Dataset Information

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

ABSTRACT: 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.

SUBMITTER: Liu S

PROVIDER: S-EPMC5486679 | biostudies-literature | 2017

REPOSITORIES: biostudies-literature

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

Liu Shudong S He Sangang S Chen Lei L Li Wenrong W Di Jiang J Liu Mingjun M

Genes & genomics 20170417 7

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 (<i>r</i><sup>2</sup> ≥ 0.25) across the whole genome was observed ...[more]

PMID: 28706593

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Project description:BackgroundThe use of molecular genetic technologies for broodstock management and selective breeding of aquaculture species is becoming increasingly more common with the continued development of genome tools and reagents. Several laboratories have produced genetic maps for rainbow trout to aid in the identification of loci affecting phenotypes of interest. These maps have resulted in the identification of many quantitative/qualitative trait loci affecting phenotypic variation in traits associated with albinism, disease resistance, temperature tolerance, sex determination, embryonic development rate, spawning date, condition factor and growth. Unfortunately, the elucidation of the precise allelic variation and/or genes underlying phenotypic diversity has yet to be achieved in this species having low marker densities and lacking a whole genome reference sequence. Experimental designs which integrate segregation analyses with linkage disequilibrium (LD) approaches facilitate the discovery of genes affecting important traits. To date the extent of LD has been characterized for humans and several agriculturally important livestock species but not for rainbow trout.ResultsWe observed that the level of LD between syntenic loci decayed rapidly at distances greater than 2 cM which is similar to observations of LD in other agriculturally important species including cattle, sheep, pigs and chickens. However, in some cases significant LD was also observed up to 50 cM. Our estimate of effective population size based on genome wide estimates of LD for the NCCCWA broodstock population was 145, indicating that this population will respond well to high selection intensity. However, the range of effective population size based on individual chromosomes was 75.51 - 203.35, possibly indicating that suites of genes on each chromosome are disproportionately under selection pressures.ConclusionsOur results indicate that large numbers of markers, more than are currently available for this species, will be required to enable the use of genome-wide integrated mapping approaches aimed at identifying genes of interest in rainbow trout.

Project description:BackgroundRecent developments of high-density SNP chips across a number of species require accurate genetic maps. Despite rapid advances in genome sequence assembly and availability of a number of tools for creating genetic maps, the exact genome location for a number of SNPs from these SNP chips still remains unknown. We have developed a locus ordering procedure based on linkage disequilibrium (LODE) which provides estimation of the chromosomal positions of unaligned SNPs and scaffolds. It also provides an alternative means for verification of genetic maps. We exemplified LODE in cattle.ResultsThe utility of the LODE procedure was demonstrated using data from 1,943 bulls genotyped for 73,569 SNPs across three different SNP chips. First, the utility of the procedure was tested by analysing the masked positions of 1,500 randomly-chosen SNPs with known locations (50 from each chromosome), representing three classes of minor allele frequencies (MAF), namely >0.05, 0.01<MAF < or = 0.05 and 0.001<MAF < or = 0.01. The efficiency (percentage of masked SNPs that could be assigned a location) was 96.7%, 30.6% and 2.0%; with an accuracy (the percentage of SNPs assigned correctly) of 99.9%, 98.9% and 33.3% in the three classes of MAF, respectively. The average precision for placement of the SNPs was 914, 3,137 and 6,853 kb, respectively. Secondly, 4,688 of 5,314 SNPs unpositioned in the Btau4.0 assembly were positioned using the LODE procedure. Based on these results, the positions of 485 unordered scaffolds were determined. The procedure was also used to validate the genome positions of 53,068 SNPs placed on Btau4.0 bovine assembly, resulting in identification of problem areas in the assembly. Finally, the accuracy of the LODE procedure was independently validated by comparative mapping on the hg18 human assembly.ConclusionThe LODE procedure described in this study is an efficient and accurate method for positioning SNPs (MAF>0.05), for validating and checking the quality of a genome assembly, and offers a means for positioning of unordered scaffolds containing SNPs. The LODE procedure will be helpful in refining genome sequence assemblies, especially those being created from next-generation sequencing where high-throughput SNP discovery and genotyping platforms are integrated components of genome analysis.

Project description:BackgroundGenomic technologies, such as high-throughput genotyping based on SNP arrays, have great potential to decipher the genetic architecture of complex traits and provide background information concerning genome structure in domestic animals, including the extent of linkage disequilibrium (LD) and haplotype blocks. The objective of this study was to estimate LD, the population evolution (past effective population size) and the level of inbreeding in Spanish Churra sheep.ResultsA total of 43,784 SNPs distributed in the ovine autosomal genome was analyzed in 1,681 Churra ewes. LD was assessed by measuring r2 between all pairs of loci. For SNPs up to 10 ?kb apart, the average r2 was 0.329; for SNPs separated by 200-500? kb the average r2 was 0.061. When SNPs are separated by more than 50 Mbp, the average r2 is the same as between non-syntenic SNP pairs (0.003). The effective population size has decreased through time, faster from 1,000 to 100 ?years ago and slower since the selection scheme started (15-25 generations ago). In the last generation, four years ago, the effective population size was estimated to be 128 animals. Inbreeding coefficients, although differed depending on the estimation approaches, were generally low and showed the same trend, which indicates that since 2003, inbreeding has been slightly increasing in the studied resource population.ConclusionsThe extent of LD in Churra sheep persists over much more limited distances than reported in dairy cattle and seems to be similar to other ovine populations. Churra sheep show a wide genetic base, with a long-term viable effective population size that has been slightly decreasing since selection scheme began in 1986. The genomic dataset analyzed provided useful information for identifying low-level inbreeding in the sample, whereas based on the parameters reported here, a higher marker density than that analyzed here will be needed to successfully conduct accurate mapping of genes underlying production traits and genomic selection prediction in this sheep breed. Although the Ovine Assembly development is still in a draft stage and future refinements will provide a more accurate physical map that will improve LD estimations, this work is a first step towards the understanding of the genetic architecture in sheep.

Project description:BackgroundThe success of genome-wide scans depends on the strength and magnitude of linkage disequilibrium (LD) present within the populations under investigation. High density SNP arrays are currently in development for the sheep genome, however little is known about the behaviour of LD in this livestock species. This study examined the behaviour of LD within five sheep populations using two LD metrics, D' and x2'. Four economically important Australian sheep flocks, three pure breeds (White Faced Suffolk, Poll Dorset, Merino) and a crossbred population (Merino x Border Leicester), along with an inbred Australian Merino museum flock were analysed.ResultsShort range LD (0 - 5 cM) was observed in all five populations, however the persistence with increasing distance and magnitude of LD varied considerably between populations. Average LD (x2') for markers spaced up to 20 cM exceeded the non-syntenic average within the White Faced Suffolk, Poll Dorset and Macarthur Merino. LD decayed faster within the Merino and Merino x Border Leicester, with LD below or consistent with observed background levels. Using marker-marker LD as a guide to the behaviour of marker-QTL LD, estimates of minimum marker spacing were made. For a 95% probability of detecting QTL, a microsatellite marker would be required every 0.1 - 2.5 centimorgans, depending on the population used.ConclusionSheep populations were selected which were inbred (Macarthur Merino), highly heterogeneous (Merino) or intermediate between these two extremes. This facilitated analysis and comparison of LD (x2') between populations. The strength and magnitude of LD was found to differ markedly between breeds and aligned closely with both observed levels of genetic diversity and expectations based on breed history. This confirmed that breed specific information is likely to be important for genome wide selection and during the design of successful genome scans where tens of thousands of markers will be required.

Project description:Single nucleotide polymorphisms (SNPs) may be correlated due to linkage disequilibrium (LD). Association studies look for both direct and indirect associations with disease loci. In a Random Forest (RF) analysis, correlation between a true risk SNP and SNPs in LD may lead to diminished variable importance for the true risk SNP. One approach to address this problem is to select SNPs in linkage equilibrium (LE) for analysis. Here, we explore alternative methods for dealing with SNPs in LD: change the tree-building algorithm by building each tree in an RF only with SNPs in LE, modify the importance measure (IM), and use haplotypes instead of SNPs to build a RF.We evaluated the performance of our alternative methods by simulation of a spectrum of complex genetics models. When a haplotype rather than an individual SNP is the risk factor, we find that the original Random Forest method performed on SNPs provides good performance. When individual, genotyped SNPs are the risk factors, we find that the stronger the genetic effect, the stronger the effect LD has on the performance of the original RF. A revised importance measure used with the original RF is relatively robust to LD among SNPs; this revised importance measure used with the revised RF is sometimes inflated. Overall, we find that the revised importance measure used with the original RF is the best choice when the genetic model and the number of SNPs in LD with risk SNPs are unknown. For the haplotype-based method, under a multiplicative heterogeneity model, we observed a decrease in the performance of RF with increasing LD among the SNPs in the haplotype.Our results suggest that by strategically revising the Random Forest method tree-building or importance measure calculation, power can increase when LD exists between SNPs. We conclude that the revised Random Forest method performed on SNPs offers an advantage of not requiring genotype phase, making it a viable tool for use in the context of thousands of SNPs, such as candidate gene studies and follow-up of top candidates from genome wide association studies.

Dataset Information

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

Publications

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

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