Transcriptome-based association study reveals a regulatory network for the shape of garlic clove

A total of 102 garlic accession were performed for mRNA sequencing, and then were used for scoring the variations in both gene sequence (SNPs) and expression (GE) in this population. Thereafter, SNPs and GE are used for carrying out association analysis with the phenotype of shape of garlic clove, respectively, which comes to a joint decision for the candidate genes that are involved in trait. In addition, SNPs and GE data is used as genotype and phenotype, respectively, for performing eQTL analysis to ascertain the interaction among trait-controlled genes, which finally brings a regulatory network for the shape of garlic clove. Overall design: Firstly, a total of 102 garlic accession were performed for mRNA-seq by Illumina sequencing. Then, the read sequencing were aligned into the referenced transcriptome, which resulted in the identification of the variations in both gene sequence (SNPs) and expression (GE).