Gao, S and Wu, J and Stiller, J and Zheng, Z and Zhou, M and Wang, YG and Liu, C, Identifying barley pan-genome sequence anchors using genetic mapping and machine learning, Theoretical and Applied Genetics, 133, (9) pp. 2535-2544. ISSN 0040-5752 (2020) [Refereed Article]
© Springer-Verlag GmbH Germany, part of Springer Nature 2020
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:||Refereed Article|
|Keywords:||barley, pan-genome, machine learning|
|Research Division:||Agricultural, Veterinary and Food Sciences|
|Research Group:||Crop and pasture production|
|Research Field:||Agrochemicals and biocides (incl. application)|
|Objective Division:||Plant Production and Plant Primary Products|
|Objective Group:||Grains and seeds|
|UTAS Author:||Gao, S (Mr Shang Gao)|
|UTAS Author:||Zhou, M (Professor Meixue Zhou)|
|Web of Science® Times Cited:||4|
|Deposited By:||TIA - Research Institute|
Repository Staff Only: item control page