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Star Trek
The adventures of the Starship Enterprise continue in this new story that picks up where the 2009 film left off. Featuring the new cast of the film, these missions re-imagine the stories from the original series in the alternate timeline created by the film, along with new threats and characters never seen before. With creative collaboration from Star Trek writer/producer Roberto Orci, this new series begins the countdown to the much-anticipated movie sequel premiering in 2012.
Book
Mapping and identification of a potential candidate gene for a novel maturity locus, E10, in soybean
Key message
E10 is a new maturity locus in soybean and FT4 is the predicted/potential functional gene underlying the locus.
Flowering and maturity time traits play crucial roles in economic soybean production. Early maturity is critical for north and west expansion of soybean in Canada. To date, 11 genes/loci have been identified which control time to flowering and maturity; however, the molecular bases of almost half of them are not yet clear. We have identified a new maturity locus called “
E10
” located at the end of chromosome Gm08. The gene symbol
E10e10
has been approved by the Soybean Genetics Committee. The
e10e10
genotype results in 5–10 days earlier maturity than
E10E10
. A set of presumed
E10E10
and
e10e10
genotypes was used to identify contrasting SSR and SNP haplotypes. These haplotypes, and their association with maturity, were maintained through five backcross generations. A functional genomics approach using a predicted protein–protein interaction (PPI) approach (Protein–protein Interaction Prediction Engine, PIPE) was used to investigate approximately 75 genes located in the genomic region that SSR and SNP analyses identified as the location of the
E10
locus. The PPI analysis identified FT4 as the most likely candidate gene underlying the
E10
locus. Sequence analysis of the two FT4 alleles identified three SNPs, in the 5′UTR, 3′UTR and fourth exon in the coding region, which result in differential mRNA structures. Allele-specific markers were developed for this locus and are available for soybean breeders to efficiently develop earlier maturing cultivars using molecular marker assisted breeding.
Journal Article
New Locus for Early Maturity in Soybean
The genetic model for maturity in soybean [Glycine max (L.) Merr.] is a series of near-isogenic lines, but they do not span the natural variation for early maturity. The objectives of this study were to determine if a single gene in OT98-17 controls early maturity and if this is a new locus. A cross was made between ‘Maple Presto’ and OT98-17, an early-maturing Maple Presto–derived backcross line. A total of 201 F3 progeny rows from this population and Maple Presto were grown at Ottawa, ON, in 1999. In 2000, F4 progeny rows were grown and 150 late-maturing and 51 early-maturing families were observed to fit a 3:1 ratio (n = 201, X2 = 0.01, P = 0.90). The early-maturing allele was transferred to a ‘Harosoy’ background, and isolines were grown from 2002 to 2006 at Ottawa, ON. The isolines were 9 and 6 d earlier maturing in Maple Presto and Harosoy backgrounds, respectively. To determine the independence of this locus, simple sequence repeat molecular markers were used to identify three candidate regions. The gene E8 specifically mapped to linkage group C1 between Sat_404 and Satt136. No other maturity gene has been mapped to this region. The two other candidate regions were both related to maturity quantitative trait loci on molecular linkage group L and may be inadvertently selected along with early maturity. The gene symbol E8e8 has been assigned by the Soybean Genetics Committee. E8E8 results in later maturity and e8e8 results in early maturity. The earliest Harosoy maturity isoline is now rated as maturity group 000.
Journal Article
PIPE4: Fast PPI Predictor for Comprehensive Inter- and Cross-Species Interactomes
The need for larger-scale and increasingly complex protein-protein interaction (PPI) prediction tasks demands that state-of-the-art predictors be highly efficient and adapted to inter- and cross-species predictions. Furthermore, the ability to generate comprehensive interactomes has enabled the appraisal of each PPI in the context of all predictions leading to further improvements in classification performance in the face of extreme class imbalance using the Reciprocal Perspective (RP) framework. We here describe the PIPE4 algorithm. Adaptation of the PIPE3/MP-PIPE sequence preprocessing step led to upwards of 50x speedup and the new Similarity Weighted Score appropriately normalizes for window frequency when applied to any inter- and cross-species prediction schemas. Comprehensive interactomes for three prediction schemas are generated: (1) cross-species predictions, where
Arabidopsis thaliana
is used as a proxy to predict the comprehensive
Glycine max
interactome, (2) inter-species predictions between
Homo sapiens-
HIV1, and (3) a combined schema involving both cross- and inter-species predictions, where both
Arabidopsis thaliana
and
Caenorhabditis elegans
are used as proxy species to predict the interactome between
Glycine max
(the soybean legume) and
Heterodera glycines
(the soybean cyst nematode). Comparing PIPE4 with the state-of-the-art resulted in improved performance, indicative that it should be the method of choice for complex PPI prediction schemas.
Journal Article
New DArT markers for oat provide enhanced map coverage and global germplasm characterization
Background: Genomic discovery in oat and its application to oat improvement have been hindered by a lack of genetic markers common to different genetic maps, and by the difficulty of conducting whole-genome analysis using high-throughput markers. This study was intended to develop, characterize, and apply a large set of oat genetic markers based on Diversity Array Technology (DArT). Results: Approximately 19,000 genomic clones were isolated from complexity-reduced genomic representations of pooled DNA samples from 60 oat varieties of global origin. These were screened on three discovery arrays, with more than 2000 polymorphic markers being identified for use in this study, and approximately 2700 potentially polymorphic markers being identified for use in future studies. DNA sequence was obtained for 2573 clones and assembled into a non-redundant set of 1770 contigs and singletons. Of these, 705 showed highly significant (Expectation < 10E-10) BLAST similarity to gene sequences in public databases. Based on marker scores in 80 recombinant inbred lines, 1010 new DArT markers were used to saturate and improve the 'Kanota' x 'Ogle' genetic map. DArT markers provided map coverage approximately equivalent to existing markers. After binning markers from similar clones, as well as those with 99% scoring similarity, a set of 1295 non-redundant markers was used to analyze genetic diversity in 182 accessions of cultivated oat of worldwide origin. Results of this analysis confirmed that major clusters of oat diversity are related to spring vs. winter type, and to the presence of major breeding programs within geographical regions. Secondary clusters revealed groups that were often related to known pedigree structure. Conclusion: These markers will provide a solid basis for future efforts in genomic discovery, comparative mapping, and the generation of an oat consensus map. They will also provide new opportunities for directed breeding of superior oat varieties, and guidance in the maintenance of oat genetic diversity.
Journal Article
Genetic Analysis of High Protein Content in ‘AC Proteus’ Related Soybean Populations Using SSR, SNP, DArT and DArTseq Markers
Key message: Several AC Proteus derived genomic regions (QTLs, SNPs) have been identified which may prove useful for further development of high yielding high protein cultivars and allele-specific marker developments. High seed protein content is a trait which is typically difficult to introgress into soybean without an accompanying reduction in seed yield. In a previous study, ‘AC Proteus’ was used as a high protein source and was found to produce populations that did not exhibit the typical association between high protein and low yield. Five high x low protein RIL populations and a high x high protein RIL population were evaluated by either quantitative trait locus (QTL) analysis or bulk segregant analyses (BSA) following phenotyping in the field. QTL analysis in one population using SSR, DArT and DArTseq markers found two QTLs for seed protein content on chromosomes 15 and 20. The BSA analyses suggested multiple genomic regions are involved with high protein content across the five populations, including the two previously mentioned QTLs. In an alternative approach to identify high protein genes, pedigree analysis identified SNPs for which the allele associated with high protein was retained in seven high protein descendants of AC Proteus on chromosomes 2, 17 and 18. Aside from the two identified QTLs (five genomic regions in total considering the two with highly elevated test statistic, but below the statistical threshold and the one with epistatic interactions) which were some distance from Meta-QTL regions and which were also supported by our BSA analysis within five populations. These high protein regions may prove useful for further development of high yielding high protein cultivars.
Journal Article
Relationship between asparagine metabolism and protein concentration in soybean seed
The relationship between asparagine metabolism and protein concentration was investigated in soybean seed. Phenotyping of a population of recombinant inbred lines adapted to Illinois confirmed a positive correlation between free asparagine levels in developing seeds and protein concentration at maturity. Analysis of a second population of recombinant inbred lines adapted to Ontario associated the elevated free asparagine trait with two of four quantitative trait loci determining population variation for protein concentration, including a major one on chromosome 20 (linkage group I) which has been reported in multiple populations. In the seed coat, levels of asparagine synthetase were high at 50 mg and progressively declined until 150 mg seed weight, suggesting that nitrogenous assimilates are pre-conditioned at early developmental stages to enable a high concentration of asparagine in the embryo. The levels of asparaginase B1 showed an opposite pattern, being low at 50 mg and progressively increased until 150 mg, coinciding with an active phase of storage reserve accumulation. In a pair of genetically related cultivars, ∼2-fold higher levels of asparaginase B1 protein and activity in seed coat, were associated with high protein concentration, reflecting enhanced flux of nitrogen. Transcript expression analyses attributed this difference to a specific asparaginase gene,ASPGB1a. These results contribute to our understanding of the processes determining protein concentration in soybean seed.
Journal Article
Novel QTL for Low Seed Cadmium Accumulation in Soybean
Soybean is a valuable crop, used in animal feed and for human consumption. Selecting soybean cultivars with low seed cadmium (Cd) concentration is important for the purpose of minimizing the transfer of Cd into the human body. To ensure international trade, farmers need to produce soybean that meets the European Union (EU) Cd limit of 0.2 mg kg−1. In this study, we evaluated two populations of recombinant inbred lines (RILs), X5154 and X4050, for seed Cd accumulation. Linkage maps were constructed with 325 and 280 polymorphic simple sequence repeat (SSR) markers, respectively, and used to identify a novel minor quantitative trait locus (QTL) on chromosome 13 in the X4050 population between SSR markers Satt522 and Satt218. Based on a gene ontology search within the QTL region, seven genes were identified as candidates responsible for low seed Cd accumulation, including Glyma.13G308700 and Glyma.13G309100. In addition, we confirmed the known major gene, Cda1, in the X5154 population and developed KASP and CAPS/dCAPS allele-specific markers for efficient marker-assisted breeding for Cda1.
Journal Article
Selection for Cold Tolerance during Flowering in Short‐Season Soybean
Cold temperatures during early reproductive development may result in reduced pod and seed formation in soybean [Glycine max (L.) Merr.]. The objectives of this work were to quantify cold tolerance of six potential parents, to screen breeding populations for cold tolerance, to search for associations between molecular markers and cold tolerance phenotypes, and to evaluate field performance of breeding lines. Six cultivars were evaluated for pod and seed set after exposure to 0 to 6 wk cold periods (15/5°C day/night), which began at flowering in growth cabinets. Evaluation at 6 vs. 2 wk following the end of a 3 or 6 wk cold period best discriminated between cold tolerant (CT) and cold sensitive (CS) cultivars. Two recombinant inbred line populations were cold stressed in growth cabinets with divergent selection performed over the F5 through F7 generations to select CT and CS lines. Bulked segregant analysis identified six chromosomal regions, four of which are related by homology, as potentially impacting the trait. Over 8 yr in the field at Ottawa, Canada, CT lines yielded 379 kg ha−1 more but matured 5.5 d later than CS lines without visual symptoms of cold damage. Following selection for early maturity, random lines from an additional four populations developed from a selected CT and CS line each crossed to another CT and CS parent were field tested in three environments. Cold tolerant × CT lines yielded about 8% more than CS × CS lines, again without visual cold damage symptoms.
Journal Article
Simple sequence repeat (SSR) markers linked to E1, E3, E4, and E7 maturity genes in soybean
Soybean near isogenic lines (NILs), contrasting for maturity and photoperiod sensitivity loci, were genotyped with approximately 430 mapped simple sequence repeats (SSRs), also known as microsatellite markers. By analysis of allele distributions across the NILs, it was possible to confirm the map location of the Dt1 indeterminate growth locus, to refine the SSR mapping of the T tawny pubescence locus, to map E1 and E3 maturity loci with molecular markers, and to map the E4 and E7 maturity loci for the first time. Molecular markers flanking these loci are now available for marker-assisted breeding for these traits. Analysis of map locations identified a putative homologous relationship among four chromosomal regions; one in the middle of linkage group (LG) C2 carrying E1 and E7, one on LG I carrying E4, one at the top of LG C2, at which there is a reproductive period quantitative trait locus (QTL), and the fourth on LG B1. Other evidence suggests that homology also exists between the E1 + E7 region on LG C2 and a region on LG L linked to a pod maturity QTL. Homology relationships predict possible locations in the soybean genome of additional maturity loci, as well as which maturity loci may share a common evolutionary origin and similar mechanism(s) of action.Key words: soybean, maturity, photoperiod, microsatellite marker, near isogenic line.
Journal Article