Unlocking the secrets of Brassica oleracea crops : A genomic journey DOI Open Access
Chengcheng Cai

Published: May 30, 2023

Evidence for two domestication lineages supporting a middle-eastern origin Brassica oleracea crops from diversified kale populations C h p t e r 3 4 9Chromosome-scale genome assemblies of five different morphotypes provide insights in intraspecific diversification 8 3Fine mapping meiotic crossovers reveals patterns and variations depending on direction combination crosses 5 1 5Metabolomic transcriptomic profiles diverse into genetic regulation glucosinolate variation 6 1General Discussion which includes three consecutive steps: 1) overlap graph construction potentially overlapping reads searching, 2) merging simplification, 3) DNA sequence deriving error correction (Jung et al., 2019).Although long-read by far surpass short-read contiguity completeness, solely long are still not sufficient to resolve complex genomes at the chromosome level.Usually, additional long-range information is required create super-scaffolds or chromosome-scale assemblies.One such technology currently commonly used Bionano Genomics optical mapping, uses fluorescently labelled enzymes produce fingerprints fragments multiple hundreds kb imaging locations restriction sites under light microscopes (Jiao 2017, Jiao andSchneeberger, 2017).The molecules can be assembled genomewide maps that serve as skeleton order orient contig sequences.Bionano Genomics' new Direct Label Stain (DLS) Labeling Enzyme (DLE-1) attach single fluorophore specific motifs does make sequence-specific nicks via nicking endonucleases.Thus, this method damage (Deschamps 2018).The DLSlabeled much longer than those endonuclease approach, with longest ones becoming larger 2 Mbp.Another Hi-C, generates genome-wide libraries originally close-by loci nucleus using proximity ligation approach (Lieberman-Aiden 2009, Logsdon 2020).The between pairs provided Hi-C sequencing data reach tens megabases apart same (Ghurye 2019, 2020).Currently, longrange scaffolding technologies becomes common standard generate high quality (Rousseau-Gueutin 2020). Genome plants B. oleraceaIn 2000, first plant A. thaliana was released (Arabidopsis Initiative, 2000).Initially, it difficult assemble short reads, especially species large repeat-rich levels ploidy.However, due advances computational algorithms, field has grown rapidly past 20 years, more 800 being date (Marks 2021).Among these genomes, sugar pine (Pinus lambertiana) largest size, an assembly size 27.6 Gb (Stevens 2016).The have relatively medium-sized genomes.For example, estimated around 600 Mb based flow cytometry

Language: Английский

Comprehensive dissection of meiotic DNA double-strand breaks and crossovers in cucumber DOI Creative Commons
Yanling Wang,

Zhaonian Dong,

Yalin Ma

et al.

PLANT PHYSIOLOGY, Journal Year: 2023, Volume and Issue: 193(3), P. 1913 - 1932

Published: Aug. 2, 2023

Meiotic recombination drives genetic diversity and crop genome optimization. In plant breeding, parents with favorable traits are crossed to create elite varieties. Different hybridizations produce diverse types of segment reshuffling between homologous chromosomes. However, little is known about the factors that cause hybrid-specific changes in crossovers (COs). Here, we constructed 2 F2 populations from crosses a semiwild domesticated cucumber (Cucumis sativus) accessions examined CO events. COs mainly occurred around genes differed unevenly along chromosomes hybrids. Fine-scale distributions were suppressed regions heterozygous structural variations (SVs) accelerated by high sequence polymorphism. C. sativus RADiation sensitive 51A (CsRAD51A) binding, histone H3 lysine 4 trimethylation (H3K4me3) modification, chromatin accessibility, hypomethylation positively associated global landscapes local DNA double-strand break (DSB) hotspots genes. The frequency suppression could be roughly predicted based on multiomic information. Differences events hybrids partially traced distinct epigenetic features significantly specific DSB SVs. Our findings identify genomic contribute formation divergence provide theoretical support for selecting parental combinations manipulating at target during breeding.

Language: Английский

Citations

4
Alternating between even and odd ploidy levels switches on and off the recombination control, even near the centromeres DOI
Franz Boideau, Virginie Huteau, Loeiz Maillet

et al.

The Plant Cell, Journal Year: 2024, Volume and Issue: 36(10), P. 4472 - 4490

Published: Aug. 9, 2024

Abstract Meiotic recombination is a key biological process in plant evolution and breeding, as it generates genetic diversity each generation through the formation of crossovers (COs). However, due to their importance genome stability, COs are highly regulated frequency distribution. We previously demonstrated that this strict regulation can be modified, both terms CO distribution, allotriploid Brassica hybrids (2n = 3x 29; AAC) resulting from cross between napus 4x 38; AACC) rapa 2x 20; AA). Using recently updated B. now including pericentromeres, we occur these cold regions allotriploids, close 375 kb centromere. Reverse transcription quantitative PCR (RT-qPCR) various meiotic genes indicated Class I likely involved increased observed allotriploids. also modified landscape maintained via successive generations allotriploidy (odd ploidy level). This deregulated behavior reverts allotetraploid (even level) progeny second generation. Overall, provide an easy way manipulate tight control polyploid crop.

Language: Английский

Citations

1
Playing with the ploidy level enables to switch on and off the strict recombination control even in the vicinity ofBrassicacentromeres DOI Creative Commons
Franz Boideau, Virginie Huteau, Anael Brunet

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: Feb. 21, 2024

Abstract Meiotic recombination is a key biological process in plant evolution and breeding, as it generates novel genetic diversity at each generation. However, due to its importance chromosome segregation genomic stability, crossovers are highly regulated both frequency distribution. We previously demonstrated that this strict regulation not fatality can be naturally modified (3.6-fold increased altered distribution) an allotriploid Brassica hybrid (2 n =3 x =29; AAC), resulting from cross between B. napus =4 =38; AACC) rapa =2 =20; AA). Taking advantage of the recently updated genome assembly, which now includes pericentromeric regions, we unambiguously occur these normally cold regions allotriploids, with presence close 375 kb centromere. deciphered landscape (both maintained successive generations allotriploidy, even slight increase crossover frequency. also showed deregulated meiotic behavior may revert back strictly one when recovering allotetraploid progeny second Overall, provide here for first time practical natural way switch on off tight control polyploid crop. discuss potential role speciation success.

Language: Английский

Citations

0
Genomic divergence shaped the genetic regulation of meiotic homologous recombination inBrassicaallopolyploids DOI Creative Commons
Alexandre Pelé, Matthieu Falque, Maryse Lodé-Taburel

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: Dec. 15, 2024

Summary The tight regulation of meiotic recombination between homologs is disrupted in Brassica AAC allotriploids, a genomic configuration that may have facilitated the formation rapeseed ( napus L.) ∼7,500 years ago. Indeed, presence haploid C genome induces supernumerary crossovers homologous A chromosomes with dramatically reshaped distribution. However, genetic mechanisms driving this phenomenon and their divergence nascent established lineages remain unclear. To address these concerns, we generated hybrids carrying additional derived either from an lineage allotetraploid B. or its diploid progenitor oleracea . We then assessed variation across twelve populations by mapping male using Single Nucleotide Polymorphism markers evenly distributed sequenced genome. Our findings reveal C09 chromosome responsible for near pericentromeric regions. Interestingly, counterpart shows no significant effect on own, despite having similar content genes. showed influences crossover through inter-chromosomal epistatic interactions other specific chromosomes. These results provide new insights into emphasize role since allopolyploid

Language: Английский

Citations

0
Analysis of the winter oilseed rape recombination landscape suggests maternal–paternal bias DOI
Nayyer Abdollahi Sisi, Eva Herzog, Amine Abbadi

et al.

Genome, Journal Year: 2024, Volume and Issue: unknown

Published: Oct. 21, 2024

Recombination, the reciprocal exchange of DNA between homologous chromosomes, is a mandatory step necessary for meiosis progression. Crossovers chromosomes generate new combinations alleles and maintain genetic diversity. Due to genetic, epigenetic, environmental factors, recombination landscape highly heterogeneous along it also differs populations sexes. Here, we investigated characteristics across 19 model allopolyploid crop species oilseed rape ( Brassica napus L.), using two unique multiparental derived from genetically divergent founder pools, each which comprised 50 diverse accessions. A fully balanced, pairwise chain-crossing scheme was utilized create populations. total 3213 individuals, spanning five successive generations, were genotyped 15K SNP array. We observed uneven distribution with some genomic regions undergoing substantially more frequent in both In populations, maternal events than paternal recombination. This study provides insight into at chromosomal level reveals maternal–paternal bias number implications breeding.

Language: Английский

Citations

0
Broad-scale signatures of linked selection under divergent recombination landscapes and mating systems in natural populations of rye and barley DOI Creative Commons
Christina Waesch, Steven Dreißig

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2023, Volume and Issue: unknown

Published: Feb. 27, 2023

Abstract Understanding the interactions between patterns of recombination, mating systems, and signatures natural selection is a central aim in evolutionary biology. Patterns recombination shape evolution genomes by affecting efficacy selection. Within populations, genetic shuffling achieved through meiotic random chromosome segregation, frequency outbreeding. Recombination landscapes vary species are further influenced systems. Here, we use populations two related grass species, rye ( Secale cereale ) barley Hordeum vulgare ssp. spontaneum ), that differ their system, to analyse linked under divergent landscapes. Rye (outbreeding) (inbreeding) members Poaceae diverged approximately 15 M years ago. We estimated population rates, analysed diversity, identified selection, quantified fraction functional class genes affected In this comparison, detected low-recombining regions both species. inbreeding barley, genome was more than 2-fold larger outbreeding rye. Furthermore, considering differences gene density across genome, 1.5 times were genomic harbour mostly involved basic cellular processes. provide empirical evidence for quantitative closely discuss consequences Significance statement The ability disentangle beneficial from deleterious mutations shaped yet our understanding magnitude interaction incomplete. work, show differs them.

Language: Английский

Citations

0
Unlocking the secrets of Brassica oleracea crops : A genomic journey DOI Open Access
Chengcheng Cai

Published: May 30, 2023

Evidence for two domestication lineages supporting a middle-eastern origin Brassica oleracea crops from diversified kale populations C h p t e r 3 4 9Chromosome-scale genome assemblies of five different morphotypes provide insights in intraspecific diversification 8 3Fine mapping meiotic crossovers reveals patterns and variations depending on direction combination crosses 5 1 5Metabolomic transcriptomic profiles diverse into genetic regulation glucosinolate variation 6 1General Discussion which includes three consecutive steps: 1) overlap graph construction potentially overlapping reads searching, 2) merging simplification, 3) DNA sequence deriving error correction (Jung et al., 2019).Although long-read by far surpass short-read contiguity completeness, solely long are still not sufficient to resolve complex genomes at the chromosome level.Usually, additional long-range information is required create super-scaffolds or chromosome-scale assemblies.One such technology currently commonly used Bionano Genomics optical mapping, uses fluorescently labelled enzymes produce fingerprints fragments multiple hundreds kb imaging locations restriction sites under light microscopes (Jiao 2017, Jiao andSchneeberger, 2017).The molecules can be assembled genomewide maps that serve as skeleton order orient contig sequences.Bionano Genomics' new Direct Label Stain (DLS) Labeling Enzyme (DLE-1) attach single fluorophore specific motifs does make sequence-specific nicks via nicking endonucleases.Thus, this method damage (Deschamps 2018).The DLSlabeled much longer than those endonuclease approach, with longest ones becoming larger 2 Mbp.Another Hi-C, generates genome-wide libraries originally close-by loci nucleus using proximity ligation approach (Lieberman-Aiden 2009, Logsdon 2020).The between pairs provided Hi-C sequencing data reach tens megabases apart same (Ghurye 2019, 2020).Currently, longrange scaffolding technologies becomes common standard generate high quality (Rousseau-Gueutin 2020). Genome plants B. oleraceaIn 2000, first plant A. thaliana was released (Arabidopsis Initiative, 2000).Initially, it difficult assemble short reads, especially species large repeat-rich levels ploidy.However, due advances computational algorithms, field has grown rapidly past 20 years, more 800 being date (Marks 2021).Among these genomes, sugar pine (Pinus lambertiana) largest size, an assembly size 27.6 Gb (Stevens 2016).The have relatively medium-sized genomes.For example, estimated around 600 Mb based flow cytometry

Language: Английский

Citations

0