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Molecular basis of adaptation to high soil boron in wheat landraces and elite cultivars

Nature volume 514, pages 88–91 (2014)Cite this article

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Abstract

Environmental constraints severely restrict crop yields in most production environments, and expanding the use of variation will underpin future progress in breeding. In semi-arid environments boron toxicity constrains productivity, and genetic improvement is the only effective strategy for addressing the problem1. Wheat breeders have sought and used available genetic diversity from landraces to maintain yield in these environments; however, the identity of the genes at the major tolerance loci was unknown. Here we describe the identification of near-identical, root-specific boron transporter genes underlying the two major-effect quantitative trait loci for boron tolerance in wheat, Bo1 and Bo4 (ref. 2). We show that tolerance to a high concentration of boron is associated with multiple genomic changes including tetraploid introgression, dispersed gene duplication, and variation in gene structure and transcript level. An allelic series was identified from a panel of bread and durum wheat cultivars and landraces originating from diverse agronomic zones. Our results demonstrate that, during selection, breeders have matched functionally different boron tolerance alleles to specific environments. The characterization of boron tolerance in wheat illustrates the power of the new wheat genomic resources to define key adaptive processes that have underpinned crop improvement.

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Figure 1: Effect of Bo1 allele type on root length at high boron concentrations.
Figure 2: Variation in Bot-B5/D5 alleles.
Figure 3: Wheat Bot-B5 allele origin and dispersion, and Australian distribution pattern.

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Primary accessions

GenBank/EMBL/DDBJ

Data deposits

Sequence data are deposited with NCBI GenBank under accession numbers KF148623–KF148633 and GF112200–GF112209.

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Acknowledgements

We thank N. Collins, J. Dvorjak, H. Kuchel, D. Mares, S. Wu, the John Innes Centre, the Biotechnology and Biological Sciences Research Council, the Institut National de la Recherche Agronomique and the International Wheat Genome Sequencing Consortium for resources, and J. Tiong, T. Oz and A. Pohlen for assistance. The authors are supported by grants from the Australian Research Council, the Grains Research and Development Corporation and the South Australian Government.

Author information

Author notes

  1. Margaret Pallotta and Thorsten Schnurbusch: These authors contributed equally to this work.

Authors and Affiliations

  1. Australian Centre for Plant Functional Genomics, School of Agriculture, Food and Wine, University of Adelaide, Waite Campus, Urrbrae, South Australia 5064, Australia,

    Margaret Pallotta, Thorsten Schnurbusch, Julie Hayes, Alison Hay, Ute Baumann, Peter Langridge & Tim Sutton

  2. Genebank Department, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstrasse 3, D-06466 Gatersleben, Germany,

    Thorsten Schnurbusch

  3. School of Agriculture, Food and Wine, University of Adelaide, Waite Campus, Urrbrae, South Australia 5064, Australia,

    Jeff Paull

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Contributions

M.P., T.Sc., J.H., J.P., P.L. and T.S. designed experiments. M.P., T.Sc., J.H. and A.H. performed experiments. M.P., T.Sc., J.H., A.H., U.B., J.P. and T.S. analysed data. M.P., T.S., J.H. and P.L. wrote the manuscript. T.Sc., U.B. and J.P. commented on the manuscript.

Corresponding author

Correspondence to Tim Sutton.

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The authors declare no competing financial interests.

Extended data figures and tables

Extended Data Figure 1 Southern analysis of Bot-D2a and Bot-B5 genes.

a, Genomic DNA from Chinese Spring nullisomic–tetrasomic (N-T) chromosome substitution lines digested with DraI and hybridized with the probe AWW469, a 261-bp cDNA fragment of Bot-D2 amplified from Cranbrook, which does not cross-hybridize to Bot-B5 or Bot-D5 at high stringency. Lane 1, Ae. tauschii; lane 2, Chinese Spring; lane 3, CS N7B-T7D; lane 4, CS N3A-T3D; lane 5, CS N3B-T3A; lane 6, CS N3D-T3B; lane 7, CS N4B-T4D; lane 8, CS N4D-T4A; lane 9, CS N5A-T5B. The chromosomal location of each detected fragment is indicated. b, Genomic DNA was digested with HindIII and hybridized with the probe AWW471, a 357-bp genomic DNA fragment of Bot-D5b that hybridizes to Bot-B5 at high stringency. Lane M, HindIII-digested Lambda DNA as size marker; lane 1, Cranbrook; lane 2, Halberd; lane 3, Chinese Spring; lane 4, CS nulli–tetra line N7B-T7A; lane 5, Langdon. The chromosomal location of strongly detected fragments is indicated. Minor bands are the result of low-level hybridization to paralogous sequences on 3A, 3B, 3D, 4B, 4D and 5A.

Extended Data Figure 2 Mapping of Bot-B5 to 7BL (Bo1) and 4AL (Bo4).

a, Fine mapping of the Bo1 locus on chromosome 7BL in a Cranbrook × Halberd F2 population. Markers are listed below the line, and numbers above indicate recombinants identified for each marker interval. Previously unpublished markers are indicated in bold (see Supplementary Table 1). Markers in black font are derived from genes that are syntenous in rice, Brachypodium and wheat. The marker in green font is derived from a gene that is absent in rice but syntenous in Brachypodium and wheat. Marker AWW461 (orange font) is a fragment of Bot-D5b and is absent in both rice and Brachypodium. In both rice and Brachypodium the genes that are syntenous with AWW220 and AWW246 are immediately adjacent to each other, whereas large insertion or inversion events have separated these genes in wheat. b, Partial genetic maps of chromosomes 4AL and 7BL in a G61450 × Kenya Farmer RIL population showing markers closely associated with Bot-B5 alleles. Genetic distances in centimorgans are shown on the left side of the chromosome between markers. In brackets after the marker name we show LOD score and the percentage of total trait variation explained by the marker as derived using simple marker regression analysis for absolute longest root length in high-boron hydroponics. Data are shown for markers with a LOD score of >2.0. No significant marker-trait association was detected at the 7BL locus in this population.

Extended Data Figure 3 Bot-B5 is localized to the plasma membrane and is responsive to boron.

a, Confocal image of an onion epidermal cell with transient expression of 35S:Bot-B5b:GFP fusion protein before (upper panel) and after (lower panel) partial plasmolysis. Expression is confined to the plasma membrane. The lower panel shows Hechtian strands (thin membrane strands) connecting the cell wall to the plasmalemma after plasmolysis. The apparent signal in the sides of the cell in the upper panel is the result of a broad optical section imaged by the confocal microscope. This has resulted in an apparent broad distribution of green fluorescent protein (GFP) signal due to the curvature in cell wall towards the cell surface within the focal plane captured. b, Semi-quantitative RT–PCR in a Chinese Spring developmental series32 using the Bot-B5-specific marker qRT–PCR-Bot-B5 (36 cycles, upper panel) and a wheat GAPDH marker (28 cycles, lower panel), indicating specific expression of Bot-B5 in root tissues. Lane M, 2.5 μl of HyperLadder II from Bioline (Aust) Pty. Ltd; lane 1, root from 2-day-old germinating seeds; lane 2, embryo from 2-day-old germinating seeds; lane 3, coleoptiles from 2-day-old germinating seeds; lane 4, root from seedlings with shoots 10 cm long; lane 5, crown from seedlings with shoots 10 cm long; lane 6, leaf from seedlings with shoots 10 cm long; lane 7, immature inflorescences 2–3 cm long; lane 8, floral bracts 2 days before anthesis; lane 9, anthers 2 days before anthesis; lane 10, caryopsis 3–5 days after pollination; lane 11, embryo 22 days after pollination; lane 12, endosperm 22 days after pollination; lanes 13 and 14, water controls. A low level of product visible in the dissected embryo (lane 2) was probably due to contamination from root tissue. c, Northern analysis of Bot-B5 mRNA levels in whole roots from 17-day-old Halberd and G61450 plants from hydroponics experiments 1 and 2 (see Methods). Seedlings were grown in nutrient solution for 17 days and treated either with no supplementary boron or with 2 mM supplementary boron for 22 h or 7 days before tissue collection. Lanes 1 and 2, Halberd plants from experiment 2 with no supplementary boron (two independent Halberd replicates are loaded); lanes 3 and 4, Halberd plants grown in experiment 2 and treated with 2 mM supplementary boron for 22 h (two independent Halberd replicates are loaded); lanes 5–7, Halberd plants grown in experiment 1 and treated with no supplementary boron, 2 mM supplementary boron for 22 h, and 2 mM supplementary boron for 7 days, respectively; lanes 8–10, G61450 plants grown in experiment 1 and treated with no supplementary boron, 2 mM supplementary boron for 22 h, and 2 mM supplementary boron for 7 days, respectively. Total RNA was revealed with ethidium bromide to indicate loading (lower panel) and analysed by northern hybridization (upper panel) using a 268-bp cDNA probe (AWW548) derived from Halberd, comprising 65 bp of coding sequence and 203 bp of 3′ UTR.

Extended Data Figure 4 Phylogeny and genome organization of monocot boron transporter genes.

a, Unrooted phylogenetic tree of boron transporter ORF sequences in selected monocot species (Ta, T. aestivum; Aet, Ae. tauschii; Hv, Hordeum vulgare; Bradi, B. distachyon; Sb, S. bicolor; LOC_Os, O. sativa). Local bootstrap values (1,000 replicates) are shown as percentages adjacent to the branch line. The tree is drawn to scale, with branch lengths measured in the number of substitutions per site. TaBot-B5 and TaBot-D5 genes are indicated in orange font. Orthologous sequences in Triticum uratu are represented by a dagger. As in bread wheat, no 7A gene is present in T. uratu. In addition to AetBot-D5b, orthologous sequences in Ae. tauschii are represented by an asterisk. b, Chromosomes of rice (green), Brachypodium (blue), barley (yellow) and wheat (orange), showing the approximate location of boron transporter sequences (red boxes) and grouped vertically by macro synteny. The dispersed duplication of Bot-B5 from 7BL to 4AL is shown by the solid arrow, and a putative ancient duplication between group 3 and group 7 chromosomes in wheat40 is shown by the grey dashed arrow.

Extended Data Figure 5 Mutations in Bot-B5b reduce root growth at high boron.

a, Length of the longest root of wheat EMS mutant lines EMS388 and EMS405 in 0.015 mM boron and 10 mM boron in comparison with the standard cultivars Cranbrook and Halberd (n = 16; means ± s.e.m.). Numbers above the black columns are relative root lengths (root length in 10 mM boron expressed as a percentage of the root length in 0.015 mM boron). Letters denote significant (P < 0.01) differences between genotypes at high boron. There were no genotypic differences at low boron. b, Root length of plants segregating for mutant Bot-B5b alleles. Box plots show root lengths of seedlings segregating for Bot-B5b-EMS388 (n = 93) and Bot-B5b-EMS405 (n = 131). The boundaries of the boxes indicate 75th and 25th centiles, and lines within mark the median. Bars above and below the boxes indicate 90th and 10th centiles; outliers are shown as black circles. The longest root of a minimum of 20 individuals was measured for each group after hydroponic culture supplemented with 8 mM boron for 8 days (EMS388) or 13 days (EMS405). Numbers of plants measured for each allele class are indicated in parentheses.

Extended Data Figure 6 Analysis of protein function and boron tolerance of AeBot-D5b from synthetic wheat SW58.

a, Serial dilutions of yeast expressing Bot-B5b from Halberd (upper panels) or Bot-D5b from SW58 (lower panels), grown on solid medium containing no additional boron (left panels) and 20 mM supplementary boron (right panels). Each plate shows three independent yeast clones expressing either Bot-B5b or Bot-D5b at the top of the plate, and three independent clones expressing a truncated non-functional sequence (Bot-B5a-sv) at the bottom of the plate. Aliquots of 10 μl of tenfold serial dilutions of saturated cultures were spotted across the plates (right to left in each panel). b, Longest root length (n = 16; means ± s.e.m.) of 10-day-old seedlings of SW58, Halberd, Cranbrook and Langdon grown in 0.015 mM boron and 10 mM boron. Letters denote statistically distinct groups within each boron treatment (Tukey’s Honestly Significant Difference test, α = 0.05).

Extended Data Table 1 Wheat boron transporter nomenclature
Full size table

Supplementary information

Supplementary Information

This file contains a Supplementary Discussion. (PDF 195 kb)

Supplementary Table 1

This table displays PCR markers and probes for genotyping and expression analysis. a, Primer sequences and expected amplicon sizes for PCR markers derived from Bot-B5/D5 which were used for allele typing and Bot-B5 expression analysis. b, primer sequences for probe generation and c, primer sequences for PCR markers used for F2 recombinant screening and semi-quantitative RT-PCR analysis. (XLSX 14 kb)

Supplementary Table 2

This table shows wild and cultivated barleys screened for TaBot-B5b orthologues. Name and source of genotypes screened by Southern analysis with AWW548. (XLSX 20 kb)

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Pallotta, M., Schnurbusch, T., Hayes, J. et al. Molecular basis of adaptation to high soil boron in wheat landraces and elite cultivars. Nature 514, 88–91 (2014). https://doi.org/10.1038/nature13538

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