Transcriptome-referenced association study of clove shape traits in garlic

Abstract

Genome-wide association studies are a powerful approach for identifying genes related to complex traits in organisms, but are limited by the requirement for a reference genome sequence of the species under study. To circumvent this problem, we propose a transcriptome-referenced association study (TRAS) that utilizes a transcriptome generated by single-molecule long-read sequencing as a reference sequence to score population variation at both transcript sequence and expression levels. Candidate transcripts are identified when both scores are associated with a trait and their potential interactions are ascertained by expression quantitative trait loci analysis. Applying this method to characterize garlic clove shape traits in 102 landraces, we identified 22 candidate transcripts, most of which showed extensive interactions. Eight transcripts were long non-coding RNAs (lncRNAs), and the others were proteins involved mainly in carbohydrate metabolism, protein degradation, etc. TRAS, as an efficient tool for association study independent of a reference genome, extends the applicability of association studies to a broad range of species.

A transcriptomic variation map provides insights into the genetic basis of Pinus massoniana Lamb. evolution and the association with oleoresin yield

“…Associative transcriptomics has contributed significantly to identifying sequence polymorphisms and transcript abundances linked to phenotypic variation, especially in non-model species [22,23]. In addition, high-quality full-length transcripts are critical for functional assays and for understanding genetic diversity [24].…”

Transcriptome Atlas by Long-Read RNA Sequencing: Contribution to a Reference Transcriptome

“…Ultimately, cost-effective long-read transcriptome sequencing can be the gold standard for transcript completeness, characterization of transcriptome, and draft genome annotation. To identify trait-associated transcripts in species for which a reference genome is lacking (i.e., garlic), this approach was used as a reference sequence for scoring the variation in both SNP and expression level in the population [36], reporting the characterization of transcripts (lncRNAs) associated with garlic clove shape traits.…”

A Transcriptomic Variation Map Provides Insights into The Genetic Basis of Pinus massoniana Evolution and Association of Oleoresin Yield

“…Associative transcriptomics has largely contributed to identify sequence polymorphisms and transcript abundance linked to phenotypic variation, especially for non-model species [22,23]. In addition, high quality full length transcripts are critical and useful for functional assays and understanding of genetic diversity [24].…”