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

Gao, S, Wu, J, Stiller, J, Zheng, Z, Zhou, M ORCID: 0000-0003-3009-7854, Wang, YG and Liu, C 2020 , 'Identifying barley pan-genome sequence anchors using genetic mapping and machine learning' , Theoretical and Applied Genetics, vol. 133, no. 9 , pp. 2535-2544 , doi: 10.1007/s00122-020-03615-y.

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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 importance of the PAV and non-PAV tags varied for different traits. The pan-genome sequence anchors based on GBS tags can facilitate the construction of a comprehensive pan-genome and greatly assist various genetic studies including identification of structural variation, genetic mapping and breeding in barley.Key message: We identified 1.844 million barley pan-genome sequence anchors from 12,306 genotypes using genetic mapping and machine learning.

Item Type: Article
Authors/Creators:Gao, S and Wu, J and Stiller, J and Zheng, Z and Zhou, M and Wang, YG and Liu, C
Keywords: barley, pan-genome, machine learning
Journal or Publication Title: Theoretical and Applied Genetics
Publisher: Springer-Verlag
ISSN: 0040-5752
DOI / ID Number: 10.1007/s00122-020-03615-y
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© Springer-Verlag GmbH Germany, part of Springer Nature 2020

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