Haplotype-based genotyping-by-sequencing in oat genome research.
Haplotype-based genotyping-by-sequencing in oat genome research.
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DOI：
10.1111/pbi.12888
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发表时间：
2018-08
影响因子：
13.8
通讯作者：
Tinker NA
中科院分区：
文献类型：
--
作者：
Bekele WA;Wight CP;Chao S;Howarth CJ;Tinker NA
在4,657份栽培燕麦种质的标签水平短单倍型的测序分析中，我们发现了164741个标签水平(TL)遗传变异，包含241224个SNPs。在此基础上，通过增加70000多个座位，提高了燕麦共识图谱的标记密度。635个品系的TL基因图谱用于推断染色体水平(CL)单倍型图谱。这些图谱揭示了单倍型块的数量和大小的差异，以及染色体和多样性面板亚组之间单倍型多样性的差异。然后，我们探索了SNP、TL和CL GBS变异在定位、高分辨率基因组分析和燕麦基因组选择方面的潜在优势。一项利用TL单倍型和单个SNP标记对来自多个地点的抽穗期进行的联合全基因组关联研究发现了184个显著关联。利用TL单倍型、CL单倍型块及其组合进行的比较分析表明，利用TL单倍型标记具有一定的优越性。使用基于主成分的全基因组扫描，识别包含选择特征的基因组区域。这些区域可能含有导致燕麦在当地适应北美条件的基因。使用TL单倍型或SNP标记进行抽穗期基因组选择，预测精度可达r=0.74，具有可比性。在一个独立的抽穗期校准和测试群体中进行的基因组选择给出了有希望的预测精度，范围在r=0.42到0.67之间。总之，TL单倍型GBS衍生标记有助于燕麦基因组分析和基因组选择。
In a de novo genotyping‐by‐sequencing (GBS) analysis of short, 64‐base tag‐level haplotypes in 4657 accessions of cultivated oat, we discovered 164741 tag‐level (TL) genetic variants containing 241224 SNPs. From this, the marker density of an oat consensus map was increased by the addition of more than 70000 loci. The mapped TL genotypes of a 635‐line diversity panel were used to infer chromosome‐level (CL) haplotype maps. These maps revealed differences in the number and size of haplotype blocks, as well as differences in haplotype diversity between chromosomes and subsets of the diversity panel. We then explored potential benefits of SNP vs. TL vs. CL GBS variants for mapping, high‐resolution genome analysis and genomic selection in oats. A combined genome‐wide association study (GWAS) of heading date from multiple locations using both TL haplotypes and individual SNP markers identified 184 significant associations. A comparative GWAS using TL haplotypes, CL haplotype blocks and their combinations demonstrated the superiority of using TL haplotype markers. Using a principal component‐based genome‐wide scan, genomic regions containing signatures of selection were identified. These regions may contain genes that are responsible for the local adaptation of oats to Northern American conditions. Genomic selection for heading date using TL haplotypes or SNP markers gave comparable and promising prediction accuracies of up to r = 0.74. Genomic selection carried out in an independent calibration and test population for heading date gave promising prediction accuracies that ranged between r = 0.42 and 0.67. In conclusion, TL haplotype GBS‐derived markers facilitate genome analysis and genomic selection in oat.
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影响因子：
10.7
作者：
Duforet-Frebourg N;Luu K;Laval G;Bazin E;Blum MG
通讯作者：
Blum MG
影响因子：
4.4
作者：
Cuyabano BC;Su G;Lund MS
通讯作者：
Lund MS
DOI：
10.1186/1297-9686-45-5
发表时间：
2013-03-06
期刊：
Genetics, selection, evolution : GSE
影响因子：
--
作者：
Edriss V;Fernando RL;Su G;Lund MS;Guldbrandtsen B
通讯作者：
Guldbrandtsen B
影响因子：
3.7
作者：
Huang YF;Poland JA;Wight CP;Jackson EW;Tinker NA
通讯作者：
Tinker NA
影响因子：
56.9
作者：
Gabriel, SB;Schaffner, SF;Altshuler, D
通讯作者：
Altshuler, D