scholarly journals The Genomics of Selfing in Maize (Zea mays ssp. mays): Catching Purging in the Act

2019 ◽  
Author(s):  
Kyria Roessler ◽  
Aline Muyle ◽  
Concepcion M. Diez ◽  
Garren R.J. Gaut ◽  
Alexandros Bousios ◽  
...  
Keyword(s):  
Arabidopsis Thaliana ◽  
Zea Mays ◽  
Inbreeding Depression ◽  
Recombination Rate ◽  
Principal Component ◽  
Genetic Tool ◽  
Deleterious Alleles ◽  
Self Fertilization ◽  
Genomic Scale ◽  
Short Timeframe

ABSTRACTIn plants, self-fertilization is both an important reproductive strategy and a valuable genetic tool. In theory, selfing increases homozygosity at a rate of 0.50 per generation. Increased homozygosity can uncover recessive deleterious variants and lead to inbreeding depression, unless it is countered by the loss of these variants by genetic purging. Here we investigated the dynamics of purging on genomic scale by testing three predictions. The first was that heterozygous, putatively deleterious SNPs were preferentially lost from the genome during continued selfing. The second was that the loss of deleterious SNPs varied as a function of recombination rate, because recombination increases the efficacy of selection by uncoupling linked variants. Finally, we predicted that genome size (GS) decreases during selfing, due to the purging of deleterious transposable element (TE) insertions. We tested these three predictions by following GS and SNP variants in a series of selfed maize (Zea mays ssp. mays) lines over six generations. In these lines, putatively deleterious alleles were purged, and purging was more pronounced in highly recombining regions. Homozygosity increased more slowly than expected; instead of increasing by 50% each generation, it increased by 35% to 40%. Finally, three lines showed dramatic decreases in GS, losing an average of 398 Mb from their genomes over the short timeframe of our experiment. TEs were the principal component of loss, and GS loss was more likely for lineages that began with more TE and more chromosomal knob repeats. Overall, this study documented remarkable GS loss – as much DNA as three Arabidopsis thaliana genomes, on average - in only a few generations of selfing.

scholarly journals Effects of Recombination Rate and Gene Density on Transposable Element Distributions in Arabidopsis thaliana

2003 ◽  
Vol 13 (8) ◽  
pp. 1897-1903 ◽  
Author(s):  
Stephen I. Wright ◽  
Newton Agrawal ◽  
Thomas E. Bureau
Keyword(s):  
Gene Expression ◽  
Arabidopsis Thaliana ◽  
Recombination Rate ◽  
Random Distribution ◽  
Gene Density ◽  
Ectopic Recombination ◽  
Self Fertilization ◽  
Competing Models ◽  
Eukaryotic Genomes ◽  
Made In

Transposable elements (TEs) comprise a major component of eukaryotic genomes, and exhibit striking deviations from random distribution across the genomes studied, including humans, flies, nematodes, and plants. Although considerable progress has been made in documenting these patterns, the causes are subject to debate. Here, we use the genome sequence of Arabidopsis thaliana to test for the importance of competing models of natural selection against TE insertions. We show that, despite TE accumulation near the centromeres, recombination does not generally correlate with TE abundance, suggesting that selection against ectopic recombination does not influence TE distribution in A. thaliana. In contrast, a consistent negative correlation between gene density and TE abundance, and a strong under-representation of TE insertions in introns suggest that selection against TE disruption of gene expression is playing a more important role in A. thaliana. High rates of self-fertilization may reduce the importance of recombination rate in genome structuring in inbreeding organisms such as A. thaliana and Caenorhabditis elegans.

scholarly journals Epistasis, inbreeding depression and the evolution of self-fertilization

2019 ◽  
Author(s):  
Diala Abu Awad ◽  
Denis Roze
Keyword(s):  
Inbreeding Depression ◽  
Stabilizing Selection ◽  
Linkage Disequilibria ◽  
Deleterious Alleles ◽  
Mating System Evolution ◽  
Special Cases ◽  
Self Fertilization ◽  
Mean Fitness ◽  
Selection For ◽  
Individual Based Simulation

ABSTRACTInbreeding depression resulting from partially recessive deleterious alleles is thought to be the main genetic factor preventing self-fertilizing mutants from spreading in outcrossing hermaphroditic populations. However, deleterious alleles may also generate an advantage to selfers in terms of more efficient purging, while the effects of epistasis among those alleles on inbreeding depression and mating system evolution remain little explored. In this paper, we use a general model of selection to disentangle the effects of different forms of epistasis (additive-by-additive, additive-by-dominance and dominance-by-dominance) on inbreeding depression and on the strength of selection for selfing. Models with fixed epistasis across loci, and models of stabilizing selection acting on quantitative traits (generating distributions of epistasis) are considered as special cases. Besides its effects on inbreeding depression, epistasis may increase the purging advantage associated with selfing (when it is negative on average), while the variance in epistasis favors selfing through the generation of linkage disequilibria that increase mean fitness. Approximations for the strengths of these effects are derived, and compared with individual-based simulation results.

scholarly journals Heterosis from local drift load is likely insufficient to favor reversions to outcrossing

2018 ◽  
Author(s):  
Alexander Harkness ◽  
Emma E. Goldberg ◽  
Yaniv J Brandvain
Keyword(s):  
Inbreeding Depression ◽  
Population Genetic ◽  
Allelic Variation ◽  
Initial Increase ◽  
Short Term ◽  
Genetic Theory ◽  
Evolutionary Trajectory ◽  
Deleterious Alleles ◽  
Self Fertilization ◽  
Cross Fertilization

AbstractThe evolutionary trajectory from cross-to self-fertilization is widely documented in nature, but results from several taxa also suggest that outcrossing may evolve in a formerly selfing population. Population genetic theory explains that selfing can evolve when its advantages overcome its immediate cost of inbreeding depression, but that this process will not run in reverse because a self-fertilizing population purges itself of inbreeding depression. That is, the primary short-term advantage of cross-fertilization over self-fertilization depends on the existence of deleterious alleles exposed upon inbreeding. Here, we explore whether outcrossing can evolve in selfing populations if allelic variation exists as divergence among populations. We consider two monomorphic populations of entirely self-fertilizing individuals, introduce a modifier allele that increases the rate of cross-fertilization, and investigate whether the heterosis among populations is sufficient for the modifier to invade and fix. We find that, despite an initial increase in the frequency of the outcrossing modifier, its fixation is possible only when populations harbor extremely large unique fixed genetic loads. These rare reversions to outcrossing become more likely as the load becomes more polygenic, or when the modifier appears on a rare background, such as by dispersal of an outcrossing genotype into a selfing population.

scholarly journals Selection, Load and Inbreeding Depression in a Large Metapopulation

Genetics ◽  
2002 ◽  
Vol 160 (3) ◽  
pp. 1191-1202 ◽  
Author(s):  
Michael C Whitlock
Keyword(s):  
Population Structure ◽  
Inbreeding Depression ◽  
Population Subdivision ◽  
Response To Selection ◽  
Mutation Load ◽  
Deleterious Alleles ◽  
Subdivided Population ◽  
Soft Selection ◽  
Mean Fitness ◽  
The Mean

Abstract The subdivision of a species into local populations causes its response to selection to change, even if selection is uniform across space. Population structure increases the frequency of homozygotes and therefore makes selection on homozygous effects more effective. However, population subdivision can increase the probability of competition among relatives, which may reduce the efficacy of selection. As a result, the response to selection can be either increased or decreased in a subdivided population relative to an undivided one, depending on the dominance coefficient FST and whether selection is hard or soft. Realistic levels of population structure tend to reduce the mean frequency of deleterious alleles. The mutation load tends to be decreased in a subdivided population for recessive alleles, as does the expected inbreeding depression. The magnitude of the effects of population subdivision tends to be greatest in species with hard selection rather than soft selection. Population structure can play an important role in determining the mean fitness of populations at equilibrium between mutation and selection.

Mitsuaria sp. and Burkholderia sp. from Arabidopsis rhizosphere enhance drought tolerance in Arabidopsis thaliana and maize (Zea mays L.)

2017 ◽  
Vol 419 (1-2) ◽  
pp. 523-539 ◽  
Author(s):  
Xing-Feng Huang ◽  
Dongmei Zhou ◽  
Erin R. Lapsansky ◽  
Kenneth F. Reardon ◽  
Jianhua Guo ◽  
...  
Keyword(s):  
Arabidopsis Thaliana ◽  
Zea Mays ◽  
Drought Tolerance ◽  
Zea Mays L

Towards efficient photosynthesis: overexpression of Zea mays phosphoenolpyruvate carboxylase in Arabidopsis thaliana

2016 ◽  
Vol 130 (1-3) ◽  
pp. 47-72 ◽  
Author(s):  
Deepika Kandoi ◽  
Sasmita Mohanty ◽  
Govindjee ◽  
Baishnab C. Tripathy
Keyword(s):  
Arabidopsis Thaliana ◽  
Zea Mays ◽  
Phosphoenolpyruvate Carboxylase

scholarly journals The Hermes transposable element from the house fly, Musca domestica, is a short inverted repeat-type element of the hobo, Ac, and Tam3 (hAT) element family

1994 ◽  
Vol 64 (2) ◽  
pp. 87-97 ◽  
Author(s):  
William D. Warren ◽  
Peter W. Atkinson ◽  
David A. O'Brochta
Keyword(s):  
Zea Mays ◽  
Transposable Element ◽  
Musca Domestica ◽  
House Fly ◽  
Inverse Pcr ◽  
Sequence Motif ◽  
Terminal Sequence ◽  
Repeat Type ◽  
Genetic Tool ◽  
Element System

SummaryThe genome of the house fly, Musca domestica, contains an active transposable element system, called Hermes. Using PCR and inverse PCR we amplified and sequenced overlapping segments of several Hermes elements and from these data we have constructed a 2749 bp consensus Hermes DNA sequence. Hermes termini are composed of 17 bp imperfect inverted repeats that are almost identical to the inverted terminal repeats of the hobo element of Drosophila melanogaster. Full length Hermes elements contain a single long ORF capable of encoding a protein of 612 amino acids which is 55% identical to the amino acid sequence of the hobo transposase. Comparison of the ends of the Hermes and hobo elements to those of the Ac element of Zea mays, and the Tam3 element of Antirrhinum majus, as well as several other plant and insect elements, revealed a conserved terminal sequence motif. Thus Hermes is clearly a member of the hobo, Ac and Tam3 (hAT) transposable element family, other members of which include the Tagl element from Arabidopsis thaliana and the Bg element from Zea mays. The evolution of this class of transposable elements and the potential utility of Hermes as a genetic tool in M. domestica and related species are discussed.

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