Genome-wide association mapping of flowering time and northern corn leaf blight (Setosphaeria turcica) resistance in a vast commercial maize germplasm set

BACKGROUND: Setosphaeria turcica is a fungal pathogen that causes northern corn leaf blight (NCLB) which is a serious foliar disease in maize. In order to unravel the genetic architecture of the resistance against this disease, a vast association mapping panel comprising 1487 European maize inbred lines was used to (i) identify chromosomal regions affecting flowering time (FT) and northern corn leaf blight (NCLB) resistance, (ii) examine the epistatic interactions of the identified chromosomal regions with the genetic background on an individual molecular marker basis, and (iii) dissect the correlation between NCLB resistance and FT. RESULTS: The single marker analyses performed for 8 244 single nucleotide polymorphism (SNP) markers revealed seven, four, and four SNP markers significantly (α=0.05, amplicon wise Bonferroni correction) associated with FT, NCLB, and NCLB resistance corrected for FT, respectively. These markers explained individually between 0.36 and 14.29% of the genetic variance of the corresponding trait. CONCLUSIONS: The very well interpretable pattern of SNP associations observed for FT suggested that data from applied plant breeding programs can be used to dissect polygenic traits. This in turn indicates that the associations identified for NCLB resistance might be successfully used in marker-assisted selection programs. Furthermore, the associated genes are also of interest for further research concerning the mechanism of resistance to NCLB and plant diseases in general, because some of the associated genes have not been mentioned in this context so far

Expression of cell wall related genes in basal and ear internodes of silking brown-midrib-3, caffeic acid O-methyltransferase (COMT) down-regulated, and normal maize plants

<p>Abstract</p> <p>Background</p> <p>Silage maize is a major forage and energy resource for cattle feeding, and several studies have shown that lignin content and structure are the determining factors in forage maize feeding value. In maize, four natural <it>brown-midrib </it>mutants have modified lignin content, lignin structure and cell wall digestibility. The greatest lignin reduction and the highest cell wall digestibility were observed in the <it>brown-midrib-3 </it>(<it>bm3</it>) mutant, which is disrupted in the caffeic acid <it>O</it>-methyltransferase (COMT) gene.</p> <p>Results</p> <p>Expression of cell wall related genes was investigated in basal and ear internodes of normal, COMT antisens (AS225), and <it>bm3 </it>maize plants of the INRA F2 line. A cell wall macro-array was developed with 651 gene specific tags of genes specifically involved in cell wall biogenesis. When comparing basal (older lignifying) and ear (younger lignifying) internodes of the normal line, all genes known to be involved in constitutive monolignol biosynthesis had a higher expression in younger ear internodes. The expression of the COMT gene was heavily reduced, especially in the younger lignifying tissues of the ear internode. Despite the fact that AS225 transgene expression was driven only in sclerenchyma tissues, COMT expression was also heavily reduced in AS225 ear and basal internodes. COMT disruption or down-regulation led to differential expressions of a few lignin pathway genes, which were all over-expressed, except for a phenylalanine ammonia-lyase gene. More unexpectedly, several transcription factor genes, cell signaling genes, transport and detoxification genes, genes involved in cell wall carbohydrate metabolism and genes encoding cell wall proteins, were differentially expressed, and mostly over-expressed, in COMT-deficient plants.</p> <p>Conclusion</p> <p>Differential gene expressions in COMT-deficient plants highlighted a probable disturbance in cell wall assembly. In addition, the gene expressions suggested modified chronology of the different events leading to cell expansion and lignification with consequences far beyond the phenylpropanoid metabolism. The reduced availability of monolignols and S units in <it>bm3 </it>or AS225 plants led to plants also differing in cell wall carbohydrate, and probably protein, composition. Thus, the deficiency in a key-enzyme of the lignin pathway had correlative effects on the whole cell wall metabolism. Furthermore, the observed differential expression between <it>bm3 </it>and normal plants indicated the possible involvement in the maize lignin pathway of genes which up until now have not been considered to play this role.</p

Investigating the unusually high cell wall digestibility of the old INRA early flint F4 maize inbred line

The old INRA flint early line F4, which belongs to the northern flint group, is typified by its high cell wall digest- ibility which reaches values as high as those observed in several brown-midrib bm3 mutant lines. The F4 line thus appeared as a model that could contribute to the understanding of genetic mechanisms involved in variation of secondary wall traits. Different strategies and results were thus gathered including especially cell wall biochemical and digestibility investigations, expression approaches, QTL investigations, and colocalizations between QTLs and candidate genes. Lignin content was lower in F4 than in other lines, with a tendency to lower p-coumarate content. The Syringyl/Guaiacyl lignin unit ratio was similar in F4 as in other lines, but this ratio was nearly not reduced in F4bm3, conversely to what is observed in bm3 mutants. In comparison with the INRA F2 control line, expressions of three PAL genes including the ZmPAL, of the ZmF5H1 and the ZmCOMT genes were significantly reduced in F4 lignifying ear internodes at early silking stage. In the F7025 x F4 RIL progeny, seven QTLs were shown with favorable alleles (increasing cell wall digestibility) originating from F4. Two strong QTLs were located in bins 1.03 and 2.03 colocalizing with the ZmMYB019 and ZmSWN6 transcription factors, respectively. Orthologs of ZmMYB019 have been shown to be involved in lignin biosynthesis, and the PpMYB8 ortholog was shown to regu- late PAL gene expression in maritime pine. The ZmSWN6 NAC transcription factor is an upstream master regulator of the secondary wall biosynthetic programs. At the other QTL positions, colocalizations were also shown with other secondary wall related ZmMYB, but also with BAHD genes involved in arabinoxylan feruloylation, and with the position of the bm6 mutation. Three QTL positions were shown with favorable alleles originating from F7025, which colocalized with ZmMYB and ZmNAC transcriptions factors. As a tentative conclusion, the F4 unusually high cell wall digestibility is likely greatly related to the altered working of at least two major transcription factors regulating cell wall biosynthesis and assembly

Nucleotide diversity of the ZmPox3 maize peroxidase gene: Relationships between a MITE insertion in exon 2 and variation in forage maize digestibility

BACKGROUND: Polymorphisms were investigated within the ZmPox3 maize peroxidase gene, possibly involved in lignin biosynthesis because of its colocalization with a cluster of QTL related to lignin content and cell wall digestibility. The purpose of this study was to identify, on the basis of 37 maize lines chosen for their varying degrees of cell wall digestibility and representative of temperate regions germplasm, ZmPox3 haplotypes or individual polymorphisms possibly associated with digestibility. RESULTS: Numerous haplotypes with high diversity were identified. Frequency of nucleotide changes was high with on average one SNP every 57 bp. Nucleotide diversity was not equally distributed among site categories: the estimated π was on average eight times higher for silent sites than for non-synonymous sites. Numerous sites were in linkage disequilibrium that decayed with increasing physical distance. A zmPox3 mutant allele, carrying an insertion of a transposable element in the second exon, was found in lines derived from the early flint inbred line, F7. This element possesses many structural features of miniature inverted-repeat transposable elements (MITE). The mutant allele encodes a truncated protein lacking important functional sites. An ANOVA performed with a subset of 31 maize lines indicated that the transposable element was significantly associated with cell wall digestibility. This association was confirmed using an additional set of 25 flint lines related to F7. Moreover, RT-PCR experiments revealed a decreased amount of corresponding mRNA in plants with the MITE insertion. CONCLUSION: These results showed that ZmPox3 could possibly be involved in monolignol polymerisation, and that a deficiency in ZmPox3 peroxidase activity seemingly has a negative effect on cell wall digestibility. Also, genetic diversity analyses of ZmPox3 indicated that this peroxidase could be a relevant target for grass digestibility improvement using specific allele introgressions

Genome wide association mapping for arabinoxylan content in a collection of tetraploid wheats

BACKGROUND: Arabinoxylans (AXs) are major components of plant cell walls in bread wheat and are important in bread-making and starch extraction. Furthermore, arabinoxylans are components of soluble dietary fibre that has potential health-promoting effects in human nutrition. Despite their high value for human health, few studies have been carried out on the genetics of AX content in durum wheat. RESULTS: The genetic variability of AX content was investigated in a set of 104 tetraploid wheat genotypes and regions attributable to AX content were identified through a genome wide association study (GWAS). The amount of arabinoxylan, expressed as percentage (w/w) of the dry weight of the kernel, ranged from 1.8% to 5.5% with a mean value of 4.0%. The GWAS revealed a total of 37 significant marker-trait associations (MTA), identifying 19 quantitative trait loci (QTL) associated with AX content. The highest number of MTAs was identified on chromosome 5A (seven), where three QTL regions were associated with AX content, while the lowest number of MTAs was detected on chromosomes 2B and 4B, where only one MTA identified a single locus. Conservation of synteny between SNP marker sequences and the annotated genes and proteins in Brachypodium distachyon, Oryza sativa and Sorghum bicolor allowed the identification of nine QTL coincident with candidate genes. These included a glycosyl hydrolase GH35, which encodes Gal7 and a glucosyltransferase GT31 on chromosome 1A; a cluster of GT1 genes on chromosome 2B that includes TaUGT1 and cisZog1; a glycosyl hydrolase that encodes a CelC gene on chromosome 3A; Ugt12887 and TaUGT1genes on chromosome 5A; a (1,3)-β-D-glucan synthase (Gsl12 gene) and a glucosyl hydrolase (Cel8 gene) on chromosome 7A. CONCLUSIONS: This study identifies significant MTAs for the AX content in the grain of tetraploid wheat genotypes. We propose that these may be used for molecular breeding of durum wheat varieties with higher soluble fibre content.Ilaria Marcotuli, Kelly Houston, Robbie Waugh, Geoffrey B. Fincher, Rachel A. Burton, Antonio Blanco, Agata Gadalet

Characterization of a cinnamoyl-CoA reductase 1 (CCR1) mutant in maize: effects on lignification, fibre development, and global gene expression

Cinnamoyl-CoA reductase (CCR), which catalyses the first committed step of the lignin-specific branch of monolignol biosynthesis, has been extensively characterized in dicot species, but few data are available in monocots. By screening a Mu insertional mutant collection in maize, a mutant in the CCR1 gene was isolated named Zmccr1–. In this mutant, CCR1 gene expression is reduced to 31% of the residual wild-type level. Zmccr1– exhibited enhanced digestibility without compromising plant growth and development. Lignin analysis revealed a slight decrease in lignin content and significant changes in lignin structure. p-Hydroxyphenyl units were strongly decreased and the syringyl/guaiacyl ratio was slightly increased. At the cellular level, alterations in lignin deposition were mainly observed in the walls of the sclerenchymatic fibre cells surrounding the vascular bundles. These cell walls showed little to no staining with phloroglucinol. These histochemical changes were accompanied by an increase in sclerenchyma surface area and an alteration in cell shape. In keeping with this cell type-specific phenotype, transcriptomics performed at an early stage of plant development revealed the down-regulation of genes specifically associated with fibre wall formation. To the present authors’ knowledge, this is the first functional characterization of CCR1 in a grass species

Addition of Aegilops U and M chromosomes affects protein and dietary fiber content of wholemeal wheat flour

Cereal grain fiber is an important health-promoting component in the human diet. One option to improve dietary fiber content and composition in wheat is to introduce genes from its wild relatives Aegilops biuncialis and Aegilops geniculata. This study showed that the addition of chromosomes 2Ug, 4Ug, 5Ug, 7Ug, 2Mg, 5Mg, and 7Mg of Ae. geniculata and 3Ub, 2Mb, 3Mb, and 7Mb of Ae. biuncialis into bread wheat increased the seed protein content. Chromosomes 1Ug and 1Mg increased the proportion of polymeric glutenin proteins, while the addition of chromosomes 1Ub and 6Ub led to its decrease. Both Aegilops species had higher proportions of β-glucan compared to arabinoxylan (AX) than wheat lines, and elevated β-glucan content was also observed in wheat chromosome addition lines 5U, 7U, and 7M. The AX content in wheat was increased by the addition of chromosomes 5Ug, 7Ug, and 1Ub while water-soluble AX was increased by the addition of chromosomes 5U, 5M, and 7M, and to a lesser extent by chromosomes 3, 4, 6Ug, and 2Mb. Chromosomes 5Ug and 7Mb also affected the structure of wheat AX, as shown by the pattern of oligosaccharides released by digestion with endoxylanase. These results will help to map genomic regions responsible for edible fiber content in Aegilops and will contribute to the efficient transfer of wild alleles in introgression breeding programs to obtain wheat varieties with improved health benefits

Effect of allelic variation at the Glu-3/Gli-1 loci on breadmaking quality parameters in hexaploid wheat (Triticum aestivum L.)

Low molecular weight glutenin subunits (LMW-GS) encoded by the Glu-3 loci are known to contribute to wheat breadmaking quality. However, the specific effect of individual Glu-3 alleles is not well understood due to their complex protein banding patterns in SDS-PAGE and tight linkage with gliadins at the Gli-1 locus. Using DNA markers and a backcross program we developed a set of nine near isogenic lines (NILs) including different Glu-A3/GliA-1 or Glu-B3/Gli-B1 alleles in the genetic background of the Argentine variety ProINTA Imperial. The nine NILs and the control were evaluated in three different field trials in Argentina. Significant genotype-by-environment interactions were detected for most quality parameters indicating that the effects of the Glu-3/Gli-1 alleles are modulated by environmental differences. None of the NILs showed differences in total flour protein content, but relative changes in the abundance of particular classes of proteins cannot be ruled out. On average, the Glu-A3f, Glu-B3b, Glu-B3g and Glu-B3i(Man) alleles were associated with the highest values in gluten strength-related parameters, while Glu-A3e, Glu-B3a and Glu-B3i(Chu) were consistently associated with weak gluten and low quality values. The value of different Glu3/Gli-1 allele combinations to improve breadmaking quality is discussed

The contribution of wheat to human diet and health

Wheat is the most important staple crop in temperate zones and is in increasing demand in countries undergoing urbanization and industrialization. In addition to being a major source of starch and energy, wheat also provides substantial amounts of a number of components which are essential or beneficial for health, notably protein, vitamins (notably B vitamins), dietary fiber, and phytochemicals. Of these, wheat is a particularly important source of dietary fiber, with bread alone providing 20% of the daily intake in the UK, and well-established relationships between the consumption of cereal dietary fiber and reduced risk of cardio-vascular disease, type 2 diabetes, and forms of cancer (notably colo-rectal cancer). Wheat shows high variability in the contents and compositions of beneficial components, with some (including dietary fiber) showing high heritability. Hence, plant breeders should be able to select for enhanced health benefits in addition to increased crop yield

The historical and political significance of the reconstruction of the Cathedral of Christ the Saviour in Moscow

A cathedral appeared in the centre of Moscow almost overnight. Where did it come from? Today’s cathedral of Christ the Saviour is perceived as a chudo, a ‘miracle’, because it is the re-appearance of a building last seen in 1931. In the intervening years it was one of the "blank spots” in official Soviet history. The way silence was broken and information about the cathedral became widespread, is part of the case I wish to make, but, for the purpose of this introduction, a very brief summary of the cathedral’s biography is useful. Tsar Alexander I, in a Manifesto issued on 25 December 1812, vowed to found a cathedral named Christ the Saviour, to thank God for having saved Russia from ruin in the hands of Napoleon's numerous and fierce troops; the church was also meant to uphold eternally for future generations the memory of "the unprecedented zeal, loyalty and love towards Faith and Fatherland" displayed by the Russian people in the course of battle. The young artist Alexander Vitberg was the architect of a first project, a classical-looking church composed of three parts expressing the trinity of suffering, death, and eternal life. To accommodate its colossal size (matching Russia's grandeur), it was located on Vorob’evy Gory (Sparrow Hills), across the river from the Kremlin. But the project foundered amid financial scandals and allegations of technical incompetence. Continued in thesis ..