Assignment of chromosomal locations for unassigned SNPs/scaffolds based on pair-wise linkage disequilibrium estimates

Abstract

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 ≤ 0.05 and 0.001<MAF ≤ 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.

Linkage disequilibrium maps to guide contig ordering for genome assembly

“…Misspecification of the inter-contig distance does not appear problematic unless, for linked segments, the assumed distance between contigs exceeds the swept radius. Alternative approaches which exploit LD information to guide genome assembly include "Locus ordering by linkage disequilibrium" (LODE) (Khatkar et al, 2010, Jones et al, 2017. LODE uses LD data to place 'orphan' SNPs within genetic linkage map scaffolds, increasing marker coverage which facilitates positioning of short sequence contigs.…”

“…Once assigned to a chromosome the location with strongest association is selected as a candidate location for the orphan SNP. This approach is also successful for validating genome assembly by testing the strength of evidence for the positions of SNPs already located within the assembly (Khatkar et al, 2010). Applying this method, Jones et al (2017) constructed an integrated linkage/LD map for the Pacific white shrimp (Litopenaeus vannamei) for which a minimum of 75 individuals provided accurate LD estimates to place several hundred SNPs within the linkage scaffold.…”

The Challenge of Genome Sequence Assembly

“…Khatkar et al, [41] and Jones et al, [42] employ the LODE (Locus Ordering by Linkage Disequilibrium) algorithm to position 'orphan' SNPs within genetic linkage map scaffolds. This approach has been shown to improve assembly by locally increasing marker coverage and therefore aiding the positioning of shorter sequence contigs.…”

The identification of SNPs with indeterminate positions using the Equine SNP50 BeadChip

“…The results indicate that such an approach can identify regions of potential concern within the genome assembly, and these regions can then be subjected to more rigorous investigation. Whilst it has been suggested that pairwise LD measures can be used to assign chromosomal locations for unassigned SNPs (Khatkar et al. 2010) and to correct locations of misplaced SNPs (Bohmanova et al.…”