Blib is a multi-module simulation platform for genetics studies and intelligent breeding

Previous studies of immunity in wild populations have focused primarily on genes of the major histocompatibility complex (MHC); however, studies of model species have identified additional immune-related genes that also affect fitness. In this study, we sequenced five non-MHC immune genes in six greater prairie-chicken (Tympanuchus cupido) populations that have experienced varying degrees of genetic drift as a consequence of population bottlenecks and fragmentation. We compared patterns of geographic variation at the immune genes with six neutral microsatellite markers to investigate the relative effects of selection and genetic drift. Global F(ST) outlier tests identified positive selection on just one of five immune genes (IAP-1) in one population. In contrast, at other immune genes, standardized G'(ST) values were lower than those at microsatellites for a majority of pairwise population comparisons, consistent with balancing selection or with species-wide positive or purifying selection resulting in similar haplotype frequencies across populations. The effects of genetic drift were also evident as summary statistics (e.g., Tajima's D) did not differ from neutrality for the majority of cases, and immune gene diversity (number of haplotypes per gene) was correlated positively with population size. In summary, we found that both genetic drift and selection shaped variation at the five immune genes, and the strength and type of selection varied among genes. Our results caution that neutral forces, such as drift, can make it difficult to detect current selection on genes.

Neutral genetic drift is an evolutionary mechanism which can strongly aid the escape from local optima. This makes neutral genetic drift an increasingly important property of Evolutionary Computational methods as more challenging applications are approached. Cartesian Genetic Programming (CGP) is a Genetic Programming technique which contains explicit, as well as the more common implicit, genetic redundancy. As explicit genetic redundancy is easily identified and manipulated it represents a useful tool for investigating neutral genetic drift. The contributions of this paper are as follows. Firstly the paper presents a substantial evaluation of the role and benefits of neutral genetic drift in CGP. Here it is shown that the benefits of explicit genetic redundancy are additive to the benefits of implicit genetic redundancy. This is significant as it indicates that that levels of implicit genetic redundancy present in other Evolutionary Computational methods may be insufficient to fully utilise neutral genetic drift. It is also shown than the identification and manipulation of explicit genetic redundancy is far easier than for implicit genetic redundancy. This is significant as it makes the investigations here possible and leads to new possibilities for allowing more effective use of neutral genetic drift. This is the case not only for CGP, but many other Evolutionary Computational methods which contain explicit genetic redundancy. Finally, it is also shown that neutral genetic drift has additional benefits other than aiding the escape from local optima.

Rice chromosome segment substitution lines (CSSLs) are ideal for creating natural variation and dissecting complex quantitative traits. In addition, it builds a bridge for molecular breeding and accurate identification of quantitative trait loci (QTLs). In this study, to construct an indica rice library of single-segment substitution lines (SSSLs) spanning the whole genome, a rice CSSL-Z691 carrying four substitution segments (4.07 Mb of average length) was identified by marker-assisted selection (MAS) from indica restorer line "Jinhui35" in the "Xihui18" genetic background. Compared with large panicle type Xihui18, seed setting ratio, grain width, and 1000-grain weight increased in Z691. In contrast, the number of primary branches, spikelet number per panicle, grain number per panicle, grain length, rate of length to width, and yield per plant decreased in Z691. Then, 11 QTLs were identified in the secondary F2 population from Xihui18/Z691. Again, four QTLs (qGW6, qGL4, qRLW4, and qGWT4) were validated by three SSSLs (S1-S3) developed in F3. In addition, 11 new QTLs were detected by the three SSSLs that were not identified in the F2 population. Moreover, the different QTLs in D1-D3 showed various genetic models. Some QTLs, e.g., qGWT6 (a = 0.96 g) and qGWT7 (a = -0.29 g), displayed independent inheritance, while others exhibited various epistatic interactions. Thus, it is vital to identify different QTLs and their genetic models. Resolving the epistasis effects among different QTLs is crucial for screening QTLs for breeding by design. Finally, qGL4 and qGW6 were fine-mapped to 160- and 240-kb intervals on chromosomes 4 and 6, and two candidate genes were determined by DNA sequencing. These results provide valuable genetic and breeding materials for cloning qGL4 and qGW6 and for future molecular breeding by design.

Habitat fragmentation may disrupt original patterns of gene flow and lead to drift-induced differentiation among local population units. Top predators such as the jaguar may be particularly susceptible to this effect, given their low population densities, leading to small effective sizes in local fragments. On the other hand, the jaguar's high dispersal capabilities and relatively long generation time might counteract this process, slowing the effect of drift on local populations over the time frame of decades or centuries. In this study, we have addressed this issue by investigating the genetic structure of jaguars in a recently fragmented Atlantic Forest region, aiming to test whether loss of diversity and differentiation among local populations are detectable, and whether they can be attributed to the recent effect of drift. We used 13 microsatellite loci to characterize the genetic diversity present in four remnant populations, and observed marked differentiation among them, with evidence of recent allelic loss in local areas. Although some migrant and admixed individuals were identified, our results indicate that recent large-scale habitat removal and fragmentation among these areas has been sufficiently strong to promote differentiation induced by drift and loss of alleles at each site. Low estimated effective sizes supported the inference that genetic drift could have caused this effect within a short time frame. These results indicate that jaguars' ability to effectively disperse across the human-dominated landscapes that separate the fragments is currently very limited, and that each fragment contains a small, isolated population that is already suffering from the effects of genetic drift.

Regression interval mapping and multiple interval mapping are compared with regard to mapping linked quantitative trait loci (QTL) in inbred-line cross experiments. For that purpose, a simulation study was performed using genetic models with two linked QTL. Data were simulated for F(2) populations of different sizes and with all QTL and marker alleles fixed for alternative alleles in the parental lines. The criteria for comparison are power of QTL identification and the accuracy of the QTL position and effect estimates. Further, the estimates of the relative QTL variance are assessed. There are distinct differences in the QTL position estimates between the two methods. Multiple interval mapping tends to be more powerful as compared to regression interval mapping. Multiple interval mapping further leads to more accurate QTL position and QTL effect estimates. The superiority increased with wider marker intervals and larger population sizes. If QTL are in repulsion, the differences between the two methods are very pronounced. For both methods, the reduction of the marker interval size from 10 to 5 cM increases power and greatly improves QTL parameter estimates. This contrasts with findings in the literature for single QTL scenarios, where a marker density of 10 cM is generally considered as sufficient. The use of standard (asymptotic) statistical theory for the computation of the standard errors of the QTL position and effect estimates proves to give much too optimistic standard errors for regression interval mapping as well as for multiple interval mapping.

The interactions of evolutionary forces are difficult to analyse in free-living populations. However, when properly understood, they provide valuable insights into evolutionary biology and conservation genetics. This is particularly important for the interplay of genetic drift and natural selection in immune genes that confer resistance to disease. The Galápagos Islands are inhabited by four closely related species of mockingbirds (Mimus spp.). We used 12 different-sized populations of Galápagos mockingbirds and one population of their continental relative northern mockingbird (Mimus polyglottos) to study the effects of genetic drift on the molecular evolution of immune genes, the Toll-like receptors (TLRs: TLR1B, TLR4 and TLR15). We found that neutral genetic diversity was positively correlated with island size, indicating an important effect of genetic drift. However, for TLR1B and TLR4, there was little correlation between functional (e.g., protein) diversity and island size, and protein structural properties were largely conserved, indicating only a limited effect of genetic drift on molecular phenotype. By contrast, TLR15 was less conserved and even its putative functional polymorphism correlated with island size. The patterns observed for the three genes suggest that genetic drift does not necessarily dominate selection even in relatively small populations, but that the final outcome depends on the degree of selection constraint that is specific for each TLR locus.

The Greater Limpopo Transfrontier Conservation Area (GLTFCA) is one of the last refuges for the endangered African wild dog and hosts roughly one-tenth of the global population. Wild dogs in this area are currently threatened by human encroachment, habitat fragmentation and scarcity of suitable connecting habitat between protected areas. We derived genetic data from mitochondrial and nuclear markers to test the following hypotheses: (i) demographic declines in wild dogs have caused a loss of genetic variation, and (ii) Zimbabwean and South African populations in the GLTFCA have diverged due to the effects of isolation and genetic drift. Genetic patterns among five populations, taken with comparisons to known information, illustrate that allelic richness and heterozygosity have been lost over time, presumably due to effects of inbreeding and genetic drift. Genetic structuring has occurred due to low dispersal rates, which was most apparent between Kruger National Park and the Zimbabwean Lowveld. Immediate strategies to improve gene flow should focus on increasing the quality of habitat corridors between reserves in the GLTFCA and securing higher wild dog survival rates in unprotected areas, with human-mediated translocation only undertaken as a last resort.

New Technologies, Tools and Approaches for Improving Crop Breeding

In a previous study on maize (Zea mays, L.) several quantitative trait loci (QTL) showing high dominance-additive ratio for agronomic traits were identified in a population of recombinant inbred lines derived from B73 × H99. For four of these mapped QTL, namely 3.05, 4.10, 7.03 and 10.03 according to their chromosome and bin position, families of near-isogenic lines (NILs) were developed, i.e., couples of homozygous lines nearly identical except for the QTL region that is homozygote either for the allele provided by B73 or by H99. For two of these QTL (3.05 and 4.10) the NILs families were produced in two different genetic backgrounds. The present research was conducted in order to: (i) characterize these QTL by estimating additive and dominance effects; (ii) investigate if these effects can be affected by genetic background, inbreeding level and environmental growing conditions (low vs. high plant density). The six NILs’ families were tested across three years and in three Experiments at different inbreeding levels as NILs per se and their reciprocal crosses (Experiment 1), NILs crossed to related inbreds B73 and H99 (Experiment 2) and NILs crossed to four unrelated inbreds (Experiment 3). Experiment 2 was conducted at two plant densities (4.5 and 9.0 plants m-2). Results of Experiments 1 and 2 confirmed previous findings as to QTL effects, with dominance-additive ratio superior to 1 for several traits, especially for grain yield per plant and its component traits; as a tendency, dominance effects were more pronounced in Experiment 1. The QTL effects were also confirmed in Experiment 3. The interactions involving QTL effects, families and plant density were generally negligible, suggesting a certain stability of the QTL. Results emphasize the importance of dominance effects for these QTL, suggesting that they might deserve further studies, using NILs’ families and their crosses as base materials.

Genome-wide association studies (GWAS) with plant species have employed inbred lines panels. We evaluated the efficiency of GWAS in non-inbred and inbred populations and assessed factors affecting GWAS. Fifty samples of 800 individuals from populations with linkage disequilibrium were simulated. Individuals were genotyped for 10,000 single nucleotide polymorphisms (SNPs) and phenotyped for traits controlled by ten quantitative trait loci (QTLs) and 90 minor genes, assuming different degrees of dominance and broad sense heritabilities of 40 and 80%. The average SNP density was 0.1 centiMorgan (cM) and the QTL heritabilities ranged from 3.2 to 11.8%. The results for random cross populations evidenced that to increase the QTL detection power, the additive-dominance model must be fitted for traits controlled by dominance effects but must not be fitted for traits showing no dominance. The power of detection was maximized by increasing the sample size to 400 and the false discovery rate (FDR) to 5%. The average power of detection for the low, intermediate, and high heritability QTLs achieved 52.4, 87.0, and 100.0%, respectively. Assuming sample sizes of 400 and 800, the observed FDR was equal to or lower than the specified level of significance. The association mapping was highly precise, since at least 97% of the declared QTLs were detected by the SNP inside it (average bias of 0.4 cM). Besides controlling the FDR, relatedness (and identity by state) efficiently controls the number of significant associations outside the QTL interval (not all false positive associations). The analysis of the inbred random cross population provided essentially the same results as the non-inbred populations.

Quantitative Genetics

Proteins are evolvable in the sense that they are readily able to acquire new or improved functions through the process of mutation and selection. Here, I examine what properties influence the ability of proteins to evolve new functions. I show that proteins with similar biochemical properties can differ substantially in their capacities to withstand mutations and evolve new functions. Specifically, more stable proteins are both more mutationally robust and more evolvable, due to improved tolerance for mutations. This fact can be exploited in protein engineering. I then show how evolutionary theory can be modified to describe how a protein's mutational robustness changes during the normal course of neutral genetic drift. One of the main theoretical predictions is that proteins evolving in larger populations will gain excess stability and mutational robustness, a prediction which I confirm experimentally. Finally, I turn to the question of how neutral genetic drift can alter protein functions that are not under selection. I show that promiscuous functions can change significantly during genetic drift, a phenomenon that may aid in the evolution of beneficial new functions. Overall, this work establishes two mechanisms whereby initially neutral mutations can influence the course of future evolution.

Optimal selection on a single identified quantitative trait locus (QTL) with four modes of inheritance: normal autosomal, sex-limited, imprinting and X-linked, was evaluated in four breeding structures: single line selection (SLS), two-way crossing (2WC), three-way crossing (3WC) and reciprocal crossing (RC) by comparing extra benefit from mate selection over index selection to demonstrate effectiveness of mate selection in exploiting non-additive QTL. The results showed that the superiority varied at different QTL inheritance modes, initial favourable allele frequencies and breeding structures. The superiority tended to decrease with the increase of the favourable allele frequency except for over-dominant QTL and imprinted QTL in all breeding structures. Less superiority (below 9%) was observed for a recessive and a fully dominant QTL than for an over-dominant QTL (up to 27.11%). Normal autosomal and sex-linked QTL led to a similar trend of superiority from mate selection but the magnitude of the superiority with the latter was slightly higher than with the former for most combinations of the parameters. A high superiority (6.41-41.54%) was observed from mate selection over index selection for an imprinted QTL. A maternally imprinted QTL tended to lead to higher superiority from mate selection than a paternally imprinted QTL. X-linked QTL led to less superiority from mate selection than the other modes of QTL. A larger superiority from mate selection was observed for a recessive and a fully dominant QTL in structures 3WC and 2WC than structures RC and SLS. The superiority from autosomal QTL and X-linked QTL was lower in the structure RC than in other structures examined.

A new approach for multi-environment quantitative trait locus (QTL) analysis based on an appropriate genetic model is presented. To accommodate a multi-environment analysis, the size of a QTL effect is assumed to be a random effect. The approach results in a multiplicative mixed model for QTL × environment interaction of the factor analytic type. The full genetic model may also include a factor analytic model for the residual genotype × environment interaction, whereas the environmental model for the non-genetic variation involves local, global, and extraneous variation. The approach is used to determine QTLs for yield in the Arapiles × Franklin doubled haploid population of the National Barley Molecular Marker Program. Analysis leads to the determination of 8 QTLs. Many of these QTLs are associated with other traits.

Validation of a quantitative trait locus (QTL) for outcrossing perennial plants is rarely reported due to complexity of plausible genetic models and reliance on field designs already available. Here, a particular marker-QTL haplotype exerted a large, positive effect on height for Pinus taeda and its origin could be traced to a founder, GP(3), in a three-generation QTL pedigree. To validate this QTL effect, we used an extended GP(3)-based pedigree. In the validation cross, each of the 46 offspring was clonally propagated from developing seeds using somatic embryogenesis technology. Subsequent analyses were conducted separately for seedlings and for other somatic emblings. For seedlings, the original QTL effect could not be fully validated. For somatic emblings, a strong negative QTL effect was detected in the validation cross; some evidence from another cross-supported the original positive QTL effect. From this part of the analysis, three distinct marker-QTL haplotypes at a single locus could be inferred. Validating QTL haplotypes in readily available field tests was feasible despite the genetic model complexity inherent to outcrossing long-lived perennials.