Expression quantitative trait locus mapping in recombinant gametes using single nucleus RNA sequencing

• DOI: 10.1101/2024.08.02.606310
• Publication Date: 2024-08-07T00:16:06Z
• Authors: Matthew T. Parker; Samija Amar; José A. Campoy; Kristin Krause; Sergio Tusso; Magdalena Marek; Bruno Huettel; Korbinian Schneeb...

Abstract Phenotypic differences between individuals of a species are often caused by in gene expression, which turn genetic variation. Expression quantitative trait locus (eQTL) analysis is methodology we can identify such causal variants. Scaling eQTL costly due to the expense generating mapping populations, and collection matched transcriptomic genomic information. We developed rapid approach using single-cell/nucleus RNA sequencing gametes from small number heterozygous individuals. Patterns inherited polymorphisms used infer recombinant genomes thousands individual how different haplotypes correlate with variation expression. Applied Arabidopsis pollen nuclei, our uncovers both cis - trans -eQTLs, ultimately master regulator sperm cell development that affects expression hundreds genes. This establishes snRNA-sequencing as powerful, cost-effective method for meiotic recombination, addressing scalability challenges enabling specific cell-types.