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DOI | 10.3389/fgene.2024.1361418 |
Comparison of ddRADseq and EUChip60K SNP genotyping systems for population genetics and genomic selection in Eucalyptus dunnii (Maiden) | |
发表日期 | 2024 |
EISSN | 1664-8021 |
起始页码 | 15 |
卷号 | 15 |
英文摘要 | Eucalyptus dunnii is one of the most important Eucalyptus species for short-fiber pulp production in regions where other species of the genus are affected by poor soil and climatic conditions. In this context, E. dunnii holds promise as a resource to address and adapt to the challenges of climate change. Despite its rapid growth and favorable wood properties for solid wood products, the advancement of its improvement remains in its early stages. In this work, we evaluated the performance of two single nucleotide polymorphism, (SNP), genotyping methods for population genetics analysis and Genomic Selection in E. dunnii. Double digest restriction-site associated DNA sequencing (ddRADseq) was compared with the EUChip60K array in 308 individuals from a provenance-progeny trial. The compared SNP set included 8,011 and 19,008 informative SNPs distributed along the 11 chromosomes, respectively. Although the two datasets differed in the percentage of missing data, genome coverage, minor allele frequency and estimated genetic diversity parameters, they revealed a similar genetic structure, showing two subpopulations with little differentiation between them, and low linkage disequilibrium. GS analyses were performed for eleven traits using Genomic Best Linear Unbiased Prediction (GBLUP) and a conventional pedigree-based model (ABLUP). Regardless of the SNP dataset, the predictive ability (PA) of GBLUP was better than that of ABLUP for six traits (Cellulose content, Total and Ethanolic extractives, Total and Klason lignin content and Syringyl and Guaiacyl lignin monomer ratio). When contrasting the SNP datasets used to estimate PAs, the GBLUP-EUChip60K model gave higher and significant PA values for six traits, meanwhile, the values estimated using ddRADseq gave higher values for three other traits. The PAs correlated positively with narrow sense heritabilities, with the highest correlations shown by the ABLUP and GBLUP-EUChip60K. The two genotyping methods, ddRADseq and EUChip60K, are generally comparable for population genetics and genomic prediction, demonstrating the utility of the former when subjected to rigorous SNP filtering. The results of this study provide a basis for future whole-genome studies using ddRADseq in non-model forest species for which SNP arrays have not yet been developed. |
英文关键词 | double digest restriction-site associated DNA sequencing; genotyping by sequencing; SNP array; genomic prediction; ABLUP; GBLUP |
语种 | 英语 |
WOS研究方向 | Genetics & Heredity |
WOS类目 | Genetics & Heredity |
WOS记录号 | WOS:001200316200001 |
来源期刊 | FRONTIERS IN GENETICS
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文献类型 | 期刊论文 |
条目标识符 | http://gcip.llas.ac.cn/handle/2XKMVOVA/305262 |
作者单位 | Instituto Nacional de Tecnologia Agropecuaria (INTA); Consejo Nacional de Investigaciones Cientificas y Tecnicas (CONICET); Universidad de la Republica, Uruguay; Instituto Nacional de Tecnologia Agropecuaria (INTA); Instituto Nacional de Tecnologia Agropecuaria (INTA); Instituto Nacional de Tecnologia Agropecuaria (INTA); Universidade de Lisboa; Centro de Estudos Florestais; Universidade de Lisboa; Empresa Brasileira de Pesquisa Agropecuaria (EMBRAPA); Consejo Nacional de Investigaciones Cientificas y Tecnicas (CONICET) |
推荐引用方式 GB/T 7714 | . Comparison of ddRADseq and EUChip60K SNP genotyping systems for population genetics and genomic selection in Eucalyptus dunnii (Maiden)[J],2024,15. |
APA | (2024).Comparison of ddRADseq and EUChip60K SNP genotyping systems for population genetics and genomic selection in Eucalyptus dunnii (Maiden).FRONTIERS IN GENETICS,15. |
MLA | "Comparison of ddRADseq and EUChip60K SNP genotyping systems for population genetics and genomic selection in Eucalyptus dunnii (Maiden)".FRONTIERS IN GENETICS 15(2024). |
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