An integrated analysis of QTL mapping and RNA sequencing provides further insights and promising candidates for pod number variation in rapeseed (Brassica napus L.)

Abstract

BackgroundAs the most important yield component in rapeseed (Brassica napus L.), pod number is determined by a series of successive growth and development processes. Pod number shows extensive variation in rapeseed natural germplasm, which is valuable for genetic improvement. However, the genetic and especially the molecular mechanism for this kind of variation are poorly understood. In this study, we conducted QTL mapping and RNA sequencing, respectively, using the BnaZNRIL population and its two parental cultivars Zhongshuang11 and No.73290 which showed significant difference in pod number, primarily due to the difference in floral organ number.ResultA total of eight QTLs for pod number were identified using BnaZNRIL population with a high-density SNP linkage map, each was distributed on seven linkage groups and explained 5.8–11.9% of phenotypic variance. Then, they were integrated with those previously detected in BnaZNF2 population (deriving from same parents) and resulted in 15 consensus-QTLs. Of which, seven QTLs were identical to other studies, whereas the other eight should be novel.RNA sequencing of the shoot apical meristem (SAM) at the formation stage of floral bud primordia identified 9135 genes that were differentially expressed between the two parents. Gene ontology (GO) analysis showed that the top two enriched groups were S-assimilation, providing an essential nutrient for the synthesis of diverse metabolites, and polyamine metabolism, serving as second messengers that play an essential role in flowering genes initiation. KEGG analysis showed that the top three overrepresented pathways were carbohydrate (707 genes), amino acid (390 genes) and lipid metabolisms (322 genes). In silico mapping showed that 647 DEGs were located within the confidence intervals of 15 consensus QTLs. Based on annotations of Arabidopsis homologs corresponding to DEGs, nine genes related to meristem growth and development were considered as promising candidates for six QTLs.ConclusionIn this study, we discovered the first repeatable major QTL for pod number in rapeseed. In addition, RNA sequencing was performed for SAM in rapeseed, which provides new insights into the determination of floral organ number. Furthermore, the integration of DEGs and QTLs identified promising candidates for further gene cloning and mechanism study.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-3402-y) contains supplementary material, which is available to authorized users.

Integrating GWAS, linkage mapping and gene expression analyses reveals the genetic control of growth period traits in rapeseed (Brassica napus L.)

“…However, transcriptome analysis often obtained a large number of differentially expressed genes (DEGs) between samples. Therefore, the integration of DEGs with GWAS or linkage mapping has been considered to be an effective way to identify candidate genes related to complex traits [16][17][18][19].…”

Whole‐transcriptome analysis reveals genetic factors underlying flowering time regulation in rapeseed (Brassica napus L.)

“…It can be used as an alternative to other transcript quantification approaches with the benefit of higher sensitivity and the potential to distinguish between very similar paralogs of a gene differing only in a few nucleotides. In one of such studies, RNA‐seq was performed on shoot apical meristem of two semiwinter rapeseed lines (Ye et al, ) that resulted in the identification of 9,135 differentially expressed genes (DEGs) between both lines, out of which 647 DEGs were within QTLs for pod number. In another study, Yu et al () performed transcriptome analysis on apetalous and an early flowering rapeseed line and developed an early flowering gene network composed of mainly vernalization and photoperiod pathway genes.…”

RAD-Seq-Based High-Density Linkage Maps Construction and Quantitative Trait Loci Mapping of Flowering Time Trait in Alfalfa (Medicago sativa L.)

“…Therefore, the strategy of QTL mapping combined with RNA-seq is considered to be a promising method to rapidly identify potential candidate genes. For example, integration of RNA-seq and QTLs mapping have been carried out to identify candidate genes associated with cadmium tolerance in barley (Hordeum vulgare) ( Derakhshani et al, 2020 ), genes for pod number variation in rapeseed ( Brassica napus L.) ( Ye et al, 2017 ), and high-temperature stress-responsive genes in tomato ( Solanum lycopersicum L.) ( Wen et al, 2019 ).…”