The Relationship between Population Structure and Aluminum Tolerance in Cultivated Sorghum

Background: Acid soils comprise up to 50% of the world's arable lands and in these areas aluminum (Al) toxicity impairs root growth, strongly limiting crop yield. Food security is thereby compromised in many developing countries located in tropical and subtropical regions worldwide. In sorghum, SbMATE, an Al-activated citrate transporter, underlies the Alt(SB) locus on chromosome 3 and confers Al tolerance via Al-activated root citrate release. Methodology: Population structure was studied in 254 sorghum accessions representative of the diversity present in cultivated sorghums. Al tolerance was assessed as the degree of root growth inhibition in nutrient solution containing Al. A genetic analysis based on markers flanking Alt(SB) and SbMATE expression was undertaken to assess a possible role for Alt(SB) in Al tolerant accessions. In addition, the mode of gene action was estimated concerning the Al tolerance trait. Comparisons between models that include population structure were applied to assess the importance of each subpopulation to Al tolerance. Conclusion/Significance: Six subpopulations were revealed featuring specific racial and geographic origins. Al tolerance was found to be rather rare and present primarily in guinea and to lesser extent in caudatum subpopulations. Alt(SB) was found to play a role in Al tolerance in most of the Al tolerant accessions. A striking variation was observed in the mode of gene action for the Al tolerance trait, which ranged from almost complete recessivity to near complete dominance, with a higher frequency of partially recessive sources of Al tolerance. A possible interpretation of our results concerning the origin and evolution of Al tolerance in cultivated sorghum is discussed. This study demonstrates the importance of deeply exploring the crop diversity reservoir both for a comprehensive view of the dynamics underlying the distribution and function of Al tolerance genes and to design efficient molecular breeding strategies aimed at enhancing Al tolerance.CGIAR[G3007.04]McKnight FoundationFundacao de Amparo a Pesquisa do Estado de Minas Gerais (FAPEMIG)National Council for Scientific and Technological Development (CNPq

Association mapping provides insights into the origin and the fine structure of the sorghum aluminum tolerance locus, AltSB

Root damage caused by aluminum (Al) toxicity is a major cause of grain yield reduction on acid soils, which are prevalent in tropical and subtropical regions of the world where food security is most tenuous. In sorghum, Al tolerance is conferred by SbMATE, an Al-activated root citrate efflux transporter that underlies the major Al tolerance locus, AltSB, on sorghum chromosome 3. We used association mapping to gain insights into the origin and evolution of Al tolerance in sorghum and to detect functional variants amenable to allele mining applications. Linkage disequilibrium across the AltSB locus decreased much faster than in previous reports in sorghum, and reached basal levels at approximately 1000 bp. Accordingly, intra-locus recombination events were found to be extensive. SNPs and indels highly associated with Al tolerance showed a narrow frequency range, between 0.06 and 0.1, suggesting a rather recent origin of Al tolerance mutations within AltSB. A haplotype network analysis suggested a single geographic and racial origin of causative mutations in primordial guinea domesticates in West Africa. Al tolerance assessment in accessions harboring recombinant haplotypes suggests that causative polymorphisms are localized to a ∼6 kb region including intronic polymorphisms and a transposon (MITE) insertion, whose size variation has been shown to be positively correlated with Al tolerance. The SNP with the strongest association signal, located in the second SbMATE intron, recovers 9 of the 14 highly Al tolerant accessions and 80% of all the Al tolerant and intermediately tolerant accessions in the association panel. Our results also demonstrate the pivotal importance of knowledge on the origin and evolution of Al tolerance mutations in molecular breeding applications. Allele mining strategies based on associated loci are expected to lead to the efficient identification, in diverse sorghum germplasm, of Al tolerant accessions able maintain grain yields under Al toxicity

Recovery of Al tolerant and intermediate accessions by loci associated with Al tolerance.

<p>In bold are the least frequent alleles, which are linked in coupling with Al tolerance except for loci with borderline association probabilities and/or small effects on <i>RNRG_5d</i> (MII, 5947 and 24804). For each associated locus are shown the minor allele frequencies (MAF), the total number of accessions (n), the number of Al tolerant (T, <i>RNRG_5d</i> >80%), intermediate (I, 30%<<i>RNRG_5d</i> <80%) and sensitive (S, <i>RNRG_5d</i> <30%) accessions. The proportions based on phenotypic selection (phenotypic) are shown at the bottom of the table. Given their genotypes, the Al tolerant accessions in the association panel marked with ‘<b>+</b>’ possess the Al tolerant <i>Alt_SB</i> allele. The Al tolerant lines CMS226, CMS227 and 9929034, which are breeding derivatives from SC283 (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0087438#pone.0087438.s001" target="_blank">Table S1</a> in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0087438#pone.0087438-Caniato1" target="_blank">[16]</a>), were excluded from this analysis.</p

LD decay in the <i>Alt_SB</i> region.

<p>In red is the prediction obtained by fitting a nonlinear regression model of the squared correlation of allele frequencies (<i>r²</i>) as a function of physical distance between pairs of loci based on the drift-recombination model <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0087438#pone.0087438-Remington1" target="_blank">[40]</a>. The regression coefficient (<i>b₁</i>, **<i>p</i><0.0001) and the fraction of the total variance explained by the nonlinear model (1– SS_R/SS_T) are shown, where SS_R and SS_T are the sum of squares of error and total, respectively.</p

Model comparison for type I error control.

<p>Type I error distribution obtained with the naïve, Q₆, K and Q₆+ K models using 38 SSR loci and phenotypic traits related to Al tolerance. Under the expectation that the randomly distributed SSR loci are not associated with Al tolerance, models that properly control the type I error should show a uniform distribution of <i>p-</i>values along a diagonal line in the cumulative plot. Loci with MAF >0.1 were used.</p

Association analysis for polymorphisms in the <i>Alt_SB</i> region and Al tolerance.

<p>Association analysis with the Q₆+ K model was performed with <i>RNRG_5d</i>. (<b>A</b>) Statistical significance is expressed as –log₁₀(<i>p</i>) and the <i>p</i><0.01 threshold is represented by the red horizontal line. Polymorphisms are shown along the x-axis and are linked to the schematic below this graph which depicts their physical location in the 24.6 kb region where <i>SbMATE</i> (exons shown as gray boxes connected to black lines representing introns) was mapped on chromosome 3 (A1 to A5 depict amplicons harboring polymorphisms, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0087438#pone.0087438.s005" target="_blank">Table S5</a>). The corresponding physical positions in the sorghum genome are shown below the scale and were obtained by sequence similarity analysis (<a href="http://www.phytozome.net" target="_blank">http://www.phytozome.net</a>). The alleles at each loci are shown in the x-axis following the locus designation, with indels represented by the number of repeats, except for the MITE insertion, which was coded as described in the Material and Methods session. (<b>B</b>) Linkage disequilibrium expressed by pairwise <i>D’</i> estimates <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0087438#pone.0087438-Lewontin1" target="_blank">[65]</a> among loci associated with Al tolerance. <i>p</i>-values obtained with the Fisher exact test are shown. (<b>C</b>) Allele substitution effect for the 6083 locus. The slope of the linear regression line indicates an allele substitution effect of 53.9% <i>RNRG_5d</i> (<i>p</i><2E-16).</p

Quantificação de açúcares solúveis totais, açúcares redutores e amido nos grãos verdes de cultivares de milho na colheita Quantification of total soluble sugars, reducing sugars and starch in immature kernels of corn cultivars

O objetivo deste trabalho foi quantificar os teores de açúcares solúveis totais (AST), açúcares redutores (AR) e amido em nove cultivares de milho colhidos no estádio verde, uma vez que estes influenciam diretamente o sabor, o aroma e a aceitação do consumidor. O experimento foi conduzido em Ponte Nova, MG, no ano agrícola 2002/2003. Para a determinação das características, foi retirada uma amostra de três espigas de cada unidade experimental. O ponto de colheita foi identificado por método empírico, quando o estilo-estigma se desprendia da espiga com facilidade. As cultivares apresentaram umidades diferentes no momento da colheita, variando de 56 a 64%. Não foi detectada diferença entre as cultivares quanto aos teores de AR, porém, P3232 e AG4051 apresentaram boa relação entre AR e AST, destacando-se para esta finalidade.<br>Total soluble sugars (TSS), reducing sugars (RS), moisture and starch directly influence flavor and consumption. In this work, TSS, RS and starch were determined at harvest in young kernels of nine corn cultivars. The experiment was carried out in Ponte Nova, MG, Brazil. To determine chemical characters of young kernels a sample was obtained of three cobs from each experimental plot. Corn ears were harvested using an empirical method, when the silk was loose from the ear. Moisture varied among samples of different cultivars at harvest. Moisture content ranged from 56 to 64%. There were no differences among cultivars regarding RS. However, cultivars P3232 and AG4051 showed good RS to TSS ratio, being adequate for fresh consumption