bluuebunny/crossref_metadata_2025_split huggingface dataset:
Cost Efficiency of Cryopreservation as a Long‐Term Conservation Method for Coffee Genetic Resources
Authors: Dulloo M. E. , Ebert A. W. , Dussert S. , Gotor E. , Astorga C. , Vasquez N. , Rakotomalala J. J. , Rabemiafara A. , Eira M. , Bellachew B. , Omondi C. , Engelmann F. , Anthony F. , Watts J. , Qamar Z. , Snook L. 
Published: October 2009

ABSTRACTCoffee (Coffea spp.) is one of the world's most valuable agricultural export commodities produced by small‐scale farmers. Its germplasm, which holds useful traits for crop improvement, has traditionally been conserved in field genebanks, which presents many challenges for conservation. New techniques of in vitro and cryopreservation have been developed to improve the long‐term conservation of coffee. But a question remains as to whether these new techniques are more cost effective than field collections and more efficient at reducing genetic erosion. This study compared the costs of maintaining one of the world's largest coffee field collections with those of establishing a coffee cryo‐collection at the Centro Agronómico Tropical de Investigación y Enseñanza (CATIE) in Costa Rica. The results indicate that cryopreservation costs less (in perpetuity per accession) than conservation in field genebanks. A comparative analysis of the costs of both methods showed that the more accessions there are in cryopreservation storage, the lower the per‐accession cost. In addition to cost, the study examined the advantages of cryopreservation over field collection and showed that for species that are difficult to conserve using seeds, and that can only be conserved as live plants, cryopreservation may be the method of choice for long‐term conservation of genetic diversity.
Bumble Bee Pollinators in Red Clover Seed Production
Authors: Rao Sujaya , Stephen William P. 
Published: October 2009

ABSTRACTBumble bees pollinate red clover (Trifolium pratense L.) but impact on seed production depends on the species, abundance, and synchrony with bloom. The objectives of the current study were to examine pollination by a native bumble bee, Bombus vosnesenskii (Radoszkowski), determine the bumble bee fauna associated with red clover in Oregon, and assess if seed set is limiting. In a cage study, yields with B. vosnesenskii (average = 661 kg ha−1) and honey bees (Apis mellifera L.) (average = 640 kgha−1) were comparable. Yields were lower compared with open pollinated plots (average = 1127 kg ha−1), which was likely due to cage effect, as seed set (# seeds/# florets per seed head) was similar in all three treatments (excluding control). Examination of the diversity of endemic bumble bees through field counts and trapping in red clover fields indicated the presence of six species. Over 92% of these were B. vosnesenskii indicating that it is the key pollinator in Oregon. Seed set across four commercial fields was high (0.84–0.88) documenting that existing pollinators, including rented honey bees, and indigenous bumble bees and solitary bees, provide close to maximum pollination of red clover in Oregon. Higher yields will require improved production practices and new cultivars with more heads per plant. Sustainability of high yields in Oregon will depend on protection of indigenous bee pollinators through conservation of habitats that provide nesting sites, judicious pesticide use, and provision of floral resources before red clover bloom.
A Conceptual Model for Describing Processes of Crop Improvement in Database Structures
Authors: DeLacy Ian H. , Fox P. N. , McLaren Graham , Trethowan Richard , White Jeffrey W. 
Published: October 2009

ABSTRACTRising research costs, broadening goals, intellectual property rights, and other concerns increase the need for robust management of crop improvement data. The data model of the International Crop Information System (ICIS) allows breeding processes to be recorded unambiguously in a relational database. This paper describes this model, which underlies the Genealogical Management System (GMS) of ICIS. The model recognizes three classes of methods by which genetic material is advanced. Generative methods such as crossing or mutagenesis increase variation. Derivative methods usually involve selection, and maintenance methods conserve the genetic makeup of germplasm, such as in seed multiplications. Unlike systems that only track pedigrees, the model describes steps of selection. Applications are illustrated for self‐pollinating, outcrossing, and clonally propagated crops. The ICIS GMS is in use for species including rice (Oryza sativa L.), wheat (Triticum aestivum L.), maize (Zea mays L.), potato (Solanum tuberosum L.), common bean (Phaseolus vulgaris L.), lesquerella [Lesquerella fendleri (Gray) S. Wats.], and witloof chicory (Cichorium intybus L.). The International Rice Information System, based on ICIS, holds more than 2.6 million unique identifiers for germplasm accessions, crosses, populations, and lines, requiring about 900 megabytes of storage space, which can easily be managed on a personal computer. The GMS model appears suited for widespread use in managing data on crop improvement.
Two Alleles of ahFAD2B Control the High Oleic Acid Trait in Cultivated Peanut
Authors: Chu Ye , Holbrook C. Corley , Ozias‐Akins Peggy 
Published: October 2009

ABSTRACTA high oleic:linoleic acid ratio (O/L) in peanut (Arachis hypogaea L.) seeds is controlled primarily by two recessive genes, ahFAD2A and ahFAD2B (ol1 and ol2). Marker‐assisted breeding for high O/L could become routine provided that user‐friendly and economical markers could be developed that would target mutant alleles underlying the trait. Previously, a mutant allele of ahFAD2A was characterized as having a 448G>A transition, and two ahFAD2B alleles were found with either a nonsense mutation caused by a single nucleotide insertion (441_442insA) (high O/L line F435) or a transposable element insertion (Flavorunner 458). A cleaved amplified polymorphic sequence (CAPS) marker targeting the 441_442insA site in ahFAD2B was designed. ‘Georgia‐02C’ and ‘Georgia Hi‐O/L’, derivatives of irradiation‐induced high O/L mutants, showed CAPS marker and sequence data diagnostic for the genetic mutations in ahFAD2 found in the spontaneous mutant line F435. In addition, conflicting reports regarding the organization of ahFAD2 genes and ahFAD2B mutations were reexamined. Our data clearly show that molecular markers can be used to screen for known ahFAD2 mutations and that only two mutant ahFAD2B alleles are present in the U.S. high O/L cultivars. Genetic markers based on these mutations have utility for detecting seed mixtures and heterozygotes, and can accelerate introduction of the high O/L trait into peanut breeding lines.
Microsatellite‐based Analysis of Tobacco (Nicotiana tabacum L.) Genetic Resources
Authors: Moon H. S. , Nifong J. M. , Nicholson J. S. , Heineman A. , Lion K. , van der Hoeven R. , Hayes A. J. , Lewis R. S. 
Published: October 2009

ABSTRACTLittle is currently known about the genetic variation within diverse gene pools of cultivated tobacco (Nicotiana tabacum L.). Knowledge in this area could aid in future germplasm maintenance activities, provide additional information in the area of N. tabacum population genetics, and assist in selection of materials for breeding or genetic investigations. To this end, 702 N. tabacum accessions from the U.S. Nicotiana Germplasm Collection were genotyped with 70 microsatellite markers. A total of 1031 alleles were detected, with an average of 14.7 alleles per marker. Average gene diversity was quite large (0.7362) and was three times the value for a diverse population of U.S. flue‐cured tobacco. Cluster analysis using various distance coefficients generated seven consistent groups. Patterns of geographic‐specific clustering were frequent but not universal. An analysis of molecular variance for tobacco collected from Central and South America revealed that 92% of the total genetic variation among samples could be attributed to country‐specific subpopulations. There was also a significant level of population subdivision between country‐specific subpopulations, however. Tobacco samples collected from Peru had both the largest average gene diversity and the largest mean genetic distance, although N. tabacum collected from Mexico had the greatest allelic richness. Tobacco samples collected from Argentina were the most divergent subpopulation.
When Is Early Generation Selection Effective in Self‐Pollinated Crops?
Authors: Yang Rong‐Cai 
Published: October 2009

ABSTRACTDespite widespread use of early generation testing and selection (EGT) in breeding for self‐pollinated crops, its effectiveness remains largely an unresolved issue. This issue is tackled here using elaborated genetic models that enable genetic and nongenetic effects to be assessed for the effectiveness of EGT in terms of (i) the selection response at one or more early generations relative to the response to direct selection at homozygosity and (ii) the probability of retaining superior lines selected during EGT. The selection response to EGT is analyzed for a model with quadratic genetic components due to additive, dominance, additive × additive, and linkage effects in selfed populations derived from a cross between two inbreds. The response to one cycle of EGT is less than the response to direct selection and decreases with nonadditive effects, repulsion linkage and reduced heritabilities. The cumulative response to two or more cycles of EGT is greater than the response to direct selection unless there are strong nonadditive effects, strong repulsion linkage, and low heritabilities. The probability of retaining a superior line at EGT decreases with increased nonadditive effects and low heritabilities. The proportion of lines needed to minimize the risk of erroneously culling superior lines increases with increased nonadditive effects and low heritabilities. Thus, EGT should be used for populations or traits with little nonadditive effect, coupling linkage and high heritability.
Dynamics of the Evolution of the Genus of Agrostis Revealed by GISH/FISH
Authors: He Shibin , Huang Min , Huang Jing , Li Jun , Hu Yong , Zhang Lu , Zhang Chunzhen , Fei Shui‐zhang , Li Lijia 
Published: October 2009

ABSTRACTGenomic changes in related species undergoing human‐driven and natural selection are important and biologically interesting. The genus Agrostis is an ideal model for studying the evolution of plants since it has not undergone artificial selection for the past thousands of years. Fluorescence in situ hybridization (FISH) or genomic in situ hybridization (GISH) technology is an effective method for analyzing genome homology and organization, detecting genomic rearrangements, and karyotyping based on visual features. In this study, GISH was performed on two tetraploid species, A. capillaris (2n = 4x = 28, A1A1 A2A2) and A. stolonifera (2n = 4x = 28, A2A2 A3A3), using genomic DNA from a putative ancestral diploid species A. canina (2n = 2x = 14, A1A1) as a probe. Genomic in situ hybridization results revealed that the two tetraploid species underwent intergenomic translocations and genomic rearrangements and demonstrated that the A1 genome is highly homologous to the A2 genome. We discovered the phenomenon of concentric parental genome separation in the nucleus of A. stolonifera in which the two parental genomes (A2 and A3) were spatially separated with limited intermixing and were of concentric arrangements. The FISH results showed that the distribution of 45S rDNA loci varied among the three species. The results of our study suggest that substantial genomic alterations occurred during the evolution of the genus of Agrostis
DNA Polymorphisms Reveal Geographic Races of Reed Canarygrass
Authors: Casler M. D. , Phillips M. M. , Krohn A. L. 
Published: October 2009

ABSTRACTReed canarygrass (Phalaris arundinacea L.) is a cool‐season perennial with a circumglobal distribution in the northern hemisphere, native to Europe, Asia, and North America. Repeated introductions of European germplasm into North America have created confusion over the origins of reed canarygrass germplasm found in wetlands, pastures, and breeding programs. The objectives of this study were to identify sources of DNA marker variation among reed canarygrass cultivars from Europe and North America and between landraces and improved cultivars from North America. Analysis of 205 reed canarygrass plants from 15 cultivars based on 102 amplified fragment length polymorphic (AFLP) DNA markers revealed two groups of cultivars. One group consisted of three closely related but geographically diverse North American landraces that were completely separated from all other plants in only two dimensions of the AFLP incidence matrix. The complete discrimination of these plants from all European plants suggests their possible origin from native North American germplasm. These results were supported by chloroplast DNA sequence analysis, which additionally revealed separation of a potential Scandinavian cytoplasmic race from the continental European cytoplasmic race. This is the strongest evidence to date suggesting that native North American reed canarygrass germplasm has been preserved within cultivars of this species.
New and Old Soybean Cultivar Responses to Plant Density and Intercepted Light
Authors: De Bruin Jason L. , Pedersen Palle 
Published: October 2009

ABSTRACTGenetic gain for new soybean [Glycine max (L.) Merr.] cultivars is substantial, and research suggests this is partially explained by greater tolerance to increased plant densities. We conducted an experiment to determine if greater tolerance to increased plant density and more efficient use of cumulative intercepted photosynthetically active radiation (CIPAR) partially explained the yield difference of two old soybean cultivars and two new cultivars. Soybean cultivars were grown in 38‐cm spaced rows at final plant densities of 4.9, 14.8, 24.7, 34.6, and 44.5 plants m−2 for 2 yr in Ames, IA. New cultivars averaged 914 kg ha−1 and 4.9 g plant−1 greater yield compared with old cultivars averaged across years and plant densities. Yield plateaus occurred at plant densities of 23.0 plants m−2 for new cultivars and 19.9 plants m−2 for old cultivars. Each cultivar group showed a similar yield decline per plant to increased plant density. New and old cultivars showed a similar response to increasing values of CIPAR, attaining a 95% relative yield plateau at 466 MJ m−2 Soybean yield response to increased plant density and CIPAR has not changed over time, and genetic gain from new cultivars is associated with more efficient use of light.
Inheritance Characteristics of Brown Patch Resistance in Tall Fescue
Authors: Bokmeyer Jonathan M. , Bonos Stacy A. , Meyer William A. 
Published: October 2009

ABSTRACTBrown patch disease, caused by Rhizoctonia solani Kühn, is one of the most devastating fungal pathogens that occur on tall fescue [Lolium arundinaceum (Schreb.) Darbysh. = Schedonorus arundinaceus (Schreb.) Dumort]. The development of genetic resistance to brown patch would provide the most effective long term control to this disease; however, the genetic mechanism of brown patch resistance in tall fescue is not known. For this study, a diallel cross involving six parents was conducted to investigate the genetic inheritance characteristics of brown patch resistance in tall fescue. Parents and their progeny were evaluated for brown patch resistance in a field experiment conducted over two years in which the field experiment was inoculated with a single isolate of R. solani Both general combining ability (GCA) and specific combining ability (SCA) effects were significant; however, the GCA accounted for a greater proportion of the sum of squares. Moderate narrow‐sense heritability estimates [0.62 (2007) and 0.57 (2008)] were calculated from mid‐parent‐progeny regression analysis. Estimates of the minimum number of effective genes ranged from 1.0 to 3.2 depending on the parents used in the crosses. The presence of a major gene for resistance was not detected in the study. These results support the idea that brown patch resistance is quantitatively inherited.
Evaluation and Characterization of Seedling Resistances to Stem Rust Ug99 Races in Wheat–Alien Species Derivatives
Authors: Xu S. S. , Jin Y. , Klindworth D. L. , Wang R. R.‐C. , Cai X. 
Published: October 2009

ABSTRACTStem rust (caused by Puccinia graminis Pers.:Pers. f. sp. tritici Eriks. & E. Henn.), a devastating disease of wheat (Triticum aestivum L.), was effectively controlled worldwide for the past 50 yr by deployment of stem rust resistance (Sr) genes in wheat cultivars. However, a new stem rust race, TTKSK (known as Ug99 or TTKS) that emerged in eastern Africa, is a cause of concern because it has broad virulence to currently deployed Sr genes. To identify potentially new sources of effective Sr genes against Ug99, we evaluated and characterized the seedling responses to TTKSK of 62 wheat lines derived from crosses of common or durum wheat (T. turgidum L. ssp. durum) with the species Thinopyrum junceum, Th. intermedium, Th. bessarabicum, Th. elongatum, Th. ponticum, Elymus rectisetus, Aegilops caudata, and Ae. speltoides For stem rust evaluation, we first tested all lines for reactions to races TTTT and TTKSK. Lines initially showing resistance to TTKSK were then retested with eight races, including three races in the TTKS lineage (TTKSK, TTKST, and TTTSK) and five North American races (QFCS, QTHJ, RCRS, RKQQ, and TPMK). Thirty wheat–alien species derivatives had resistance to TTKSK, TTKST, and TTTSK. The comparisons of wheat–alien species derivatives and their parental lines for reactions to different races suggested that 12 partial amphiploids or amphiploids and four disomic addition lines may carry novel genes for stem rust resistance. These resistant lines represent materials for introducing stem rust resistance genes into wheat breeding.
Comparison of Weighting in Two‐Stage Analysis of Plant Breeding Trials
Authors: Möhring J. , Piepho H.‐P. 
Published: October 2009

ABSTRACTSeries of plant breeding trials are often unbalanced and have a complex genetic structure. To reduce computing cost, it is common practice to employ a two‐stage approach, where adjusted means per location are estimated and then a mixed model analysis of these adjusted means is performed. An important question is how means from the first step should be weighted in the second step. Our objective therefore was the comparison of different weighting methods in the analysis of four typical series of plant breeding trials using mixed models with fixed or random genetic effects. We used four published weighting methods and proposed three new methods. Four evaluation criteria were computed to compare methods, using one‐stage analysis as benchmark. We found that the two‐stage analysis gave acceptable results with fixed genetic effects. When genetic effects were taken as random in stage two, in three of four datasets the two‐stage analysis gave acceptable results. In both cases differences between weighting methods were small and the best weighting method depended on the dataset but not on the evaluation criteria. A two‐stage analysis without weighting also produced acceptable results, but weighting mostly performed better. In the fourth dataset the missing data pattern was informative, resulting in violation of the missing‐at‐random (MAR) assumption in one‐ and two‐stage analysis. In this case both analyses were not strictly valid.
An Alternate Wetting and Moderate Soil Drying Regime Improves Root and Shoot Growth in Rice
Authors: Zhang Hao , Xue Yaguang , Wang Zhiqin , Yang Jianchnag , Zhang Jianhua 
Published: October 2009

ABSTRACTA major challenge in rice (Oryza sativa L.) production is to achieve the dual goal of increasing food production and saving water. This study aimed to investigate if alternate wetting and drying regimes could improve root and shoot growth and consequently increase grain yield and water use efficiency (WUE). Two rice varieties were field‐grown at Yangzhou, China in 2005 and 2006. Three irrigation regimes, alternate wetting and moderate soil drying (WMD, re‐watered when soil water potential reached −15 kPa at 15–20 cm depth), alternate wetting and severe soil drying (WSD, re‐watered when soil water potential reached −30 kPa), and a conventional irrigation (CI, continuously flooded), were imposed during the whole growing season. Compared with the CI, the WMD regime significantly increased, whereas the WSD regime reduced, root oxidation activity, cytokinin concentrations in roots and shoots, leaf photosynthetic rate, and activities of key enzymes involved in sucrose‐to‐starch conversion in grains. Grain yield of the two varieties, on the average, was increased by 11% under the WMD regime, and was reduced by 32% under the WSD regime when compared with that under the CI regime. Averaged WUE of the two varieties was increased by 55% under the WMD regime and 36% under the WSD regime. We conclude that a moderate wetting and drying regime can enhance root growth which benefits other physiological processes and result in higher grain yield and WUE.
Meta‐Analysis of QTL Associated with Fusarium Head Blight Resistance in Wheat
Authors: Liu Shuyu , Hall Marla D. , Griffey Carl A. , McKendry Anne L. 
Published: October 2009

ABSTRACTQuantitative trait loci (QTL) associated with resistance to Fusarium head blight (FHB), which is mainly caused by Fusarium graminearum Schwabe [telomorph: Gibberella zeae Schw. (Petch)], have been identified in wheat (Triticum aestivum L.) from different countries. Due to the differences of genetic backgrounds and analysis methods, the linked marker and significance levels of QTL are not consistent across studies. Such discrepancies make it difficult to select diagnostic flanking markers. Meta‐analysis has been used to estimate the confidence intervals (CIs) of QTL in plant and animal genomes. The objective of this study was to cluster 249 FHB resistance QTL identified in 46 unique lines from 45 studies based on the estimated QTL CI by meta‐analysis. A total of 209 QTL conditioning FHB resistance type I, II, III and IV were classified into 43 clusters on 21 chromosomes. Among them, 119 QTL were significant and 116 QTL explained more than 10% of phenotypic variation. There are 19 confirmed QTL located on chromosomes 3A, 5A, 7A, 1B, 3BS, 5B, 6B, and 2D. The results provide chromosome locations and linked markers for overlapping and unique QTL. Markers flanking QTL clusters can be used to pyramid diverse QTL more efficiently through marker‐assisted breeding.
Water Use by Five Warm‐Season Legumes in the Southern Great Plains
Authors: Rao Srinivas C. , Northup Brian K. 
Published: October 2009

ABSTRACTGrowing warm‐season legumes during fallow periods associated with traditional continuous systems of winter wheat (Triticum aestivum L.) in the southern Great Plains (SGP) can provide supplemental forage, biological N, and protection from soil erosion, provided the legumes can tolerate drought stress and not deplete the available water in the soil profile. Our objective was to quantify water use by five species of pulse legumes {pigeon pea [(Cajanus Cajan (L.) Millsp.) cv. GA‐2], guar [Cyamopsis tetragonobloba (L.) Taub., cv. Kinman], cowpea [Vigna unguiculata (L.) Walp., cv. Chinese red], mung bean [Vigna radiate (L.) Wilcz., cv. Berkins], and soybean [Glycine max (L.) Merr., cv. Hutcheson (the control)]}. Seeds were inoculated and planted after wheat harvest in mid‐June 2003 through 2006. The amount of water in the upper 65 cm of the soil profile was measured on nine dates [from 45 d before planting legumes to 195 d since planting (DSP)]. Significant (P < 0.01) differences in soil water were recorded among treatments, dates, and years. Differences in soil water among fallow, cowpea, and mung bean were less following the 2003 and 2004 summer seasons and most noticeable in 2005 and 2006. Mung bean, guar, soybean, and pigeon pea used the greatest amounts of water in 2005, the wettest season, while cowpea and mung bean used the least in 2003. Mung bean, cowpea, and guar generated smaller water deficits and used less soil water, in three of four years, and could be effective in wheat‐summer legume rotations in the SGP.