Identifying barley pan-genome sequence anchors using genetic mapping and machine learning.

Identifying barley pan-genome sequence anchors using genetic mapping and machine learning. Theor Appl Genet. 2020 May 24;: Authors: Gao S, Wu J, Stiller J, Zheng Z, Zhou M, Wang YG, Liu C Abstract KEY MESSAGE: We identified 1.844 million barley pan-genome sequence anchors from 12,306 genotypes using genetic mapping and machine learning. There is increasing evidence that genes from a given crop genotype are far to cover all genes in that species; thus, building more comprehensive pan-genomes is of great importance in genetic research and breeding. Obtaining a thousand-genotype scale pan-genome using deep-sequencing data is currently impractical for species like barley which has a huge and highly repetitive genome. To this end, we attempted to identify barley pan-genome sequence anchors from a large quantity of genotype-by-sequencing (GBS) datasets by combining genetic mapping and machine learning algorithms. Based on the GBS sequences from 11,166 domesticated and 1140 wild barley genotypes, we identified 1.844 million pan-genome sequence anchors. Of them, 532,253 were identified as presence/absence variation (PAV) tags. Through aligning these PAV tags to the genome of hulless barley genotype Zangqing320, our analysis resulted in a validation of 83.6% of them from the domesticated genotypes and 88.6% from the wild barley genotypes. Association analyses against flowering time, plant height and kernel size showed that the relative import...
Source: TAG. Theoretical and Applied Genetics - Category: Genetics & Stem Cells Authors: Tags: Theor Appl Genet Source Type: research