Phenotypic selection

The core of Darwin’s theory includes two ideas about natural selection: that it explains the evolution of the organisms’ characteristics and that it pushes these characteristics towards an optimum of organization and design. While the first idea is formalised in Population Genetics models, only informal descriptions support the second one. Moreover, Population Genetics models focus on loose characteristics and cannot explain the coordination among their functions, nor do they suggest that natural selection leads to the optimization of the organism design. Facing this bicephalous and at first sight contradictory situation, Grafen’s Formal Darwinism Project provides a mathematical foundations for the argument of design, through an optimization model, and shows that the results of the optimization are coherent with these from Population Genetics. It therefore formally demonstrates that natural selection, modifying genetic frequencies, optimizes the individual characteristics and leads them to complex designs: in other words, that Darwin was right in claiming that the ‘struggle for life’ is the source of the variety and the complexity of the biological world. However, Grafen’s model is not universally accepted: additionally to the critics around its hypothesis and conclusions that can be found in the literature, others can be advanced regarding the lack of precise definitions of some of the concepts used. Nevertheless, his program, irrespective of whether it will prove adequate or not, contributes to the reflection around central subjects within the Philosophy of Biology.

Bayesian analysis via Gibbs sampling, restricted maximum likelihood (REML), and Method R were used to estimate variance components for several models of simulated data. Four simulated data sets that included direct genetic effects and different combinations of maternal, permanent environmental, and dominance effects were used. Parents were selected randomly, on phenotype across or within contemporary groups, or on BLUP of genetic value. Estimates by Bayesian analysis and REML were always empirically unbiased in large data sets. Estimates by Method R were biased only with phenotypic selection across contemporary groups; estimates of the additive variance were biased upward, and all the other estimates were biased downward. No empirical bias was observed for Method R under selection within contemporary groups or in data without contemporary group effects. The bias of Method R estimates in small data sets was evaluated using a simple direct additive model. Method R gave biased estimate...

Molecular markers (RAPD, AFLP and microsatellites) were used to generate a linkage map and to identify QTLs associated to witches' broom (Crinipellis perniciosa) resistance in cacao (Theobroma cacao), using 82 individuals of an F2 population derived from the clones ICS-1 (susceptible) and Scavina-6 (resistant). Fifteen evaluations of the number of brooms have been carried out in six years (1997–2002). In order to increase the precision and accuracy in the measures of resistance, each F2 plant was cloned in three replications in a randomized block design with single-tree plots and evaluated over 2 years. Three hundred and forty-two markers were obtained, being 33 microsatellites, 77 AFLPs and 232 RAPDs. The distribution of the number of brooms in the F2 population was skewed to resistance, suggesting the involvement of major genes controlling resistance and the repeatability estimated for resistance was 44%. A strong putative QTL was detected as being related to witches' broom resistance. Associated to this QTL, the microsatellite mTcCIR35 explained 35.5% of the phenotypic variation in resistance. This marker is being used for marker-assisted selection in Scavina-6 progenies, including those selected in private plantations, as an auxiliary tool to the phenotypic selection.

Application of Marker-Assisted Selection in Crop Breed- ing. Muhammad Azrai. DNA-based technology has dramat- ically enhanced the efficiency of plant breeding, especially when selections are to be done under unfavourable condi- tions. Although significant strides have been made in crop improvement trough phenotypic selections for ergonomic- ally important traits, this often encounters considerable diffi- culties, particularly those posed by genotype x environment interactions. Besides testing procedure may be many times difficult, unreliable or expensive due to the nature of the target traits (e.g. abiotic and biotic stresses) or the target environment. The most widespread use of Marker Assisted Selection (MAS) to date is to assist backcrossing of major gene already proven elite cultivars. If individual genes or Quantitative Trait Loci (QTL) significantly influencing spe- cific target traits can be identified based on their linkage to molecular markers, the efficiency of incorporati...

The relative strength of different types of directional selection has seldom been compared directly in natural populations. A recent meta-analysis of phenotypic selection studies in natural populations suggested that directional sexual selection may be stronger in magnitude than directional natural selection, although this pattern may have partly been confounded by the different time scales over which selection was estimated. Knowledge about the strength of different types of selection is of general interest for understanding how selective forces affect adaptive population divergence and how they may influence speciation. We studied divergent selection on morphology in parapatric, natural damselfly (Calopteryx splendens) populations. Sexual selection was stronger than natural selection measured on the same traits, irrespective of the time scale over which sexual selection was measured. Visualization of the fitness surfaces indicated that population divergence in overall morphology i...

Background. In order to properly direct the breeding work of cultivars of a given potato earliness group it is necessary to know the range of variability and relationships between their characteristics, both in a given
year and between years. Therefore, the purpose of this study was to determine the structure of the variability of the quantitative traits of mid-early potato cultivars, which would facilitate in selecting cultivars with the highest stability of the desired characteristics.
Material and methods. The analysis was based on a strict field experiment carried out in the years 2010-2012 at the Experimental Station in Uhnin (Lublin Province), (51°34' N; 23°02' E), on lessive soil, slightly acidic. The experiment was performed in randomized blocks in three repetitions. Eighteen potato cultivars were studied, four very early cultivars and six early cultivars. Cultivation techniques were conducted in accordance with the principles of Good Agricultural Practice and conservation measures in line with the recommendations of the IOR-PIB. Organic fertilizers and minerals for potato were at the same level each
year (20 Mg·ha-1 white mustard for ploughing, 90 kg N, 39.3 kg P, and 112.0 kg K·ha-1.
Results. The dominant role in the variability of tuber yield and its structure was played by the interaction between the cultivar and the environment (3.2%-92.7%). Genotype accounted for 2.9%-27.9% of variance in the total variance of the studied characteristics, and the test conditions for 3.7%-73.9%. Interaction between the genotype and the environment was the most conducive to: total yield, commercial yield, yield of seed potatoes, and proportion of tuber mass of <4, 5-6 and >6 cm in diameter. It did not, however, significantly affect the number of shoots per plant. The most stable characteristic of the activity of the tested cultivars was mass proportion of commercial tubers, and the most variable one was their yield. Conclusion. Analysis of the main components identified five groups of cultivars with specific characteristics that can be used in decision-making in the breeding of new cultivars.

The advent of molecular markers as a tool to aid selection has provided plant breeders with the opportunity to rapidly deliver superior genetic solutions to problems in agricultural production systems. However, a major constraint to the implementation of marker-assisted selection (MAS) in pragmatic breeding programs in the past has been the perceived high relative cost of MAS compared to conventional phenotypic selection. In this paper, computer simulation was used to design a genetically effective and economically efficient marker-assisted breeding strategy aimed at a specific outcome. Under investigation was a strategy involving the integration of both restricted backcrossing and doubled haploid (DH) technology. The point at which molecular markers are applied in a selection strategy can be critical to the effectiveness and cost efficiency of that strategy. The application of molecular markers was considered at three phases in the strategy: allele enrichment in the BC1F1 population, gene selection at the haploid stage and the selection for recurrent parent background of DHs prior to field testing. Overall, incorporating MAS at all three stages was the most effective, in terms of delivering a high frequency of desired outcomes and at combining the selected favourable rust resistance, end use quality and grain yield alleles. However, when costs were included in the model the combination of MAS at the BC1F1 and haploid stage was identified as the optimal strategy. A detailed economic analysis showed that incorporation of marker selection at these two stages not only increased genetic gain over the phenotypic alternative but actually reduced the over all cost by 40%.