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Cotton fiber represents the largest single cell in plants and they serve as models to study cell development. This study investigated the distribution and evolution of fiber Unigenes anchored to recombination hotspots between tetraploid cotton (Gossypium hirsutum) At and Dt subgenomes, and within a parental diploid cotton (Gossypium raimondii) D genome. Comparative analysis of At vs D and Dt vs D showed that 1) the D genome provides many fiber genes after its merger with another parental diploid cotton (Gossypium arboreum) A genome although the D genome itself does not produce any spinnable fiber; 2) similarity of fiber genes is higher between At vs D than between Dt vs D genomic hotspots. This is the first report that fiber genes have higher similarity between At and D than between Dt and D. The finding provides new insights into cotton genomic regions that would facilitate genetic improvement of natural fiber properties.

The discovery of sequence variants and their functionality has been increasing with new genotyping technologies and mapping studies across plant species. Sequence polymorphisms associated with trait variation can be converted into Functional Markers (FMs), which are derived from polymorphic sites within genes or regulatory sequences causally affecting phenotypic trait variation. The effects of FMs on the phenotypic variation of complex inherited traits, however, are usually dependent on epistatic and environment interactions. In this review, we propose the term “potential” to define effects of FMs. The potential of a FM is based on distribution of allelic effects across environments and backgrounds, and the probability of achieving a phenotype of interest. The use of FM in plant breeding programs and how FMs may be combined with Genomic Selection to increase genetic gain are also discussed.

Detection of quantitative trait loci (QTL) controlling complex traits followed by selection has become a common approach for selection in crop plants. The QTL are most often identified by linkage mapping using experimental F(2), backcross, advanced inbred, or doubled haploid families. An alternative approach for QTL detection are genome-wide association studies (GWAS) that use pre-existing lines such as those found in breeding programs. We explored the implementation of GWAS in oat (Avena sativa L.) to identify QTL affecting β-glucan concentration, a soluble dietary fiber with several human health benefits when consumed as a whole grain. A total of 431 lines of worldwide origin were tested over 2 years and genotyped using Diversity Array Technology (DArT) markers. A mixed model approach was used where both population structure fixed effects and pair-wise kinship random effects were included. Various mixed models that differed with respect to population structure and kinship were tested for their ability to control for false positives. As expected, given the level of population structure previously described in oat, population structure did not play a large role in controlling for false positives. Three independent markers were significantly associated with β-glucan concentration. Significant marker sequences were compared with rice and one of the three showed sequence homology to genes localized on rice chromosome seven adjacent to the CslF gene family, known to have β-glucan synthase function. Results indicate that GWAS in oat can be a successful option for QTL detection, more so with future development of higher-density markers.

The landscape of plant genomes, while slowly being characterized and defined, is still composed primarily of regions of undefined function. Many eukaryotic genomes contain isochore regions, mosaics of homogeneous GC content that can abruptly change from one neighboring isochore to the next. Isochores are broken into families which are characterized by their GC levels. We identified 4,339 compositionally distinct domains and 331 of these were identified as Long Homogeneous Genome Regions (LHGRs). We assigned these to four families based on finite mixture models of GC content. We then characterized each family with respect to exon length, gene content, and transposeable elements. The LHGR pattern of soybeans is unique in that while the majority of the genes within LHGRs are found within a single LHGR family with a narrow GC-range (Family B), that family is not the highest in GC content as seen in vertebrates and invertebrates. Instead Family B has a mean GC content of 35%. The range of GC content for all LHGRs is 16-59% GC which is a larger range than what is typical of vertebrates. This is the first study in which LHGRs have been identified in soybeans and the functions of the genes within the LHGRs have been analyzed.

Plant breeders have an interest in the identification of genomic regions associated with the expression of quantitative traits because they recognize that such information coud be used to improve realized heritability and reduce time per cyle of selection. The development of molecular marker technologies may provide tools to accomplish these goals. Maize (Zea mays L.) breeders develop new inbred parents of hybrids through topcrossed and per se evaluation of numerous quantitative traits in segregating progeny from planned breeding crosses [...]

Segregating soybean [ (L.) Merr.] breeding populations are frequently inbred by either single-seed descent or by bulking progeny at each generation. During inbreeding, repetitive sampling of individual genotypes, or natural selection, may decrease the potential for genetic gain in a population. This is most likely to occur in populations that are inbred by the bulk method. This study examines the genetic structure of two soybean populations, each containing 261 segregating lines. One population was derived from a cross of two elite lines and was inbred by a multiple-seed descent (MSD) strategy that is frequently employed by soybean breeders. A second population was derived from an elite × unadapted genotype cross that was inbred by single-seed descent (SSD). The genetic composition of each line and the genetic distances among lines were estimated using 100 RFLP markers. The genetic contribution of each parent to each population was equivalent regardless of the inbreeding procedure. No individual in either population obtained greater than 75% of its genes from a particular parent. Close genetic relationships among lines were not observed in the SSD population, but were common in the MSD population. Cluster analysis of individual lines within the MSD population indicated that about 18% of the lines were due to repetitive sampling and, therefore, did not represent independent lineages. The repetitive sampling appeared to be caused by stochastic processes, as opposed to systematic factors such as differential fecundity among genotypes. Genetic marker analysis of population structure provides a method for directly assessing the effectiveness of inbreeding strategies.

Gray leaf spot (GLS) (caused by Cercospora zeae-maydis Theon & Daniels) is a fungal disease of the maize (Zea mays L.) that can cause significant grain yield reductions. Quantitative resistance to GLS does exist; therefore, one method of controlling the disease is to develop hybrids with genetic resistance. The objective of this study was to identify quantitative trait loci (QTL) and type-of-gene action for GLS resistance in segregating families of three single-cross populations of maize using restriction fragment length polymorphisms (RFLPs) (.)

Soybean RFLP markers have been primarily developed and genetically mapped using wide crosses between exotic and adapted genotypes. We have screened 38 soybean lines at 128 RFLP marker loci primarily to characterize germ plasm structure but also to evaluate the utility of RFLP markers identified in unadapted populations. Of these DNA probes 70% detected RFLPs in this set of soybean lines with an average polymorphism index of 0.30. This means that only 1 out of 5 marker loci was informative between any particular pair of adapted soybean lines. The variance associated with the estimation of RFLP genetic distance (GDR) was determined, and the value obtained suggested that the use of more than 65-90 marker loci for germ plasm surveys will add little precision. Cluster analysis and principal coordinate analysis of the GDR matrix revealed the relative lack of diversity in adapted germ plasm. Within the cultivated lines, several lines adapted to Southern US maturity zones also appeared as a separate group. GDR data was compared to the genetic distance estimates obtained from pedigree analysis (GDP). These two measures were correlated with r = 0.54 for all 38 lines, but the correlation increased to r = 0.73 when only adapted lines were analyzed.

Although genetic studies have been critically important for the identification of therapeutic targets in Mendelian disorders, genetic approaches aiming to identify targets for common, complex diseases have traditionally had much more limited success. However, during the past year, a novel genetic approach — genome-wide association (GWA) — has demonstrated its potential to identify common genetic variants associated with complex diseases such as diabetes, inflammatory bowel disease and cancer. Here, we highlight some of these recent successes, and discuss the potential for GWA studies to identify novel therapeutic targets and genetic biomarkers that will be useful for drug discovery, patient selection and stratification in common diseases.

Comparative genomics is an emerging and powerful approach to achieve crop improvement. Using comparative genomics, information from model plant species can accelerate the discovery of genes responsible for disease and pest resistance, tolerance to plant stresses such as drought, and enhanced nutritional value including production of anti-oxidants and anti-cancer compounds. We demonstrate here how to use the Legume Information System for a comparative genomics study, leveraging genomic information from Medicago truncatula (barrel medic), the model legume, to find candidate genes involved with sudden death syndrome (SDS) in Glycine max (soybean). Specifically, genetic maps, physical maps, and annotated tentative consensus and expressed sequence tag (EST) sequences from G. max and M. truncatula can be compared. In addition, the recently published M. truncatula genomic sequences can be used to identify M. truncatula candidate genes in a genomic region syntenic to a quantitative trait loci region for SDS in soybean. Genomic sequences of candidate genes from M. truncatula can then be used to identify ESTs with sequence similarities from soybean for primer design and cloning of potential soybean disease causing alleles.

Genomics and bioinformatics are expected to revolutionize crop improvement. We have to admit, howere, tha while information from the various "omics" is being used by developmental and evolutionary biologists, the information is not being used routinely byn translational plant biologists or applied plant breeders. This is due to a failure to provide information from omics technologies in formats that can be used to develop more effective and efficient assays that the breeder can use for selection. A similar situation exits in biomedical research where more efficacious therapies will be realized if omics information is translated into biomarker-based diagnostics. Because data are stil lacking in plant science, herein we describe the development of an integrated web-based system that supports translational research using a biomedical example that can serve as a model for translational plant research. We also discuss how the bioinformatic system is agnostic with respect to data content and is capable of accepting omics data that eventually will be generated by plant biologists for use by plant breeders to develop diagnostic biomarkers for use in selection.

Comparative genomics is an emerging and powerful approach to achieve crop improvement. Using comparative genomics, information from model plant species can accelerate the discovery of genes responsible for disease and pest resistance, tolerance to plant stresses such as drought, and enhanced nutritional value including production of anti-oxidants and anti-cancer compounds. We demonstrate here how to use the Legume Information System for a comparative genomics study, leveraging genomic information from Medicago truncatula (barrel medic), the model legume, to find candidate genes involved with sudden death syndrome (SDS) in Glycine max (soybean). Specifically, genetic maps, physical maps, and annotated tentative consensus and expressed sequence tag (EST) sequences from G. max and M. truncatula can be compared. In addition, the recently published M. truncatula genomic sequences can be used to identify M. truncatula candidate genes in a genomic region syntenic to a quantitative trait loci region for SDS in soybean. Genomic sequences of candidate genes from M. truncatula can then be used to identify ESTs with sequence similarities from soybean for primer design and cloning of potential soybean disease causing alleles.

The Legume Information System (LIS) (http://www.comparative-legumes.org), developed by the National Center for Genome Resources in cooperation with the USDA Agricultural Research Service (ARS), is a comparative legume resource that integrates genetic and molecular data from multiple legume species enabling cross-species genomic and transcript comparisons. The LIS virtual plant interface allows simplified and intuitive navigation of transcript data from Medicago truncatula, Lotus japonicus, Glycine max and Arabidopsis thaliana. Transcript libraries are represented as images of plant organs in different developmental stages, which are selected to query the analyzed and annotated data. Complex queries can be accomplished by adding modifiers, keywords and sequence names. The LIS also contains annotated genomic data featuring transcript alignments to validate gene predictions as well as motif and similarity analyses. The genomic browser supports comparative analysis via novel dynamic functional annotation comparisons. CMap, developed as part of the GMOD project (http://www.gmod.org/cmap/index.shtml), has been incorporated to support comparative analyses of community linkage and physical map data. LIS is being expanded to incorporate gene expression and biochemical pathways which will be seamlessly integrated forming a knowledge discovery framework.

A molecular understanding of porcine reproduction is of biological interest and economic importance. Our Midwest Consortium has produced cDNA libraries containing the majority of genes expressed in major female reproductive tissues, and we have deposited into public databases 21,499 expressed sequence tag (EST) gene sequences from the 3' end of clones from these libraries. These sequences represent 10,574 different genes, based on sequence comparison among these data, and comparison with existing porcine ESTs and genes indicate as many as 4652 of these EST clusters are novel. In silico analysis identified sequences that are expressed in specific pig tissues or organs and confirmed the broad expression in pig for many genes ubiquitously expressed in human tissues. Furthermore, we have developed computer software to identify sequence similarity of these pig genes with their human counterparts, and to extract the mapping information of these human homologues from genome databases. We demonstrate the utility of this software for comparative mapping by localizing 61 genes on the porcine physical map for Chromosomes (Chrs) 5, 10, and 14.

Applied breeding programs evaluate large numbers of progeny derived from multiple related crosses for a wide range of agronomic traits and for tens to hundreds of molecular markers. This study was conducted to determine how these phenotypic and genetic data could be used for routinely mapping quantitative trait loci (QTLs). With dense maps, haplotype sharing of parents in a certain region is a good indicator for QTL-allele sharing, albeit not 100% perfect. With this in mind, an approximate and simple method has been developed where ancestral genome blocks in the parents of the crosses can be identified via haplotype analysis and where the effect of a putative QTL is then modeled and estimated per ancestral genome block. A simulation of an early-generation maize breeding scheme demonstrates the potential of the present approach for QTL detection in existing breeding programs. With this new QTL mapping strategy, the power, precision, and accuracy associated with large numbers of progeny may be attained, inferences about QTLs can be drawn across the breeding program rather than being limited to the sample of progeny from a single cross, and results may be much more valuable for marker-assisted breeding because the QTLs apply to agronomically challenging situations in the field.

The effects of intermating on recombination and the development of linkage maps were assessed in maize. Progeny derived from a common population (B73 x Mo17) before and after five generations of intermating were genotyped at the same set of 190 RFLP loci. Intermating resulted in nearly a four-fold increase in the genetic map distance and increased the potential for improved genetic resolution in 91% of the intervals evaluated. This mapping population and related information should connect research involving dense genetic maps, physical mapping, gene isolation, comparative genomics, analysis of quantitative trait loci and investigations of heterosis.

Reductionist approaches to biological questions have provided important insights to genetic mechanisms and genome structures. These approaches have also led to the engineering of technologies that generate data at rates that far exceed our ability to comprehend their meaning. If biologists are going to address the fundamental questions concerning the complexity that underlies growth, development and phenotypic variability, then there is an unprecedented need to acquire, understand, manipulate, and exploit high-value genomic information. Further, for genomics to deliver the promise of using biological processes to make agricultural systems more efficient, sustainable, and environmentally friendly, various types of biological data will need to be integrated to reveal the functional relationships between DNA, RNA, proteins, environment and phenotypes. Such integrative approaches will rely heavily on development of information systems (IS) and data analysis methods that will require the same rigor and resources that have been applied to development of laboratory experimental protocols. In addition, software and process engineering will need to be applied to information systems development much in the same way as engineering principles have been applied to data production in biological laboratories, resulting in a shift from cottage industry to industrial scale biological data factories.

As the world’s population continues to rise, and it becomes increasingly desirable to avoid excessive use of chemical inputs, plant breeding can provide biological solutions to the necessities of food production and help conserve environmental resources. Continued improvements in the genetic basis of agronomic productivity must be achieved. Applied genetic research has been instrumental in progressing varietal performance and breeding efficiency. Productivity has risen as breeders have brought together in single varieties chromosomal regions exerting positive effects on traits that have a favorable impact on agronomic performance in specific and general environments. Russell (1984), Duvick (1987), Anderson et al (1988), and Tollenaar (1989) have shown that newer varieties outperform older varieties even in low input environments. Older varieties more readily exhibit sterility, lodging, and increased damage from pests when confronted with stress conditions (Patch et al, 1941; Russell, 1974; Austin et al, 1980; Duvick, 1984).

The purpose of this chapter is to enable the investigator to obtain and utilize restriction fragment-length polymorphism (RFLP) probes for the ultimate goal of cloning genes by transposon tagging. Probes for transposable elements often yield a complex RFLP pattern in maize DNA, and this chapter presents methods for interpreting such patterns. While purely genetic methods can be used to establish an association between an autonomous transposable element and a mutant locus (McClintock 1965), molecular methods such as those presented here are often required to perform a similar analysis with nonautonomous elements. The latter elements cause far more mutations in maize than do their autonomous counterparts.

We report that plant height quantitative trait loci (QTLs) identified in a given small population are not consistent with QTLs identified in other small populations, and that most QTLs are in close proximity to mapped qualitative genetic loci. These observations provide evidence to support the hypothesis that qualitative genetic loci are the same loci that affect quantitative traits, and affirm that these modest experiments probably identify real QTLs.

Recently, maize (Zea mays L.) genetic maps based primarily upon segregating restriction fragment length polymorphisms (RFLPs) have been developed by several research groups. Some of the reported maps were based upon data from a single segregating population, whereas others were based upon information from several segregating populations. Potential problems with pooling information from several segregating populations have not been reported. These include the fact that few genetic markers are polymorphic in all populations, estimates of linkage may differ among populations, and population sizes may differ. We utilize the log-likelihood statistic to genetically map partially overlapping sets of informative genetic markers, to test homogeneity of recombination among populations, and to present a composite RFLP linkage map based upon data pooled from four F2 populations.

Applied breeding programs evaluate large numbers of progeny derived from multiple related crosses for a wide range of agronomic traits and for tens to hundreds of molecular markers. This study was conducted to determine how these phenotypic and genetic data could be used for routinely mapping quantitative trait loci (QTLs). With dense maps, haplotype sharing of parents in a certain region is a good indicator for QTL-allele sharing, albeit not 100% perfect. With this in mind, an approximate and simple method has been developed where ancestral genome blocks in the parents of the crosses can be identified via haplotype analysis and where the effect of a putative QTL is then modeled and estimated per ancestral genome block. A simulation of an early-generation maize breeding scheme demonstrates the potential of the present approach for QTL detection in existing breeding programs. With this new QTL mapping strategy, the power, precision, and accuracy associated with large numbers of progeny may be attained, inferences about QTLs can be drawn across the breeding program rather than being limited to the sample of progeny from a single cross, and results may be much more valuable for marker-assisted breeding because the QTLs apply to agronomically challenging situations in the field.

Cytoplasmic genes of crop species exhibit non-Mendelian inheritance and affect quantitative traits such as biomass and grain yield. Photosynthesis and respiration are physiological processes responsible, in part, for the expression of such quantitative traits and are regulated by enzymes encoded in both the cytoplasm and nucleus. Cytoplasmic genes are located in the chloroplast and mitochondrial genomes. Unlike the nuclear genome, the cytoplasmic genomes consist of single, circular, double-stranded molecules of DNA, and in many crop species, the cytoplasmic genomes are inherited solely through the maternal parent. Maternal inheritance of cytoplasmic genomes and Mendelian inheritance of the nuclear genome were used to model the genotypic value of an individual. The model then was utilized to derive genetic variances and covariances for a random-mating population. Finally, the use of reciprocal mating designs to estimate variance components was investigated.

This study was initiated to determine the itiuence of vesiculararbuscular mycorrhizal (VAM) fungi on a rhizobhun-legume interaction. Inoculation of subclover with Glomus fascicddus resulted in 2 times as many rhizobium nodules on roots as on nonmycorrhizal controls. Inocuhtion with Glomus mosseue resulted in 1.4 times greater nodule formation compared to the noninoculated controls. Plants inoculated with G. mosseue + G. fusckulatus had 1.9 times more nodules than the controls. Furthermore, inoculation with G. fasciculatus or G. mosswe+ G. fasciculatus resulted in shoot weights and total plant weights nearly double that of the controls. The conclusion is that inoculation with the correct VAM fungal species is as important as the selection of the rhizobium species for subclover growth and development. The increased demand for energy resources has resulted in large tracts of arid and semiarid rangelands being disturbed by the quest for coal and oil shale. Both the 1972 federal mining law and state regulations require the reclamation of these lands to acceptable standards for forage and wildlife habitat. Western rangelands are generally deficient in nitrogen and phosphorus throughout their soil profiles; as a result, standard rehabilitation operations must use large applications of these inorganic fertilizers to establish site productivity (Bauer et al. 1978). However, the costs of fertilizer often exceed the actual benefits derived from their use in reseeding projects in arid locations. Abbott and Robson studied the growth of subterranean clover inoculated with two types of vesicular arbuscular endophytes and compared them with that of noninoculated plants at 5 levels of applied superphospate in a high phosphate fixing soil. A greater growth response of plants inoculated with a fungus resembling G. mosseue was associated with a greater amount of mycorrhizal roots. Responses in nodulation closely paralleled responses in growth. This study was initiated to determine the potential of using existing biological systems in place of expensive fertilizer applications for site rehabilitation. Legumes will, with associated rhizobium, fix large quantities of nitrogen; this association might be useful as a biological system for supplying nitrogen. However, the legume-rhizobium interaction requires relatively high levels of phosphorus (van Schreven 1958). Since vesicular-arbuscular mycorrhizal (VAM) fungi increase the uptake of phosphorus by their host plants, a study was initiated to determine the influence of VAM fungis on a rhizobium-legume assoc$tion under low phosphorus conditions. The use of mist chambers for root studies Authors arc. respectively, associate professor, graduate research assistant, and former student. Debartment of Ranne Manaeement. Humboldt State Universitv. Arcata, Califorttia 45521, and projecy leader, ‘kocky ‘Mountain Forest and Ran& Experiment Station. Albuquerque,, New Mexico 87106. William Beavis is presently a research assistant. Iowa State Untversity, Ames Xl01 I. This research was funded by the Rocky Mountain Forest and Range Experiment Station, at the Station’s Research Work Unit in Albuquerque, incooperation with the University of New Mexico. Station headquarters is in Fort Collins. in cooperation with Colorado State University. Manuscript received December 4. 1981. avoids the confounding effects of edaphic factors (Graham et al. 1976). Materials and Methods Spores of Glomus mosseae (Nichol. and Gerd.) Gerdemannand Trappe and Glomusfascicuhtus (7haxter sensu Gerdemann) Gerdemann and Trappe, collected in the state of Washington, were multiplied in pot culture on wheat (Graham et al. 1976). Spores were extracted by wet sieving and decanting (Gerdemann and Nicholson 1963) and stored in Ringer’s solution (Daniels and Graham 1976) for about 3-5 months before use. Seeds of subclover (Trifolium subterranean L. cv. Mount Barker) were surface disinfected in a 0.5% sodium hypochlorite solution and rinsed 5 times in sterile, distilled water. The moistened seeds were inoculated with a commercial preparation of Rhizobium trifolii (Dungeard) by placing them in the preparation and thoroughly coating each seed. The inoculated seeds were then planted in 3-inch pots containing a 1 to I mixture (vol/vol) of sterile autoclaved sand and vermiculite. When the seedlings reached the two-leaf stage, they were carefully tapped out of the pots, and the roots were rinsed free of sand and vermiculite with tap water. The seedlings were then placed in 3-inch pots with one root subtended through a l/2-inch hole drilled in the base of each pot. One to 3 lateral roots were left confined within the pot. The confined roots were covered with l/2-inch of moistened vermiculite, and the potted plants were then placed in a misted-root culture chamber (Hansen et al. 1979). The roots were sprayed continuously with a fine mist of a 40-fold dilution of a modified Hoaglands number 2 solution to allow healing of any abrasions on the roots (Graham et al. 1976). After 7 days, the vermiculite covering the confined roots was carefully rinsed out of the pots with tap water. Roots of the plants used for controls were recovered with moistened vermiculite and placed back on the misted-root chambers. Plants for the VAM fungi treatments were inoculated by placing lo-15 spores of each selected VAM fungal species directly on the rootlets confined within the pot. The inoculated roots were covered with moistened vermiculite, and the pots again placed in the root-chamber and misted with the same diluted Hoglands solutions (available phosphorus maintained at 10e6 M concentration). Treatments, in addition to the R. trifolii inoculation already done, were (1) control-no VAM inoculation; (2) G. mosseae; (3) G. fasciculatus; (4) G. mosseae -IG.fascicularus-inoculated with 15 spores each of the VAM fungi G. mosseae and G. fasciculatus. All root lengths were measured every 2 weeks until all of the plants were harvested 12 weeks following inoculation, when the following data were also collected: Number of nodules/root system, root dry weight, shoot dry weight, and total plant dry weight. Presence of VAM mycelium was determined by trypan blue staining techniques. Two completely randomized blocks of 92 plants/block were used, which represents a total of 23 plants per treatment, replicated twice. 576 JOURNAL OF RANGE MANAGEMENT 36(5), September 1963