RNA-seq and Bulked Segregant Analysis of a Gene Related to High Growth in Ginkgo biloba Half-siblings.

Abstract

The lifetime of G. biloba is very long, and its growth is relatively slow. However, little is known about growth-related genes in this species. We combined mRNA sequencing (RNA-Seq) with bulked segregant analysis (BSA) to fine map significant agronomic trait genes by developing polymorphism molecular markers at the transcriptome level. RNA-Seq data provides BSA with genotype information in RNA Pool to screen out linked genes (low in false positives) after data analysis, and the efficiency of development and verification of the linked polymorphism marker is greatly improved. This combined approach (named BSR) has been applied to plant transcriptome sequencing in sunflower, corn, wheat, and Arabidopsis thaliana. In this study, transcriptome sequencing of high growth (GD) and low growth (BD) samples of G. biloba half-sib families was performed. After assembling the clean reads, 601 differential expression genes were detected and 513 of them were assigned functional annotations. Single nucleotide polymorphism (SNP) analysis identified SNPs associated with 119 genes in the GD and BD groups; 58 of these genes were annotated. This study provides molecular level data that could be used for seed selection of high growth G.biloba half-sib families for future breeding programs.