They were associated with 719 genes involved in 61 unique KEGG pathways and 51 unique enzymes. Likewise, 1060 non-synonymous SNPs were found to distinguish the low- and high-trigonelline bulks. SAM, xanthine and IMP) which participate in the caffeine biosynthesic pathways. Based on KEGG pathway-based analysis, 40 caffeine-associated SNPs were discovered, among which nine SNPs were tightly associated with genes encoding enzymes involved in the conversion of substrates (i.e. Gene annotation analysis with Blast2GO revealed that these SNPs corresponding to 908 genes with 56 unique KEGG pathways and 49 unique enzymes. eugenioides (CC and CE) identified 1351 non-synonymous SNPs that distinguished the low- and high-caffeine bulks. Sequencing and mapping using the combined reference genomes of C. DNA extracted from extreme phenotypes was bulked (high and low caffeine, and high and low trigonelline) based on biochemical analysis of the germplasm collection. The X-axis scale is logarithmic.ДЄssociation analysis was performed at the whole genome level to identify loci affecting the caffeine and trigonelline content of Coffea arabica beans. Bars in lighter colours represent sub-categories within the top level categories. Top level GO categories (Biological process, Molecular function and Cellular component) are shadowed. B: Distribution of the main GO categories in annotated contigs (on the left) and singlets (on the right). Annotation: Sequences with BLAST hits >1e-6 which were successfully assigned GO terms. No Annotation: Sequences with blastx hits >1e-6 and associated GO terms lying below the GO annotation rule thresholds described in the Methods section. No Mapping: Sequences with blastx hits >1e-6, but for which no GO terms could be associated to the BLAST results. No BLAST Hits: Sequences with no significant blastx hit to non-redundant protein database described in the methods. A: Numbers and proportions of sequences successfully passing the subsequent steps of the annotation procedure of BLAST2GO as described in the Methods (contigs on the left and singlets on the right). We discuss the potential to extend the analysis to identify a вЂњcore setвЂќ of ancestrally derived homeolog specific variants in white clover. This represents a significant resource for white clover genomics and genetics studies. In total, 208,854 independent SNPs in 31,715 reference sequences were discovered, approximately three quarters of which were categorised as representing allelic or homeolog-specific variation using two inbred lines. The potential for using haplotype reconstruction and progenitor genome comparison to assign haplotypes to specific ancestral sub-genomes of white clover is demonstrated for sequences corresponding to genes encoding dehydration responsive element binding protein and acyl-coA oxidase. Mapping these reads to the reference transcript set allowed us to develop a significant SNP resource for white clover, and to partition the SNPs from the inbred lines into categories reflecting allelic or homeolog-specific variation. We subsequently performed Illumina sequencing on three further white clover samples, generating 14 million transcript reads from a mixed sample comprising 24 divergent white clover genotypes, and 50 million reads on two further eighth generation white clover inbred lines. These were assembled and partially annotated to yield a reference transcript set comprising 71,545 sequences. We used 454-pyrosequencing sequencing to generate ~760,000 transcript sequences from an 8th generation white clover inbred line. We illustrate one potential approach in this study. Robust methods for categorising single nucleotide variants as allelic or homeolog-specific in large transcript datasets are required. This is especially true for the development of genetic markers based on single nucleotide polymorphisms (SNPs), since it is difficult to distinguish between homeolog-specific and allelic variants. The apparent existence of highly similar homeolog copies for the majority of genes in white clover is problematic for the development of genome-based resources in the species. White clover (Trifolium repens L.) is an allotetraploid species possessing two highly collinear ancestral sub-genomes.

J line unitarans