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. 2024 Mar 19;15:1342359. doi: 10.3389/fpls.2024.1342359

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Copyright © 2024 Salami, Heidari, Alizadeh, Batley, Wang, Tan, Dadkhodaie and Richards

This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

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Genome-wide association study (GWAS) reveals the genetic basis of seed yield and yield-related traits in rapeseed (Brassica napus). (A) Phenotypes of siliques in rapeseed which are considered the major contributing factors for increasing rapeseed yield. (B–D) GWAS of plant weight (PW) using the 119 rapeseed varieties under well-watered conditions in 2020. (B) Manhattan plot and corresponding quantile–quantile (QQ) plot displaying the GWAS result of PW in 19 chromosomes (1–10 stand for rapeseed chromosomes of A01–A10, and 11–19 stand for rapeseed chromosomes of C01–C09 at the horizontal axis). SNPs on different chromosomes are denoted by different colors. (C) Locus zoom plot for PW associations in the chromosome 14 (C04). (D) A representation of pairwise r ² value (displayed as percentages) among polymorphic sites of chromosome 14 (C04) for PW. (E) Schematic diagram of the region of chromosome 14 (C04) genotyped in this study, showing the associated gene ABCG16 (LOC106391243). Chromosomal position based on the National Center for Biotechnology Information (NCBI). (F) Gene model of ABCG16. Solid boxes indicate exons, and open boxes indicate untranslated regions (UTRs). The red stars mark the positions of Chr14:35642269, Chr14:35642321, Chr14:35642324, and Chr14:35643023. (G) The influence of Chr14:35642269, Chr14:35642321, Chr14:35642324, and Chr14:35643023 on plant weight. (H) Haplotype block based on 11 significant SNPs on chromosome 14 (C04). (I) Four different haplotype variants (Hap1–Hap4) are present at different frequencies in the analyzed population. Boxplots for plant weight indicate the phenotype values corresponding to the four different haplotype groups. Significant differences among haplotypes were identified using one-way ANOVA. Different letters indicate distinct groups. (J–L) GWAS of seed weight/plant (SWPP) under drought stress conditions in 2020. (J) Manhattan plot and corresponding quantile–quantile (QQ) plot displaying the GWAS result of SWPP in 19 chromosomes. (K) Locus zoom plot for SWPP associations in chromosome 8 (A08). (L) A representation of the pairwise r ² value (displayed as percentages) among polymorphic sites of chromosome 8 (A08) for SWPP. (M-Q) GWAS of seed yield (SY) under drought stress conditions in 2017. (M) Manhattan plot and corresponding quantile–quantile (QQ) plot displaying the GWAS result of SY in 19 chromosomes. (N) Locus zoom plot for SY associations in chromosome 11 (C01). (O) A representation of pairwise r ² value (displayed as percentages) among polymorphic sites of chromosome 11 (C01) for SY. (P) Locus zoom plot for SY associations in the chromosome 14 (C04). (Q) A representation of pairwise r ² value (displayed as percentages) among polymorphic sites of chromosome 14 (C04) for SY.