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, 15 (1), 153

Genetic Dissection of Al Tolerance QTLs in the Maize Genome by High Density SNP Scan

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Genetic Dissection of Al Tolerance QTLs in the Maize Genome by High Density SNP Scan

Claudia T Guimaraes et al. BMC Genomics.

Abstract

Background: Aluminum (Al) toxicity is an important limitation to food security in tropical and subtropical regions. High Al saturation on acid soils limits root development, reducing water and nutrient uptake. In addition to naturally occurring acid soils, agricultural practices may decrease soil pH, leading to yield losses due to Al toxicity. Elucidating the genetic and molecular mechanisms underlying maize Al tolerance is expected to accelerate the development of Al-tolerant cultivars.

Results: Five genomic regions were significantly associated with Al tolerance, using 54,455 SNP markers in a recombinant inbred line population derived from Cateto Al237. Candidate genes co-localized with Al tolerance QTLs were further investigated. Near-isogenic lines (NILs) developed for ZmMATE2 were as Al-sensitive as the recurrent line, indicating that this candidate gene was not responsible for the Al tolerance QTL on chromosome 5, qALT5. However, ZmNrat1, a maize homolog to OsNrat1, which encodes an Al(3+) specific transporter previously implicated in rice Al tolerance, was mapped at ~40 Mbp from qALT5. We demonstrate for the first time that ZmNrat1 is preferentially expressed in maize root tips and is up-regulated by Al, similarly to OsNrat1 in rice, suggesting a role of this gene in maize Al tolerance. The strongest-effect QTL was mapped on chromosome 6 (qALT6), within a 0.5 Mbp region where three copies of the Al tolerance gene, ZmMATE1, were found in tandem configuration. qALT6 was shown to increase Al tolerance in maize; the qALT6-NILs carrying three copies of ZmMATE1 exhibited a two-fold increase in Al tolerance, and higher expression of ZmMATE1 compared to the Al sensitive recurrent parent. Interestingly, a new source of Al tolerance via ZmMATE1 was identified in a Brazilian elite line that showed high expression of ZmMATE1 but carries a single copy of ZmMATE1.

Conclusions: High ZmMATE1 expression, controlled either by three copies of the target gene or by an unknown molecular mechanism, is responsible for Al tolerance mediated by qALT6. As Al tolerant alleles at qALT6 are rare in maize, marker-assisted introgression of this QTL is an important strategy to improve maize adaptation to acid soils worldwide.

Figures

Figure 1
Figure 1
Al tolerance QTLs detected using a multiple regression model. QTLs were assigned as significant at p < 0.001.
Figure 2
Figure 2
Near-isogenic lines introgressed with ZmMATE2 , using Cateto Al237 and L53 as the donor and recurrent parents, respectively. A) Aluminum tolerance measured as relative seminal root growth after five days under {39} μM Al3+. B) ZmMATE2 relative expression evaluated in root tips after 6 hours of treatment with {39} μM Al3+. Expression of L53 was used as calibrator. Error bars indicate standard deviation.
Figure 3
Figure 3
Spatial and temporal expression profiles of ZmNrat1 in two contrasting maize lines for Al tolerance. A) Expression of ZmNrat1 in different tissues under controlled conditions, and after 6 hours at {39} μM Al3+. B) Time course of ZmNrat1 expression following treatment of root tips with {39} μM Al3+. Expression of L53 under controlled condition (−Al) was used as calibrator. Error bars indicate standard deviation.
Figure 4
Figure 4
Near-isogenic lines introgressed with qALT6 , using Cateto Al237 and L53 as the donor and recurrent parents, respectively. A) Aluminum tolerance measured as relative seminal root growth after five days under {39} μM Al3+. B) ZmMATE1 relative expression evaluated in root tips after 6 hours of treatment with {39} μM Al3+ (dark gray) and under control condition (light gray). Expression of L53 under controlled condition (−Al) was used as calibrator. C) ZmMATE1 copy-number estimated based on qPCR. Error bars indicate standard deviation.
Figure 5
Figure 5
Aluminum tolerance and ZmMATE1 relative expression among 37 maize lines. Aluminum tolerance measured as relative seminal root growth after five days under {39} μM Al3+ and ZmMATE1 relative expression evaluated in root tips after 6 hours of treatment with {39} μM Al3+.
Figure 6
Figure 6
ZmMATE1 copy-number estimate based on quantitative PCR in Cateto Al237, L53, L228-3, L228-3-derived lines (line designations starting with numbers), and B73. The primers for CNV2 and CNV4 amplify a portion of exon 2 and 3′UTR region of ZmMATE1, respectively.

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