Integrating QTL mapping with transcriptome analysis mined candidate genes of growth stages in castor (Ricinus communis L.)

TL;DR

This study identifies genetic regions and candidate genes involved in growth stages of castor plants, offering insights for improving crop yield.

Contribution

The study combines QTL mapping and transcriptome analysis to identify candidate genes for growth stages in castor.

Findings

Twenty QTLs for four growth traits were identified in the F2 population, explaining up to 25.46% phenotypic variation.

Five QTLs for PSMD and PBSMD were found in the BC1 population, clustered in two marker intervals.

Four candidate genes (RcSYN3, RcNTT, RcGG3, RcSAUR76) were identified as potentially regulating growth stages.

Abstract

The growth stages largely determine the crop yield, while little is known about their genetic mechanisms in castor. In this study, the QTL mapping and candidate gene mining of growth stages were conducted using populations F2 and BC1, combining with differential expression analysis and weighted gene co-expression network analysis (WGCNA). The traits studied included the emergence date (ED), the budding date of primary spike (PSBD), the flowering date of primary spike (PSFD), the maturation date of primary spike (PSMD), and the maturation date of primary branch spike (PBSMD).

A total of 20 QTLs conferring four traits (ED, PSBD, PSFD and PBSMD) were identified in the F2 population, with a phenotypic variation explained (PVE) of single QTL ranged from 0.24 to 25.46%. Five QTLs underlying PSMD and PBSMD were identified in the BC1 population, with a PVE of single QTL ranged from 4.74 to 10.82%. To our surprise, almost all the identified QTLs were clustered within two marker intervals, the RCM1769-RCM1838 on linkage group 6 and RCM950-RCM917 on linkage group 3. Subsequently, 473 open reading frames (ORFs) were searched out within these two clusters and 110 differentially expressed genes (DEGs) were screened out from these ORFs by the comparative transcriptome clean data (a total of 140.86 G) at the budding date, the initial flowering date and the full flowering date between parental racemes. With these DEGs, five distinct gene co-expression modules were generated using WGCNA. Showing significant differential expression between parents, four candidate genes (LOC8261128, LOC8278994, LOC8281165 and LOC8259049) in module MEturquoise, were recognized and were annotated as RcSYN3, RcNTT, RcGG3 and RcSAUR76 respectively. This finding implies their potential role in regulating the growth stages of castor.

In this study, numerous QTLs conferring growth stages were detected and four candidate genes were mined, which need to be functionally validated. The results provided a new insight into the genetic structure of ED, PSBD, PSFD, PSMD and PBSMD, offered the candidate genes and molecular markers for their improvement as well in castor.

The online version contains supplementary material available at 10.1186/s12864-025-11348-9.

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