GenBank genomics highlight the genomic features, genetic diversity and regulation of morphological, metabolic and disease-resistance traits in Nicotiana tabacum

• Published in: bioRxiv
• Main Authors: Zan, Yanjun, Chen, Shuai, Ren, Min, Liu, Guoxiang, Liu, Yutong, Si, Huan, Liu, Zhengwen, Liu, Dan, Zhang, Xingwei, Tong, Ying, Li, Yuan, Jiang, Caihong, Wen, Liuying, Xiao, Zhiliang, Sun, Yangyang, Geng, Ruimei, Feng, Quanfu, Wang, Yuanying, Chen, Yong, Cheng, Lirui, Yang, Aiguo
• Format: Paper
• Language: English
• Published: Cold Spring Harbor Cold Spring Harbor Laboratory Press 23.02.2023
• Subjects: Amino acids; Association analysis; Biodiesel fuels; Biofuels; Chromosomes; Disease resistance; Epigenetics; Genetic diversity; Genetic structure; Genomes; Genomics; Genotypes; Morphology; Nicotiana tabacum; Phenotypes; Phenotyping; Plant breeding; Point mutation; Polygenic inheritance; Polyploidy; Positive selection; Single-nucleotide polymorphism
• DOI: 10.1101/2023.02.21.529366

Nicotiana tabacum is a model organism in plant molecular and pathogenic research, and has significant potential in producing biofuels and active pharmaceutical compounds in synthetic biology. Challenged by the large allotetraploid genome, the genomic features, genetic diversity and genetic regulation of many complex traits remain unknown. In this study, we present the nearly complete chromosome-scale assembly of N. tabacum, and provide evidence that homoeologous exchange between subgenomes and epigenetic remodeling are likely mechanisms in genome stabilization and subgenome coordination following polyploidization. By leveraging GenBank scale sequencing and phenotyping data, geography at the continent scale, rather than types named after curing crop practices, was found to be the most important correlate of genetic structure. Using 178 marker-trait associations detected in genome-wide association analysis, a reference genotype-to-phenotype map was built for 39 plant morphological, developmental, and disease-resistant traits. A novel gene, auxin response factor 9 (Arf9), associated with wider leaves after being knocked out was fine-mapped to a SNP. This point mutation alters the translated amino acid from Ala203 to Pro203, likely preventing the formation of a homodimer in DNA binding. Our analysis also revealed signatures of positive selection and polygenic selection for multiple traits during the process of selective breeding. Overall, this study demonstrated the power of leveraging GenBank genomics to gain insights into the genomic features, genetic diversity, and regulation of complex traits in N. tabacum, laying a foundation for future research in plant functional genomics, crop breeding, and the production of bio-pharmaceuticals and biofuels.Competing Interest StatementThe authors have declared no competing interest.