Novel throughput phenotyping platforms in plant genetic studies

Unraveling the genetic basis of complex traits in plants is limited by the lack of appropriate phenotyping platforms that enable high-throughput screening of many genotypes in multilocation field trials. Near-infrared spectroscopy on agricultural harvesters and spectral reflectance of plant canopies have recently been reported as promising components of novel phenotyping platforms. Understanding the genetic basis of complex traits is now within reach with the use of these new techniques.     

Linkage disequilibrium in two European F<Subscript>2</Subscript> flint maize populations under modified recurrent full-sib selection

According to quantitative genetic theory, linkage disequilibrium (LD) can hamper the short- and long-term selection response in recurrent selection (RS) programs. We analyzed LD in two European flint maize populations, KW1265 × D146 (A × B) and D145 × KW1292 (C × D), under modified recurrent full-sib selection. Our objectives were to investigate (1) the decay of initial parental LD present in F₂ populations by three generations of intermating, (2) the generation of new LD in four (A × B) and seven (C × D) selection cycles, and (3) the relationship between LD changes and estimates of the additive genetic variance. We analyzed the F₂ and the intermated populations as well as all selection cycles with 104 (A × B) and 101 (C × D) simple sequence repeat (SSR) markers with a uniform coverage of the entire maize genome. The LD coefficient D and the composite LD measure Δ were estimated and significance tests for LD were performed. LD was reduced by intermating as expected from theory. A directional generation of negative LD between favorable alleles could not be observed during the selection cycles. However, considerable undirectional changes in D were observed, which we attributed to genetic sampling due to the finite population size used for recombination. Consequently, a long-term reduction of the additive genetic variance due to negative LD was not observed. Our experimental results support the hypothesis that in practical RS programs with maize, LD generated by selection is not a limiting factor for obtaining a high selection response.     

Hybrid maize breeding with doubled haploids: II. Optimum type and number of testers in two-stage selection for general combining ability

Optimum allocation of test resources is of crucial importance for the efficiency of breeding programs. Our objectives were to (1) determine the optimum allocation of the number of lines, test locations, as well as number and type of testers in hybrid maize breeding using doubled haploids with two breeding strategies for improvement of general combining ability (GCA), (2) compare the maximum selection gain (ΔG) achievable under both strategies, and (3) give recommendations for the optimum implementation of doubled haploids in commercial hybrid maize breeding. We calculated ΔG by numerical integration for two two-stage selection strategies with evaluation of (1) testcross performance in both stages (BS1) or (2) line per se performance in the first stage followed by testcross performance in the second stage (BS2). Different assumptions were made regarding the budget, variance components (VCs), and the correlation between line per se performance and GCA. Selection gain for GCA increased with a broader genetic base of the tester. Hence, testers combining a large number of divergent lines are advantageous. However, in applied breeding programs, the use of single- or double-cross testers in the first and inbred testers in the second selection stage may be a good compromise between theoretical and practical requirements. With a correlation between line per se performance and GCA of 0.50, ΔG for BS1 is about 5% higher than for BS2, if an economic weight of line per se performance is neglected. With increasing economic weight of line per se performance, relative efficiency of BS2 increased rapidly resulting in a superiority of BS2 over BS1 already for an economic weight for line per se performance larger than 0.1. Considering the importance of an economic seed production, an economic weight larger than 0.1 seems realistic indicating the necessity of separate breeding strategies for seed and pollen parent heterotic groups. C. Friedrich H. Longin and H. Friedrich Utz have contributed equally to this work.     

Structure and characterization of a novel chicken biotin-binding protein A (BBP-A)

Background  

The chicken genome contains a BBP-A gene showing similar characteristics to avidin family genes. In a previous study we reported that the BBP-A gene may encode a biotin-binding protein due to the high sequence similarity with chicken avidin, especially at regions encoding residues known to be located at the ligand-binding site of avidin.     

Exploiting Nonlinear Recurrence and Fractal Scaling Properties for Voice Disorder Detection

Background  

Voice disorders affect patients profoundly, and acoustic tools can potentially measure voice function objectively. Disordered sustained vowels exhibit wide-ranging phenomena, from nearly periodic to highly complex, aperiodic vibrations, and increased "breathiness". Modelling and surrogate data studies have shown significant nonlinear and non-Gaussian random properties in these sounds. Nonetheless, existing tools are limited to analysing voices displaying near periodicity, and do not account for this inherent biophysical nonlinearity and non-Gaussian randomness, often using linear signal processing methods insensitive to these properties. They do not directly measure the two main biophysical symptoms of disorder: complex nonlinear aperiodicity, and turbulent, aeroacoustic, non-Gaussian randomness. Often these tools cannot be applied to more severe disordered voices, limiting their clinical usefulness.     

The role of epistasis in the manifestation of heterosis: a systems-oriented approach

Heterosis is widely used in breeding, but the genetic basis of this biological phenomenon has not been elucidated. We postulate that additive and dominance genetic effects as well as two-locus interactions estimated in classical QTL analyses are not sufficient for quantifying the contributions of QTL to heterosis. A general theoretical framework for determining the contributions of different types of genetic effects to heterosis was developed. Additive x additive epistatic interactions of individual loci with the entire genetic background were identified as a major component of midparent heterosis. On the basis of these findings we defined a new type of heterotic effect denoted as augmented dominance effect di* that comprises the dominance effect at each QTL minus half the sum of additive x additive interactions with all other QTL. We demonstrate that genotypic expectations of QTL effects obtained from analyses with the design III using testcrosses of recombinant inbred lines and composite-interval mapping precisely equal genotypic expectations of midparent heterosis, thus identifying genomic regions relevant for expression of heterosis. The theory for QTL mapping of multiple traits is extended to the simultaneous mapping of newly defined genetic effects to improve the power of QTL detection and distinguish between dominance and overdominance.     

QTL mapping for resistance against the European corn borer (Ostrinia nubilalis H.) in early maturing European dent germplasm

The European corn borer (ECB, Ostrinia nubilalis Hübner) is a major pest of maize in Central Europe. We mapped and characterized quantitative trait loci (QTLs) involved in resistance of maize against ECB damage, compared them with QTLs for agronomic traits, and evaluated the usefulness of marker-assisted selection (MAS) for improving ECB resistance in early maturing European maize germplasm. A total 226 F₃ families from the cross D06 (resistant) × D408 (susceptible), together with 93 RFLP and two SSR markers were used for the QTL analyses. For each F₃ family we measured the length of tunnels produced by larval stalk mining (TL), stalk damage ratings (SDR), and relative grain yield (RGY) in field experiments, with two replications in two environments in 1 year. The agronomic traits comprised grain yield under insecticide protection (GYP) and manual ECB larval infestation (GYI), the date of anthesis (ANT), and the in vitro digestibility of organic matter (IVDOM) of stover. Estimates of genotypic variance (σ² _g) were highly significant for all traits. Six QTLs for TL and five QTLs for SDR were detected, explaining about 50.0% of σ² _g. Most QTLs showed additive gene action for TL and dominance for SDR. No QTL was found for RGY. The number of QTLs detected for the agronomic traits ranged from two for GYI to 12 for ANT, explaining 12.5 to 57.3% of σ² _g, respectively. Only a single QTL was in common between the two resistance traits, as expected from the moderate trait correlation and the moderate proportions of σ² _g explained. Based on these results, MAS for improving ECB resistance can be competitive when cost-effective PCR-based marker systems are applied. However, it remains to be established whether the putative QTL regions for ECB resistance detected in the population D06 × D408 are consistent across other early maturing European maize germplasms. Received: 20 December 1999 / Accepted: 6 June 2000     

Mean, genetic variance, and usefulness of selfing progenies from intra- and inter-pool crosses in faba beans (Vicia faba L.) and their prediction from parental parameters

 Determining the genetic potential of a base population from the properties of their parental lines would improve the efficiency of a breeding program. In the present study, we investigated whether the means of the parents and the genetic distance determined from RAPD data (GD) or multivariate analysis (Mahalanobis D²), mid-parent heterosis (MPH), and the absolute difference between means of the parents (∣P₁−P₂∣) can be used for predicting the means and genetic variances (σ^² _g ) of F_3:4 lines derived from different crosses in faba beans. The material comprised 18 intra- and 18 inter-pool crosses among lines from the Minor, Major, and Mediterranean germplasm pools. Fifty F_3:4 lines from each cross were evaluated for days to anthesis, plant height, seeds per plant, and seed yield in German (GE) and Mediterranean (ME) environments. GD estimates between parent lines ranged from 0.38 to 0.58, while D² ranged from 45.5 to 134.7. Correlations between means of the parents and F_3:4 lines were highly significant for most traits. Estimates of σ² _g for all traits showed non-significant correlations with MPH, GD, D². In one ME, ∣P₁−P₂∣ had significant associations with σ^² _g for seed yield and days to anthesis. The predicted usefulness of crosses, defined as the sum of the population mean and selection responses, was most closely associated with the means of F_3:4 lines. We conclude from this study that the means of F_3:4 lines can be predicted from the means of the parents, whereas the prediction of genetic variance is still an unsolved problem Received: 12 December 1997 / Accepted: 13 July 1998     

RFLP analyses of early-maturing European maize germ plasm

Summary Thirty inbred lines representing a wide range of early-maturing European elite germ plasm of maize (Zea mays L.) were assayed for RFLPs using 203 clone-enzyme combinations (106 DNA clones with restriction enzymes EcoR1 and HindIII). The genetic materials comprised 14 flint, 12 dent, and 4 lines of miscellaneous origin. Objectives were to (1) characterize the genetic diversity for RFLPs in these materials, (2) compare the level of genetic diversity found within and between the flint and the dent heterotic groups, and (3) examine the usefulness of RFLPs for assigning inbreds to heterotic groups. All but two DNA clones yielded polymorphism with at least one restriction enzyme. A total of 82 and 121 clone-enzyme combinations gave single-banded and multiple-banded RFLP patterns, respectively, with an average of 3.9 and 7.7 RFLP patterns per clone-enzyme combination across all 30 inbreds, respectively. Genetic similarity (GS) between lines, estimated from RFLP data as Dice's similarity coefficient, showed considerable variation (0.32 to 0.58) among unrelated inbreds. The mean GS for line combinations of type flint x dent (0.41) was significantly smaller than for unrelated flint lines (0.46) and dent lines (0.46), but there was considerable variation in GS estimates of individual line combinations within each group. Cluster and principal coordinate analyses based on GS values resulted in separate groupings of flint and dent lines in accordance with phylogenetic information. Positioning of lines of miscellaneous origin was generally consistent with expectations based on known breeding behavior and pedigrees. Results from this study corroborated that RFLP data can be used for assigning inbreds to heterotic groups and revealing pedigree relationships among inbreds.