Genome-Wide Association Study for Root Morphology and Phosphorus Acquisition Efficiency in Diverse Maize Panels.

Maximizing soil exploration through modifications of the root system is a strategy for plants to overcome phosphorus (P) deficiency. Genome-wide association with 561 tropical maize inbred lines from Embrapa and DTMA panels was undertaken for root morphology and P acquisition traits under low- and high-P concentrations, with 353,540 SNPs. P supply modified root morphology traits, biomass and P content in the global maize panel, but root length and root surface area changed differentially in Embrapa and DTMA panels. This suggests that different root plasticity mechanisms exist for maize adaptation to low-P conditions. A total of 87 SNPs were associated to phenotypic traits in both P conditions at -log10(p-value) ≥ 5, whereas only seven SNPs reached the Bonferroni significance. Among these SNPs, S9_137746077, which is located upstream of the gene GRMZM2G378852 that encodes a MAPKKK protein kinase, was significantly associated with total seedling dry weight, with the same allele increasing root length and root surface area under P deficiency. The C allele of S8_88600375, mapped within GRMZM2G044531 that encodes an AGC kinase, significantly enhanced root length under low P, positively affecting root surface area and seedling weight. The broad genetic diversity evaluated in this panel suggests that candidate genes and favorable alleles could be exploited to improve P efficiency in maize breeding programs of Africa and Latin America.

Analysis of BAC-end sequences in common bean (Phaseolus vulgaris L.) towards the development and characterization of long motifs SSRs.

The increasing volume of genomic data on the Phaseolus vulgaris species have contributed to its importance as a model genetic species and positively affected the investigation of other legumes of scientific and economic value. To expand and gain a more in-depth knowledge of the common bean genome, the ends of a number of bacterial artificial chromosome (BAC) were sequenced, annotated and the presence of repetitive sequences was determined. In total, 52,270 BESs (BAC-end sequences), equivalent to 32 Mbp (~6 %) of the genome, were processed. In total, 3,789 BES-SSRs were identified, with a distribution of one SSR (simple sequence repeat) per 8.36 kbp and 2,000 were suitable for the development of SSRs, of which 194 were evaluated in low-resolution screening. From 40 BES-SSRs based on long motifs SSRs (≥ trinucleotides) analyzed in high-resolution genotyping, 34 showed an equally good amplification for the Andean and for the Mesoamerican genepools, exhibiting an average gene diversity (H E) of 0.490 and 5.59 alleles/locus, of which six classified as Class I showed a H E ≥ 0.7. The PCoA and structure analysis allowed to discriminate the gene pools (K = 2, FST = 0.733). From the 52,270 BESs, 2 % corresponded to transcription factors and 3 % to transposable elements. Putative functions for 24,321 BESs were identified and for 19,363 were assigned functional categories (gene ontology). This study identified highly polymorphic BES-SSRs containing tri- to hexanucleotides motifs and bringing together relevant genetic characteristics useful for breeding programs. Additionally, the BESs were incorporated into the international genome-sequencing project for the common bean.

In silico characterization and expression analysis of the multigene family encoding the Bowman-Birk protease inhibitor in soybean.

The Bowman-Birk (BBI) protease inhibitors can be used as source of sulfur amino acids, can regulate endogenous protease activity during seed germination and during the defense response of plants to pathogens. In soybean this family has not been fully described. The goal of this work was to characterize in silico and analyze the expression of the members of this family in soybean. We identified 11 potential BBI genes in the soybean genome. In each one of them at least a characteristic BBI conserved domain was detected in addition to a potential signal peptide. The sequences have been positioned in the soybean physical map and the promoter regions were analyzed with respect to known regulatory elements. Elements related to seed-specific expression and also to response to biotic and abiotic stresses have been identified. Based on the in silico analysis and also on quantitative RT-PCR data it was concluded that BBI-A, BBI-CII and BBI-DII are expressed specifically in the seed. The expression profiles of these three genes are similar along seed development. Their expressions reach a maximum in the intermediate stages and decrease as the seed matures. The BBI-DII transcripts are the most abundant ones followed by those of BBI-A and BBI-CII.

Development of new molecular markers for the Colletotrichum genus using RetroCl1 sequences.

A nonautonomous element of 624 bp, called RetroCl1 (Retroelement Colletotrichum lindemuthianum 1), was identified in the plant pathogenic fungus Colletotrichum lindemuthianum. RetroCl1 contains terminal direct repeats (223 bp) that are surrounded by CTAGT sequences. It has a short internal domain of 178 bp and shows characteristics of terminal-repeat retrotransposon in miniature (TRIM) family. We used RetroCl1 sequence to develop molecular markers for the Colletotrichum genus. IRAP (Inter-Retrotransposon Amplified Polymorphism) and REMAP (Retrotransposon-Microsatellite Amplified Polymorphism) markers were used to analyze the genetic diversity of C. lindemuthianum. Fifty-four isolates belonging to different races were used. A total of 45 loci were amplified. The Nei index showed significant differences among the populations divided according to race, indicating that they are structured according to pathotype. No clear correlation between IRAP and REMAP markers with pathogenic characterization was found. C. lindemuthianum has high genetic diversity, and the analysis of molecular variance showed that 51% of variability is found among the populations of different races. The markers were also tested in different Colletotrichum species. In every case, multiple bands were amplified, indicating that these markers can be successfully used in different species belonging to the Colletotrichum genus.

Inheritance of Anthracnose Resistance in Common Bean Differential Cultivar AB 136.

Inheritance of anthracnose resistance of the common bean (Phaseolus vulgaris L.) differential cultivar AB 136 to races 89, 64, and 73 (binary system designation) was studied in crosses with the susceptible differential cultivars Michelite (race 89), Mexico 222 (race 64), and Cornell 49-242 (race 73). In each cross two progenitors, the F1, F2, and backcross-derived plants were inoculated with the respective race under environmentally controlled greenhouse conditions. The results indicate that single dominant gene(s) control resistance to races 89 and 64, giving a segregation ratio of 3:1 in the F2, 1:0 in the backcrosses to AB 136, and 1:1 in the backcross to Michelite (race 89), and to Mexico 222 (race 64). For race 73, the following segregation ratios between resistant and susceptible plants were observed: 13:3 in the F2, 1:0 in the backcross to AB 136, and 1:1 in the backcross to Cornell 49-242. Such results suggest that two independent genes may determine resistance of AB 136 to race 73, one dominant (Co-6) and one recessive that is proposed to be assigned co-8. Genotypes Co-6_ or co-8 co-8 would condition resistance, whereas susceptibility would be present in genotypes co-6 co-6 Co-8_. Given the dominant nature of anthracnose resistance genes present in line AB 136 and its resistance to 25 races of Colletotrichum lindemuthianum identified in Brazil by other researchers, we included this cultivar as one of the donor parents in our molecular marker-assisted backcross breeding program, to develop common bean cultivars resistant to anthracnose and adapted to Central Brazil.

Method optimization for proteomic analysis of soybean leaf: Improvements in identification of new and low-abundance proteins.

The most critical step in any proteomic study is protein extraction and sample preparation. Better solubilization increases the separation and resolution of gels, allowing identification of a higher number of proteins and more accurate quantitation of differences in gene expression. Despite the existence of published results for the optimization of proteomic analyses of soybean seeds, no comparable data are available for proteomic studies of soybean leaf tissue. In this work we have tested the effects of modification of a TCA-acetone method on the resolution of 2-DE gels of leaves and roots of soybean. Better focusing was obtained when both mercaptoethanol and dithiothreitol were used in the extraction buffer simultaneously. Increasing the number of washes of TCA precipitated protein with acetone, using a final wash with 80% ethanol and using sonication to ressuspend the pellet increased the number of detected proteins as well the resolution of the 2-DE gels. Using this approach we have constructed a soybean protein map. The major group of identified proteins corresponded to genes of unknown function. The second and third most abundant groups of proteins were composed of photosynthesis and metabolism related genes. The resulting protocol improved protein solubility and gel resolution allowing the identification of 122 soybean leaf proteins, 72 of which were not detected in other published soybean leaf 2-DE gel datasets, including a transcription factor and several signaling proteins.

Separomics applied to the proteomics and peptidomics of low-abundance proteins: Choice of methods and challenges - A review.

The enrichment and isolation of proteins are considered limiting steps in proteomic studies. Identification of proteins whose expression is transient, those that are of low-abundance, and of natural peptides not described in databases, is still a great challenge. Plant extracts are in general complex, and contaminants interfere with the identification of proteins involved in important physiological processes, such as plant defense against pathogens. This review discusses the challenges and strategies of separomics applied to the identification of low-abundance proteins and peptides in plants, especially in plants challenged by pathogens. Separomics is described as a group of methodological strategies for the separation of protein molecules for proteomics. Several tools have been used to remove highly abundant proteins from samples and also non-protein contaminants. The use of chromatographic techniques, the partition of the proteome into subproteomes, and an effort to isolate proteins in their native form have allowed the isolation and identification of rare proteins involved in different processes.

Covalent immobilization of alpha-galactosidase from Penicillium griseoroseum and its application in oligosaccharides hydrolysis.

Partially purified alpha-Galactosidase from Penicillium griseoroseum was immobilized onto modified silica using glutaraldehyde linkages. The effective activity of immobilized enzyme was 33%. Free and immobilized alpha-galactosidase showed optimal activity at 45 degrees C and pH values of 5 and 4, respectively. Immobilized alpha-galactosidase was more stable at higher temperatures and pH values. Immobilized alpha-galactosidase from P. griseoroseum maintained 100% activity after 24 h of incubation at 40 degrees C, while free enzyme showed only 32% activity under the same incubation conditions. Defatted soybean flour was treated with free and immobilized alpha-galactosidase in batch reactors. After 8 h of incubation, stachyose was completely hydrolyzed in both treatments. After 8 h of incubation, 39% and 70% of raffinose was hydrolyzed with free and immobilized alpha-galactosidase respectively. Immobilized alpha-galactosidase was reutilized eight times without any decrease in its activity.

Biochemical composition and indigestible oligosaccharides in Phaseolus vulgaris L. seeds.

Common beans have a high nutritional value, but contain galactooligosaccharides (GO), which cause flatulence and intestinal discomfort in humans. The biochemical composition of ten bean cultivars was determined to select those of high protein and low GO contents. The cultivars varied in carbohydrate (47.02-60.17%), GO (3.12-5.71%), protein (22.17-33.50%), lipid (1.13-1.81%), moisture (11.42-12.93%) and ash contents (4.08-5.61%). 'Mexico 222' presented the highest alpha-galactosidase activity. Protein and GO contents were positively correlated. 'Perry Marrow' combined high protein and low GO concentrations, indicating it can be used in improvement programs aiming at high-quality cultivars for human consumption.