Artificial Directional Selection Research Articles

Demographic history and distinct selection signatures of two domestication genes in mungbean.

Domestication is the long and complex process underlying the evolution of crops, in which artificial directional selection transformed wild progenitors into the desired form, affecting genomic variation and leaving traces of selection at targeted loci. However, whether genes controlling important domestication traits follow the same evolutionary pattern expected under the standard selective sweep model remains unclear. With whole-genome re-sequencing of mungbean (Vigna radiata), we investigated this issue by resolving its global demographic history and targeted dissection of the molecular footprints of genes underlying two key traits representing different stages of domestication. Mungbean originated in Asia, and the Southeast Asian wild population migrated to Australia about 50 thousand generations ago (kga). Later in Asia, the cultivated form diverged from the wild progenitor. We identified the gene associated with the pod shattering resistance trait, VrMYB26a, with lower expression across cultivars and reduced polymorphism in the promoter region, reflecting a hard selective sweep. On the other hand, the stem determinacy trait was associated with VrDet1. We found two ancient haplotypes of this gene have lower gene expression and exhibited intermediate frequencies in cultivars, consistent with selection favoring independent haplotypes in a soft selective sweep. In mungbean, contrasting signatures of selection were identified from the detailed dissection of two important domestication traits. The results suggest complex genetic architecture underlying the seemingly simple process of directional artificial selection and highlight the limitations of genome-scan methods relying on hard selective sweeps.

Integrated Analysis of mRNAs and Long Non-Coding RNAs Expression of Oviduct That Provides Novel Insights into the Prolificacy Mechanism of Goat (Capra hircus).

Artificial directional selection has replaced natural selection and resulted in trait differences across breeds in domestic animal breeding. However, the molecular mechanism by which the oviduct regulates litter size remains largely elusive in goats during the follicular phase. Accumulating data have linked lncRNAs to reproductive activities; however, little is known about the modulation mechanism in the oviduct. Herein, RNA-seq was used to measure mRNA and lncRNA expression levels in low- and high-fecundity goats. We observed distinctive differences in mRNA and lncRNA in terms of different kidding numbers and detected the differential expression of 1640 mRNA transcripts and 271 lncRNA transcripts. Enrichment analysis of differentially expressed mRNAs (DEGs) suggested that multiple pathways, such as the AMPK, PI3K–Akt, calcium signaling pathway, oocyte meiosis, ABC transporter, and ECM–receptor interaction pathways, directly or indirectly affected goat reproduction. Additionally, coexpression of differentially expressed lncRNAs (DEL)-genes analysis showed that XLOC_021615, XLOC_119780, and XLOC_076450 were trans-acting as the DEGs ATAD2, DEPDC5, and TRPM6, respectively, and could regulate embryo development. Moreover, XLOC_020079, XLOC_107361, XLOC_169844, XLOC_252348 were the trans-regulated elements of the DEGs ARHGEF2 and RAPGEF6, and the target DEGs CPEB3 of XLOC_089239, XLOC_090063, XLOC_107409, XLOC_153574, XLOC_211271, XLOC_251687 were associated with prolificacy. Collectively, our study has offered a thorough dissection of the oviduct lncRNA and mRNA landscapes in goats. These results could serve as potential targets of the oviduct affecting fertility in goats.

Whole-genome resequencing of Osmanthus fragrans provides insights into flower color evolution

Osmanthus fragrans is a well-known ornamental plant that has been domesticated in China for 2500 years. More than 160 cultivars have been found during this long period of domestication, and they have subsequently been divided into four cultivar groups, including the Yingui, Jingui, Dangui, and Sijigui groups. These groups provide a set of materials to study genetic evolution and variability. Here, we constructed a reference genome of O. fragrans ‘Liuyejingui’ in the Jingui group and investigated its floral color traits and domestication history by resequencing a total of 122 samples, including 119 O. fragrans accessions and three other Osmanthus species, at an average sequencing depth of 15×. The population structure analysis showed that these 119 accessions formed an apparent regional cluster. The results of linkage disequilibrium (LD) decay analysis suggested that varieties with orange/red flower color in the Dangui group had undergone more artificial directional selection; these varieties had the highest LD values among the four groups, followed by the Sijigui, Jingui, and Yingui groups. Through a genome-wide association study, we further identified significant quantitative trait loci and genomic regions containing several genes, such as ethylene-responsive transcription factor 2 and Arabidopsis pseudoresponse regulator 2, that are positively associated with petal color. Moreover, we found a frameshift mutation with a 34-bp deletion in the first coding region of the carotenoid cleavage dioxygenase 4 gene. This frameshift mutation existed in at least one site on both alleles in all varieties of the Dangui group. The results from this study shed light on the genetic basis of domestication in woody plants, such as O. fragrans.

A joint analysis strategy reveals genetic changes associated with artificial selection between egg-type and meat-type ducks.

Egg-type ducks and meat-type ducks are predominantly commercial or indigenous and have been subjected to artificial directional selection. These two duck types differ substantially in body shape, production performance and reproductivity. However, the genetic changes associated with phenotypic differences remain unclear. Here, we compared the two duck types at the genomic and transcriptomic levels. We identified a large number of SNPs and genes in genomic divergent regions in terms of FST and θπ values. The corresponding genes were mainly enriched in embryonic development function and metabolic pathway. RNA-seq analysis also revealed differential gene expression in the liver and gonads. The differentially expressed genes were functionally associated with signal transmission and substance metabolism respectively. Furthermore, we found that seven genes were related to differentiation between the two types by both g genome and transcriptome analysis and were plausible candidate genes. These genes were annotated to GO categories of cell development and disease immunity. These findings will enable a better understanding of the artificial selection history of meat and egg ducks and provide a valuable resource for future research on the breeding of these two lineages.

Genome assembly of wild tea tree DASZ reveals pedigree and selection history of tea varieties

Wild teas are valuable genetic resources for studying domestication and breeding. Here we report the assembly of a high-quality chromosome-scale reference genome for an ancient tea tree. The further RNA sequencing of 217 diverse tea accessions clarifies the pedigree of tea cultivars and reveals key contributors in the breeding of Chinese tea. Candidate genes associated with flavonoid biosynthesis are identified by genome-wide association study. Specifically, diverse allelic function of CsANR, CsF3’5’H and CsMYB5 is verified by transient overexpression and enzymatic assays, providing comprehensive insights into the biosynthesis of catechins, the most important bioactive compounds in tea plants. The inconspicuous differentiation between ancient trees and cultivars at both genetic and metabolic levels implies that tea may not have undergone long-term artificial directional selection in terms of flavor-related metabolites. These genomic resources provide evolutionary insight into tea plants and lay the foundation for better understanding the biosynthesis of beneficial natural compounds.

Whole-genome sequencing of European autochthonous and commercial pig breeds allows the detection of signatures of selection for adaptation of genetic resources to different breeding and production systems

BackgroundNatural and artificial directional selection in cosmopolitan and autochthonous pig breeds and wild boars have shaped their genomes and resulted in a reservoir of animal genetic diversity. Signatures of selection are the result of these selection events that have contributed to the adaptation of breeds to different environments and production systems. In this study, we analysed the genome variability of 19 European autochthonous pig breeds (Alentejana, Bísara, Majorcan Black, Basque, Gascon, Apulo-Calabrese, Casertana, Cinta Senese, Mora Romagnola, Nero Siciliano, Sarda, Krškopolje pig, Black Slavonian, Turopolje, Moravka, Swallow-Bellied Mangalitsa, Schwäbisch-Hällisches Schwein, Lithuanian indigenous wattle and Lithuanian White old type) from nine countries, three European commercial breeds (Italian Large White, Italian Landrace and Italian Duroc), and European wild boars, by mining whole-genome sequencing data obtained by using a DNA-pool sequencing approach. Signatures of selection were identified by using a single-breed approach with two statistics [within-breed pooled heterozygosity (HP) and fixation index (FST)] and group-based FST approaches, which compare groups of breeds defined according to external traits and use/specialization/type.ResultsWe detected more than 22 million single nucleotide polymorphisms (SNPs) across the 23 compared populations and identified 359 chromosome regions showing signatures of selection. These regions harbour genes that are already known or new genes that are under selection and relevant for the domestication process in this species, and that affect several morphological and physiological traits (e.g. coat colours and patterns, body size, number of vertebrae and teats, ear size and conformation, reproductive traits, growth and fat deposition traits). Wild boar related signatures of selection were detected across all the genome of several autochthonous breeds, which suggests that crossbreeding (accidental or deliberate) occurred with wild boars.ConclusionsOur findings provide a catalogue of genetic variants of many European pig populations and identify genome regions that can explain, at least in part, the phenotypic diversity of these genetic resources.

Twenty years of artificial directional selection have shaped the genome of the Italian Large White pig breed.

In this study, we investigated at the genome-wide level if 20years of artificial directional selection based on boar genetic evaluation obtained with a classical BLUP animal model shaped the genome of the Italian Large White pig breed. The most influential boars of this breed (n=192), born from 1992 (the beginning of the selection program of this breed) to 2012, with an estimated breeding value reliability of >0.85, were genotyped with the Illumina Porcine SNP60 BeadChip. After grouping the boars in eight classes according to their year of birth, filtered single nucleotide polymorphisms (SNPs) were used to evaluate the effects of time on genotype frequency changes using multinomial logistic regression models. Of these markers, 493 had a PBonferroni <0.10. However, there was an increasing number of SNPs with a decreasing level of allele frequency changes over time, representing a continuous profile across the genome. The largest proportion of the 493 SNPs was on porcine chromosome (SSC) 7, SSC2, SSC8 and SSC18 for a total of 204 haploblocks. Functional annotations of genomic regions, including the 493 shifted SNPs, reported a few Gene Ontology terms that might underly the biological processes that contributed to increase performances of the pigs over the 20years of the selection program. The obtained results indicated that the genome of the Italian Large White pigs was shaped by a directional selection program derived by the application of methodologies assuming the infinitesimal model that captured a continuous trend of allele frequency changes in the boar population.

Local neutral networks help maintain inaccurately replicating ribozymes.

The error threshold of replication limits the selectively maintainable genome size against recurrent deleterious mutations for most fitness landscapes. In the context of RNA replication a distinction between the genotypic and the phenotypic error threshold has been made; where the latter concerns the maintenance of secondary structure rather than sequence. RNA secondary structure is treated as a proxy for function. The phenotypic error threshold allows higher per digit mutation rates than its genotypic counterpart, and is known to increase with the frequency of neutral mutations in sequence space. Here we show that the degree of neutrality, i.e. the frequency of nearest-neighbour (one-step) neutral mutants is a remarkably accurate proxy for the overall frequency of such mutants in an experimentally verifiable formula for the phenotypic error threshold; this we achieve by the full numerical solution for the concentration of all sequences in mutation-selection balance up to length 16. We reinforce our previous result that currently known ribozymes could be selectively maintained by the accuracy known from the best available polymerase ribozymes. Furthermore, we show that in silico stabilizing selection can increase the mutational robustness of ribozymes due to the fact that they were produced by artificial directional selection in the first place. Our finding offers a better understanding of the error threshold and provides further insight into the plausibility of an ancient RNA world.

Dynamics of Adaptive Alleles in Divergently Selected Body Weight Lines of Chickens

By studying genomic changes over time in populations subjected to strong artificial directional selection, we can gain insights to the dynamics of beneficial alleles originating from the founder population or emerging as novel mutations undergoing ongoing selection. The Virginia lines are a chicken resource population generated by long-term bi-directional, single-trait selection for juvenile body weight. We studied genome-wide allele frequency changes from generation 40 to 53 using genome-wide genotypes from directional and relaxed selection lines. Overall, there were small changes in allele frequencies at individual loci over the studied time period; but, on average, the changes were greater in lines with larger phenotypic changes. This is consistent with previous findings that much of the response to selection over the first 40 years of selection was attributable to utilization of standing genetic variation at many loci in the genome, indicating a mostly polygenic architecture for body weight. Over the course of the selection experiment, the largest phenotypic response to selection was observed in the high-weight selected line, and in this line we detected a single locus where the allele frequency changed rapidly during a late stage of the experiment. This locus likely contains a novel, beneficial mutation that appeared between generations 40 and 45 and was driven to fixation in 5 to 10 generations. This result illustrates the dependence of continued long-term selection response on standing genetic variation at many loci as well as strong, novel, beneficial mutations.

Changes in correlations between commercially valuable characters of the sable Martes zibellina L. during artificial selection

A farm population of the sable Martes zibellina L. has been selected for darker coat color during 40 years. Correlations between fitness characters and correlations of these characters with the selected character have been monitored. Correlation analysis has shown that the female fertility in the first year of reproduction is a promising predictor of how valuable the female will be for further breeding. Artificial directional selection has been shown to change the correlations that have been formed in natural populations of the sable. The relationship of this phenomenon with a decrease in the overall fitness during selection that has been observed in the sable population is discussed.

Bidirectional Selection for Novel Pheromone Blend Ratios in the Almond Moth, Cadra cautella

The sex pheromone of the almond moth, Cadra cautella, is a blend of (Z,E)-9,12-tetradecadienyl acetate (Z9,E12-14:Ac, the major component capable of inducing attraction alone) and (Z)-9-tetradecenyl acetate (Z9-14:Ac, the minor component, which is unattractive alone but augments attraction of the major component). In this study, the ratio of the two components responded to artificial directional selection in five of six selected lines, whereas no change was observed in the three control lines. The mean ratio (+/-SE) of Z9,E12-14:Ac to Z9-14:Ac went from 13.72 +/- 1.02:1 to 20.13 +/- 0.68:1 in high line 1, an increase of 47%. In the second high-selected line, the mean ratio (+/-SE) increased from 9.87 +/- 0.54:1 to 15.89 +/- 0.85:1, an increase of 61%. In low line 1, the mean ratio (+/-SE) in the parental generation was 10.74 +/- 0.78:1 and 7.35 +/- 0.41:1 in the last selected generation, a decrease of 32%. The response to selection was greater in low line 2, as the mean ratio (+/-SE) decreased from 10.11 +/- 0.66:1 to 5.65 +/- 0.55:1 in the last generation, a decrease of 44%. In low line 3, the mean ratio (+/-SE) in the parental generation was 13.63 +/- 0.82:1 and 6.47 +/- 0.26:1 in the last generation, a decrease of 53%. The response to selection was approximately symmetrical with a mean increase of 54% and a mean decrease of 43%. The increases in ratio observed in the high lines were caused by an increase in the titer of the Z9,E12-14:Ac component with no concurrent change in the titer of the component Z9-14:Ac. Among the low selected lines, the titers of both components increased; however, there was a greater relative increase in the titer of the component Z9-14:Ac. The absolute and relative titers of the sex pheromone components had decreased significantly in the F10 generation in some of the selected lines, five generations after the discontinuation of selection.

Directional-disruptive selection in Drosophila melanogaster.

Artificial directional selection for increased sternopleural chaetae number in Drosophila melanogaster is compared with a mode of directional selection which incorporates an element of disruptive selection. Compared with directional selection, this directional-disruptive selection results in a similar response but with a lower selection differential, and higher realised heritability. The differences might be attributed to a higher genetic variance maintained by the directional-disruptive selection.

Artificial selection with differing population structures

SUMMARYThe effect of subdivision of a population on response to artificial directional selection for abdominal bristle number inDrosophila melanogasterwas compared using large, replicated lines. Three different population structures were compared: (i) selection in an Undivided, large population with 50 pairs of parents (treatment U); (ii) selection in each of 10 sublines which were reconstituted every 6th generation by Crossing after Culling the 5 lowest sublines (treatment CC); and (iii) selection in each of 10 sublines which were reconstituted every 6th generation by Crossing after Retaining all 10 sublines (treatment CR). At the end of three cycles of selection and crossing, neither CR nor CC was superior to U; sublining did not increase response to selection. These results agree with the predictions arising from an entirely additive model and provide no evidence for the presence of epistasis.A comparison of 50-pair lines (U) with several 5-pair lines was made over 31 generations. For the 50-pair lines, there was close agreement between response predicted from the base population (usingih2σp) and observed response throughout all 31 generations of selection. Although the best of the 5-pair lines exceeded the 50-pair lines in the early generations, average response to directional selection in the 5-pair lines soon fell behind that predicted fromih2σp, and soon reached a plateau.

Size of population required for artificial selection.

SUMMARYIt is widely acknowledged that genetic drift is an important source of variation in response to artificial directional selection. How large should a selection line be in order to reduce the effect of genetic drift to an acceptably low level?This paper investigates two criteria that can be used to answer this question in relation to short-term response to selection. The first criterion is coefficient of variation of response, and the second criterion is chance of success, where a successful selection programme is one in which the observed response is greater than a certain proportion, β, of expected response.For a simple mass selection programme with intensityiand heritabilityh2, the size of population required in order for the coefficient of variation of response to be γ aftertgenerations, is approximately 2/(γih)2t, and the size required for the chance of success to be α aftertgenerations is approximately 2{zα/(β−l)ih}2/t, wherezαis the standard normal deviate corresponding to the probability α.As an example, suppose it is required that aftertgenerations the coefficient of variation of response be 10% or that there be a 90% chance of achieving at least 9/10 of expected response. Sinceih≤ 2 in most selection programmes, the size of population required is at least 50/tor 82/trespectively. Ifih≤ 1, the corresponding sizes are 200/tand 328/t.Results are extended to enable the calculation of size of population required for any type of artificial directional selection programme, including those in which generations overlap.