Functional genomics in forage and turf - present status and future prospects

The recent advances in plant genomics have greatly influenced basic research in many agriculturally important crops. Along with the availability of complete genome information from the model grass species rice and the model legume species M. trucncatula, the functional genomics activities in other crop species will accelerate the genomics studies of forage and turf. Brachypodium distachyon was recently proposed as a new model plant for forage and turf grass genomics studies. The combination of bioinformatics and genomics will enhance our understanding of the molecular functions of forage and turf species. This review focuses on recent advances and applications of functional genomics for large-scale EST projects, global gene expression analyses, proteomics, and metabolic profiling, as well as the impact of functional genomics on improvement of forage and turf crops. Key words: Functional genomics, forage and turf grasses, ESTs, microarray, proteomics, metabolomics, Medicago truncatula, legume. African Journal of Biotechnology Vol. 2 (12), pp. 521-527, December 200

Soybean Amino Acids in Health, Genetics, and Evaluation

Soybean is an important source of protein and amino acids for humans and livestock because of its well-balanced amino acid profile. This chapter outlines the strengths and weaknesses of soybean as a complete amino acid source as well as the relative importance of individual amino acids. Special attention is paid to the sulfur-containing amino acids, methionine and cysteine. Breeding and genetic engineering efforts are summarized to highlight previous accomplishments in amino acid improvement and potential avenues for future research. Agronomic properties and processing methods that affect amino acid levels in soybean food and feed are also explained. A brief introduction into current amino acid evaluation techniques is provided. By understanding the complexities of amino acids in soybean, protein quality for humans and livestock can be maximized

Phenotypic Characterization of a Major Quantitative Disease Resistance Locus for Partial Resistance to Phytophthora sojae

Major quantitative disease resistance loci (QDRLs) are rare in the Phytophthora sojae (Kaufmann and Gerdemann)–soybean [Glycine max (L). Merr.] pathosystem. A major QDRL on chromosome 18 (QDRL-18) was identified in PI 427105B and PI 427106. QDRL-18 represents a valuable resistance source for breeding programs. Thus, our objectives were to determine its isolate specificity and measure its effect on yield and resistance to both P. sojae and other soybean pathogens. We characterized near isogenic lines (NILs) developed from F7 recombinant inbred lines heterozygous at QDRL-18; NILs represent introgressions from PI 427105B, PI 427106, and susceptible ‘OX20- 8’. The introgressions from PI 427105B and PI 427106 increased resistance to P. sojae by 11 to 20% and 35 to 40%, respectively, based on laboratory and greenhouse assays, and increased yield by 13 to 29% under disease conditions. The resistant introgression from PI 427105B was also effective against seven P. sojae isolates with no isolate specificity detected. Based on quantitative polymerase chain reaction assays, NILs with the susceptible introgression had significantly higher relative levels of P. sojae colonization 48 h after inoculation. No pleiotropic effects for resistance to either soybean cyst nematode or Fusarium graminearum were detected. This information improves soybean breeders’ ability to make informed decisions regarding the deployment of QDRL-18 in their respective breeding programs

Introgression of a Danbaekkong high-protein allele across different genetic backgrounds in soybean

Soybean meal is a major component of livestock feed due to its high content and quality of protein. Understanding the genetic control of protein is essential to develop new cultivars with improved meal protein. Previously, a genomic region on chromosome 20 significantly associated with elevated protein content was identified in the cultivar Danbaekkong. The present research aimed to introgress the Danbaekkong high-protein allele into elite lines with different genetic backgrounds by developing and deploying robust DNA markers. A multiparent population consisting of 10 F5-derived populations with a total of 1,115 recombinant inbred lines (RILs) was developed using “Benning HP” as the donor parent of the Danbaekkong high-protein allele. A new functional marker targeting the 321-bp insertion in the gene Glyma.20g085100 was developed and used to track the Danbaekkong high-protein allele across the different populations and enable assessment of its effect and stability. Across all populations, the high-protein allele consistently increased the content, with an increase of 3.3% in seed protein. A total of 103 RILs were selected from the multiparent population for yield testing in five environments to assess the impact of the high-protein allele on yield and to enable the selection of new breeding lines with high protein and high yield. The results indicated that the high-protein allele impacts yield negatively in general; however, it is possible to select high-yielding lines with high protein content. An analysis of inheritance of the Chr 20 high-protein allele in Danbaekkong indicated that it originated from a Glycine soja line (PI 163453) and is the same as other G. soja lines studied. A survey of the distribution of the allele across 79 G. soja accessions and 35 Glycine max ancestors of North American soybean cultivars showed that the high-protein allele is present in all G. soja lines evaluated but not in any of the 35 North American soybean ancestors. These results demonstrate that G. soja accessions are a valuable source of favorable alleles for improvement of protein composition

Effects of full-fat high-oleic soybean meal in layer diets on nutrient digestibility and egg quality parameters of a white laying hen strain

This study was conducted to understand the impact of including full fat high-oleic soybean meal in layer hen diets on nutrient digestibility and added nutritional value in eggs. Forty-eight layers (∼36 wk old) were randomly assigned to one of 4 isonitrogenous (18.5% crude protein) treatment diets with 12 replicate birds per treatment in a 3-wk study. Treatments were 1) solvent extracted defatted soybean meal + corn diet, 2) dry extruded defatted soybean meal + corn, 3) full-fat soybean meal + corn, 4) high-oleic full-fat soybean meal + corn diet. Apparent ileal digestibility of crude fat (CF) and crude protein (CP) were determined using celite (∼2%) as an indigestible marker. Tibia strength and egg quality parameters (egg weight, shell strength, Haugh unit, shell color, and yolk color) were recorded during the study. Fatty acid profiles, including the monounsaturated fatty acid, oleic acid (C18:1, cis), in eggs and adipogenic tissue (liver, muscle, and fat pad) were measured using gas chromatography (GC-FID). Digestibility values of CF ranged from 71 to 84% and CP varied from 67 to 72% for treatment diets, with treatment mean values being no different (P \u3e 0.05) between treatment diets. No differences between treatment diets in tibia strength or egg quality parameters (egg weight, shell strength, and Haugh unit) were observed (P \u3e 0.05) except for yolk color. Similarly, there were no differences in the total lipids in egg yolk (P \u3e 0.05) between treatment diets. However, oleic acid percentage of total lipid in egg and tissue was significantly higher (P \u3c 0.001) in hens given the high-oleic full-fat soybean meal diet than in other treatment groups. No difference was observed in oleic acid percentage of total lipid in egg between the other 3 treatment diets (P \u3e 0.05). Overall, the results exhibited that the eggs and tissue of layer hens fed the full-fat high-oleic acid soybean meal diet were higher in oleic acid while the CF and CP digestibility remained similar to the digestibility of the other diets

Geographic Distribution of Soybean Aphid Biotypes in the United States and Canada during 2008–2010

Soybean aphid (Aphis glycines Matsumura) is a native pest of soybean [Glycine max (L.) Merr.] in eastern Asia and was detected on soybeans in North America in 2000. In 2004, the soybean cultivar Dowling was described to be resistant to soybean aphids with the Rag1 gene for resistance. In 2006, a virulent biotype of soybean aphid in Ohio was reported to proliferate on soybeans with the Rag1 gene. The objective was to survey the occurrence of virulent aphid populations on soybean indicator lines across geographies and years. Nine soybean lines were identified on the basis of their degree of aphid resistance and their importance in breeding programs. Naturally occurring soybean aphid populations were collected in 10 states (Kansas, Illinois, Indiana, Iowa, Michigan, Minnesota, North Dakota, Ohio, South Dakota, and Wisconsin) and the Canadian province of Ontario. The reproductive capacity of field-collected soybean aphid populations was tested on soybean lines; growth rates were compared in no-choice field cages at each geographic region across 3 yr. The occurrence of soybean aphid biotypes was highly variable from year to year and across environments. The frequency of Biotypes 2, 3, and 4 was 54, 18, and 7%, respectively, from the 28 soybean aphid populations collected across 3 yr and 11 environments. Plant introduction (PI) 567598B, a natural gene pyramid of rag1c and rag4, had lowest frequency of soybean aphid colonization (18%). Several factors may have contributed to the variability, including genetic diversity of soybean aphids, parthenogenicity, abundance of the overwintering host buckthorn (Rhamnus spp.), and migratory patterns of soybean aphids across the landscape

Analysis of tall fescue ESTs representing different abiotic stresses, tissue types and developmental stages

<p>Abstract</p> <p>Background</p> <p>Tall fescue (<it>Festuca arundinacea </it>Schreb) is a major cool season forage and turf grass species grown in the temperate regions of the world. In this paper we report the generation of a tall fescue expressed sequence tag (EST) database developed from nine cDNA libraries representing tissues from different plant organs, developmental stages, and abiotic stress factors. The results of inter-library and library-specific <it>in silico </it>expression analyses of these ESTs are also reported.</p> <p>Results</p> <p>A total of 41,516 ESTs were generated from nine cDNA libraries of tall fescue representing tissues from different plant organs, developmental stages, and abiotic stress conditions. The <it>Festuca </it>Gene Index (FaGI) has been established. To date, this represents the first publicly available tall fescue EST database. <it>In silico </it>gene expression studies using these ESTs were performed to understand stress responses in tall fescue. A large number of ESTs of known stress response gene were identified from stressed tissue libraries. These ESTs represent gene homologues of heat-shock and oxidative stress proteins, and various transcription factor protein families. Highly expressed ESTs representing genes of unknown functions were also identified in the stressed tissue libraries.</p> <p>Conclusion</p> <p>FaGI provides a useful resource for genomics studies of tall fescue and other closely related forage and turf grass species. Comparative genomic analyses between tall fescue and other grass species, including ryegrasses (<it>Lolium </it>sp.), meadow fescue (<it>F. pratensis</it>) and tetraploid fescue (<it>F. arundinacea var glaucescens</it>) will benefit from this database. These ESTs are an excellent resource for the development of simple sequence repeat (SSR) and single nucleotide polymorphism (SNP) PCR-based molecular markers.</p

Genetic Architecture of Soybean Yield and Agronomic Traits

Soybean is the world’s leading source of vegetable protein and demand for its seed continues to grow. Breeders have successfully increased soybean yield, but the genetic architecture of yield and key agronomic traits is poorly understood. We developed a 40-mating soybean nested association mapping (NAM) population of 5,600 inbred lines that were characterized by single nucleotide polymorphism (SNP) markers and six agronomic traits in field trials in 22 environments. Analysis of the yield, agronomic, and SNP data revealed 23 significant marker-trait associations for yield, 19 for maturity, 15 for plant height, 17 for plant lodging, and 29 for seed mass. A higher frequency of estimated positive yield alleles was evident from elite founder parents than from exotic founders, although unique desirable alleles from the exotic group were identified, demonstrating the value of expanding the genetic base of US soybean breeding

Combining Next-Generation Sequencing Strategies for Rapid Molecular Resource Development from an Invasive Aphid Species, Aphis glycines

Aphids are one of the most important insect taxa in terms of ecology, evolutionary biology, genetics and genomics, and interactions with endosymbionts. Additionally, many aphids are serious pest species of agricultural and horticultural plants. Recent genetic and genomic research has expanded molecular resources for many aphid species, including the whole genome sequencing of the pea aphid, Acrythosiphon pisum. However, the invasive soybean aphid, Aphis glycines, lacks in any significant molecular resources.Two next-generation sequencing technologies (Roche-454 and Illumina GA-II) were used in a combined approach to develop both transcriptomic and genomic resources, including expressed genes and molecular markers. Over 278 million bp were sequenced among the two methods, resulting in 19,293 transcripts and 56,688 genomic sequences. From this data set, 635 SNPs and 1,382 microsatellite markers were identified. For each sequencing method, different soybean aphid biotypes were used which revealed potential biotype specific markers. In addition, we uncovered 39,822 bp of sequence that were related to the obligatory endosymbiont, Buchnera aphidicola, as well as sequences that suggest the presence of Hamiltonella defensa, a facultative endosymbiont.Molecular resources for an invasive, non-model aphid species were generated. Additionally, the power of next-generation sequencing to uncover endosymbionts was demonstrated. The resources presented here will complement ongoing molecular studies within the Aphididae, including the pea aphid whole genome, lead to better understanding of aphid adaptation and evolution, and help provide novel targets for soybean aphid control