scholarly journals Deleterious Mutations Accumulate Faster in Allopolyploid than Diploid Cotton (Gossypium) and Unequally Between Subgenomes

2021 ◽  
Author(s):  
Justin L Conover ◽  
Jonathan F Wendel
Keyword(s):  
Amino Acid Level ◽  
Masking Effect ◽  
Whole Genome ◽  
Deleterious Mutations ◽  
Ploidy Levels ◽  
Gene Copies ◽  
A Genome ◽  
Redundant Gene ◽  
Wide Perspective ◽  
Whole Genome Resequencing

Whole genome duplication (polyploidization) is among the most dramatic mutational processes in nature, so understanding how natural selection differs in polyploids relative to diploids is an important goal. Population genetics theory predicts that recessive deleterious mutations accumulate faster in allopolyploids than diploids due to the masking effect of redundant gene copies, but this prediction is hitherto unconfirmed. Here, we use the cotton genus (Gossypium), which contains seven allopolyploids derived from a single polyploidization event 1-2 million years ago, to investigate deleterious mutation accumulation. We use two methods of identifying deleterious mutations at the nucleotide and amino acid level, along with whole-genome resequencing of 43 individuals spanning six allopolyploid species and their two diploid progenitors, to demonstrate that deleterious mutations accumulate faster in allopolyploids than in their diploid progenitors. We find that, unlike what would be expected under models of demographic changes alone, strongly deleterious mutations show the biggest difference between ploidy levels, and this effect diminishes for moderately and mildly deleterious mutations. We further show that the proportion of nonsynonymous mutations that are deleterious differs between the two co-resident subgenomes in the allopolyploids, suggesting that homoeologous masking acts unequally between subgenomes. Our results provide a genome-wide perspective on classic notions of the significance of gene duplication that likely are broadly applicable to allopolyploids, with implications for our understanding of the evolutionary fate of deleterious mutations. Finally, we note that some measures of selection (e.g. dN/dS, 𝛑N/𝛑S) may be biased when species of different ploidy levels are compared.

scholarly journals Accumulation of Deleterious Mutations in Landlocked Threespine Stickleback Populations

2020 ◽  
Vol 12 (4) ◽  
pp. 479-492
Author(s):  
Kohta Yoshida ◽  
Mark Ravinet ◽  
Takashi Makino ◽  
Atsushi Toyoda ◽  
Tomoyuki Kokita ◽  
...  
Keyword(s):  
Gasterosteus Aculeatus ◽  
Substantial Reduction ◽  
Threespine Stickleback ◽  
Phylogenomic Analysis ◽  
Whole Genome ◽  
Deleterious Mutations ◽  
Genome Resequencing ◽  
Isolated Populations ◽  
X Chromosomes ◽  
Whole Genome Resequencing

Abstract Colonization of new habitats often reduces population sizes and may result in the accumulation of deleterious mutations by genetic drift. Compared with the genomic basis for adaptation to new environments, genome-wide analysis of deleterious mutations in isolated populations remains limited. In the present study, we investigated the accumulation of deleterious mutations in five endangered freshwater populations of threespine stickleback (Gasterosteus aculeatus) in the central part of the mainland of Japan. Using whole-genome resequencing data, we first conducted phylogenomic analysis and confirmed at least two independent freshwater colonization events in the central mainland from ancestral marine ecotypes. Next, analyses of single nucleotide polymorphisms showed a substantial reduction of heterozygosity in freshwater populations compared with marine populations. Reduction in heterozygosity was more apparent at the center of each chromosome than the peripheries and on X chromosomes compared with autosomes. Third, bioinformatic analysis of deleterious mutations showed increased accumulation of putatively deleterious mutations in the landlocked freshwater populations compared with marine populations. For the majority of populations examined, the frequencies of putatively deleterious mutations were higher on X chromosomes than on autosomes. The interpopulation comparison indicated that the majority of putatively deleterious mutations may have accumulated independently. Thus, whole-genome resequencing of endangered populations can help to estimate the accumulation of deleterious mutations and inform us of which populations are the most severely endangered. Furthermore, analysis of variation among chromosomes can give insights into whether any particular chromosomes are likely to accumulate deleterious mutations.

scholarly journals The fate of deleterious variants in a barley genomic prediction population

2018 ◽  
Author(s):  
TJY Kono ◽  
C Liu ◽  
EE Vonderharr ◽  
D Koenig ◽  
JC Fay ◽  
...  
Keyword(s):  
Genomic Prediction ◽  
Genetic Variants ◽  
Recombination Rate ◽  
Exome Capture ◽  
Whole Genome ◽  
Genome Resequencing ◽  
Initial Frequency ◽  
A Genome ◽  
Hordeum Murinum ◽  
Whole Genome Resequencing

AbstractTargeted identification and purging of deleterious genetic variants has been proposed as a novel approach to animal and plant breeding. This strategy is motivated, in part, by the observation that demographic events and strong selection associated with cultivated species pose a “cost of domestication.” This includes an increase in the proportion of genetic variants where a mutation is likely to reduce fitness. Recent advances in DNA resequencing and sequence constraint-based approaches to predict the functional impact of a mutation permit the identification of putatively deleterious SNPs (dSNPs) on a genome-wide scale. Using exome capture resequencing of 21 barley 6-row spring breeding lines, we identify 3,855 dSNPs among 497,754 total SNPs. In order to polarize SNPs as ancestral versus derived, we generated whole genome resequencing data of Hordeum murinum ssp. glaucum as a phylogenetic outgroup. The dSNPs occur at higher density in portions of the genome with a higher recombination rate than in pericentromeric regions with lower recombination rate and gene density. Using 5,215 progeny from a genomic prediction experiment, we examine the fate of dSNPs over three breeding cycles. Average derived allele frequency is lower for dSNPs than any other class of variants. Adjusting for initial frequency, derived alleles at dSNPs reduce in frequency or are lost more often than other classes of SNPs. The highest yielding lines in the experiment, as chosen by standard genomic prediction approaches, carry fewer homozygous dSNPs than randomly sampled lines from the same progeny cycle. In the final cycle of the experiment, progeny selected by genomic prediction have a mean of 5.6% fewer homozygous dSNPs relative to randomly chosen progeny from the same cycle.Author SummaryThe nature of genetic variants underlying complex trait variation has been the source of debate in evolutionary biology. Here, we provide evidence that agronomically important phenotypes are influenced by rare, putatively deleterious variants. We use exome capture resequencing and a hypothesis-based test for codon conservation to predict deleterious SNPs (dSNPS) in the parents of a multi-parent barley breeding population. We also generated whole-genome resequencing data of Hordeum murinum, a phylogenetic outgroup to barley, to polarize dSNPs by ancestral versus derived state. dSNPs occur disproportionately in the gene-rich chromosome arms, rather than in the recombination-poor pericentromeric regions. They also decrease in frequency more often than other variants at the same initial frequency during recurrent selection for grain yield and disease resistance. Finally, we identify a region on chromosome 4H that strongly associated with agronomic phenotypes in which dSNPs appear to be hitchhiking with favorable variants. Our results show that targeted identification and removal of dSNPs from breeding programs is a viable strategy for crop improvement, and that standard genomic prediction approaches may already contain some information about unobserved segregating dSNPs.

scholarly journals Analysis of the Segregation Distortion of FcRAN1 Genotypes Based on Whole-Genome Resequencing of Fig (Ficus carica L.) Breeding Parents

2021 ◽  
Vol 12 ◽  
Author(s):  
Hidetoshi Ikegami ◽  
Kenta Shirasawa ◽  
Hiroshi Yakushiji ◽  
Shiori Yabe ◽  
Masaru Sato ◽  
...  
Keyword(s):  
Segregation Distortion ◽  
Segregation Ratio ◽  
High Impact ◽  
Ficus Carica ◽  
Normal Embryo ◽  
Whole Genome ◽  
Genome Resequencing ◽  
A Genome ◽  
Whole Genome Resequencing ◽  
And Function

The common fig (Ficus carica L.) has a gynodioecious breeding system, and its sex phenotype is an important trait for breeding because only female plant fruits are edible. During breeding to select for female plants, we analyzed the FcRAN1 genotype, which is strongly associated with the sex phenotype. In 12 F1 populations derived from 13 cross combinations, the FcRAN1 genotype segregation ratio was 1:1, whereas the M119-226 × H238-107 hybridization resulted in an extremely male-biased segregation ratio (178:7 = male:female). This finding suggests that the segregation distortion was caused by some genetic factor(s). A whole-genome resequencing of breeding parents (paternal and maternal lines) identified 9,061 high-impact SNPs in the parents. A genome-wide linkage analysis exploring the gene(s) responsible for the distortion revealed 194 high-impact SNPs specific to Caprifig6085 (i.e., seed parent ancestor) and 215 high-impact SNPs specific to H238-107 (i.e., pollen parent) in 201 annotated genes. A comparison between the annotated genes and the genes required for normal embryo or gametophyte development and function identified several candidate genes possibly responsible for the segregation distortion. This is the first report describing segregation distortion in F. carica.

scholarly journals Whole genome resequencing and custom genotyping unveil clonal lineages in ‘Malbec’ grapevines (Vitis vinifera L.)

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Luciano Calderón ◽  
Nuria Mauri ◽  
Claudio Muñoz ◽  
Pablo Carbonell-Bejerano ◽  
Laura Bree ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Somatic Mutations ◽  
Clonal Propagation ◽  
Variant Calling ◽  
Vitis Vinifera L ◽  
Whole Genome ◽  
Single Nucleotide Variants ◽  
Genome Resequencing ◽  
Diversity Pattern ◽  
Whole Genome Resequencing

AbstractGrapevine cultivars are clonally propagated to preserve their varietal attributes. However, genetic variations accumulate due to the occurrence of somatic mutations. This process is anthropically influenced through plant transportation, clonal propagation and selection. Malbec is a cultivar that is well-appreciated for the elaboration of red wine. It originated in Southwestern France and was introduced in Argentina during the 1850s. In order to study the clonal genetic diversity of Malbec grapevines, we generated whole-genome resequencing data for four accessions with different clonal propagation records. A stringent variant calling procedure was established to identify reliable polymorphisms among the analyzed accessions. The latter procedure retrieved 941 single nucleotide variants (SNVs). A reduced set of the detected SNVs was corroborated through Sanger sequencing, and employed to custom-design a genotyping experiment. We successfully genotyped 214 Malbec accessions using 41 SNVs, and identified 14 genotypes that clustered in two genetically divergent clonal lineages. These lineages were associated with the time span of clonal propagation of the analyzed accessions in Argentina and Europe. Our results show the usefulness of this approach for the study of the scarce intra-cultivar genetic diversity in grapevines. We also provide evidence on how human actions might have driven the accumulation of different somatic mutations, ultimately shaping the Malbec genetic diversity pattern.

scholarly journals Three founding ancestral genomes involved in the origin of sugarcane

2021 ◽  
Author(s):  
Nicolas Pompidor ◽  
Carine Charron ◽  
Catherine Hervouet ◽  
Stéphanie Bocs ◽  
Gaëtan Droc ◽  
...  
Keyword(s):  
Evolutionary Model ◽  
Saccharum Officinarum ◽  
Modern Cultivar ◽  
Ploidy Levels ◽  
Saccharum Spp ◽  
Bac Clones ◽  
B Genome ◽  
A Genome ◽  
Genomic Regions ◽  
Complex Genome

Abstract Background and Aims Modern sugarcane cultivars (Saccharum spp.) are high polyploids, aneuploids (2n = ~12x = ~120) derived from interspecific hybridizations between the domesticated sweet species Saccharum officinarum and the wild species S. spontaneum. Methods To analyse the architecture and origin of such a complex genome, we analysed the sequences of all 12 hom(oe)ologous haplotypes (BAC clones) from two distinct genomic regions of a typical modern cultivar, as well as the corresponding sequence in Miscanthus sinense and Sorghum bicolor, and monitored their distribution among representatives of the Saccharum genus. Key Results The diversity observed among haplotypes suggested the existence of three founding genomes (A, B, C) in modern cultivars, which diverged between 0.8 and 1.3 Mya. Two genomes (A, B) were contributed by S. officinarum; these were also found in its wild presumed ancestor S. robustum, and one genome (C) was contributed by S. spontaneum. These results suggest that S. officinarum and S. robustum are derived from interspecific hybridization between two unknown ancestors (A and B genomes). The A genome contributed most haplotypes (nine or ten) while the B and C genomes contributed one or two haplotypes in the regions analysed of this typical modern cultivar. Interspecific hybridizations likely involved accessions or gametes with distinct ploidy levels and/or were followed by a series of backcrosses with the A genome. The three founding genomes were found in all S. barberi, S. sinense and modern cultivars analysed. None of the analysed accessions contained only the A genome or the B genome, suggesting that representatives of these founding genomes remain to be discovered. Conclusions This evolutionary model, which combines interspecificity and high polyploidy, can explain the variable chromosome pairing affinity observed in Saccharum. It represents a major revision of the understanding of Saccharum diversity.

scholarly journals Whole genome resequencing of black Angus and Holstein cattle for SNP and CNV discovery

BMC Genomics ◽  
2011 ◽  
Vol 12 (1) ◽  
Author(s):  
Paul Stothard ◽  
Jung-Woo Choi ◽  
Urmila Basu ◽  
Jennifer M Sumner-Thomson ◽  
Yan Meng ◽  
...  
Keyword(s):  
Holstein Cattle ◽  
Whole Genome ◽  
Genome Resequencing ◽  
Whole Genome Resequencing
Sign in / Sign up

Export Citation Format

Share Document