The RNA-seq and BSA-seq analysis reveals genes associated to the control of early fruiting in walnut (Juglans regia L.)

Abstract

Walnut is an important nut worldwide. The duration of the juvenile phase has a considerable impact on walnut yield. Floral transition is critical for walnut flowering and fruit setting. To improve walnut breeding, it is critical to study the mechanisms of early blooming and fruiting in early-fruiting (EF) walnuts and shorten their juvenile stages. This work used EF and later-fruiting (LF) walnuts to screen for genes associated with walnut early fruiting using RNA sequencing (RNA-seq) and bulk segregant analysis sequencing (BSA-seq). Thirty-seven key differential genes were analyzed using weighted gene co-expression network association (WGCNA) in RNA-seq, and FT, CAL, FUL, and APRR9 genes were found to be able to shorten the juvenile phase of plants by affecting the floral transition process and influencing plant fruiting time. BSA-seq was utilized to identify 3305656 SNPs and 596640 InDels in EF walnut and 925347 SNPs and 514751 InDels in LF walnut. A combined analysis of RNA-seq and BSA-seq revealed 49 structurally varied DEGs in both kinds, with 47 genes in the NC_049914.1 region, one gene in NC_049901.1, one gene locus in NC_049908.1, and eight structurally variant DEGs found solely in early fruiting walnuts. The analysis of candidate genes and verification of RT-qPCR expression revealed that JrLOC109015871 (JrPBL12), JrLOC108983551 (WRI1-like), JrLOC109016788 (WRKY12), and AP2-like genes are likely to be related to early fruiting of walnut, with WRKY12 being expressed at the highest level during the flowering peak of early fruiting walnut. It is likely that the WRKY12 gene regulates the flowering transition of walnut through the ageing pathway, allowing walnut to complete the transition from nutrient growth to reproductive growth more quickly and realize early fruiting to increase walnut yield, laying the groundwork for the study of the molecular mechanism of walnut's early fruiting trait.