GWAS and WGCNA analysis uncover candidate genes associated with drought in Brassica juncea L.
Bibliographic record
Abstract
Drought poses a major challenge to crop growth and yield, and exploring the drought tolerance of crops is an effective and economical approach to mitigating the effects of drought. To screen drought-tolerant germplasm resources and key functional genes related to drought tolerance in Brassica juncea L.(193 accessions), three treatments were applied at the germination and seedling stages:control(CK), moderate drought stress (M), and severe drought stress (S). Drought tolerance identification, GWAS, and RNA-Seq analysis of these materials under different treatments showed that drought stress significantly reduced the germination rate, aboveground and underground fresh weight at the seedling stage, harvest index at maturity, and expanded the root/shoot ratio. From the 193 materials, 24 drought-tolerant, 139 drought-tolerant medium, and 30 drought-sensitive materials were identified. The 77 SNPs identified by GWAS were associated with the relative germination rate at the germination stage, and the fresh weight of the aboveground and underground parts at the seedling stage, which could be integrated into 27 QTLs. WGCNA identified 15, 0, and 5 modules significantly related to drought tolerance in the aboveground and underground parts at the germination and seedling stages, respectively. By correlating the significant GWAS SNPs with the significant WGCNA modules, a total of 11 genes related to drought tolerance under moderate and severe drought stress were identified. These genes were involved in the regulation of auxin-responsive protein ( SAUR ), LEA protein, glucosidase, AP2/ERF , WRKY and GATA transcription factors, FLZ zinc finger domain, PRP , and b561 proteins. Among them, the BjuB035910 gene was detected in the underground parts of the seedling and germination stages under moderate drought stress. GWAS and selective sweep analysis jointly identified the 23.955-24.089 Mb region of chromosome B06, where four genes ( BjuB022264, BjuB022292, BjuB022282 , and BjuB022235 ) were located, as confirmed by WGCNA analysis. A total of 125 SNPs with high linkage disequilibrium were found in this region, and 12 haplotypes were detected, with Hap1 being present exclusively in drought-tolerant materials and Hap3-Hap12 distributed in drought-sensitive materials. These findings provide new insights into the drought tolerance mechanisms of B. juncea and will contribute to the breeding of drought-tolerant rapeseed varieties.
Fetched live from OpenAlex and de-inverted. Abstracts are not stored in this database: the inverted indexes are 8.6 GB of the frame’s 9.3 GB of text, and the host has 13 GB free.
How this classification was reachedexpand
Full frame machine prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. The Gemma side is a direct model label for every work in the frame, read from the title-only record. The Codex side is a classifier learned from the 10,348 direct Codex labels and calibrated to design-weighted sample rates; fields without enough sample support carry no Codex call. Candidate is the union of the two sides; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels.
Distilled classifier scores by category (both heads)
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.000 | 0.000 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.001 | 0.001 |
| Bibliometrics | 0.001 | 0.002 |
| Science and technology studies | 0.001 | 0.000 |
| Scholarly communication | 0.000 | 0.000 |
| Open science | 0.000 | 0.000 |
| Research integrity | 0.000 | 0.000 |
| Insufficient payload (model declined to judge) | 0.002 | 0.000 |
Machine scores (provisional)
The two teacher heads of the student model, read on this work. A score orders the frame for review; it never asserts a category, and the validation status ships verbatim with every row.
Baseline scores from an immature model (maturity gate not passed, 7 training rounds). Scores rank; they never assert a category.
score_only:v0-immature-baseline · verbatim from the scoring run: score_only means the number may rank works, and no category label ships from itClassification
machine, unvalidatedMachine predicted; a candidate call from one source (direct Gemma or distilled Codex), not a consensus.
How this classification was reached, model by model and score by score, is at the end of the page under "How this classification was reached".