide polymorphism markers

This study attempted to infer the population structure of Japanese Black cattle by using genotype data on 33,063 genomewide single nucleotide polymorphism (SNP) markers of totally 4,348 fattened steers slaughtered at carcass markets in Tokyo, Osaka, Hyogo, Tottori, and Hiroshima prefectures. We evaluated allele frequency, heterozygosity, linkage disequilibrium, correlation of linkage phase, and genotype concordance among the steers. The distribution of allele frequencies in the steers sampled in Hyogo differed from the others, showing >10% of the SNPs as monomorphic. Observed heterozygosity was lowest and degree of linkage disequilibrium was highest in Hyogo. Genotypes were more similar among Hyogo steers than between other steer pairs. These results show the genetic characteristics of the Japanese Black cattle populations inferred from genotype data on genome-wide SNPs obtained using a commercial chip.

Population structure and geographic origin assignment of Mytilus galloprovincialis mussels using SNPs

Seafood traceability represents a major goal for regulators and fishing industries worldwide who seek to prevent commercial fraud, protect marine resources and ensure consumer safety. Genetic approaches can be used to trace the provenance of seafood based on the ability of DNA markers to assign samples back to their population of origin. Here, we have used thousands of genome-wide Single Nucleotide Polymorphism markers to provide a detailed genetic structure of the highly farmed Mediterranean mussel Mytilus galloprovincialis in part of its native (Atlantic and Mediterranean areas) and introduced ranges (South-eastern Pacific area). Also, we have assessed the power of the newly developed markers to assign samples to their geographic origin. Results showed a clear differentiation between the Atlantic and the Mediterranean M. galloprovincialis populations, with significant differences also observed between the Mediterranean and South-eastern Pacific individuals. In addition, we found 90–100% of individuals could be correctly assigned to the Atlantic or Mediterranean/South-eastern Pacific populations when using only 10 to 25 SNPs. Our results support the possibility of the development of an accurate and cost-effective origin assignment tool with global uses in aquaculture management, seafood traceability and food safety.

Characterization of the genetic basis of local adaptation of wheat landraces from Iran and Pakistan using genome-wide association study.

Characterization of genomic regions underlying adaptation of landraces can reveal a quantitative genetics framework for local wheat (Triticum aestivum L.) adaptability. A collection of 512 wheat landraces from the eastern edge of the Fertile Crescent in Iran and Pakistan were genotyped using genome-wide single nucleotide polymorphism markers generated by genotyping-by-sequencing. The minor allele frequency (MAF) and the heterozygosity (H) of Pakistani wheat landraces (MAF=0.19, H=0.008) were slightly higher than the Iranian wheat landraces (MAF=0.17, H=0.005), indicating that Pakistani landraces were slightly more genetically diverse. Population structure analysis clearly separated the Pakistani landraces from Iranian landraces, which indicates two separate adaptability trajectories. The large-scale agro-climatic data of seven variables were quite dissimilar between Iran and Pakistan as revealed by the correlation coefficients. Genome-wide association study identified 91 and 58 loci using agroclimatic data, which likely underpin local adaptability of the wheat landraces from Iran and Pakistan, respectively. Selective sweep analysis identified significant hits on chromosomes 4A, 4B, 6B, 7B, 2D, and 6D, which were colocalized with the loci associated with local adaptability and with some known genes related to flowering time and grain size. This study provides insight into the genetic diversity with emphasis on the genetic architecture of loci involved in adaptation to local environments, which has breeding implications.

Development of genome-wide single nucleotide polymorphism markers for variety identification of F1 hybrids in cucumber (Cucumis sativus L.)

Plant variety identification is essential for the official registration of new cultivars and for variety protection. It is therefore imperative to have rapid and highly reliable methods for plant variety identification. In this study, a core 96-SNP set optimized for use with Fluidigm EP1TM assay was developed to facilitate cultivar identification in cucumber. Genotyping-by-sequencing (GBS) of 88 F1 hybrids comprising nine cultivar groups (Korean Gasi, Korean Nakhap, Korean Baekdadagi, Japanese Gasi, Chinese Gasi, Chinese Baekdadagi, Southeast Asian slice, European slice, and pickle groups) was carried out, and a total of 10,996 high-quality SNPs were generated. Population structure, principle component analysis, and hierarchical clustering indicated that the nine cultivar groups were clearly divided into four subpopulations (subpopulation G for Gasi type, B for Baekdadagi type, N for Nakhap type, and E for slice and pickle types). Population differentiation measures based on pairwise FST values indicated that the closest relationship (0.124) was between subpopulations B and N and subpopulations E (0.140) and G, while subpopulations B and E were the most clearly distinct from each other (0.208). The metrics of genetic differentiation measured by AMOVA also indicated that significant genetic division exists among the subpopulations, while variation among cultivars within each subpopulation is extremely low, indicating high genetic exchange within the subpopulations. By applying filtering criteria to the SNPs, including FST and linkage disequilibrium decay values, 240 SNPs were filtered from the original 10,996 for use with a Fluidigm assay, from which a core 96-SNP set was obtained. This set demonstrated high reproducibility and discrimination power. Hierarchical clustering confirmed that the core 96-SNP set could distinguish all 88 cultivars and delineate them clearly according to their population structures. A Mantel test based on 10,996 SNPs and 37 traits revealed a high level of correlation (r = 0.57) between molecular and morphological distance. Our core 96-SNP set is not only suitable for generating signature profiles of released cucumber cultivars, but also represents a promising supplement to morphological trait-based distinctness, uniformity, and stability testing for cultivar identification.

Genetic diversity and population structure of eddoe taro in China using genome-wide SNP markers.

Taro (Colocasia esculenta) is an important root and tuber crop cultivated worldwide. There are two main types of taro that vary in morphology of corm and cormel, ‘dasheen’ and ‘eddoe’. The eddoe type (Colocasia esculenta var. antiquorium) is predominantly distributed throughout China. Characterizing the genetic diversity present in the germplasm bank of taro is fundamental to better manage, conserve and utilize the genetic resources of this species. In this study, the genetic diversity of 234 taro accessions from 16 provinces of China was assessed using 132,869 single nucleotide polymorphism (SNP) markers identified by specific length amplified fragment-sequencing (SLAF-seq). Population structure and principal component analysis permitted the accessions to be categorized into eight groups. The genetic diversity and population differentiation of the eight groups were evaluated using the characterized SNPs. Analysis of molecular variance showed that the variation among eight inferred groups was higher than that within groups, while a relatively small variance was found among the two morphological types and 16 collection regions. Further, a core germplasm set comprising 41 taro accessions that maintained the genetic diversity of the entire collection was developed based on the genotype. This research is expected to be valuable for genetic characterization, germplasm conservation, and breeding of taro.

DdRAD genotyping reveals hierarchical genetic population structure in anadromous Arctic char (Salvelinus alpinus) in the Lower Northwest Passage, Nunavut

Contemporary intraspecific patterns of genetic variation reflect the historical effects of population subdivision–expansion and forces like drift, gene flow, and selection. We investigated the population structure of anadromous Arctic char (Salvelinus alpinus) in the Lower Northwest Passage (LNWP), Nunavut, using 3074 genome-wide single nucleotide polymorphisms markers (SNPs). Overall, the genetic differentiation was weak to moderate among 18 sampling locales (global FST= 0.037). Populations were structured hierarchically, with a deeper genetic division between King William Island (global FST= 0.018) and mainland populations ∼200 km away to the south (global FST= 0.018), and some evidence of genetic subgroups within the former. These findings suggest a role for char migratory behaviour in shaping contemporary genetic population structure, with demographic modelling favouring an isolation with migration over a strict isolation scenario. Twenty-two SNPs were identified as potentially under divergent selection with putative functions including neurotransmission and bone development and growth during late embryogenesis. Our study is the first survey of Arctic char in the LNWP using genomics and provides baseline data for the development of a sustainable fishery within this region.

Development of SNP markers and validation assays in commercial Korean melon cultivars, using Genotyping-by-sequencing and Fluidigm analyses

Melon is an important horticultural crop across the globe, which consisted of several subspecies. Single nucleotide polymorphisms (SNPs) are the most preferred molecular markers in genetic diversity and genomic studies. Recently, Genotyping-by-sequencing (GBS) has produced sequences that detect genome-wide distribution of these SNP markers. In this study, we identified genome-wide highly efficient SNP markers to differentiate the cultivars of the melon using GBS. Here we detected 9018 SNPs by the analysis of 48 commercialized Korean melon cultivars, which released by various seed companies in South Korea. Further, precise filtering resulted in 5644 high-quality SNPs. Of these, 5293 SNPs and 351 were identified in the genic region and intergenic region, respectively. A total of 192 SNPs were identified as putative SNPs, on the basis of high polymorphism information content (PIC) and physical distance. These SNPs were further analyzed to distinguish 95 commercial melon cultivars via high-throughput Fluidigm system, thus revealed 95.83 % (184 SNPs) of validation ratio. The summary of SNP genotyping revealed estimates of PIC ranged from 0.02 to 0.53 and 179 SNPs (97.28 %) showed more than 0.3 of PIC. This is the first study in melon to develop and validate genome-wide SNP markers using GBS and Fluidigm platform, respectively. The SNP markers reported in this study will be a valuable tool for cultivar identification, genetic diversity, and marker-trait association studies in melon.

Genetic diversity, population structure and runs of homozygosity in Ethiopian short fat-tailed and Awassi sheep breeds using genome-wide 50k SNP markers

Improved Awassi sheep from Israel has been used for the improvement of the productivity of Ethiopian short-fat tailed Menz and Wollo sheep breeds through crossbreeding. High density (~50,000) single nucleotide polymorphism (SNP) markers distributed along the ovine genome were analyzed for Menz (n = =34), Wollo (n = =18), local Awassi (n = =24) and improved Awassi (n = =23) sheep breeds to assess genetic diversity and population structure. Proportion of polymorphism was highest for local Awassi (96.2%) followed by the Ethiopian breeds (91.7 to 93.0%). Lowest proportion of polymorphic SNP was found in improved Awassi (84.3%). Expected heterozygosity was high (0.37) for local Awassi followed by the local Ethiopian breeds (0.35 and 0.36) and the improved Awassi (0.35). Highest genetic differentiation measured as fixation index (FST) appeared between local Ethiopian breeds and improved Awassi (FST ~ 0.14) while the two Ethiopian breeds were closely related (FST=0.004). Surprisingly, local Awassi sheep differentiated from improved Awassi at a higher level (FST = 0.09) than it differentiated from Wollo (FST = 0.058) and Menz (FST = 0.065). Principal component, model based structure and neighbor net analysis revealed clustering of populations according to their geographic location and breed development history. Strong selection pressure on the Awassi sheep resulted in significant differentiation from local Awassi, less within population variation, excess monomorphic loci and high level of runs of homozygosity (ROH) based genomic inbreeding. The high level of differentiation between local Ethiopian and improved Awassi supported the use of improved Awassi sheep to improve Menz and Wollo sheep breeds. However, importation of Awassi sheep and mating should consider strategies of controlling the level of inbreeding.

Development of SNP in spotted steed (Hemibarbus maculatus Bleeker) using GBS sequencing

Spotted steed (Hemibarbus maculatus) is a native freshwater fish widely distributed in China, but data regarding its genetic markers are scarce. In this study, we used genotyping by sequencing (GBS) to develop single nucleotide polymorphisms (SNPs) from 56 individuals. We discovered a total of 57,523 genome-wide SNP markers. After applying strict filtering criteria, 166 high-qualified SNPs were obtained. Among these SNPs markers, 42 polymorphic markers were identified and characterized. The observed and expected heterozygosity ranged from 0.063 to 0.479 and 0.100 to 0.500, respectively. Polymorphic information content ranged from 0.094 to 0.372. Among these markers, no loci were significantly deviated from Hardy–Weinberg equilibrium. This study indicated that GBS sequencing allowed fast and efficient isolation of SNPs, and these results could provide a useful resource in further population genetic studies and genetic mapping in spotted steed.