Redundant Loci Research Articles

Polygenic Selection within a Single Generation Leads to Subtle Divergence among Ecological NichesINc.

Selection on standing genetic variation may be effective enough to allow for adaptation to distinct niche environments within a single generation. Minor allele frequency changes at multiple, redundant loci of small effect can produce remarkable phenotypic shifts. Yet, demonstrating rapid adaptation via polygenic selection in the wild remains challenging. Here we harness natural replicate populations that experience similar selection pressures and harbor high within-, yet negligible among-population genetic variation. Such populations can be found among the teleost Fundulus heteroclitus that inhabits marine estuaries characterized by high environmental heterogeneity. We identify 10,861 single nucleotide polymorphisms in F. heteroclitus that belong to a single, panmictic population yet reside in environmentally distinct niches (one coastal basin and three replicate tidal ponds). By sampling at two time points within a single generation, we quantify both allele frequency change within as well as spatial divergence among niche subpopulations. We observe few individually significant allele frequency changes yet find that the “number” of moderate changes exceeds the neutral expectation by 10–100%. We find allele frequency changes to be significantly concordant in both direction and magnitude among all niche subpopulations, suggestive of parallel selection. In addition, within-generation allele frequency changes generate subtle but significant divergence among niches, indicative of local adaptation. Although we cannot distinguish between selection and genotype-dependent migration as drivers of within-generation allele frequency changes, the trait/s determining fitness and/or migration likelihood appear to be polygenic. In heterogeneous environments, polygenic selection and polygenic, genotype-dependent migration offer conceivable mechanisms for within-generation, local adaptation to distinct niches.

Polygenic adaptation: From sweeps to subtle frequency shifts.

Evolutionary theory has produced two conflicting paradigms for the adaptation of a polygenic trait. While population genetics views adaptation as a sequence of selective sweeps at single loci underlying the trait, quantitative genetics posits a collective response, where phenotypic adaptation results from subtle allele frequency shifts at many loci. Yet, a synthesis of these views is largely missing and the population genetic factors that favor each scenario are not well understood. Here, we study the architecture of adaptation of a binary polygenic trait (such as resistance) with negative epistasis among the loci of its basis. The genetic structure of this trait allows for a full range of potential architectures of adaptation, ranging from sweeps to small frequency shifts. By combining computer simulations and a newly devised analytical framework based on Yule branching processes, we gain a detailed understanding of the adaptation dynamics for this trait. Our key analytical result is an expression for the joint distribution of mutant alleles at the end of the adaptive phase. This distribution characterizes the polygenic pattern of adaptation at the underlying genotype when phenotypic adaptation has been accomplished. We find that a single compound parameter, the population-scaled background mutation rate Θbg, explains the main differences among these patterns. For a focal locus, Θbg measures the mutation rate at all redundant loci in its genetic background that offer alternative ways for adaptation. For adaptation starting from mutation-selection-drift balance, we observe different patterns in three parameter regions. Adaptation proceeds by sweeps for small Θbg ≲ 0.1, while small polygenic allele frequency shifts require large Θbg ≳ 100. In the large intermediate regime, we observe a heterogeneous pattern of partial sweeps at several interacting loci.

Genome-wide identification of simple sequence repeat (SSR) markers in Capsicum chinense Jacq. with high potential for use in pepper introgression breeding

Capsicum chinense, is closely related to Capsicum annuum L., and the two species share a common gene pool. There are a limited number of cultivated C. chinense varieties; yet, it is acknowledged that C. chinense germplasm harbors useful alleles for important traits such as fruit yield, disease resistance, accumulation of secondary metabolites and technological fruit characters. Besides, it is feasible to obtain fertile progeny from interspecific crosses of C. chinense and C. annuum. Consequently, C. chinense has high breeding potential for improvement of several different traits in pepper breeding. In the present work, C. chinense genome assembly was mined for trinucleotide simple sequence repeats (SSRs) and repeat loci were converted to 53,749 PCR markers. Marker transferability to C. annuum genome was analyzed with high-stringency cross-species mapping parameters, identifying 17,992 transferable markers. Selecting for interspecific polymorphisms and eliminating redundant loci resulted in 4994 SSR markers distributed over the 12 pepper chromosomes with high potential for interspecific polymorphisms between the two pepper species. Laboratory experiments with a subset of candidate polymorphic markers (36 markers) resulted in an amplification rate of 100% from both pepper species and 31 markers produced polymorphic alleles. Thus, in silico marker development and cross-species mapping analyses proved highly efficient in accuracy of primer design and detection of interspecific sequence divergence. The large set of genome-anchored SSR markers introduced in the present work has high potential for polymorphisms. Therefore, the marker set constitutes a useful genomic resource for broadening the genetic base of cultivated pepper with favorable C. chinense alleles.

Recessive Antimorphic Alleles Overcome Functionally Redundant Loci to Reveal TSO1 Function in Arabidopsis Flowers and Meristems

Arabidopsis TSO1 encodes a protein with conserved CXC domains known to bind DNA and is homologous to animal proteins that function in chromatin complexes. tso1 mutants fall into two classes due to their distinct phenotypes. Class I, represented by two different missense mutations in the CXC domain, leads to failure in floral organ development, sterility, and fasciated inflorescence meristems. Class II, represented by a nonsense mutation and a T-DNA insertion line, develops wild-type–like flowers and inflorescences but shows severely reduced fertility. The phenotypic variability of tso1 alleles presents challenges in determining the true function of TSO1. In this study, we use artificial microRNA, double mutant analysis, and bimolecular fluorescence complementation assay to investigate the molecular basis underlying these two distinct classes of phenotypes. We show that the class I mutants could be converted into class II by artificial microRNA knockdown of the tso1 mutant transcript, suggesting that class I alleles produce antimorphic mutant proteins that interfere with functionally redundant loci. We identified one such redundant factor coded by the closely related TSO1 homolog SOL2. We show that the class I phenotype can be mimicked by knocking out both TSO1 and its homolog SOL2 in double mutants. Such antimorphic alleles targeting redundant factors are likely prevalent in Arabidopsis and maybe common in organisms with many sets of paralogous genes such as human. Our data challenge the conventional view that recessive alleles are always hypomorphic or null and that antimorphic alleles are always dominant. This study shows that recessive alleles can also be antimorphic and can produce a phenotype more severe than null by interfering with the function of related loci. This finding adds a new paradigm to classical genetic concepts, with important implications for future genetic studies both in basic research as well as in agriculture and medicine.

Genomic breeding value estimation using genetic markers, inferred ancestral haplotypes, and the genomic relationship matrix

With the introduction of new single nucleotide polymorphism (SNP) chips of various densities, more and more genotype data sets will include animals genotyped for only a subset of the SNP. Imputation techniques based on unobserved ancestral haplotypes may be used to infer missing genotypes. These ancestral haplotypes may also be used in the genomic prediction model, instead of using the SNP. This may increase the reliability of predictions because the ancestral haplotype may capture more linkage disequilibrium with quantitative trait loci than SNP. The aim of this paper was to study whether using unobserved ancestral haplotypes in a genomic prediction model would provide more reliable genomic predictions than using SNP, and to determine how many loci in the genomic prediction model would be redundant. Genotypes of 8,960 bulls and cows for 39,557 SNP were analyzed with a hidden Markov model to associate each individual at each locus to 2 ancestral haplotypes. The number of ancestral haplotypes per locus was fixed at 10, 15, or 20. Subsequently, a validation study was performed in which the phenotypes of 3,251 progeny-tested bulls for 16 traits were used in a genomic prediction model to predict the estimated breeding values of at least 753 validation bulls. The squared correlation between genomic prediction and deregressed daughter performance estimated breeding value, when averaged across traits, was slightly higher when 15 or 20 ancestral haplotypes per locus were used in the prediction model instead of the SNP genotypes, whereas the prediction model using a genomic relationship matrix gave the lowest squared correlations. The number of redundant loci [i.e., loci that had less than 18 jumps (0.1%) from one ancestral haplotype to another ancestral haplotype at the next locus], was 18,793 (48%), which means that only 20,764 loci would need to be included in the genomic prediction model. This provides opportunities for greatly decreasing computer requirements of genomic evaluations with very large numbers of markers.

Nonadditive Expression of Homoeologous Genes Is Established Upon Polyploidization in Hexaploid Wheat

Effects of polyploidy in allohexaploid wheat (Triticum aestivum L.) have primarily been ascribed to increases in coding sequence variation and potential to acquire new gene functions through mutation of redundant loci. However, regulatory variation that arises through new promoter and transcription factor combinations or epigenetic events may also contribute to the effects of polyploidization. In this study, gene expression was characterized in a synthetic T. aestivum line and the T. turgidum and Aegilops tauschii parents to establish a timeline for such regulatory changes and estimate the frequency of nonadditive expression of homoeologous transcripts in newly formed T. aestivum. Large-scale analysis of nonadditive gene expression was assayed by microarray expression experiments, where synthetic T. aestivum gene expression was compared to additive model values (mid-parent) calculated from parental T. turgidum and Ae. tauschii expression levels. Approximately 16% of genes were estimated to display nonadditive expression in synthetic T. aestivum. A certain fraction of the genes (2.9%) showed overdominance or underdominance. cDNA-single strand conformation polymorphism analysis was applied to measure expression of homoeologous transcripts and further verify microarray data. The results demonstrate that allopolyploidization, per se, results in rapid initiation of differential expression of homoeologous loci and nonadditive gene expression in T. aestivum.

Two distinct functional spliced leader RNA gene arrays in Leishmaniatarentolae are found in several lizard Leishmania species

A second distinct array of spliced leader RNA genes has been found in several Leishmania species particular to lizards. This is the first report of two non-allelic arrays of spliced leader RNA genes within a species cell line. The arrays are identical to each other in their transcribed spliced leader RNA gene sequences, but variable in their non-transcribed spacer sequences. In the two arrays from Leishmania tarentolae UC strain the promoter regions are similar, but not identical, at positions shown previously to be critical for spliced leader RNA transcription. These arrays contain similar numbers of genes and are both transcribed in L. tarentolae in vitro transcription extract as well as in vivo. The −66/−58 regions of both genes, which contain an element of the spliced leader RNA gene promoter, bind proteins likely to be transcription factors in a specific manner. A survey of lizard Leishmania spp. revealed a second spliced leader RNA gene array in three of four species. Phylogenetic analyses of these sequences with each other and with the spliced leader RNA gene sequences of non-lizard Leishmania spp. and their near-relatives showed that the lizard groups are more closely related to each other than to arrays from other Leishmania spp. As the transcripts of the two arrays are identical, they may co-exist to fulfil the substantial requirement for spliced leader RNA production; however, they have the potential for differential usage modulated by their distinct promoter elements. The presence of two distinct spliced leader RNA gene arrays within a single cell type may represent dissociated evolution of two redundant loci, or a previously unsuspected level of control in the post-transcriptional gene expression within some kinetoplastids.

A limited number of Caenorhabditis elegans genes are readily mutable to dominant, temperature-sensitive maternal-effect embryonic lethality.

Dominant gain-of-function mutations can give unique insights into the study of gene function. In addition, gain-of-function mutations, unlike loss-of-function alleles, are not biased against the identification of genetically redundant loci. To identify novel genetic functions active during Caenorhabditis elegans embryogenesis, we have collected a set of dominant temperature-sensitive maternal-effect embryonic lethal mutations. In a previous screen, we isolated eight such mutations, distributed among six genes. In the present study, we describe eight new dominant mutations that identify only three additional genes, yielding a total of 16 dominant mutations found in nine genes. Therefore, it appears that a limited number of C. elegans genes mutate to this phenotype at appreciable frequencies. Five of the genes that we identified by dominant mutations have loss-of-function alleles. Two of these genes may lack loss-of-function phenotypes, indicating that they are nonessential and so may represent redundant loci. Loss-of-function mutations of three other genes are associated with recessive lethality, indicating nonredundancy.

Genetic and molecular organization of the 5S locus and mutants in D. melanogaster

The topography of an entire redundant locus was analyzed by both genetic and molecular means. Three mutants ( min 0, min 1, min 2 ) allelic to the 5S rRNA genetic locus on chromosome 2 of D. melanogaster were isolated. Flies exhibit a mutant phenotype when hemizygous for a min allele, but flies having two doses are wild-type. Saturation hybridization experiments show that the alleles are gross deficiencies each deleting an equal amount of 5S DNA. Each of the three mutant min alleles produces a distinct temperature-sensitive viability phene, and thus they are suggested to be pseudoalleles within the same redundant locus. Using the segmental aneuploid method (Lindsley et al., 1972), the 5S gene cluster was subdivided into proximal and distal halves. Both saturation hybridization experiments and genetic tests show that each half contains about eighty 5S genes. The complementation of the min alleles with the proximal and distal halves of the cluster indicates that both halves function independently. We present evidence which supports the model that all of the 160 5S genes are arranged as a single continuous cluster of tandem repeats with no large interdispersive DNA segments not complementary to 5S rRNA.

Temperature-sensitive bobbed mutants in Drosophila melanogaster

Temperature-sensitive mutants allelic to the NO region were isolated on the Y chromosome ofDrosophila melanogaster. Thebbts − 1 allele showed a minimal viability and extremebobbed phenotype at 18°C whereas at 29°C the viability and phenotype approached the wild-type condition. This allele is a typical cold-sensitive mutant. Thebbts − 2 allele had a maximum viability at both 18° and 29°C and a reduced viability at 25°C. The lethal phase of thebbts − 1 allele occurs during the late pupal stage. Thebbts − 1 allele showed no discrete temperature-sensitive period during the life cycle of the organism. This is compatible with the expectation that ats mutant in rRNA synthesis would not demonstrate a definite temperature-sensitive period since rRNA synthesis occurs during the entire life cycle. The number of rRNA genes for thets alleles was 117 forbbts − 1 and 127 forbbts − 2. These amounts represent deficiencies of rDNA of approximately 45 and 41%, respectively. This is the first report that partial deletions of a highly redundant locus can demonstrate a temperature-sensitive phenotype.

Chromosome structure in phage T4, II. Terminal redundancy and heterozygosis.

In a previous communnication' it was suggested that the chromosome of each particle of phage T4 is terminally redundant, and that after several rounds of replication (following infection), progeny chromosomes arise which have circularly permuted genetic sequences. Among the niembers of a population of phage particles, the ends of the chromosomes would be randomly distributed over the genome, and a phage particle carryinig different alleles at one of its redundant loci would be heterozygous. Nomura and Benizer2 have reported that heterozygotes for rII deletioni mutants (from mixed infections with r+ phage) occur with about a third of the frequency of those for rII point mutants. It thus seemed likely that heterozygosity in phage T4 is of at least two kinds. One kind may be the result of heterozygosity within the molecule, as was first suggested by Levinthal, whereas another kind may be due to the terminal redundancy described above. Deletion mutants may be unable to form heterozygotes of the internial kind since these would involve violations of duplex complementarity (regardless of their precise molecular structure), whereas point mutants may form heterozygotes of both kinds. The chromosome of a phage particle will be termimnally redundant and heterozygous for marker a provided that (1) the chromosome terminates near marker a and includes marker a, and (2) the last recomnbinatiomnal event, occurring somewhere within the chromosome, has been such that the other end of the chromosome contains marker a+. Terminal-redundancy heterozygotes are formed and lost by the process of recombination; their frequency (as a function of time after infection) will depend on the rate of recombination but not on the rate of replication. In a pool of vegetative chromosomes, the frequency of terminally redundant heterozygotes would be expected to change in time as does the frequency of recombination for very distanitly liniked markers; it would be expected to increase until an equilibrium value was reached and to remain constant after that. Because of the high frequency of recombination in phage T4, onne would expect that the equilibrium value would be reached very early during the latent period. Internal heterozygotes are most probably formed by an event that results in the recombination of markers on either side of the heterozygous region;3 thus, they may well represent the primary products of recombination. They would be expected to disappear upon the semiconservative replication of the chromosome bearing them. The chromosome of a phage particle will be internally heterozygous for marker a provided that (1) a recombinational event leading to internal heterozygosis will have occurred at the site of marker a, and (2) the chromosome is incorporated into a mature particle before it unidergoes replication. Internal heterozygotes are formed by recombination and are lost by replication: their frequency (as a function of