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

• Published in: Theoretical and applied genetics 2020-09, Vol.133 (9), p.2535-2544
• Main Authors: Gao, Shang, Wu, Jinran, Stiller, Jiri, Zheng, Zhi, Zhou, Meixue, Wang, You-Gan, Liu, Chunji
• Format: Article
• Language: English
• Subjects: Agriculture; Algorithms; Barley; Biochemistry; Biomedical and Life Sciences; Biotechnology; Chromosome Mapping; Construction; Data mining; Domestication; Flowering; Gene mapping; Genes; Genetic diversity; Genetic research; Genome, Plant; Genomes; Genomics; Genotype; Genotype & phenotype; Genotypes; Hordeum - genetics; Learning algorithms; Life Sciences; Linkage Disequilibrium; Machine Learning; Nucleotide sequence; Original Article; Plant Biochemistry; Plant breeding; Plant Breeding/Biotechnology; Plant Genetics and Genomics
• ISSN: 0040-5752; 1432-2242
• DOI: 10.1007/s00122-020-03615-y

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 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.