Polymorphisms within three candidate genes for lignin biosynthesis were investigated to identify alleles useful for the improvement of maize digestibility. The allelic diversity of two caffeoyl-CoA 3-O-methyltransferase genes, CCoAOMT2 and CCoAOMT1, as well as that of the aldehyde O-methyltransferase gene, AldOMT, was evaluated for 34 maize lines chosen for their varying degrees of cell wall digestibility. Frequency of nucleotide changes averaged one SNP every 35 bp. Ninety-one indels were identified in non-coding regions and only four in coding regions. Numerous distinct and highly diverse haplotypes were identified at each locus. Numerous sites were in linkage disequilibrium that declined rapidly within a few hundred bases. For F4, an early flint French line with high cell wall digestibility, the CCoAOMT2 first exon presented many non-synonymous polymorphisms. Notably we found an 18-bp indel, which resembled a microsatellite and was associated with cell wall digestibility variation. Additionally, the CCoAOMT2 gene co-localized with a QTL for cell wall digestibility and lignin content. Together, these results suggest that genetic diversity investigated on a broader genetic basis could contribute to the identification of favourable alleles to be used in the molecular breeding of elite maize germplasm.

In most production areas, Alternaria leaf blight (ALB) is recognized as the most common and destructive foliage disease in carrot. To assess the genetic architecture of carrot ALB resistance, two parental coupling maps were developed with similar number of dominant markers (around 70), sizes (around 650 cM), densities (around 9.5 cM), and marker composition. The F(2:3) progenies were evaluated in field and tunnel for two scoring dates. The continuous distribution of the disease severity value indicated that ALB resistance is under polygenic control. Three QTLs regions were found on three linkage groups. Two of them were tunnel or field specific and were detected only at the second screening date suggesting that the expression of these two QTLs regions involved in resistance to Alternaria dauci might depend on environment and delay after infection.

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.

QTL detection is a good way to assess the genetic basis of quantitative traits such as the plant response to its environment, but requires large mapping populations. Experimental constraints, however, may require a restriction of the population size, risking a decrease in the quality level of QTL mapping. The purpose of this paper was to test if an advanced backcross population sample chosen by MapPop 1.0 could limit the effect of size restriction and improve the QTL detection when compared to random samples. We used the genotypic and phenotypic data obtained for 280 genotypes, considered as the reference population. The "MapPop sample" of 100 genotypes was first compared to the reference population, and genetic maps, genotypic and phenotypic data and QTL results were analysed. Despite the increase in donor allele frequency in the MapPop sample, this did not lead to an increase of the genetic map length or a biased phenotypic distribution. Three QTL among the 10 QTL found in the reference population were also detected in the MapPop sample. Next, the MapPop sample results were compared to those from 500 random samples of the same size. The main conclusion was that the MapPop software avoided the selection of biased samples and the detection of false QTL and appears particularly interesting to select a sample from an unbalanced population.

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