Classifying genotypic data from plant breeding trials: a preliminary investigation using repeated checks

Summary Several subjective choices must be made when classifying genotypes based on data from plant breeding trials. One choice involves the method used to weight the contribution each environment makes to the classification. A second involves the use of either genotype-means for each environment or genotypevalues for each block, i.e., considering each block to be a different environment. Another involves whether environments (or blocks) in which genotypes are nonsignificantly different should be included or excluded from such classifications. An alternative to the use of raw or standardized data, is proposed in which each environment is weighted by a discrimination index (DI) that is based on the concept of repeatability. In this study the effect of three weighting methods (raw, standardized and DI), the choice of using environments or blocks, and the choice of including or excluding environments or blocks in which genotypic effects were not significant, were considered in factorial combination to give 12 options. A data set comprised of five check cultivars each repeated six times in each of three blocks at six environments was used. The effect of these options on the ability of a hierarchical clustering technique to correctly classify the repeats into five groups, each consisting of all the six repeats of a particular check cultivar, was investigated. It was found that the DI weighting method generally led to better recovery of the known structure. Using block data rather than environmental data also improved structure recovery for each of the three weighting methods. The exclusive use of environments in which genotypic effects were significant decreased structure recovery while the contrary generally occurred for blocks. The best structure recovery was obtained from the DI weighting applied to blocks (whether genotypes were significant or not).     

Gas exchange characteristics, metabolic rate and water loss of the Heelwalker, Karoophasma biedouwensis (Mantophasmatodea: Austrophasmatidae)

This study presents the first physiological information for a member of the wingless Mantophasmatodea, or Heelwalkers. This species shows cyclic gas exchange with no evidence of a Flutter period (more typical of discontinuous gas exchange in insects) and no indication that the spiracles are fully occluded during quiescent metabolism. Standard metabolic rate at 20 degrees C was 21.32+/-2.73 microl CO(2)h(-1) (mean+/-S.E.), with a Q(10) (10-25 degrees C) of 1.7. Increases in V()CO(2) associated with variation in mass and with trial temperature were modulated by an increase in burst period volume and a decline in cycle frequency. Total water loss rate, determined by infrared gas analysis, was 0.876+/-0.08 mg H(2)Oh(-1) (range 0.602-1.577, n=11) whilst cuticular water loss rate, estimated by linear regression of total water loss rate and metabolic rate, was 0.618+/-0.09 mg H(2)Oh(-1) (range 0.341-1.363, n=11). Respiratory water loss rate was therefore no more than 29% of the total rate of water loss. Both total water loss rate and estimated cuticular water loss rate were significantly repeatable, with intraclass correlation coefficients of 0.745 and 0.553, respectively.     

Offspring sex ratio in the sequentially polygamous Penduline Tit Remiz pendulinus

Despite the growing literature on facultative sex-ratio adjustment in chromosomal sex-determining vertebrate taxa (birds, mammals), the consistency of results is often low between studies and species. Here, we investigate the primary and secondary offspring sex ratio of a small passerine bird, the Eurasian Penduline Tit (Remiz pendulinus) in three consecutive years. This species has a uniquely diverse breeding system, in which the male (and/or the female) abandons the nest during egg-laying, and starts a new breeding attempt. This allowed us to test (1) whether patterns of parental care, i.e., male-only care, female-only care or biparental desertion, influence offspring sex ratio, and (2) whether the offspring sex ratio is repeatable between successive clutches of males and females. Using molecular markers to sex 497 offspring in 176 broods, we show that (1) offspring sex ratio does not depend on which parent provides care, and (2) the offspring sex ratio is not repeatable between clutches of a given individual. The overall primary and secondary offspring sex ratio at a population level is not different from parity (54 ± 6% males, and 50 ± 3% (mean ± SE), respectively). We suggest that ecological and phenotypic factors, rather than individual traits of parents, may influence offspring’s sex, and conclude that there is currently no evidence for a facultative adjustment of offspring sex ratio in the Penduline Tit.     

Influence of oocyte donor on in vitro embryo production in buffalo

The aim of this research was to estimate the variability between buffalo as oocyte donors. In Experiment 1, reproductive variables were retrospectively analyzed in buffalo (n = 40) that underwent repeated ovum pick up (OPU), over 16 puncture sessions (PS). The follicular recruitment among individuals and the relationship between follicular population and oocyte production were evaluated. In Experiment 2, eight buffalo underwent OPU for 28 PS and the oocytes were processed separately to correlate follicular and oocyte population at the first PS to blastocyst (BL) production. In Experiment 1, the average number of total follicles (TFL), small follicles (SFL), cumulus-oocyte complexes (COC) and Grade A + B COC recorded in each 4-PS period had great repeatability (r = 0.52, 0.54, 0.60 and 0.57, respectively). The average number of Grade A + B COC recovered during the subsequent 15 PS was positively correlated with the first PS number of TFL (r = 0.60; P < 0.001), SFL (r = 0.68; P < 0.001), COC (r = 0.48; P < 0.01) and Grade A + B COC (r = 0.40; P < 0.05). In Experiment 2, a large variability among animals was observed in blastocyst yields. When animals were grouped according to the BL yield, the greatest BL yield group had a greater (P < 0.05) number of TFL (8.3 ± 0.9 compared with 5.6 ± 0.7) and SFL (7.3 ± 0.3 compared with 3.8 ± 0.7) at the first PS than the lesser BL yield group. The average number of BL produced over the subsequent sessions was correlated with the number of TFL (r = 0.80; P < 0.05) and COC (r = 0.76; P < 0.05) observed at the first PS. These results demonstrated a donor influence on the oocyte and BL production, suggesting a preliminary screening to select the donors with greater potential.     

Gone with the wind and the stream: Dispersal in the invasive species Ailanthus altissima

Dispersal is a key process in plant invasions and is strongly related to diaspore morphology. Often, dispersal comprises more than one step, and morphologies adapted to a primary dispersal mechanism can aid or detract from a secondary one. The aim of this work was to assess the relationship between primary wind dispersal and secondary water dispersal in Ailanthus altissima, an invasive tree species. Wind and water dispersal potential and their association with the morphological characteristics of samaras were assessed under controlled conditions to ensure the repeatability of the measurements. We found a direct positive relationship between primary wind and secondary water dispersal in A. altissima. The main morphological characteristics of the samara that affected the success of the two types of dispersal were side perimeter and mass. However, a possibility of dispersal specialisation exists, as one morphological characteristic (samara width) affects wind dispersal negatively but water dispersal positively, and dispersal potential and samara morphology have been shown to differ across individuals.     

Estimators of repeatability

Summary Analysis of variance and principal components methods have been suggested for estimating repeatability. In this study, six estimation procedures are compared: ANOVA, principal components based on the sample covariance matrix and also on the sample correlation matrix, a related multivariate method (structural analysis) based on the sample covariance matrix and also on the sample correlation matrix, and maximum likelihood estimation. A simulation study indicates that when the standard linear model assumptions are met, the estimators are quite similar except when the repeatability is small. Overall, maximum likelihood appears the preferred method. If the assumption of equal variance is relaxed, the methods based on the sample correlation matrix perform better although others are surprisingly robust. The structural analysis method (with sample correlation matrix) appears to be best.Paper number 776 from the Department of Meat and Animal Science, University of Wisconsin-Madison.     

Repeatability: Its role in evolutionary studies of mating behavior

Summary Repeatability, a concept derived from quantitative genetics theory, is a statistic that describes the degree to which variation within individuals contributes to total variation in a population. Its usual application has been to set an upper limit on heritability but it may also be useful for studies of stereotypy of behavior. The repeatability of the production of male mating signals gives information both about whether males differ sufficiently for selection to act and whether the differences could be appreciably heritable. Measures of the repeatability of female mating preferences will provide data that can describe the preference functions used in mathematical models of the evolution of sexually selected traits, as well as putting an upper bound on the heritability of preferences. A survey of the few measures in the literature shows that the repeatability of male signal production varies substantially (range 0.21–0.85) and does not necessarily reflect heritability. The repeatabilities of female preferences have not been published previously: for the response to conspecific pheromones by female flour beetles (Tribolium castaneum), my best estimate is zero. Measuring the repeatability of other traits such as parental care and foraging behavior may also lead to insights about selection on and the evolution of these traits.     

Ultrasound does not provide reliable results for the measurement of the patellar tendon cross sectional area

PurposeThis study examined the reliability of patellar tendon cross sectional area (CSA) measurement using brightness mode ultrasonography.MethodsThe patellar tendon CSA of fourteen participants was examined on two different days and at three different positions (proximal, median and distal). Five trials per day were conducted in each position, replacing the ultrasound probe on every trial. The images were examined by three different and equally experienced observers. We compared the mean of the five trials in each position to examine the day, observer and position effect. Further, Bland and Altman plots, root mean square (RMS) differences and intraclass correlation coefficients (ICC) were calculated.ResultsThere was a significant (p < 0.05) day, observer and position effect on the CSA, while the average ICC was 0.592. The Bland and Altman plots showed that differences between conditions or groups, should be in average lower than 37% or higher than 55% of the patellar tendon CSA to be important for clinical or intervention studies.ConclusionOur findings show low reliability of the method, which resulted from the low clarity and unclear visibility of tissue boundaries in the ultrasound images. Therefore, the measurement of the CSA of the patellar tendon using ultrasound does not provide accurate and reliable results.     

Heritability of fresh fruit bunch yield and its components in the oil palm (Elaeis guineensis,Jacq.)

Summary Single-plant heritability estimates of 38.9%, 31.5% and 42.3% were obtained for number of bunches (NB), fresh fruit bunch yield (FFB) and mean bunch weight (MBW) respectively. Hybrid (family) mean heritability estimates for these traits were 88.9%, 90.5% and 96% respectively. Repeatability estimates for these traits were 33%, 11% and 8% for NB, FFB and MBW respectively. Evaluation of hybrid family mean for yield components appears feasible at the third or fourth year of data collection. Phenotypic and genotypic correlations between NB and FFB were 0.80 and 0.61 respectively; between NB and MBW, –0.41 and –0.16 respectively; and between FFB and MBW, 0.66 and 0.60 respectively. The hypothesis that increased FFB can be obtained by hybridization between parents with high NB and heavy MBW is supported by this correlation set.