VfODB: a comprehensive database of ESTs, EST-SSRs, mtSSRs, microRNA-target markers and genetic maps in Vicia faba.

Faba bean (Vicia faba) is an essential food and fodder legume crop worldwide due to its high content of proteins and fibres. Molecular markers tools represent an invaluable tool for faba bean breeders towards rapid crop improvement. Although there have historically been few V. faba genome resources available, several transcriptomes and mitochondrial genome sequence data have been released. These data in addition to previously developed genetic linkage maps represent a great resource for developing functional markers and maps that can accelerate the faba bean breeding programmes. Here, we present the Vicia faba Omics database (VfODB) as a comprehensive database integrating germplasm information, expressed sequence tags (ESTs), expressed sequence tags-simple sequence repeats (EST-SSRs), and mitochondrial-simple sequence repeats (mtSSRs), microRNA-target markers and genetic maps in faba bean. In addition, KEGG pathway-based markers and functional maps are integrated as a novel class of annotation-based markers/maps. Collectively, we developed 31 536 EST markers, 9071 EST-SSR markers and 3023 microRNA-target markers based on V. faba RefTrans V2 mining. By mapping 7940 EST and 2282 EST-SSR markers against the KEGG pathways database we successfully developed 107 functional maps. Also, 40 mtSSR markers were developed based on mitochondrial genome mining. On the data curation level, we retrieved 3461 markers representing 12 types of markers (CAPS, EST, EST-SSR, Gene marker, INDEL, Isozyme, ISSR, RAPD, SCAR, RGA, SNP and SSR), which mapped across 18 V. faba genetic linkage maps. VfODB provides two user-friendly tools to identify, classify SSR motifs and in silico amplify their targets. VfODB can serve as a powerful database and helpful platform for faba bean research community as well as breeders interested in Genomics-Assisted Breeding.

Genic and Intergenic SSR Database Generation, SNPs Determination and Pathway Annotations, in Date Palm (Phoenix dactylifera L.).

The present investigation was carried out aiming to use the bioinformatics tools in order to identify and characterize, simple sequence repeats within the third Version of the date palm genome and develop a new SSR primers database. In addition single nucleotide polymorphisms (SNPs) that are located within the SSR flanking regions were recognized. Moreover, the pathways for the sequences assigned by SSR primers, the biological functions and gene interaction were determined. A total of 172,075 SSR motifs was identified on date palm genome sequence with a frequency of 450.97 SSRs per Mb. Out of these, 130,014 SSRs (75.6%) were located within the intergenic regions with a frequency of 499 SSRs per Mb. While, only 42,061 SSRs (24.4%) were located within the genic regions with a frequency of 347.5 SSRs per Mb. A total of 111,403 of SSR primer pairs were designed, that represents 291.9 SSR primers per Mb. Out of the 111,403, only 31,380 SSR primers were in the genic regions, while 80,023 primers were in the intergenic regions. A number of 250,507 SNPs were recognized in 84,172 SSR flanking regions, which represents 75.55% of the total SSR flanking regions. Out of 12,274 genes only 463 genes comprising 896 SSR primers were mapped onto 111 pathways using KEGG data base. The most abundant enzymes were identified in the pathway related to the biosynthesis of antibiotics. We tested 1031 SSR primers using both publicly available date palm genome sequences as templates in the in silico PCR reactions. Concerning in vitro validation, 31 SSR primers among those used in the in silico PCR were synthesized and tested for their ability to detect polymorphism among six Egyptian date palm cultivars. All tested primers have successfully amplified products, but only 18 primers detected polymorphic amplicons among the studied date palm cultivars.

Construction of genetic linkage map with chromosomal assigment and quantitative trait loci associated with some important agronomic traits in cotton.

Cotton is the world's leading natural fiber and second most important oilseed crop and has been a focus of genetic, systematic and breeding research. The genetic and physiological bases of some important agronomic traits in cotton were investigated by QTL mapping through constructing of genetic map with chromosomal assignment. A segregating F2 population derived from an interspecific cross (G. barbadense x G. hirsutum) between two genotypes, cvs. "Giza 83" and "Deltapine" was used in this study. Different molecular markers including SSR, EST, EST-SSR, AFLP and RAPD were employed to identify markers that reveal differences between the parents. In total 42 new markers were merged with 140 previously mapped markers to produce a new map with 182 loci covering a total length of 2370.5 cM. Among these new markers, some of them were used to assign chromosomes to the produced 26 linkage groups. The LG2, LG3, LG11 and LG26 were assigned to chromosomes 1, 6, 5 and 20 respectively. Single point analysis was used to identify genomic regions controlling traits for plant height, number of nodes at flowering time, bolling date, days to flowering and number of bolls. In total 40 significant QTL were identified for the five traits on 11 linkage groups (1, 2, 3, 4, 5, 10, 11, 12, 18, 19 and 23). This work represents an improvement of the previously constructed genetic map in addition to chromosomal assignment and detection of new significant QTL for the five traits in Egyptian cotton. The Significant QTLs detected in this study can be employed in marker assisted selection for molecular breeding programs aiming at developing cotton cultivars with improved agronomic traits.

Analysis of gene expression in soybean (Glycine max) roots in response to the root knot nematode Meloidogyne incognita using microarrays and KEGG pathways.

BACKGROUND: Root-knot nematodes are sedentary endoparasites that can infect more than 3000 plant species. Root-knot nematodes cause an estimated $100 billion annual loss worldwide. For successful establishment of the root-knot nematode in its host plant, it causes dramatic morphological and physiological changes in plant cells. The expression of some plant genes is altered by the nematode as it establishes its feeding site. RESULTS: We examined the expression of soybean (Glycine max) genes in galls formed in roots by the root-knot nematode, Meloidogyne incognita, 12 days and 10 weeks after infection to understand the effects of infection of roots by M. incognita. Gene expression was monitored using the Affymetrix Soybean GeneChip containing 37,500 G. max probe sets. Gene expression patterns were integrated with biochemical pathways from the Kyoto Encyclopedia of Genes and Genomes using PAICE software. Genes encoding enzymes involved in carbohydrate and cell wall metabolism, cell cycle control and plant defense were altered. CONCLUSIONS: A number of different soybean genes were identified that were differentially expressed which provided insights into the interaction between M. incognita and soybean and into the formation and maintenance of giant cells. Some of these genes may be candidates for broadening plants resistance to root-knot nematode through over-expression or silencing and require further examination.

Post-transcriptional gene silencing of root-knot nematode in transformed soybean roots.

RNAi constructs targeted to four different genes were examined to determine their efficacy to reduce galls formed by Meloidogyne incognita in soybean roots. These genes have high similarity with essential soybean cyst nematode (Heterodera glycines) and Caenorhabditis elegans genes. Transformed roots were challenged with M. incognita. Two constructs, targeted to genes encoding tyrosine phosphatase (TP) and mitochondrial stress-70 protein precursor (MSP), respectively, strongly interfered with M. incognita gall formation. The number of galls formed on roots transformed with constructs targeting the M. incognita TP and MSP genes was reduced by 92% and 94.7%, respectively. The diameter of M. incognita inside these transformed roots was 5.4 and 6.5 times less than the diameter of M. incognita found inside control plants transformed with the empty vector. These results indicate that silencing the genes encoding TP and MSP can greatly decrease gall formation and shows a promising solution for broadening resistance of plants against this plant-parasitic nematode.