Haplotype based genotyping-by-sequencing in oat genome research

Wubishet Abebe Bekele, Charlene P. Wight, Shiaoman Chao, Catherine Howarth, Nicholas A. Tinker

Allbwn ymchwil: Cyfraniad at gyfnodolynErthygladolygiad gan gymheiriaid

79 Dyfyniadau(SciVal)
154 Wedi eu Llwytho i Lawr (Pure)


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.
Iaith wreiddiolSaesneg
Tudalennau (o-i)1452-1463
Nifer y tudalennau12
CyfnodolynPlant Biotechnology Journal
Rhif cyhoeddi8
Dyddiad ar-lein cynnar18 Ion 2018
Dynodwyr Gwrthrych Digidol (DOIs)
StatwsCyhoeddwyd - 25 Maw 2018

Ôl bys

Gweld gwybodaeth am bynciau ymchwil 'Haplotype based genotyping-by-sequencing in oat genome research'. Gyda’i gilydd, maen nhw’n ffurfio ôl bys unigryw.

Dyfynnu hyn