A multi-part strategy for introgression of exotic germplasm into elite plant breeding programs using genomic selection

Some of the most economically important traits in plant breeding show highly polygenic inheritance. Genetic variation is a key determinant of the rates of genetic improvement in selective breeding programs. Rapid progress in genetic improvement comes at the cost of a rapid loss of genetic variation. Germplasm available through expired Plant Variety Protection (exPVP) lines is a potential resource of variation previously lost in elite breeding programs. Introgression for polygenic traits is challenging, as many genes have a small effect on the trait of interest. Here we propose a way to overcome these challenges with a multi-part pre-breeding program that has feedback pathways to optimise recurrent genomic selection. The multi-part breeding program consists of three components, namely a bridging component, population improvement, and product development. Parameters influencing the multi-part program were optimised with the use of a grid search. Haploblock effect and origin were investigated. Results showed that the introgression of exPVP germplasm using an optimised multi-part breeding strategy resulted in 1.53 times higher genetic gain compared to a two-part breeding program. Higher gain was achieved through reducing the performance gap between exPVP and elite germplasm and breaking down linkage drag. Both first and subsequent introgression events showed to be successful. In conclusion, the multi-part breeding strategy has a potential to improve long-term genetic gain for polygenic traits and therefore, potential to contribute to global food security.

Genetic redundancy resolves invasion paradox in Colorado potato beetle

The paradox of how invasive species cope with novel selective pressures with limited genetic variation is a fundamental question in molecular ecology. Several mechanisms have been proposed, but they can lack generality and predictive power. Here, we introduce an alternative mechanism, genetic redundancy, wherein changes in multiple combinations of loci can achieve a fitness optimum for polygenic traits, and thus the variations left after the founder effect may be sufficient for adaptation. We tested the potential importance of genetic redundancy in environmental adaptation of Colorado potato beetle (CPB) in introduced Eurasia. Population genomic analyses showed substantial genetic depletion following a single introduction event, which supports invasive CPB as a classic system for the paradox study. Genome-environment association analyses revealed a suite of loci and gene functions plausibly related to cold stress. Notably, a substantial portion of loci showed different contributions to similar or identical environments. Such non-parallel evolution indicates their potential redundancy to overall fitness. Furthermore, one important adaptive gene function, “phospholipid production”, was represented by more than one independent linkage cluster, suggesting some gene functional redundancy in cold resistance. Taken together, these results support the hypothesis that genetic redundancy can promote the adaptability of polygenic traits despite strong genetic depletion, thus providing a general mechanism for resolving the genetic paradox of invasion. More broadly, genetic redundancy, as an inherent feature of the genome, may have contributed to the evolutionary success of invasive species in many aspects.

On the genetic architecture of rapidly adapting and convergent life history traits in guppies

The genetic basis of traits can shape and constrain how adaptation proceeds in nature; rapid adaptation can be facilitated by polygenic traits, whereas polygenic traits may restrict re-use of the same genes in adaptation (genetic convergence). The rapidly evolving life histories of guppies in response to predation risk provide an opportunity to test this proposition. Guppies adapted to high- (HP) and low-predation (LP) environments in northern Trinidad evolve rapidly and convergently among natural populations. This system has been studied extensively at the phenotypic level, but little is known about the underlying genetic architecture. Here, we use an F2 QTL design to examine the genetic basis of seven (five female, two male) guppy life history phenotypes. We use RAD-sequencing data (16,539 SNPs) from 370 male and 267 female F2 individuals. We perform linkage mapping, estimates of genome-wide and per-chromosome heritability (multi-locus associations), and QTL mapping (single-locus associations). Our results are consistent with architectures of many-loci of small effect for male age and size at maturity and female interbrood period. Male trait associations are clustered on specific chromosomes, but female interbrood period exhibits a weak genome-wide signal suggesting a potentially highly polygenic component. Offspring weight and female size at maturity are also associated with a single significant QTL each. These results suggest rapid phenotypic evolution of guppies may be facilitated by polygenic trait architectures, but these may restrict gene-reuse across populations, in agreement with an absence of strong signatures of genetic convergence from recent population genomic analyses of wild HP-LP guppies.

A selection pressure landscape for 870 human polygenic traits

Characterizing the natural selection of complex traits is essential for understanding human evolution and biological or pathological mechanisms. To fulfill this requirement, we leveraged Genome-wide summary statistics for 870 polygenic traits and quantified the selection pressure of different forms and time scales on them in European ancestry. We found that 88% of traits underwent polygenic adaptation in the past 2000 years. At the present time and Neolithic period, selection pressure showed profound alteration. Traits related to pigmentation, impedance, and nutrition intake exhibited strong selection signals across different time scales. Our result provided an overview of selection pressure on various human polygenic traits, which served as a foundation for further populational and medical genetic studies.

Ghat: An R package for identifying adaptive polygenic traits

Identifying selection on polygenic complex traits in crops and livestock is key to understanding evolution and helps prioritize important characteristics for breeding. However, the QTL that contribute to polygenic trait variation exhibit small or infinitesimal effects. This hinders the ability to detect QTL controlling polygenic traits because enormously high statistical power is needed for their detection. Recently, we circumvented this challenge by introducing a method to identify selection on complex traits by evaluating the relationship between genome-wide changes in allele frequency and estimates of effect-size. The method involves calculating a composite-statistic across all markers that captures this relationship, followed by implementing a linkage disequilibrium-aware permutation test to evaluate if the observed pattern differs from that expected due to drift during evolution and population stratification. In this manuscript, we describe “Ghat”, an R package developed to implement the method to test for selection on polygenic traits. We demonstrate the package by applying it to test for polygenic selection on 15 published European winter wheat traits including yield, biomass, quality, morphological characteristics, and disease resistance traits. The results highlight the power of Ghat to identify selection on complex traits. The Ghat package is accessible on CRAN, The Comprehensive R Archival Network, and on GitHub.