Candidate genes for quantitative resistance to Mycosphaerella pinodes in pea (Pisum sativum L.).

Partial resistance to Mycosphaerella pinodes in pea is quantitatively inherited. Genomic regions involved in resistance (QTLs) have been previously identified in the pea genome, but the molecular basis of the resistance is still unknown. The objective of this study was to map resistance gene analogs (RGA) and defense-related (DR) genes in the JI296 x DP RIL population that has been used for mapping QTLs for resistance to M. pinodes, and identify co-localizations between candidate genes and QTLs. Using degenerate oligonucleotide primers designed on the conserved motifs P-loop and GLPL of cloned resistance genes, we isolated and cloned 16 NBS-LRR sequences, corresponding to five distinct classes of RGAs. Specific second-generation primers were designed for each class. RGAs from two classes were located on the linkage group (LG) VII. Another set of PCR-based markers was designed for four RGA sequences previously isolated in pea and 12 previously cloned DR gene sequences available in databases. Out of the 16 sequences studied, the two RGAs RGA-G3A and RGA2.97 were located on LG VII, PsPRP4A was located on LG II, Peachi21, PsMnSOD, DRR230-b and PsDof1 were mapped on LG III and peabetaglu and DRR49a were located on LG VI. Two co-localizations between candidate genes and QTLs for resistance to M. pinodes were observed on LG III, between the putative transcription factor PsDof1 and the QTL mpIII-1 and between the pea defensin DRR230-b gene and the QTL mpIII-4. Another co-localization was observed on LG VII between a cluster of RGAs and the QTL mpVII-1. The three co-localizations appear to be located in chromosomal regions containing other disease resistance or DR genes, suggesting an important role of these genomic regions in defense responses against pathogens in pea.

Genetic diversity associated with variation in silage corn digestibility for three O-methyltransferase genes involved in lignin biosynthesis.

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.

From Arabidopsis thaliana to Brassica napus: development of amplified consensus genetic markers (ACGM) for construction of a gene map.

The evolution of genomes can be studied by comparing maps of homologous genes which show changes in nucleic acid sequences and chromosome rearrangements. In this study, we developed a set of 32 amplified consensus gene markers (ACGMs) that amplified gene sequences from Arabidopsis thaliana and Brassica napus. Our methodology, based on PCR, facilitated the rapid sequencing of homologous genes from various species of the same phylogenetic family and the detection of intragenic polymorphism. We found that such polymorphism principally concerned intron sequences and we used it to attribute a Brassica oleracea or Brassica rapa origin to the B. napus sequences and to map 43 rapeseed genes. We confirm that the genetic position of homologous genes varied between B. napus and A. thaliana. ACGMs are a useful tool for genome evolution studies and for the further development of single nucleotide polymorphism suitable for use in genetic mapping and genetic diversity analyses.

Expression, mapping, and genetic variability of Brassica napus disease resistance gene analogues.

Numerous sequences analogous to resistance (R) genes exist in plant genomes and could be involved in resistance traits. The aim of this study was to identify a large number of Brassica napus sequences related to R genes and also to test the adequacy of specific PCR-based tools for studying them. Different consensus primers were compared for their efficiency in amplifying resistance-gene analogues (RGAs) related to the nucleotide-binding-site subgroup of R genes. Specific primers were subsequently designed to fine-study the different RGAs and we tested their efficiency in three species related to B. napus: Brassica oleracea, Brassica rapa, and Arabidopsis thaliana. Forty-four B. napus RGAs were identified. Among 29 examined, at least one-third were expressed. Eighteen RGAs were mapped on 10 of the 19 B. napus linkage groups. The high variability within these sequences permitted discrimination of each genotype within a B. napus collection. The RGA-specific primers amplified RGAs in the B. oleracea and B. rapa genomes, but the sequences appear to be poorly conserved in A. thaliana. Specific RGA primers are a precise tool for studying known-sequence RGAs. These sequences represent interesting markers that could be correlated with resistance traits in B. napus or related Brassica genomes.