genotypic and phenotypic data for GWAS in autotetraploid potato

This work is published in the following article:Sharma, S.K., McLean, K., Hedley, P.E., Dale, F., Daniels, S., Bryan, G.J. 2024. Genotyping-by-sequencing Targets Genic Regions and Improves Resolution of Genome-wide Association Studies in Autotetraploid Potato. Theoretical and Applied Genetics. Abstract: This study deploys recent advancements in polyploid analytical approaches to perform complex trait analyses in cultivated tetraploid potato. The study employs a ‘fixed’ SNP Infinium array platform and a ‘flexible and open’ genome complexity reduction-based sequencing method (GBS, genotyping-by-sequencing) to perform genome-wide association studies (GWAS) for several key potato traits including the assessment of population structure and linkage disequilibrium (LD) in the studied population. GBS SNPs discovered here were largely confined (~90%) to genic or gene-associated regions of the genome demonstrating the utility of using a methylation sensitive restriction enzyme (<i>Pst</i>I) for library construction. As compared to Infinium array SNPs, GBS SNPs displayed enhanced effectiveness in estimating LD decay rates and discriminating population subgroups. GWAS using a combined set of 30,363 SNPs identified 189 unique QTL marker-trait associations (QTL-MTAs) covering all studied traits. The majority of the QTL-MTAs were from GBS SNPs potentially illustrating the effectiveness of marker-dense <i>de novo</i> genotyping platforms in overcoming ascertainment bias and providing a more accurate correction for different levels of relatedness in GWAS models. GWAS also detected QTL ‘hotspots’ for several traits at previously known as well as newly identified genomic locations. Due to the current study exploiting genome-wide genotyping and <i>de novo</i> SNP discovery simultaneously on a large tetraploid panel representing a greater diversity of the cultivated potato gene pool, the reported sequence-tagged MTAs are likely to have higher transferability across a wider range of potato germplasm and increased utility for expediting genomics-assisted breeding for the several complex traits studied.

本研究成果发表于以下论文：Sharma, S.K.、McLean, K.、Hedley, P.E.、Dale, F.、Daniels, S.、Bryan, G.J.，2024年。《测序分型靶向编码区并提升同源四倍体马铃薯全基因组关联分析分辨率》，发表于《理论与应用遗传学》。摘要：本研究借助多倍体分析领域的最新进展，对栽培同源四倍体马铃薯开展复杂性状分析。本研究采用「固定型」单核苷酸多态性（SNP，Single Nucleotide Polymorphism）Infinium阵列平台，以及「灵活开放」的基于基因组复杂度降低的测序方法（GBS，测序分型genotyping-by-sequencing），针对多项关键马铃薯性状开展全基因组关联分析（GWAS，Genome-Wide Association Study），包括评估研究群体的群体结构与连锁不平衡（LD，linkage disequilibrium）水平。本研究发现的GBS SNP位点中，约90%主要定位于基因组的编码区或基因关联区域，这证明了使用甲基化敏感限制性内切酶PstI构建文库的实用性。与Infinium阵列的SNP位点相比，GBS SNP位点在估算LD衰减速率以及区分群体亚类方面表现出更优的效能。基于30363个SNP位点的合并数据集开展的GWAS分析，共鉴定出189个独特的数量性状位点-标记-性状关联（QTL-MTA，Quantitative Trait Locus-Marker-Trait Association），覆盖所有研究性状。绝大多数QTL-MTA均来自GBS SNP位点，这或可证明标记密集型从头（de novo）测序分型平台能够克服 ascertainment偏倚，并为GWAS模型中不同水平的亲缘关系提供更精准的校正。GWAS分析还在既往已知及新鉴定的基因组位点处，检测到了多个性状的QTL「热点区域」。由于本研究同时对代表栽培马铃薯基因库更多样性的大型四倍体群体开展全基因组分型与从头（de novo）SNP位点鉴定，所报道的序列标记型MTAs有望在更广范围的马铃薯种质资源间实现更高的跨群体可转移性，且能更高效地助力所研究多项复杂性状的基因组辅助育种工作。