Soybean Genomics: Developments through the Use of Cultivar “Forrest”

Legume crops are particularly important due to their ability to support symbiotic nitrogen fixation, a key to sustainable crop production and reduced carbon emissions. Soybean (Glycine max) has a special position as a major source of increased protein and oil production in the common grass-legume rotation. The cultivar “Forrest” has saved US growers billions of dollars in crop losses due to resistances programmed into the genome. Moreover, since Forrest grows well in the north-south transition zone, breeders have used this cultivar as a bridge between the southern and northern US gene pools. Investment in Forrest genomics resulted in the development of the following research tools: (i) a genetic map, (ii) three RIL populations (96 > n > 975), (iii) ∼200 NILs, (iv) 115 220 BACs and BIBACs, (v) a physical map, (vi) 4 different minimum tiling path (MTP) sets, (vii) 25 123 BAC end sequences (BESs) that encompass 18.5 Mbp spaced out from the MTPs, and 2 000 microsatellite markers within them (viii) a map of 2408 regions each found at a single position in the genome and 2104 regions found in 2 or 4 similar copies at different genomic locations (each of >150 kbp), (ix) a map of homoeologous regions among both sets of regions, (x) a set of transcript abundance measurements that address biotic stress resistance, (xi) methods for transformation, (xii) methods for RNAi, (xiii) a TILLING resource for directed mutant isolation, and (xiv) analyses of conserved synteny with other sequenced genomes. The SoyGD portal at sprovides access to the data. To date these resources assisted in the genomic analysis of soybean nodulation and disease resistance. This review summarizes the resources and their uses

The Multigeneic _Rhg1_ Locus: A Model For The Effects on Root Development, Nematode Resistance and Recombination Suppression.

Soybean (Glycine max L. Merr.) resistance to populations (HgType) of _Heterodera glycines I._, the soybean cyst nematode (SCN), requires a functional allele at rhg1. An apoptosis-like response in the giant cells formed around the nematode results 24-48 h after feeding commences. This study aimed to identify the role of the three genes within the rhg1 locus, a receptor like kinase (RLK), a laccase and an ion anti-porter. Used were near isogeneic lines (NILs) that contrasted at their rhg1 alleles. Features of the rhg1 locus, the candidate genes and their nascent transcripts and proteins in roots were elucidated. First, evidence for a syntenic gene cluster was found and the effectiveness of SNP probes for distinguishing the homeolog sequence variant on linkage group (Lg) B1 from alleles at the rhg1 locus on Lg G was shown. Analysis of plant s heterozygous at rhg1 showed that the allele for resistance was dominant. The absence of recombination events among the NILs between the RLK and other 2 genes eliminated the possibility of a monogeneic rhg1 locus. Finally, an effect on root development was discovered. A model for multigeneic resistance based on developmental control of root growth including a mechanism for segregation distortion is presented

Assessment of Genetic Biodiversity of Several Traits Using SSR Markers in Rice (Oryza sativa L.)

Eight primers (RM 315, RM 318, RM 166, RM 302, RM 201, RM 234, RM 526 and RM 144) revealed different levels of polymorphism to tag the related traits of interest as tolerant to abiotic stress, resistant to biotic stress and yield-related traits. Two primers (RM 190 and RM 278) were monomorphic. The percentage of the polymorphism was nearly 80 %. The size of detected fragments ranged from 105–325 bp. A total of 186 bands were scored from the amplification products with the ten SSR primers. Genetic diversity analyses were conducted on the basis of the scores with 176 unique bands. Phylogenic tree for the fifteen rice accessions from each group were established according to the molecular data and based on ten SSRs. A marked genetic diversity was observed in these innovative accessions (Sakha 101, IR 03N137, IR 83142-12, IR 87856-10-AJY-1-B, HHZ 12-Y4-DT1-Y2 and IR 1552), which revealed higher levels of diversity and hence can be used as donors for the effective conservation, utilization and providing favorable genes in rice breeding programs

Review of the Rpt3 Genes Encoding Part of the 26S Proteasome Associated with Loci Underlying Disease Resistance in Soybean

The 26S proteasomal complex is a multifunctional proteolytic machinery of the cell. The proteasome plays role in myriad of cellular functions, which have been further diversified by its separable proteolytic and non-proteolytic sub-complexes. Protein quality control and turnover, cell cycle regulation, gene regulation and DNA repair are among the key processes controlled by the proteasome. Disease resistance in plants invokes changes in all the processes controlled by the 26S proteasome. In this review, the potential contribution of genes encoding the proteasome to disease resistance in soybean (Glycine max L. Merr.) was examined

Using A Minimum Tile Path For Plant Transformations Encompassing the Entire Soybean Genome

Genomes like Glycine max (soybean) that have been highly conserved following increases in ploidy represent a frontier for genome analysis. Many soybean QTL analyzed to date have been composed of gene clusters each with contributing a portion of the trait rather than alleles of single genes. At the Soybean Genome Database (SoyGD) http://soybeangenome.siu.edu the genome browser that integrates and served the publicly available soybean physical map, BAC fingerprint database and genetic map associated genomic data shows a minimum tile of transformation ready BIBAC-like clones in pCLD04541 (pV41; oriV; tra; bom). Sequence resources made available through the DOE genome sequencing project have allowed the minimum tile to be revised and new functional analyses to be made. There are 3,840 MTP clones that appeared to encompass 90% of the genome (see http://soybeangenome.siu.edu/cgi-bin/gbrowse/BES_scaffolds). The BIBAC-like clones (tetR) from E. coli DH10 B were transferred en masse to Agrobacterium tumefaciens by triparental matings with EHA105 (rifR) mediated by pRK2013 (oriP) in DH10B (kanR) in 384 well plates. Although not necessary the extra helper plasmid boosted efficiency 10 fold. Individual A. tumefaciens rifampicin and tetracyclin resistant strains were used for transformation of Arabidopsis thaliana flowers in 384 well arrays. Initially kanamycin selection was used to isolate transgenic plants. Because the BACs were already tetR the recA mutants of A. tumefaciens could not be used (Tn3 insertions). Consequent to this and partial transconjugation events only some inserts are transferred completely while other transformed lines contain a substitution series of deleted inserts anchored on the Ti-left border (LB). These are maintained as kanR mixtures of seed. Phenotypes found for lines transgenic for particular BACs that were repeated include seed composition (protein, oil), development (growth, senescence) and disease resistance (suddean death syndrome (SDS) and soybean cyst nematode (SCN)

Re-annotation of the physical map of Glycine max for polyploid-like regions by BAC end sequence driven whole genome shotgun read assembly

<p>Abstract</p> <p>Background</p> <p>Many of the world's most important food crops have either polyploid genomes or homeologous regions derived from segmental shuffling following polyploid formation. The soybean (<it>Glycine max</it>) genome has been shown to be composed of approximately four thousand short interspersed homeologous regions with 1, 2 or 4 copies per haploid genome by RFLP analysis, microsatellite anchors to BACs and by contigs formed from BAC fingerprints. Despite these similar regions,, the genome has been sequenced by whole genome shotgun sequence (WGS). Here the aim was to use BAC end sequences (BES) derived from three minimum tile paths (MTP) to examine the extent and homogeneity of polyploid-like regions within contigs and the extent of correlation between the polyploid-like regions inferred from fingerprinting and the polyploid-like sequences inferred from WGS matches.</p> <p>Results</p> <p>Results show that when sequence divergence was 1–10%, the copy number of homeologous regions could be identified from sequence variation in WGS reads overlapping BES. Homeolog sequence variants (HSVs) were single nucleotide polymorphisms (SNPs; 89%) and single nucleotide indels (SNIs 10%). Larger indels were rare but present (1%). Simulations that had predicted fingerprints of homeologous regions could be separated when divergence exceeded 2% were shown to be false. We show that a 5–10% sequence divergence is necessary to separate homeologs by fingerprinting. BES compared to WGS traces showed polyploid-like regions with less than 1% sequence divergence exist at 2.3% of the locations assayed.</p> <p>Conclusion</p> <p>The use of HSVs like SNPs and SNIs to characterize BACs wil improve contig building methods. The implications for bioinformatic and functional annotation of polyploid and paleopolyploid genomes show that a combined approach of BAC fingerprint based physical maps, WGS sequence and HSV-based partitioning of BAC clones from homeologous regions to separate contigs will allow reliable de-convolution and positioning of sequence scaffolds (see BES_scaffolds section of SoyGD). This approach will assist genome annotation for paleopolyploid and true polyploid genomes such as soybean and many important cereal and fruit crops.</p

Effect of drip irrigation circuits design and lateral line length on: II-flow velocity and velocity head

The objectives of the work were to study the effect of drip irrigation circuits (DIC) and lateral lines lengths (LLL) on: Flow velocity (FV) and velocity head (VH). Laboratory tests were con- ducted at Irrigation Devices and Equipments Tests Laboratory, Agricultural Engineering Research Institute, Agriculture Research Center, Giza, Egypt. The experimental design of laboratory experiments was split in randomized complete block design with three replicates. Laboratory tests carried out on three irrigation lateral lines 40, 60, 80 m (LLL1, LLL2; LLL3) under the following three drip irrigation circuits (DIC): a) one manifold for lateral lines or closed circuits with one manifold of drip irrigation system (CM1DIS); b) closed circuits with two manifolds for lateral lines (CM2DIS), and c) traditional drip irrigation system (TDIS) as a control. Concerning FV values, DIC and LLL treatments could state in the following ascending orders: TDIS \u3c CM1DIS \u3c CM2DIS and LLL1 \u3c LLL2 \u3c LLL3, respectively. FV varied from 0.593 m·sec–1 to 1.376 m·sec–1. i.e. FV \u3c 5 ft·sec–1 and this is necessary to avoid the effect of water hammer in the main and sub-main lines, but in lateral line, it can cause silt and clay precipitation problems. The differences in FV among DIC and LLL were significant at the 1% level. The effect of interaction: DIC X LLL on FV values, were significant at the 1% level. The maximum and minimum values of FV were noticed in these interactions: CM2DIS X LLL3 and TDIS X LLL1, respectively. The following ascending orders TDIS \u3c CM1DIS \u3c CM2DIS and LLL1 \u3c LLL2 \u3c LLL3 expressed their effects on VH respectively. Differences in VH among DIC and/or LLL were significant at the 1% with few exceptions. The effects of interactions: DIC X LLL on VH were significant at the 1% level in some cases. The maximum and minimum values of VH were found in the interactions: CM2DIS X LLL3 and TDIS X LLL1, respectively

Effects of drip irrigation circuit design and lateral line lengths: I—On pressure and friction loss

Laboratory tests were conducted at the Irrigation Devices and Equipment’s Test Laboratory, Agricultural Engineering Research Institute, Agriculture Research Center, Giza, Egypt. The experimental design of laboratory experiments was split in randomized complete block design with three replicates. Laboratory tests carried out on three irrigation lateral lines of 40, 60, 80 m under the following three drip irrigation circuit (DIC) designs; 1) one manifold for lateral lines or closed circuits with one manifold of drip irrigation system (CM1DIS); 2) closed circuits with two manifolds for lateral lines (CM2DIS), and 3) traditional drip irrigation system (TDIS) as a control. The aims of the work were to study the effect of drip irrigation circuits (DIC) and lateral lines lengths (LLL; where): (LLL1 = 40 m, LLL2 = 60 m, and LLL3 = 80 m) on pressure head (PH) and friction loss (FL). Regarding to LLL and according to PH values, DIC designs could be ranked in the following ascending order: TDIS \u3c CM1DIS \u3c CM2DIS. The differences in PH among DIC de-signs were significant at the 1% level. The de-pressive effects of LLL on PH could be ranked in the following ascending order: LLL1 \u3c LLL2 ≤ LLL3. Differences in PH among LLL treatments were significant at the 1% level except that be-tween LLL2 and LLL3. The effects of interactions among: DIC × LLL on PH were significant at the 1% level with some exceptions. The highest value of PH (9.5 m) and the lowest one (6.05 m) were achieved in the interactions of CM2DIS × LLL1 and TDIS × LLL3, respectively. The shapes of the energy gradient lines were affected by DIC and LLL treatments used through their effect on ΔH/H ratio. However, they followed similar trends. According to the FL values, DIC and LLL treatments could be ranked in the following descending orders TDIS \u3e CM1DIS \u3e CM2DIS and LLL1 \u3e LLL2 \u3e LLL3. The differences in FL among DIC and LLL were significant and the effects of interactions among DIC × LLL on FL were significant at the 1% level. The maximum and mi- nimum values of FL were obtained in the inter-actions: TDIS × LLL3 and CM2DIS × LLL1, respectively. Therefore, the CM2DIS system is recommended for use where technically feasible

Effects of ultrasonic treatments on the polyphenol and antioxidant content of spinach extracts

The objective was to test ultrasound treatments on spinach leaves during extraction, and conventional extraction was used as a control. The effects of different combinations of the ultrasonic water bath factors tested on phenolic compound yields included frequency (37 and 80 kHz), exposure time (5, 10, 15, 20, 25 and 30 min), temperature (30, 40, and 50 C), and ultrasonic power (30%, 50%, and 70%). The best conditions for extraction yields were ultrasonic frequency of 37 kHz, extraction time of 30 min, reaction temperature of 40 C, and ultrasonic power of 50%. The mean yield (mg/100 g), total phenol (mg gallic acid/g DW), flavonoids (mg/g DW), % DPPH free-radical scavenging activity, and % ferric reducing antioxidant power were all high (64.88 ± 21.84, 33.96 ± 11.30, 27.37 ± 11.85, 64.18 ± 16.69 and 70.25 ± 9.68). Treatments were significantly different. The interaction among the ultrasonic parameters was significant. Temperature and power had significant effects on all other dependent variables

A sequence based synteny map between soybean and Arabidopsis thaliana

BACKGROUND: Soybean (Glycine max, L. Merr.) is one of the world's most important crops, however, its complete genomic sequence has yet to be determined. Nonetheless, a large body of sequence information exists, particularly in the form of expressed sequence tags (ESTs). Herein, we report the use of the model organism Arabidopsis thaliana (thale cress) for which the entire genomic sequence is available as a framework to align thousands of short soybean sequences. RESULTS: A series of JAVA-based programs were created that processed and compared 341,619 soybean DNA sequences against A. thaliana chromosomal DNA. A. thaliana DNA was probed for short, exact matches (15 bp) to each soybean sequence, and then checked for the number of additional 7 bp matches in the adjacent 400 bp region. The position of these matches was used to order soybean sequences in relation to the A. thaliana genome. CONCLUSION: Reported associations between soybean sequences and A. thaliana were within a 95% confidence interval of e(-30 )– e(-100). In addition, the clustering of soybean expressed sequence tags (ESTs) based on A. thaliana sequence was accurate enough to identify potential single nucleotide polymorphisms (SNPs) within the soybean sequence clusters. An EST, bacterial artificial chromosome (BAC) end sequence and marker amplicon sequence synteny map of soybean and A. thaliana is presented. In addition, all JAVA programs used to create this map are available upon request and on the WEB