Crossover-active regions of the wheat genome are distinguished by DMC1, the chromosome axis, H3K27me3, and signatures of adaptation

The hexaploid bread wheat genome comprises over 16 gigabases of sequence across 21 chromosomes. Meiotic crossovers are highly polarized along the chromosomes, with elevation in the gene-dense distal regions and suppression in the Gypsy retrotransposon-dense centromere-proximal regions. We profiled the genomic landscapes of the meiotic recombinase DMC1 and the chromosome axis protein ASY1 in wheat and investigated their relationships with crossovers, chromatin state, and genetic diversity. DMC1 and ASY1 chromatin immunoprecipitation followed by sequencing (ChIP-seq) revealed strong co-enrichment in the distal, crossover-active regions of the wheat chromosomes. Distal ChIP-seq enrichment is consistent with spatiotemporally biased cytological immunolocalization of DMC1 and ASY1 close to the telomeres during meiotic prophase I. DMC1 and ASY1 ChIP-seq peaks show significant overlap with genes and transposable elements in the Mariner and Mutator superfamilies. However, DMC1 and ASY1 ChIP-seq peaks were detected along the length of each chromosome, including in low-crossover regions. At the fine scale, crossover elevation at DMC1 and ASY1 peaks and genes correlates with enrichment of the Polycomb histone modification H3K27me3. This indicates a role for facultative heterochromatin, coincident with high DMC1 and ASY1, in promoting crossovers in wheat and is reflected in distalized H3K27me3 enrichment observed via ChIP-seq and immunocytology. Genes with elevated crossover rates and high DMC1 and ASY1 ChIP-seq signals are overrepresented for defense-response and immunity annotations, have higher sequence polymorphism, and exhibit signatures of selection. Our findings are consistent with meiotic recombination promoting genetic diversity, shaping host–pathogen co-evolution, and accelerating adaptation by increasing the efficiency of selection.

Download Full-text

Genetic diversity and matrilineal genetic signature of native Ethiopian donkeys (Equus asinus) inferred from mitochondrial DNA sequence polymorphism

Livestock Science ◽

10.1016/j.livsci.2014.06.006 ◽

2014 ◽

Vol 167 ◽

pp. 73-79 ◽

Cited By ~ 8

Author(s):

E. Kefena ◽

T. Dessie ◽

A. Tegegne ◽

A. Beja-Pereira ◽

M. Yusuf Kurtu ◽

...

Keyword(s):

Genetic Diversity ◽

Mitochondrial Dna ◽

Dna Sequence ◽

Sequence Polymorphism ◽

Mitochondrial Dna Sequence ◽

Genetic Signature ◽

Equus Asinus ◽

Dna Sequence Polymorphism

Download Full-text

Characterization of a haplotype- reference panel for genotyping by low-pass sequencing in Swiss Large White pigs

10.21203/rs.3.rs-318745/v1 ◽

2021 ◽

Author(s):

Adéla Nosková ◽

Meenu Bhati ◽

Naveen Kumar Kadri ◽

Danang Crysnanto ◽

Stefan Neuenschwander ◽

...

Keyword(s):

Genetic Diversity ◽

Principal Component ◽

Cost Effective ◽

Reference Panel ◽

Effective Population ◽

Large White ◽

Breeding Populations ◽

Low Pass ◽

Signatures Of Selection ◽

Genomic Inbreeding

Abstract Background The key-ancestor approach has been frequently applied to prioritize individuals for whole-genome sequencing based on their marginal genetic contribution to current populations. Using this approach, we selected 70 key ancestors from two lines of the Swiss Large White breed that have been selected divergently for fertility and fattening traits and sequenced their genomes with short paired-end reads. Results Using pedigree records, we estimated the effective population size of the dam and sire line to 72 and 44, respectively. In order to assess sequence variation in both lines, we sequenced the genomes of 70 boars at an average coverage of 16.69-fold. The boars explained 87.95 and 95.35% of the genetic diversity of the breeding populations of the dam and sire line, respectively. Reference-guided variant discovery using the GATK revealed 26,862,369 polymorphic sites. Principal component, admixture and FST analyses indicated considerable genetic differentiation between the lines. Genomic inbreeding quantified using runs of homozygosity was higher in the sire than dam line (0.28 vs 0.26). Using two complementary approaches (CLR and iHS), we detected 51 signatures of selection. However, only six signatures of selection overlapped between both lines. We used the sequenced haplotypes of the 70 key ancestors as a reference panel to call 22,618,811 genotypes in 175 pigs that had been sequenced at very low coverage (1.11-fold) using GLIMPSE. The genotype concordance, non-reference sensitivity and non-reference discrepancy between thus inferred and Illumina PorcineSNP60 BeadChip-called genotypes was 97.60, 98.73 and 3.24%, respectively. The low-pass sequencing-derived genomic relationship coefficients were highly correlated (r > 0.99) with those obtained from microarray genotyping. Conclusions We assessed genetic diversity within and between two lines of the Swiss Large White pig breed. Our analyses revealed considerable differentiation, even though the split into two populations occurred only few generations ago. The sequenced haplotypes of the key ancestor animals enabled us to implement genotyping by low-pass sequencing which offers an intriguing cost-effective approach to increase the variant density over current array-based genotyping by more than 350-fold.

Download Full-text

Population‐dependent reproducible deviation from natural bread wheat genome in synthetic hexaploid wheat

The Plant Journal ◽

10.1111/tpj.14480 ◽

2019 ◽

Vol 100 (4) ◽

pp. 801-812 ◽

Cited By ~ 2

Author(s):

Abdulqader Jighly ◽

Reem Joukhadar ◽

Deepmala Sehgal ◽

Sukhwinder Singh ◽

Francis C. Ogbonnaya ◽

...

Keyword(s):

Bread Wheat ◽

Hexaploid Wheat ◽

Wheat Genome ◽

Synthetic Hexaploid Wheat ◽

Synthetic Hexaploid ◽

Bread Wheat Genome

Download Full-text

Assessment of genetic diversity and Signatures of Selection in Korean Cattle Populations

Journal of Animal Breeding and Genomics ◽

10.12972/jabng.20190013 ◽

2019 ◽

Vol 3 (4) ◽

Keyword(s):

Genetic Diversity ◽

Korean Cattle ◽

Signatures Of Selection

Download Full-text

Genetic diversity and signatures of selection of drug resistance in Plasmodium populations from both human and mosquito hosts in continental Equatorial Guinea

Malaria Journal ◽

10.1186/1475-2875-12-114 ◽

2013 ◽

Vol 12 (1) ◽

pp. 114 ◽

Cited By ~ 10

Author(s):

Cristina Mendes ◽

Patrícia Salgueiro ◽

Vicenta Gonzalez ◽

Pedro Berzosa ◽

Agustin Benito ◽

...

Keyword(s):

Genetic Diversity ◽

Drug Resistance ◽

Equatorial Guinea ◽

Signatures Of Selection ◽

Selection Of

Download Full-text

Natural selection and genetic diversity in the butterfly Heliconius melpomene

10.1101/042796 ◽

2016 ◽

Cited By ~ 2

Author(s):

Simon Henry Martin ◽

Markus Moest ◽

Wiliam J Palmer ◽

Camilo Salazar ◽

W. Owen McMillan ◽

...

Keyword(s):

Genetic Diversity ◽

Complete Understanding ◽

Recombination Rates ◽

Synonymous Mutations ◽

Evolutionary Forces ◽

Heliconius Melpomene ◽

Adaptive Diversity ◽

Different Populations ◽

Signatures Of Selection ◽

Linked Selection

A combination of selective and neutral evolutionary forces shape patterns of genetic diversity in nature. Among the insects, most previous analyses of the roles of drift and selection in shaping variation across the genome have focused on the genus Drosophila. A more complete understanding of these forces will come from analysing other taxa that differ in population demography and other aspects of biology. We have analysed diversity and signatures of selection in the neotropical Heliconius butterflies using resequenced genomes from 58 wild-caught individuals of H. melpomene, and another 21 resequenced genomes representing 11 related species. By comparing intra-specific diversity and inter-specific divergence, we estimate that 31% of amino acid substitutions between Heliconius species are adaptive. Diversity at putatively neutral sites is negatively correlated with gene density and positively correlated with recombination rate, indicating widespread linked selection. This process also manifests in significantly reduced diversity on longer chromosomes, consistent with lower recombination rates. Genetic hitchhiking around beneficial non-synonymous mutations has also had a significant impact on genetic variation in this species, but evidence for strong selective sweeps was limited overall. We did however identify two regions where distinct haplotypes have swept in different populations, leading to increased population differentiation. On the whole, our study suggests that positive selection is less pervasive in these butterflies as compared to fruit flies; a fact that curiously results in very similar levels of neutral diversity in these very different insects.

Download Full-text

Signatures of selection and genomic diversity of Muskellunge (Esox masquinongy) from two populations in North America.

10.21203/rs.3.rs-264701/v3 ◽

2021 ◽

Author(s):

Josue Chinchilla-Vargas ◽

Jonathan R. Meerbeek ◽

Max F. Rothschild ◽

Francesca Bertolini

Keyword(s):

Genetic Diversity ◽

North America ◽

Related Species ◽

Reference Genome ◽

Genetic Differences ◽

Genomic Diversity ◽

Closely Related Species ◽

Esox Masquinongy ◽

Inbreeding Rate ◽

Signatures Of Selection

Abstract Background Muskellunge (Esox masquinongy) is the largest and most prized game fish for anglers in North America. However, little is known about Muskellunge genetic diversity in Iowa’s propagation program. We used whole genome sequence from 12 brooding individuals from Iowa and publicly available RAD-seq of 625 individuals from Saint-Lawrence river in Canada to study the genetic differences between populations, analyze signatures of selection that might shed light on environmental adaptations, and evaluate the levels of genetic diversity in both populations. Given that there is no reference genome available for Muskellunge, reads were aligned to the genome of Pike (Esox lucius), a closely-related species.Results Variant calling produced 7,886,471 biallelic variants for the Iowa population and 16,867 high-quality SNPs that overlap with the Canadian samples. The Ti/Tv values were 1.09 and 1.29 for samples from Iowa and Canada, respectively. PCA and Admixture analyses showed a large genetic difference between Canadian and Iowan populations. Moreover, PCA showed clustering by sex in the Iowan population although widow-based Fst did not find outlier regions. Window-based pooled heterozygosity found 6 highly heterozygous windows containing 244 genes in the Iowa population and Fst comparing the Iowa and Canadian populations found 14 windows with Fst values larger than 0.9 containing 641 genes. One enriched GO term (sensory perception of pain) was found through pooled heterozygosity analyzes. Although not significant, several enriched GO terms associated to growth and development were found through Fst analyses.Inbreeding calculated as Froh was 0.03 on average for the Iowa population and 0.32 on average for the Canadian samples. The Canadian inbreeding rate appears to be higher, presumably due to isolation of subpopulations, than the inbreeding rate of the Iowa population.Conclusions This study was the first to document that brood stock Muskellunge from Iowa showed marked genetic differences with the Canadian population. Additionally, despite genetic differentiation based on sex has been observed, no major locus has been detected. Inbreeding does not seem to be an immediate concern for Muskellunge in Iowa, but apparent isolation of subpopulations has caused levels of homozygosity to increase in the Canadian Muskellunge population. Finally, these results prove the validity of using genomes of closely related species to perform genomic analyses when no reference genome assembly is available.

Download Full-text

Signatures of selection and genomic diversity of Muskellunge (Esox masquinongy) from two populations in North America.

10.21203/rs.3.rs-264701/v1 ◽

2021 ◽

Author(s):

Josue Chinchilla-Vargas ◽

Max F. Rothschild ◽

Francesca Bertolini

Keyword(s):

Genetic Diversity ◽

North America ◽

Related Species ◽

Reference Genome ◽

Genetic Differences ◽

Genomic Diversity ◽

Whole Genome Sequence ◽

Closely Related Species ◽

Esox Masquinongy ◽

Signatures Of Selection

Abstract Background Muskellunge (Esox masquinongy) is the largest and most prized game fish for anglers in North America. However, little is known about Muskellunge genetic diversity in Iowa’s propagation program. We used whole genome sequence from 12 brooding individuals from Iowa and publicly available RAD-seq of 625 individuals from Saint-Lawrence river in Canada to study the genetic differences between populations, analyze signatures of selection that might shed light on environmental adaptations, and evaluate the levels of genetic diversity in both populations. Given that there is no reference genome available for Muskellunge, reads were aligned to the genome of Pike (Esox lucius), a closely-related species. Results Variant calling produced 7,886,471 biallelic variants for the Iowa population and 16,867 high quality SNPs that overlap with the Canadian samples. The Ti/Tv values were 1.09 and 1.29 for samples from Iowa and Canada, respectively. PCA and Admixture analyses showed a large genetic difference between Canadian and Iowan populations. Moreover, PCA showed a clustering by sex in the Iowan population although widow-based Fst did not find outlier regions. Window based pooled heterozygosity found 6 highly heterozygous windows containing 244 genes in the Iowa population and Fst comparing the Iowa and Canadian populations found 14 windows with Fst values larger than 0.9 containing 641 genes. One enriched GO term (sensory perception of pain) was found through pooled heterozygosity analyzes. Although not significant, several enriched GO terms associated to growth and development were found through Fst analyses. Inbreeding calculated as Froh was 0.03 on average for the Iowa population and 0.32 on average for the Canadian samples. The inbreeding rate appears is presumably due to isolation of subpopulations. Conclusions This study is the first of its kind in Muskellunge from Iowa in which captured brood stock showed marked genetic differences with the Canadian population. Additionally, despite genetic differentiation based on sex has been observed, no major locus has been detected . Inbreeding does not seem to be an immediate concern for Muskellunge in Iowa, isolation of subpopulations has caused levels of homozygosity to increase in the Canadian Muskellunge population. These results prove the validity of using genomes of closely related species to perform genomic analyses when no reference genome assembly is available.

Download Full-text