Structural variation among assembled genomes facilitates development of rapid and low-cost NOR-linked markers and NOR-telomere junction mapping in Arabidopsis

• Published in: Plant cell reports Vol. 42; no. 6; pp. 1059 - 1069
• Main Authors: Saradadevi, Gargi Prasad, Fultz, Dalen, Ramgopal, Murali Krishna, Subramanian, Abirami T., Prince, Gerin, Thakur, Vivek, Mohannath, Gireesha
• Format: Journal Article
• Language: English
• Published: Berlin/Heidelberg Springer Berlin Heidelberg 01.06.2023; Springer Nature B.V
• Subjects: Arabidopsis - genetics; Base Sequence; Biomarkers; Biomedical and Life Sciences; Biotechnology; Cell Biology; Chromosome 2; Chromosome 4; Chromosome Mapping; Chromosomes; Ecotypes; Gene mapping; Genes; Genetic markers; Genome-wide association studies; Genome-Wide Association Study; Genomes; Inbreeding; Life Sciences; Low cost; Mapping; Nucleoli; Original Article; Plant Biochemistry; Plant Sciences; rRNA 45S; Telomere; Telomeres; Genetic mapping; Telomeres; Molecular marker; Ribosomal DNA (rDNA); Nanopore sequencing; Nucleolus organizer region (NOR)
• DOI: 10.1007/s00299-023-03012-x
• ISSN: 0721-7714

Key message Genome-wide structural variants we identified and new NOR-linked markers we developed would be useful for future genome-wide association studies (GWAS), and for new gene/trait mapping purposes. Bioinformatic alignment of the assembled genomes of Col-0 and Sha ecotypes of Arabidopsis thaliana revealed ~ 13,000 genome-wide structural variants involving simple insertions or deletions and repeat contractions or expansions. Using some of these structural variants, we developed new, rapid, and low-cost PCR-based molecular markers that are genetically linked to the nucleolus organizer regions (NORs). A. thaliana has two NORs, one each on chromosome 2 ( NOR2 ) and chromosome 4 ( NOR4 ). Both NORs are ~ 4 Mb each, and hundreds of 45S ribosomal RNA (rRNA) genes are tandemly arrayed at these loci. Using previously characterized recombinant inbred lines (RILs) derived from Sha x Col-0  crosses, we validated the utility of the newly developed NOR-linked markers in genetically mapping rRNA genes and the associated telomeres to either NOR2 or NOR4 . Lastly, we sequenced Sha genome using Oxford Nanopore Technology (ONT) and used the data to obtain sequences of NOR-telomere junctions, and with the help of RILs, we mapped them as new genetic markers to their respective NORs ( NOR2-TEL2N and N OR4-TEL4N ). The structural variants obtained from this study would serve as valuable data for genome-wide association studies (GWAS), and to rapidly design more genome-wide genetic (molecular) markers for new gene/trait mapping purposes.