Extent Of Linkage Disequilibrium Research Articles

Evidence for Strong Kinship Influence on the Extent of Linkage Disequilibrium in Cultivated Common Beans.

Phaseolus vulgaris is an important grain legume for human consumption. Recently, association mapping studies have been performed for the species aiming to identify loci underlying quantitative variation of traits. It is now imperative to know whether the linkage disequilibrium (LD) reflects the true association between a marker and causative loci. The aim of this study was to estimate and analyze LD on a diversity panel of common beans using ordinary and extensions which correct bias due to population structure (), kinship (), and both (). A total of 10,362 single nucleotide polymorphisms (SNPs) were identified by genotyping by sequencing (GBS), and polymorphisms were found to be widely distributed along the 11 chromosomes. In terms of , high values of LD (over 0.8) were identified between SNPs located at opposite chromosomal ends. Estimates for were lower than those for . Results for and were similar, suggesting that kinship may also include information on population structure. Over genetic distance, LD decayed to 0.1 at a distance of 1 Mb for . Inter-chromosomal LD was also evidenced. This study showed that LD estimates decay dramatically according to the population structure, and especially the degree of kinship. Importantly, the LD estimates reported herein may influence our ability to perform association mapping studies on P. vulgaris.

Exploring genotype–phenotype relationships of the CRABP2 gene on growth traits in beef cattle

Cellular retinoic acid binding protein 2 (CRABP2) is essential to myoblast differentiation. However, there was no report about the function of CRABP2 gene in cattle. This study explored the association of CRABP2 gene polymorphisms with growth traits in cattle breeds by several methods, such as DNA sequencing, PCR, PCR–RFLP and forced PCR–RFLP. Two sequence variants were determined. There were 621 individuals in six cattle breeds from China for the experiment, and three breeds were used to test validation of polymorphisms and extent of linkage disequilibrium (LD). The results showed that both SNPs (SNP1, g.2458 G > T, SNP2, g.3878 G > A) were in intron1. Two SNPs were in low linkage disequilibrium. Association analysis suggested that SNP1 had the significant difference on growth traits with body height, height at hip cross and body slanting length (P < .05), while SNP2 showed a significant difference in growth traits with body height, height at hip cross and body slanting length(P < .05). The results of this investigation displayed that the CRABP2 gene is an available candidate gene and may be used for breed selection and conservation.

Population Genomic Structure and Genome-Wide Linkage Disequilibrium in Farmed Atlantic Salmon (Salmo salar L.) Using Dense SNP Genotypes.

Chilean Farmed Atlantic salmon (Salmo salar) populations were established with individuals of both European and North American origins. These populations are expected to be highly genetically differentiated due to evolutionary history and poor gene flow between ancestral populations from different continents. The extent and decay of linkage disequilibrium (LD) among single nucleotide polymorphism (SNP) impacts the implementation of genome-wide association studies and genomic selection and provides relevant information about demographic processes of fish populations. We assessed the population structure and characterized the extent and decay of LD in three Chilean commercial populations of Atlantic salmon with North American (NAM), Scottish (SCO), and Norwegian (NOR) origin. A total of 123 animals were genotyped using a 159 K SNP Axiom® myDesignTM Genotyping Array. A total of 32 K SNP markers, representing the common SNPs along the three populations after quality control were used. The principal component analysis explained 78.9% of the genetic diversity between populations, clearly discriminating between populations of North American and European origin, and also between European populations. NAM had the lowest effective population size, followed by SCO and NOR. Large differences in the LD decay were observed between populations of North American and European origin. An r2 threshold of 0.2 was estimated for marker pairs separated by 7,800, 64, and 50 kb in the NAM, SCO, and NOR populations, respectively. In this study we show that this SNP panel can be used to detect association between markers and traits of interests and also to capture high-resolution information for genome-enabled predictions. Also, we suggest the feasibility to achieve similar prediction accuracies using a smaller SNP data set for the NAM population, compared with samples with European origin which would need a higher density SNP array.

Population genetic analyses of seven Chinese indigenous chicken breeds in a context of global breeds.

Jiangxi province in China is rich in indigenous chicken breeds, which have diverse phenotypes and represent a valuable genetic resource for further genetic improvement of modern breeds. Here, we conducted a series of analyses to reveal genetic diversity, phylogenetic relationships and population structure of seven chicken breeds in Jiangxi province in the context of nine non-local chicken breeds, using 600K SNP data. We show that Jiangxi indigenous breeds have more abundant nucleotide diversity than do European local and commercial breeds. Among Jiangxi breeds, Dongxiang Blue-eggshell (DX) and Chongren Partride (CR) display remarkably reduced genetic diversity, as the two breeds exhibit increased inbreeding coefficients, runs of homozygosity, extent of linkage disequilibrium and reduced expected heterozygosity. DX, CR and Taihe Silkie (TH) represent three ancestral lineages of the Jiangxi chicken and display genetic differentiation from the other four Jiangxi breeds, which show a signature of admixture with European commercial breeds. These findings provide insight for the establishment of an efficient conservation program for Jiangxi chicken breeds. Considering the current status of genetic diversity and ancestral representativeness, particular attention should be paid to DX, CR and TH chickens.

Potential of Genome-Wide Studies in Unrelated Plus Trees of a Coniferous Species, Cryptomeria japonica (Japanese Cedar).

A genome-wide association study (GWAS) was conducted on more than 30,000 single nucleotide polymorphisms (SNPs) in unrelated first-generation plus tree genotypes from three populations of Japanese cedar Cryptomeria japonica D. Don with genomic prediction for traits of growth, wood properties and male fecundity. Among the assessed populations, genetic characteristics including the extent of linkage disequilibrium (LD) and genetic structure differed and these differences are considered to be due to differences in genetic background. Through population-independent GWAS, several significant SNPs found close to the regions associated with each of these traits and shared in common across the populations were identified. The accuracies of genomic predictions were dependent on the traits and populations and reflected the genetic architecture of traits and genetic characteristics. Prediction accuracies using SNPs selected based on GWAS results were similar to those using all SNPs for several combinations of traits and populations. We discussed the application of genome-wide studies for C. japonica improvement.

Genome sequencing and conservation genomics in the Scandinavian wolverine population.

Genetic approaches have proved valuable to the study and conservation of endangered populations, especially for monitoring programs, and there is potential for further developments in this direction by extending analyses to the genomic level. We assembled the genome of the wolverine (Gulo gulo), a mustelid that in Scandinavia has recently recovered from a significant population decline, and obtained a 2.42Gb draft sequence representing >85% of the genome and including >21,000protein-coding genes. We then performed whole-genome resequencing of 10Scandinavian wolverines for population genomic and demographic analyses. Genetic diversity was among the lowest detected in a red-listed population (mean genome-wide nucleotide diversity of 0.05%). Results of the demographic analyses indicated a long-term decline of the effective population size (Ne ) from 10,000well before the last glaciation to <500 after this period. Current Ne appeared even lower. The genome-wide FIS level was 0.089 (possibly signaling inbreeding), but this effect was not observed when analyzing a set of highly variable SNP markers, illustrating that such markers can give a biased picture of the overall character of genetic diversity. We found significant population structure, which has implications for population connectivity and conservation. We used an integrated microfluidic circuit chip technology to develop an SNP-array consisting of 96 highly informative markers that, together with a multiplex pre-amplification step, was successfully applied to low-quality DNA from scat samples. Our findings will inform management, conservation, and genetic monitoring of wolverines and serve as a genomic roadmap that can be applied to other endangered species. The approach used here can be generally utilized in other systems, but we acknowledge the trade-off between investing in genomic resources and direct conservation actions.

Target enrichment sequencing of 307 germplasm accessions identified ancestry of ancient and modern hybrids and signatures of adaptation and selection in sugarcane (Saccharum spp.), a 'sweet' crop with 'bitter' genomes.

SummarySugarcane (Saccharum spp.) is a highly energy‐efficient crop primarily for sugar and bio‐ethanol production. Sugarcane genetics and cultivar improvement have been extremely challenging largely due to its complex genomes with high polyploidy levels. In this study, we deeply sequenced the coding regions of 307 sugarcane germplasm accessions. Nearly five million sequence variations were catalogued. The average of 98× sequence depth enabled different allele dosages of sequence variation to be differentiated in this polyploid collection. With selected high‐quality genome‐wide SNPs, we performed population genomic studies and environmental association analysis. Results illustrated that the ancient sugarcane hybrids, S. barberi and S. sinense, and modern sugarcane hybrids are significantly different in terms of genomic compositions, hybridization processes and their potential ancestry contributors. Linkage disequilibrium (LD) analysis showed a large extent of LD in sugarcane, with 962.4 Kbp, 2739.2 Kbp and 3573.6 Kbp for S. spontaneum, S. officinarum and modern S. hybrids respectively. Candidate selective sweep regions and genes were identified during domestication and historical selection processes of sugarcane in addition to genes associated with environmental variables at the original locations of the collection. This research provided an extensive amount of genomic resources for sugarcane community and the in‐depth population genomic analyses shed light on the breeding and evolution history of sugarcane, a highly polyploid species.

Suitability of existing commercial single nucleotide polymorphism chips for genomic studies in Bos indicus cattle breeds and their Bos taurus crosses.

Bos indicus cattle breeds are genetically distinct from Bos taurus breeds. We examined the performance of three SNP arrays, the Illumina BovineHD BeadChip (777k; Illumina Inc.), the Illumina BovineSNP50 BeadChip (50k) and the GeneSeek 70k Indicus chip (75Ki; GeneSeek) in four B.indicus breeds (Gir, Kankrej, Sahiwal and Red Sindhi) and their B.taurus crosses, along with two B.taurus breeds, Holstein and Jersey. More SNPs on both Illumina SNP chips were monomorphic in B.indicus breeds (average 20.3%-29.3% on the 777k chip, 35.5%-45.5% on the 50k chip) than in Holstein (19.7% on the 777k chip, 17.1% on the 50k chip). The proportion of monomorphic SNPs on the 75Ki chip was much lower, 4% (2.8%-7%) in B.indicus breeds, while it was 33.5% in Holstein. With on average 164,357 heterozygous loci in B.indicus breeds, the 777k SNP chip has sufficient heterozygous loci to design a chip customized for B.indicus breeds. Principal component analysis clearly differentiated B.indicus from B.taurus breeds. Differentiation among B.indicus breeds was only achieved by plotting the third and fifth principal components using 777k genotype data. Admixture analysis showed that many B.indicus animals, previously believed to be of pure origin, are in fact had mixed ancestry. The extent of linkage disequilibrium showed comparatively higher effective population sizes in four B.indicus breeds compared to two B.taurus breeds. The results of admixture analyses show that it is important to assess the genomic composition of a bull before using it in a breeding programme.

Extent of linkage disequilibrium and effective population size of Korean Yorkshire swine.

ObjectiveWe aimed to characterize linkage disequilibrium (LD) and effective population size (Ne) in a Korean Yorkshire population using genomic data from thousands of individuals.MethodsWe genotyped 2,470 Yorkshire individuals from four major Grand-Grand-Parent farms in Korea using the Illumina PorcineSNP60 version2 BeadChip, which covers >61,565 single nucleotide polymorphisms (SNPs) located across all chromosomes and mitochondria. We estimated the expected LD and inferred current Ne as well as ancestral Ne.ResultsWe identified 61,565 SNP from autosomes, mitochondria, and sex chromosomes and characterized the LD of the Yorkshire population, which was relatively high between closely linked markers (>0.55 at 50 kb) and declined with increasing genetic distance. The current Ne of this Korean Yorkshire population was 122.87 (106.90; 138.84), while the historical Ne of Yorkshire pigs suggests that the ancestor Ne has decreased by 99.6% over the last 10,000 generations.ConclusionTo maintain genetic diversity of a domesticated animal population, we must carefully consider appropriate breed management methods to avoid inbreeding. Although attenuated selection can affect short-term genetic gain, it is essential for maintaining the long-term genetic variability of the Korean Yorkshire population. Continuous and long-term monitoring would also be needed to maintain the pig population to avoid an unintended reduction of Ne. The best way to preserve a sustainable population is to maintain a sufficient Ne.

Genetic diversity near the DGAT1-2 gene for high oleic acid content and kernel trait variation in a maize breeding collection

Previous studies in maize have identified three quantitative trait loci (QTLs) coding for high oleic acid content (HOAC) (QTLs oleic6-1, oleic6-2, and oleic6-3) at bins 6.04–6.05, proximal to the DGAT1-2 gene. The aims of this work were (i) to discover new markers for linkage disequilibrium (LD) and haplotype analysis distal to DGAT1-2, (ii) to develop a new DGAT1-2 PCR probe to detect the allele determining HOAC (F469 insertion), (iii) to conduct cluster analysis for kernel traits, and (iv) to assess genetic diversity, LD, and association analysis for kernel traits with the DGAT1-2 PCR probe and 13 markers previously mapped near DGAT1-2 in the Argentine temperate maize collection of 111 inbred lines. The results showed high haplotype diversity distal to DGAT1-2 and relatedness between the inbred line LP199 (with HOAC) and the Non-Stiff Stalk line W22 (reference genome). The frequency of F469 was low (20%). F469 was clustered with flint-grain type characteristics, whereas HOAC was associated with F469 across linear models. Genetic diversity at bins 6.04–6.05 was high (0.62), whereas LD extent was low (r2 ≤ 0.45). This low extent of LD indicates a high level of recombination and no LD between DGAT1-2 and markers flanking QTLs oleic6-1 to 3. Nevertheless, the significant LD between markers flanking those QTLs and the cosegregation of F469 with nc009 (markers flanking QTLs oleic6-1 and 2) during inbred line conversion suggest that these QTLs might contribute to HOAC in the breeding collection. However, further studies are needed to precise mapping at bins 6.04–6.05 for breeding purposes.

Extent of linkage disequilibrium and effective population size of the Landrace population in Korea.

ObjectiveThe genetic diversity of the Landrace population, a representative maternal pig breed in Korea, is important for genetic improvement. Previously, the effective population size (Ne) has been used to infer the genetic diversity of a population of interest. In this study, we aimed to use single nucleotide polymorphism (SNP) data to characterize linkage disequilibrium (LD) and the Ne of the Korean Landrace population.MethodsWe genotyped 1,128 Landrace individuals from three representative Korean major grand-grand-parent (GGP) farms using the Illumina PorcineSNP60 version2 BeadChip, which covers >61,565 SNPs located across all autosomes and mitochondrial and sex chromosomes. We estimated the expected LD and current Ne, as well as ancestral Ne.ResultsIn the Korean Landrace population, the mean LD (r2) of 3.698 million SNP pairs was 0.135±0.204. The mean r2 decreased slowly with as the distance between SNPs increased, and remained constant beyond 3 Mb. According to the r2 calculations, 8,085 of 3.698 million SNP pairs were in complete LD. The current Ne (±standard deviation) of the Korean Landrace population is approximately 92.27 [79.46; 105.07] individuals. The ancestral Ne exhibited a slow and steady decline from 186.61 to 92.27 over the past 100 generations. Additionally, we observed more a rapid Ne decrease from the past 20 to 10 generations ago, compared with other intervals.ConclusionWe have presented an overview of LD and the current and ancestral Ne values in the Korean Landrace population. The mean LD and current Ne for the Korean Landrace population confirm the genetic diversity and reflect the history of this pig population in Korea.

Whole genome study of linkage disequilibrium in Sahiwal cattle

The linkage disequilibrium (LD) is an important tool to study quantitative trait locus (QTL) mapping and genetic selection. In this study, we identified the extent of linkage disequilibrium (LD) in Sahiwal (n = 14) cattle using the bovine high density single-nucleotide polymorphisms (SNPs) BeadChip. After data filtering, 500,968 SNPs comprising 2518.1 Mb of the genome, were used for the LD estimation. The minior allele frequency (MAF) was 0.21 in a substantial proportion of SNPs and mean distance between adjacent markers was 4.77 ± 2.83 kb. The overall mean LD between adjacent markers was 0.18 (r 2 ) and 0.55 (|D'|), respectively. The LD (r 2 ) values reduced with the increase in distance between adjacent markers from 1 kb (0.35) to 100 kb (0.12) and |D'| specified distinct decay of the LD. Chromosomes 1, 27, 28 and 29 presented the LD at some distance between markers. The extent of LD was higher, except these four chromosomes, for markers separated by 20 kb. At < 3 kb distance, the upper value of the linkage disequilibrium (LD) was observed at 0.30. High level of the linkage disequilibrium (LD) between markers was observed at high minor allele frequency (MAF) threshold (0.15), at the short distance between markers. The results of this study revealed that the Bovine high density SNPs BeadChip will be informative for the estimation of breeding value in Sahiwal cattle. Keywords: Breeding value, linkage disequilibrium, minor allele frequency, molecular marker

Rice diversity panel provides accurate genomic predictions for complex traits in the progenies of biparental crosses involving members of the panel

Key messageRice breeding programs based on pedigree schemes can use a genomic model trained with data from their working collection to predict performances of progenies produced through rapid generation advancement.So far, most potential applications of genomic prediction in plant improvement have been explored using cross validation approaches. This is the first empirical study to evaluate the accuracy of genomic prediction of the performances of progenies in a typical rice breeding program. Using a cross validation approach, we first analyzed the effects of marker selection and statistical methods on the accuracy of prediction of three different heritability traits in a reference population (RP) of 284 inbred accessions. Next, we investigated the size and the degree of relatedness with the progeny population (PP) of sub-sets of the RP that maximize the accuracy of prediction of phenotype across generations, i.e., for 97 F5–F7 lines derived from biparental crosses between 31 accessions of the RP. The extent of linkage disequilibrium was high (r2 = 0.2 at 0.80 Mb in RP and at 1.1 Mb in PP). Consequently, average marker density above one per 22 kb did not improve the accuracy of predictions in the RP. The accuracy of progeny prediction varied greatly depending on the composition of the training set, the trait, LD and minor allele frequency. The highest accuracy achieved for each trait exceeded 0.50 and was only slightly below the accuracy achieved by cross validation in the RP. Our results thus show that relatively high accuracy (0.41–0.54) can be achieved using only a rather small share of the RP, most related to the PP, as the training set. The practical implications of these results for rice breeding programs are discussed.

Estimations of linkage disequilibrium, effective population size and ROH-based inbreeding coefficients in Spanish Churra sheep using imputed high-density SNP genotypes.

In this study, the availability of the Ovine HD SNP BeadChip (HD-chip) and the development of an imputation strategy provided an opportunity to further investigate the extent of linkage disequilibrium (LD) at short distances in the genome of the Spanish Churra dairy sheep breed. A population of 1686 animals, including 16 rams and their half-sib daughters, previously genotyped for the 50K-chip, was imputed to the HD-chip density based on a reference population of 335 individuals. After assessing the imputation accuracy for beagle v4.0 (0.922) and fimpute v2.2 (0.921) using a cross-validation approach, the imputed HD-chip genotypes obtained with beagle were used to update the estimates of LD and effective population size for the studied population. The imputed genotypes were also used to assess the degree of homozygosity by calculating runs of homozygosity and to obtain genomic-based inbreeding coefficients. The updated LD estimations provided evidence that the extent of LD in Churra sheep is even shorter than that reported based on the 50K-chip and is one of the shortest extents compared with other sheep breeds. Through different comparisons we have also assessed the impact of imputation on LD and effective population size estimates. The inbreeding coefficient, considering the total length of the run of homozygosity, showed an average estimate (0.0404) lower than the critical level. Overall, the improved accuracy of theupdated LD estimates suggests that the HD-chip, combined with an imputation strategy, offers a powerful tool that will increase the opportunities to identify genuine marker-phenotype associations and to successfully implement genomic selection in Churra sheep.

Estimates of linkage disequilibrium and effective population sizes in Chinese Merino (Xinjiang type) sheep by genome-wide SNPs

Knowledge of linkage disequilibrium (LD) is important for effective genome-wide association studies and accurate genomic prediction. Chinese Merino (Xinjiang type) is well-known fine wool sheep breed. However, the extent of LD across the genome remains unexplored. In this study, we calculated autosomal LD based on genome-wide SNPs of 635 Chinese Merino (Xinjiang type) sheep by Illumina Ovine SNP50 BeadChip. A moderate level of LD (r2 ≥ 0.25) across the whole genome was observed at short distances of 0–10 kb. Further, the ancestral effective population size (Ne) was analyzed by extent of LD and found that Ne increased with the increase of generations and declined rapidly within the most recent 50 generations, which is consistent with the history of Chinese Merino sheep breeding, initiated in 1971. We also noted that even when the effective population size was estimated across different single chromosomes, Ne only ranged from 140.36 to 183.33 at five generations in the past, exhibiting a rapid decrease compared with that at ten generations in the past. These results indicated that the genetic diversity in Chinese Merino sheep recently decreased and proper protective measures should be taken to maintain the diversity. Our datasets provided essential genetic information to track molecular variations which potentially contribute to phenotypic variation in Chinese Merino sheep.

Genome Analysis Identified Novel Candidate Genes for Ascochyta Blight Resistance in Chickpea Using Whole Genome Re-sequencing Data.

Ascochyta blight (AB) is a fungal disease that can significantly reduce chickpea production in Australia and other regions of the world. In this study, 69 chickpea genotypes were sequenced using whole genome re-sequencing (WGRS) methods. They included 48 Australian varieties differing in their resistance ranking to AB, 16 advanced breeding lines from the Australian chickpea breeding program, four landraces, and one accession representing the wild chickpea species Cicer reticulatum. More than 800,000 single nucleotide polymorphisms (SNPs) were identified. Population structure analysis revealed relatively narrow genetic diversity amongst recently released Australian varieties and two groups of varieties separated by the level of AB resistance. Several regions of the chickpea genome were under positive selection based on Tajima’s D test. Both Fst genome- scan and genome-wide association studies (GWAS) identified a 100 kb region (AB4.1) on chromosome 4 that was significantly associated with AB resistance. The AB4.1 region co-located to a large QTL interval of 7 Mb∼30 Mb identified previously in three different mapping populations which were genotyped at relatively low density with SSR or SNP markers. The AB4.1 region was validated by GWAS in an additional collection of 132 advanced breeding lines from the Australian chickpea breeding program, genotyped with approximately 144,000 SNPs. The reduced level of nucleotide diversity and long extent of linkage disequilibrium also suggested the AB4.1 region may have gone through selective sweeps probably caused by selection of the AB resistance trait in breeding. In total, 12 predicted genes were located in the AB4.1 QTL region, including those annotated as: NBS-LRR receptor-like kinase, wall-associated kinase, zinc finger protein, and serine/threonine protein kinases. One significant SNP located in the conserved catalytic domain of a NBS-LRR receptor-like kinase led to amino acid substitution. Transcriptional analysis using qPCR showed that some predicted genes were significantly induced in resistant lines after inoculation compared to non-inoculated plants. This study demonstrates the power of combining WGRS data with relatively simple traits to rapidly develop “functional makers” for marker-assisted selection and genomic selection.

Genome-wide association study of rust traits in orchardgrass using SLAF-seq technology

BackgroundWhile orchardgrass (Dactylis glomerata L.) is a well-known perennial forage species, rust diseases cause serious reductions in the yield and quality of orchardgrass; however, genetic mechanisms of rust resistance are not well understood in orchardgrass.ResultsIn this study, a genome-wide association study (GWAS) was performed using specific-locus amplified fragment sequencing (SLAF-seq) technology in orchardgrass. A total of 2,334,889 SLAF tags were generated to produce 2,309,777 SNPs. ADMIXTURE analysis revealed unstructured subpopulations for 33 accessions, indicating that this orchardgrass population could be used for association analysis. Linkage disequilibrium (LD) analysis revealed an average r2 of 0.4 across all SNP pairs, indicating a high extent of LD in these samples. Through GWAS, a total of 4,604 SNPs were found to be significantly (P < 0.01) associated with the rust trait. The bulk analysis discovered a number of 5,211 SNPs related to rust trait. Two candidate genes, including cytochrome P450, and prolamin were implicated in disease resistance through prediction of functional genes surrounding each high-quality SNP (P < 0.01) associated with rust traits based on GWAS analysis and bulk analysisConclusionsThe large number of SNPs associated with rust traits and these two candidate genes may provide the basis for further research on rust resistance mechanisms and marker-assisted selection (MAS) for rust-resistant lineages.

Distinguishing recent admixture from ancestral population structure.

We develop and test two methods for distinguishing between recent admixture and ancestral population structure as explanations for greater similarity of one of two populations to an outgroup population. This problem arose when Neanderthals were found to be slightly more similar to nonAfrican than to African populations. The excess similarity is consistent with both recent admixture from Neanderthals into the ancestors of nonAfricans and subdivision in the ancestral population. Although later studies showed that there had been recent admixture, distinguishing between these two classes of models will be important in other situations, particularly when high-coverage genomes cannot be obtained for all populations. One of our two methods is based on the properties of the doubly conditioned frequency spectrum combined with the unconditional frequency spectrum. This method does not require a linkage map and can be used when there is relatively low coverage. The second method uses the extent of linkage disequilibrium among closely linked markers.

Genetic diversity, extent of linkage disequilibrium and persistence of gametic phase in Canadian pigs

BackgroundKnowledge on the levels of linkage disequilibrium (LD) across the genome, persistence of gametic phase between breed pairs, genetic diversity and population structure are important parameters for the successful implementation of genomic selection. Therefore, the objectives of this study were to investigate these parameters in order to assess the feasibility of a multi-herd and multi-breed training population for genomic selection in important purebred and crossbred pig populations in Canada. A total of 3,057 animals, representative of the national populations, were genotyped with the Illumina Porcine SNP60 BeadChip (62,163 markers).ResultsThe overall LD (r2) between adjacent SNPs was 0.49, 0.38, 0.40 and 0.31 for Duroc, Landrace, Yorkshire and Crossbred (Landrace x Yorkshire) populations, respectively. The highest correlation of phase (r) across breeds was observed between Crossbred animals and either Landrace or Yorkshire breeds, in which r was approximately 0.80 at 1 Mbp of distance. Landrace and Yorkshire breeds presented r ≥ 0.80 in distances up to 0.1 Mbp, while Duroc breed showed r ≥ 0.80 for distances up to 0.03 Mbp with all other populations. The persistence of phase across herds were strong for all breeds, with r ≥ 0.80 up to 1.81 Mbp for Yorkshire, 1.20 Mbp for Duroc, and 0.70 Mbp for Landrace. The first two principal components clearly discriminate all the breeds. Similar levels of genetic diversity were observed among all breed groups. The current effective population size was equal to 75 for Duroc and 92 for both Landrace and Yorkshire.ConclusionsAn overview of population structure, LD decay, demographic history and inbreeding of important pig breeds in Canada was presented. The rate of LD decay for the three Canadian pig breeds indicates that genomic selection can be successfully implemented within breeds with the current 60 K SNP panel. The use of a multi-breed training population involving Landrace and Yorkshire to estimate the genomic breeding values of crossbred animals (Landrace × Yorkshire) should be further evaluated. The lower correlation of phase at short distances between Duroc and the other breeds indicates that a denser panel may be required for the use of a multi-breed training population including Duroc.

Estimates of Linkage Disequilibrium and Effective Population Size in Wild and Selected Populations of the Pacific Oyster Using Single‐nucleotide Polymorphism Markers

AbstractThe level and extent of linkage disequilibrium (LD) and effective population size (Ne) were studied in three selected lines and a wild population of Pacific oyster, Crassostrea gigas, using 61 single‐nucleotide polymorphisms. Significant differences were detected in the average r2 between the selected lines and wild population for both syntenic and nonsyntenic loci with LD beyond population‐specific critical values (P&lt;0.05). Moreover, the proportions of syntenic and nonsyntenic loci with the expected LD level in the wild population were lower than that in the selected lines. Taken together, the LD level of the selected lines was higher than that of the wild population. The extent of LD analysis showed that a short range of LD (0–0.23 cM) was detected in the four populations, and the decay distance was lower in the wild population than in the selected lines. Ne values ranged from 47.6 to 58.5 in the selected lines and ranged from 527.9 to 709.6 with infinite upper limits in the wild population. Further variance analysis of LD demonstrated that genetic drift and epistatic selection might account for the increased LD levels in selected lines. The LD information will be valuable for further association study and marker‐assisted selection in oysters.