Genome-wide association study (GWAS) reveals genetic loci of lead (Pb) tolerance during seedling establishment in rapeseed (Brassica napus L.)

- Genome-wide association study (GWAS) reveals genetic loci of lead (Pb) tolerance during seedling establishment in rapeseed ( Brassica napus L.).
- Safe utilization of Pb contaminated soil by phytoremediation require Pb-tolerant rapeseed (Brassica napus L.) accessions.
- napus cultivars tolerance to Pb stress has been restricted by limited knowledge on molecular mechanisms involved in Pb tolerance.
- This work was carried out to identify genetic loci related to Pb tolerance during seedling establishment in rapeseed..
- Results: Pb tolerance, which was assessed by quantifying radicle length (RL) under 0 or 100 mg/L Pb stress condition, shown an extensive variation in 472 worldwide-collected rapeseed accessions.
- 80%, six Pb-tolerant genotypes were selected.
- Four quantitative trait loci (QTLs) associated with Pb tolerance were identified by Genome-wide association study.
- The expression level of nine promising candidate genes, including GSTUs, BCATs, UBP13, TBR and HIPP01, located in these four QTL regions, were significantly higher or induced by Pb in Pb-tolerant accessions in comparison to Pb-sensitive accessions..
- Conclusion: To our knowledge, this is the first study on Pb-tolerant germplasms and genomic loci in B.
- The findings can provide valuable genetic resources for the breeding of Pb-tolerant B.
- understanding of Pb tolerance mechanism in Brassica species..
- Several alleviating techniques such as phytoreme- diation (including Phytostabilization and Phytoextrac- tion) have been applied for safe utilization of Pb.
- Development of new cultivars tolerance to Pb toxicity will be the first step for safe utilization of Pb polluted soil by phytoremediation [8–.
- Rapeseed (Brassica napus L.
- Breeding rapeseed cultivars with Pb-tolerant re- quire germplasms and genetic loci related to Pb toler- ance.
- Whereas, more and more genotypes tolerance to Pb toxicity have been selected in rice, ramie and willow populations, very few Pb-tolerant B.
- Unlike in other plants, few data is available on molecular mechanisms involved in Pb tolerance in rapeseed.
- In Arabi- dopsis AtACBP1 (Acyl-CoA-binding domain-containing protein), AtPSAE1 (Photosystem I reaction center subunit IV A) and several ABC (ATP-binding cassette) transporter genes (AtATM3, AtPDR8, and AtPDR12) have been identi- fied as being involved in tolerance to Pb stress [24–27].
- For further exploring genetic factors responding to Pb stress, Genome-wide association study (GWAS), a powerful tool to detect the genetic architecture of complex traits, has been widely used in rice, maize and grasses .
- GWAS has also been used to study HMs concentration, tolerance to Cd and other abiotic stress related quantitative trait loci (QTLs), but not the mo- lecular mechanism of Pb tolerance in B.
- The objectives of this study were screening elite germ- plasms tolerance to Pb stress at seedling establishment stage among 472 worldwide-collected rapeseed accessions and identification of QTLs and candidate genes related to Pb tolerance by GWAS for the first time in B.
- of Pb-tolerant cultivars and understanding of the molecular mechanisms responding to Pb stress in Brassica species..
- napus germplasms tolerance to Pb stress.
- To investigate the tolerance to Pb stress of different B..
- napus genotypes, the radicle lengths (RL) of 472 acces- sions grown under 0 or 100 mg/L Pb stress condition for seven days were compared.
- Although the RL varied sig- nificantly among all the accessions under both normal and Pb stress conditions (with a range from 31.15 to 130.50 mm (mm), and 8.67 to 80.60 mm, respectively), the RL of all accessions under Pb stress condition were shorter than that under normal condition (Fig.
- The average of RL under normal growth condition was mm, whereas the aver- age of RL under Pb stress condition was mm (Fig.
- To eliminate the genetic variations in RLs under nor- mal condition, the relative radicle length (RRL) was employed to evaluate the tolerance to Pb stress of B..
- napus population exhibited a broad variation of Pb tolerance..
- To select stable Pb-tolerant genotypes for potentially used in phytoremediation or new cultivar breeding, we performed correlation analyses, and found that the RRLs of three replications were significantly correlated with each other with a correlation coefficient value over 0.85 (Fig.
- Based on the values of RRLs of all the acces- sions, six Pb-tolerant genotypes (RRL >.
- Detection of QTLs associated with Pb tolerance.
- To select a most suitable model for GWAS analysis of Pb tolerance in the population, the native, population struc- ture (Q), principal component analysis (P), kinship (K), Q + K and P + K models were tested.
- Identification of candidate genes related to Pb tolerance For the identification of candidate genes related to Pb toler- ance, all the 115 genes located in the QTL regions and 21 genes in QTL regions Pb-A09, Pb-C03–1, Pb- C03–2 and Pb-C04, respectively) were annotated by nucleic acid basic local alignment search tool (BLASTN) with A..
- All these nine candidate genes may contribute to Pb tolerance in B.
- Exploring the expression level of candidate genes.
- To investigate the expression levels of these candidate genes under both normal and Pb stress conditions in both Pb-tolerant and Pb-sensitive accessions, we.
- We observed that the expression level of BnaA09g14520D, BnaA09g14520D and BnaA09g14540D located in QTL Pb-A09, and BnaC03g02630D and BnaC03g02690D located in QTL Pb-C03–1, were extremely higher in Pb-tolerant geno- types than in Pb-sensitive genotypes (Fig.
- BnaA09g14520D and BnaC03g02690D were significantly induced by Pb stress only in two Pb-tolerant accessions (Fig.
- BnaA09g14540D and BnaC03g02630D were significantly up-regulated in a Pb-tolerant accession III- 229 and only slightly up-regulated in the other acces- sions under Pb stress (Fig.
- BnaC03g68440D, BnaC03g68450D and BnaC03g68460D located in QTL Pb-C03–2 were enriched in the same pathways.
- We found that BnaC03g68440D and BnaC03g68450D were significantly induced by Pb stress in III-229 (Fig.
- 5f, g), and the ex- pression levels of BnaC03g68440D and BnaC03g68450D in Pb-sensitive genotype EH3143 were extensively lower in comparison to Pb-tolerant genotypes (Fig.
- Simi- larly, a higher expression level of BnaC03g68460D was also observed in the two Pb-tolerant genotypes than in two Pb-sensitive genotypes (Fig.
- Under Pb stress condition, BnaC04g16200D, located in QTL Pb-C04, was remarkably up-regulated in Pb-tolerant genotype III-229 and down-regulated in Pb-sensitive genotype 6024–1 (Fig.
- Pb-tolerant accessions provide valuable resources for phytoremediation.
- Especially in the initial stages, seed germination and seedling establishment were ex- tremely inhibited by high concentration of Pb stress [22, Table 1 Genome-wide association signals of Pb tolerance.
- napus was seriously short under Pb stress in comparison to under normal condition (Fig.
- Pb tolerance, represent the ability of plants to adapt to and cope with Pb stress, was commonly evaluated by relative growth indexes under both normal and Pb stress conditions [45].
- Considering the severe inhibition of Pb stress on radicle elongation, the RRL has been employed to evaluate the tolerance of B.
- napus to Pb stress.
- Exten- sive phenotypic variation for Pb tolerance in B.
- Six Pd-tolerant genotypes (Additional file 6: Table S2) selected from the population can pro- vide valuable plant resources which is usable for the breeding of Pb-tolerant B.
- Specific QTLs for Pb tolerance were identified in B.
- napus To detect Pb tolerance related QTLs by GWAS in B.
- whether these four QTLs is specific for Pb tolerance in B..
- Thus, the four QTLs might be specific gen- etic factors for tolerance to Pb stress in B.
- Higher expression of GSTs contributes to Pb-tolerant Glutathione S-transferases (GSTs) contributed to HMs tolerance mainly by playing important roles in the cellu- lar antioxidant defense mechanisms and serving as non- enzymatic carriers for intracellular transport [55, 56]..
- qRT-PCR assays demonstrated that the ex- pression levels of these three genes were extremely higher in Pb-tolerant genotypes than in Pb-sensitive ge- notypes (Fig.
- Furthermore, an induced ex- pression of BnaA09g14520D and BnaA09g14540D by Pb exposure in Pb-tolerant accessions were also observed as reported previously [55].
- Ubiquitination and de-ubiquitination co-regulate Pb tolerance.
- Plots show the SNPs in the QTL Pb-C03 – 1 (top left of Fig.
- study, the expression level of BnaC03g02630D was sig- nificantly higher in Pb-tolerant accessions than in Pb- sensitive accessions (Fig.
- TBR protein was associated with Pb tolerance by regulating cell wall development.
- The expression level of BnaC03g02690D was significantly higher and induced by Pb in Pb- tolerant accessions than in Pb-sensitive accessions (Fig..
- Therefore, the TBR protein encoded by BnaC03g02690D contribute to Pb detoxification by in- creasing cell wall capacity through the compartmentalization of Pb in B.
- BCAA metabolism regulation can mediate Pb tolerance Branched-chain-amino-acid aminotransferase (BCAT), which catalyzes both the last anabolic step and the.
- BnaC03g68440D and BnaC03g68450D, which encoded a BCAT, were highly induced by Pb in Pb- tolerant accession III-229 (Fig.
- The expression level of BnaC03g68460D was higher in Pb tolerance genotypes than in Pb-sensitive genotypes (Fig.
- ALL these results suggest that these three genes, de- tected in QTL Pb-C03–2, contribute to Pb tolerance of B.
- BnaHIPP01 might contribute to detoxification of Pb stress It is well known that HIPPs, containing HM–binding domain (HMA, pfam00403.6), have important func- tions in plant responses to both biotic and abiotic stresses [72, 73].
- We found that BnaC04g16200D, the homolog of AtHIPP01, was sig- nificantly up-regulated in Pb-tolerant genotype III-229 and down-regulated in Pb-sensitive genotype 6024–1 under Pb stress (Fig.
- These findings suggest that, BnaC04g16200D might contribute to the detoxifica- tion of Pb stress, as did BnHIPP27 to Cd stress in B..
- Table 2 A list of the most promising candidate genes for Pb tolerance in rapeseed QTLs Candidate.
- To our knowledge, this is the first study on Pb-tolerant germplasms and genomic loci in B.
- We found that Pb tolerance shown an extensive variation in 472 worldwide-collected rapeseed accessions.
- Four QTLs associated with Pb tolerance were identified by GWAS.
- The expression level of these nine genes were sig- nificantly higher or induced by Pb in Pb-tolerant accessions in comparison to Pb-sensitive accessions..
- These findings can provide valuable genetic resources for the breeding of Pb-tolerant B.
- napus cultivar and un- derstanding of Pb tolerance mechanism in Brassica species..
- Pb tolerance evaluation of 472 B.
- 5 The relative expression level of candidate genes for Pb tolerance.
- In order to find out the opti- mal method for Pb tolerance evaluation at seedling es- tablishment stage in rapeseed, we first performed a trial..
- Thus, 100 mg/L was selected as an optimal concentration for screening Pb-tolerant rapeseed acces- sions at seedling establishment stage..
- Accessions with higher RRL were genotypes more tolerant to Pb stress.
- Genome-wide association study.
- Identification of candidate genes.
- The expression level of candidate genes in two Pb- tolerant (HANNA and III-229) and two Pb-sensitive (6024–1 and EH3143) genotypes were evaluated by quantitative real time PCR (qRT-PCR).
- Additional file 1: Figure S1.
- The details Pb-tolerant genotypes screeneded from 472 global-coolected rapeseeds.
- GWAS: Genome-wide association study.
- FZ, XX and KX performed the phenotyping of Pb tolerance.
- Genome-wide association analysis of lead accumulation in maize.
- Genome-wide.
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- differences in the response mechanisms

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