Smart breeding driven by advances in sequencing technology

Modern Agriculture, Journal Year: 2023, Volume and Issue: 1(1), P. 43 - 56

Published: March 1, 2023

Abstract Crop breeding has undergone numerous advancements throughout history with the next revolution being uncertain. This review provides an overview of techniques from traditional selective and crossbreeding to modern based on molecular marker‐assisted genomic selection. Systematic analysis mainstream genotyping approaches principle, application scenario supporting software revealed that changes in technology have led explosion data. data expansion will drive a breakthrough sequencing integrate artificial intelligence automation. The also discusses technological associated during big era, including models, technologies future intelligent breeding, provide references for crop breeders. paper highlights potential smart driven by advances technology, which lead development new strategies accelerate process.

Language: Английский

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Transgressive and parental dominant gene expression and cytosine methylation during seed development in Brassica napus hybrids

Theoretical and Applied Genetics, Journal Year: 2023, Volume and Issue: 136(5)

Published: April 18, 2023

Transcriptomic and epigenomic profiling of gene expression small RNAs during seed seedling development reveals methylation dominance levels with implications on early stage heterosis in oilseed rape. The enhanced performance hybrids through remains a key aspect plant breeding; however, the underlying mechanisms are still not fully elucidated. To investigate potential role transcriptomic patterns hybrid vigor, we investigated expression, RNA abundance genome-wide from two distant Brassica napus ecotypes developmental stages using next-generation sequencing. A total 31117, 344, 36229 7399 differentially expressed genes, microRNAs, interfering methylated regions were identified, respectively. Approximately 70% or features displayed parental where followed same as parents. Via ontology enrichment microRNA-target association analyses development, found copies reproductive, meiotic genes transgressive paternal patterns. Interestingly, maternal was more prominent hypermethylated downregulated formation, contrasting to general gamete demethylation reported gametogenesis angiosperms. Associations between allowed identification putative epialleles diverse pivotal biological functions formation. Furthermore, most regions, siRNAs transposable elements that flanked without differential expression. This suggests may help maintain context. Differential formation an F1 provide novel insights into roles heterosis.

Language: Английский

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Dosage-sensitivity shapes how genes transcriptionally respond to allopolyploidy and homoeologous exchange in resynthesized Brassica napus

Genetics, Journal Year: 2023, Volume and Issue: 225(1)

Published: June 20, 2023

The gene balance hypothesis proposes that selection acts on the dosage (i.e. copy number) of genes within dosage-sensitive portions networks, pathways, and protein complexes to maintain balanced stoichiometry interacting proteins, because perturbations stoichiometric can result in reduced fitness. This has been called selection. Dosage is also hypothesized constrain expression responses changes, making (those encoding members proteins) experience more similar changes. In allopolyploids, where whole-genome duplication involves hybridization diverged lineages, organisms often homoeologous exchanges recombine, duplicate, delete regions genome alter pairs. Although makes predictions about response exchanges, they have not empirically tested. We used genomic transcriptomic data from 6 resynthesized, isogenic Brassica napus lines over 10 generations identify analyzed responses, tested for patterns imbalance. Groups had less variable than dosage-insensitive genes, a sign their relative constrained. difference was absent pairs whose biased toward B. A subgenome. Finally, duplication, suggesting create These findings expand our knowledge impact evolution potentially connect polyploid genomes time, homoeolog bias duplicate retention.

Language: Английский

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The occurrence, inheritance, and segregation of complex genomic structural variation in synthetic Brassica napus

The Crop Journal, Journal Year: 2024, Volume and Issue: 12(2), P. 515 - 528

Published: Feb. 7, 2024

"Synthetic" allopolyploids recreated by interspecific hybridization play an important role in providing novel genomic variation for crop improvement. Such synthetic often undergo rapid structural (SV). However, how such SV arises, is inherited and fixed, it affects traits, has rarely been comprehensively quantitively studied advanced generation lines. A better understanding of these processes will aid breeders knowing to best utilize breeding programs. Here, we analyzed three genetic mapping populations (735 DH lines) derived from crosses between conventional Brassica napus (rapeseed) lines, using whole-genome sequencing determine genome composition. We observed high tolerance large variants, particularly toward the telomeres, preferential selection balanced homoeologous exchanges (duplication/deletion events C genomes resulting retention gene/chromosome dosage chromosome pairs), including stable involving whole chromosomes ("pseudoeuploidy"). Given experimental design (all shared a common parent), were able observe that parental was regularly inherited, showed hitchhiking effects on segregation, one major factors inducing adjacent larger SV. Surprisingly, occurred at low frequencies with no significant impacts fertility yield-related traits incorporating genome-wide linkage explained significantly more variance traits. Our results provide framework detecting occurrence inheritance programs, support use parents as source trait variation.

Language: Английский

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Genome‐wide patterns of homoeologous gene flow in allotetraploid coffee

Applications in Plant Sciences, Journal Year: 2024, Volume and Issue: 12(4)

Published: June 14, 2024

Allopolyploidy-a hybridization-induced whole-genome duplication event-has been a major driver of plant diversification. The extent to which chromosomes pair with their proper homolog vs. homoeolog in allopolyploids varies across taxa, and methods detect homoeologous gene flow (HGF) are needed understand how HGF has shaped polyploid lineages.

Language: Английский

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Frequent spontaneous structural rearrangements promote rapid genome diversification in a Brassica napus F1 generation

Frontiers in Plant Science, Journal Year: 2022, Volume and Issue: 13

Published: Nov. 18, 2022

In a cross between two homozygous Brassica napus plants of synthetic and natural origin, we demonstrate that novel structural genome variants from the parent cause immediate diversification among F1 offspring. Long read sequencing in twelve sister revealed five large-scale rearrangements where both parents carried different alleles but heterozygous genomes were not identical heterozygotes as expected. Such spontaneous part homoeologous exchanges or segmental deletions identified different, individual plants. The caused deletions, gene copy-number variations, diverging methylation patterns other changes large numbers genes may have been causal for unexpected phenotypic variation plants, example strong divergence plant height leaf area. This supports hypothesis de novo after polyploidization can rapidly overcome intense allopolyploidization bottlenecks to re-expand crops genetic diversity ecogeographical expansion human selection. findings imply restructuring allopolyploid interspecific hybridization, common approach breeding, considerably more drastic impact on agricultural ecosystems than extremely precise, biotechnological modifications.

Language: Английский

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Genome-wide patterns of homoeologous gene flow in allotetraploid coffee

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

Published: Sept. 12, 2023

ABSTRACT Premise Allopolyploidy – a hybridization-induced whole-genome duplication event has been major driver of plant diversification. The extent to which chromosomes pair with their proper homolog vs. homoeolog in allopolyploids varies across taxa, and methods detect homoeologous gene flow (HGF) are needed understand how HGF shaped polyploid lineages. Methods ABBA-BABA test represents classic method for detecting introgression between closely related species, but here we developed modified use the characterize direction allotetraploid Coffea arabica . Results We found that is abundant C. genome, both subgenomes serving as donors recipients variation. also highly maternally biased plastid-targeted not mitochondrial-targeted genes, would be expected if plastid-nuclear incompatibilities exist two parent species. Discussion Together our analyses provide simple framework new evidence consistent selection favoring overwriting paternally derived alleles by ameliorate incompatibilities. Natural therefore appears shape intensity allopolyploid coffee, indicating cytoplasmic inheritance long-term consequences

Language: Английский

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Regional Active Transcription Associates with Homoeologous Exchange Breakpoints in Synthetic Brassica Tetraploids

PLANT PHYSIOLOGY, Journal Year: 2024, Volume and Issue: 196(3), P. 1965 - 1979

Published: Aug. 20, 2024

Abstract Polyploidization plays a crucial role in plant evolution and is becoming increasingly important breeding. Structural variations epigenomic repatterning have been observed synthetic polyploidizations. However, the mechanisms underlying occurrence their effects on gene expression phenotype remain unknown. Here, we investigated genome-wide large deletion/duplication regions (DelDups) genomic methylation dynamics leaf organs of progeny from first eight generations tetraploids derived Chinese cabbage (Brassica rapa L. ssp. pekinensis) oleracea var. capitata). One- or two-copy DelDups, with mean size 5.70 Mb (400 kb to 65.85 Mb), occurred generation selfing thereafter. The duplication fragment one subgenome consistently coincided deletion its syntenic other subgenome, vice versa, indicating that these DelDups were generated by homoeologous exchanges (HEs). Interestingly, larger region, higher frequency further suggesting pairing fragments for HEs. Moreover, found active transcription continuously distributed genes local positively associated HE breakpoints. In addition, within exhibited dosage effect, plants extra parental generally displayed phenotypes biased toward corresponding parent. Genome-wide fluctuated remarkably, which did not clearly affect scale. Our findings provide insights into early polyploid genomes, offering valuable knowledge polyploidization-based

Language: Английский

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Tracing post-domestication historical events and screening pre-breeding germplasm from large gene pools in wheat in the absence of phenotype data

Theoretical and Applied Genetics, Journal Year: 2024, Volume and Issue: 137(10)

Published: Sept. 28, 2024

Language: Английский

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Dosage-sensitivity shapes how genes transcriptionally respond to allopolyploidy and homoeologous exchange in resynthesized Brassica napus

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2021, Volume and Issue: unknown

Published: Nov. 19, 2021

Abstract The Gene Balance Hypothesis (GBH) proposes that selection acts on the dosage (i.e. copy number) of genes within dosage-sensitive portions networks, pathways, and protein complexes to maintain balanced stoichiometry interacting proteins, because perturbations stoichiometric balance can result in reduced fitness. This has been called selection. Dosage is also hypothesized constrain expression responses changes, making (those encoding members proteins) experience more similar changes. In allopolyploids, where whole-genome duplication involves hybridization diverged lineages, organisms often homoeologous exchanges (HEs) recombine, duplicate, delete regions genome alter gene pairs. Although GBH makes predictions about response HEs, they have not empirically tested. We used genomic transcriptomic data from six resynthesized, isogenic Brassica napus lines over ten generations identify analyzed responses, tested for patterns imbalance. Groups had less variable HEs than dosage-insensitive genes, a sign their relative constrained. difference was absent pairs whose biased toward BnA subgenome. Finally, WGD, suggesting create These findings expand our knowledge impact evolution potentially connect polyploid genomes time; homoeolog bias duplicate retention.

Language: Английский

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