评估三个商业鸡群中结构变异与单核苷酸多态性之间的连锁不平衡模式。
Assessment of linkage disequilibrium patterns between structural variants and single nucleotide polymorphisms in three commercial chicken populations.
机构信息
Animal Breeding and Genetics Group, Department of Animal Sciences, University of Goettingen, Göttingen, Germany.
Center for Integrated Breeding Research, University of Goettingen, Göttingen, Germany.
出版信息
BMC Genomics. 2022 Mar 9;23(1):193. doi: 10.1186/s12864-022-08418-7.
BACKGROUND
Structural variants (SV) are causative for some prominent phenotypic traits of livestock as different comb types in chickens or color patterns in pigs. Their effects on production traits are also increasingly studied. Nevertheless, accurately calling SV remains challenging. It is therefore of interest, whether close-by single nucleotide polymorphisms (SNPs) are in strong linkage disequilibrium (LD) with SVs and can serve as markers. Literature comes to different conclusions on whether SVs are in LD to SNPs on the same level as SNPs to other SNPs. The present study aimed to generate a precise SV callset from whole-genome short-read sequencing (WGS) data for three commercial chicken populations and to evaluate LD patterns between the called SVs and surrounding SNPs. It is thereby the first study that assessed LD between SVs and SNPs in chickens.
RESULTS
The final callset consisted of 12,294,329 bivariate SNPs, 4,301 deletions (DEL), 224 duplications (DUP), 218 inversions (INV) and 117 translocation breakpoints (BND). While average LD between DELs and SNPs was at the same level as between SNPs and SNPs, LD between other SVs and SNPs was strongly reduced (DUP: 40%, INV: 27%, BND: 19% of between-SNP LD). A main factor for the reduced LD was the presence of local minor allele frequency differences, which accounted for 50% of the difference between SNP - SNP and DUP - SNP LD. This was potentially accompanied by lower genotyping accuracies for DUP, INV and BND compared with SNPs and DELs. An evaluation of the presence of tag SNPs (SNP in highest LD to the variant of interest) further revealed DELs to be slightly less tagged by WGS SNPs than WGS SNPs by other SNPs. This difference, however, was no longer present when reducing the pool of potential tag SNPs to SNPs located on four different chicken genotyping arrays.
CONCLUSIONS
The results implied that genomic variance due to DELs in the chicken populations studied can be captured by different SNP marker sets as good as variance from WGS SNPs, whereas separate SV calling might be advisable for DUP, INV, and BND effects.
背景
结构变异（SV）是一些家畜明显表型特征的原因，例如鸡的不同梳状类型或猪的颜色模式。它们对生产性状的影响也越来越受到研究。然而，准确地识别 SV 仍然具有挑战性。因此，人们有兴趣了解附近的单核苷酸多态性（SNP）是否与 SV 紧密连锁不平衡（LD），并可以作为标记。文献对于 SV 是否与 SNP 处于与 SNP 与其他 SNP 相同的 LD 水平存在不同的结论。本研究旨在从三个商业鸡群的全基因组短读测序（WGS）数据中生成精确的 SV 调用集，并评估所调用的 SV 与周围 SNP 之间的 LD 模式。这是首次评估鸡中 SV 与 SNP 之间 LD 的研究。
结果
最终的调用集包括 12,294,329 个双变量 SNP、4,301 个缺失（DEL）、224 个重复（DUP）、218 个倒位（INV）和 117 个易位断点（BND）。虽然 DEL 与 SNP 之间的平均 LD 与 SNP 与 SNP 之间的 LD 相同，但其他 SV 与 SNP 之间的 LD 则明显降低（DUP：40%、INV：27%、BND：19%的 SNP-SNP LD）。LD 降低的一个主要因素是局部等位基因频率差异的存在，这占 SNP-SNP 和 DUP-SNP LD 差异的 50%。这可能伴随着与 SNP 和 DEL 相比，DUP、INV 和 BND 的基因分型准确性较低。对标记 SNP（与感兴趣的变异体最紧密 LD 的 SNP）的存在进行评估进一步表明，DEL 被 WGS SNP 标记的程度略低于 WGS SNP 被其他 SNP 标记的程度。然而，当将潜在的标记 SNP 池减少到位于四个不同鸡基因分型阵列上的 SNP 时，这种差异就不再存在。
结论
结果表明，在所研究的鸡群中，由于 DEL 引起的基因组变异可以像 WGS SNP 引起的变异一样，通过不同的 SNP 标记集来捕获，而对于 DUP、INV 和 BND 效应，单独的 SV 调用可能是明智的。
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