Dissection of quantitative trait nucleotides and candidate genes associated with agronomic and yield-related traits under drought stress in rapeseed varieties: Integration of genome-wide association study and transcriptomic

Authors: SALAMI, MARYAM - Shiraz University; HEIDARI, BAHRAM - Shiraz University; ALIZADEH, BAHRAM - Shiraz University; BATLEY, JACQUELINE - The University Of Western Australia; WANG, JIN - Nanjing Agricultural University; TAN, XIAL-LI - Jiangsu University; Richards, Christopher; DADKHODAIE, ALI - Shiraz University

Submitted to: Frontiers in Plant Science
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 2/26/2023
Publication Date: 3/19/2024
Citation: Salami, M., Heidari, B., Alizadeh, B., Batley, J., Wang, J., Tan, X., Richards, C.M., Dadkhodaie, A. 2024. Dissection of quantitative trait nucleotides and candidate genes associated with agronomic and yield-related traits under drought stress in rapeseed varieties: Integration of genome-wide association study and transcriptomic analysis. Frontiers in Plant Science. 15. Article e1342359. https://doi.org/10.3389/fpls.2024.1342359.
DOI: https://doi.org/10.3389/fpls.2024.1342359

Interpretive Summary: The main goal of this study was to investigate the genetic identity and regulation of drought stress loci within Brassica napus. B. napus is the second most important oilseed crop world wide and its agronomic production especially in the middle east is threatened by climate change and associated drought. In order to dissect the genomic basis of drought tolerance (a highly complex quantitative trait) we surveyed phenotypic traits in contrasting irrigation environments over three growing seasons. Phenotypic data from the field plots were combined with high density individual genomic data and both leaf and seed RNAseq data to identify candidate loci that are associates with drought tolerance and genes at these QTL that show clear patterns of differential expression between treatments. The resulting set of candidate gene were further sorted by functional characteristics related to developmental processes and signaling involved in seed maturation, cell wall organization and general purpose locie involved on a range or stress related responses. These results help support the acceleration of future efforts aimed at breeding for drought tolerance in rapeseed.

Technical Abstract: An important strategy to combat yield loss challenge is the development of drought tolerance to maintain production. Improvement of crop yield under drought stress is critical to global food security. In this study, we performed multi-omics analysis in a collection of 119 diverse rapeseed (Brassica napus L.) varieties to dissect the genetic control of agronomic traits in contrasting well-watered and drought-stressed conditions for three years. Results of genome-wide association study (GWAS) using 52,157 single nucleotide polymorphisms (SNPs) revealed 1281 SNPs associated with traits. Six stable SNPs showed sequence variation for flowering time between the two irrigation conditions across years. Three novel SNPs on chromosome C04 for plant weight were located within of drought tolerance-related gene ABCG16, and their pleiotropically effects on seed weight per plant and seed yield were characterized. We identified the C02 peak as a novel signal for flowering time, harboring 52.77% of the associated SNPs. The 288 kbps LD decay distance analysis revealed 2232 candidate genes (CGs) associated with traits. The CGs BIG1-D, CAND1, DRG3, PUP10, and PUP21 involved in phytohormone signaling and pollen development with significant effects on seed number, seed weight and grain yield in drought condition. By integrating GWAS and RNA-seq, 215 promising CGs were associated with developmental process, reproductive processes, cell wall organization, and response to stress. GWAS and differentially expressed genes (DEGs) of leaf and seed in the yield contrasting accessions identified BIG1-D, CAND1, and DRG3 genes for yield variation. Results of our study provide insights into the genetic control of drought tolerance and the improvement of marker-assisted selection (MAS) for breeding high-yield and drought tolerant varieties.