Phylogenomic discovery of deleterious mutations facilitates hybrid potato breeding

Cell, Journal Year: 2023, Volume and Issue: 186(11), P. 2313 - 2328.e15

Published: May 1, 2023

Hybrid potato breeding will transform the crop from a clonally propagated tetraploid to seed-reproducing diploid. Historical accumulation of deleterious mutations in genomes has hindered development elite inbred lines and hybrids. Utilizing whole-genome phylogeny 92 Solanaceae its sister clade species, we employ an evolutionary strategy identify mutations. The deep reveals genome-wide landscape highly constrained sites, comprising ∼2.4% genome. Based on diploid diversity panel, infer 367,499 variants, which 50% occur at non-coding 15% synonymous sites. Counterintuitively, with relatively high homozygous burden can be better starting material for inbred-line development, despite showing less vigorous growth. Inclusion inferred increases genomic-prediction accuracy yield by 24.7%. Our study generates insights into incidence properties their far-reaching consequences breeding.

Language: Английский

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A review of the pangenome: how it affects our understanding of genomic variation, selection and breeding in domestic animals?

Journal of Animal Science and Biotechnology/Journal of animal science and biotechnology, Journal Year: 2023, Volume and Issue: 14(1)

Published: May 5, 2023

Abstract As large-scale genomic studies have progressed, it has been revealed that a single reference genome pattern cannot represent genetic diversity at the species level. While domestic animals tend to complex routes of origin and migration, suggesting possible omission some population-specific sequences in current genome. Conversely, pangenome is collection all DNA contains shared by individuals (core genome) also able display sequence information unique each individual (variable genome). The progress research humans, plants proved missing components identification large structural variants (SVs) can be explored through pangenomic studies. Many specific shown related biological adaptability, phenotype important economic traits. maturity technologies methods such as third-generation sequencing, Telomere-to-telomere genomes, graphic reference-free assembly will further promote development pangenome. In future, combined with long-read data multi-omics help resolve SVs their relationship main traits interest domesticated animals, providing better insights into animal domestication, evolution breeding. this review, we mainly discuss how analysis reveals variations (sheep, cattle, pigs, chickens) impacts on phenotypes contribute understanding diversity. Additionally, go potential issues future perspectives livestock poultry.

Language: Английский

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Convergent evolution of plant prickles by repeated gene co-option over deep time

Science, Journal Year: 2024, Volume and Issue: 385(6708)

Published: Aug. 1, 2024

An enduring question in evolutionary biology concerns the degree to which episodes of convergent trait evolution depend on same genetic programs, particularly over long timescales. In this work, we genetically dissected repeated origins and losses prickles-sharp epidermal projections-that convergently evolved numerous plant lineages. Mutations a cytokinin hormone biosynthetic gene caused at least 16 independent prickles eggplants wild relatives genus

Language: Английский

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Discovery of a DFR gene that controls anthocyanin accumulation in the spiny Solanum group: roles of a natural promoter variant and alternative splicing

The Plant Journal, Journal Year: 2022, Volume and Issue: 111(4), P. 1096 - 1109

Published: June 24, 2022

Anthocyanins are important pigments that impart color in plants. In Solanum, different species display various fruit or flower colors due to varying degrees of anthocyanin accumulation. Here we identified two anthocyanin-free mutants from an ethylmethane sulfonate-induced mutant library and naturally occurring Solanum melongena, with mutations the 5' splicing site second intron dihydroflavonol-4-reductase (DFR) - leading altered splicing. Further study revealed alternative was closely related accumulation 17 accessions three cultivated species: S. macrocarpon aethiopicum, their wild species. Analysis natural variations DFR, using expanded population including 282 belonging spiny group, a single-nucleotide polymorphism MYB recognition promoter region, which causes differential expression DFR affects fruits detected accessions. Our suggests that, owing years domestication, variation region gene account for during domestication.

Language: Английский

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Tomato root specialized metabolites evolved through gene duplication and regulatory divergence within a biosynthetic gene cluster

Science Advances, Journal Year: 2024, Volume and Issue: 10(17)

Published: April 24, 2024

Tremendous plant metabolic diversity arises from phylogenetically restricted specialized pathways. Specialized metabolites are synthesized in dedicated cells or tissues, with pathway genes sometimes colocalizing biosynthetic gene clusters (BGCs). However, the mechanisms by which spatial expression patterns arise and role of BGCs evolution remain underappreciated. In this study, we investigated driving acylsugar Solanaceae. Previously thought to be glandular trichomes, acylsugars were recently found cultivated tomato roots. We demonstrated that roots trichomes have different sugar cores, identified root-enriched paralogs trichome genes, characterized a key paralog required for root biosynthesis,

Language: Английский

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Solanum pan-genetics reveals paralogues as contingencies in crop engineering

Nature, Journal Year: 2025, Volume and Issue: unknown

Published: March 5, 2025

Language: Английский

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Genomics and Marker-Assisted Improvement of Vegetable Crops

Critical Reviews in Plant Sciences, Journal Year: 2021, Volume and Issue: 40(4), P. 303 - 365

Published: July 4, 2021

Vegetables are an integral part of the human diet worldwide. Traditional breeding approaches have been used extensively to develop new cultivars vegetables with desirable characteristics, including resistance/tolerance biotic and abiotic stresses, high yield, elevated content compounds beneficial health. The technological progress since early 1980s has revolutionized our ability study manipulate genetic variation in crop plants. development high-throughput sequencing platforms accompanying analytical methods led assembly a large number plant genomes, construction dense ultra-dense molecular linkage maps, identification structural variants, application markers programs. Linkage mapping genome-wide association studies identify chromosomal locations genes QTLs associated phenotypic variations important for improvement. This review provides up-to-date information on status genomics marker-assisted improvement vegetable crops focus tomato, pepper, eggplant, lettuce, spinach, cucumber, chicory. For each crop, we present most recent resources, populations, genome sequences, mapped QTLs, selection genomic selection, discuss future research prospects novel techniques approaches.

Language: Английский

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Genetics and breeding of phenolic content in tomato, eggplant and pepper fruits

Frontiers in Plant Science, Journal Year: 2023, Volume and Issue: 14

Published: March 21, 2023

Phenolic acids and flavonoids are large groups of secondary metabolites ubiquitous in the plant kingdom. They currently spotlight due to numerous health benefits associated with their consumption, as well for vital roles biological processes plant-environment interaction. Tomato, eggplant pepper top ten most consumed vegetables world, fruit accumulation profiles have been extensively characterized, showing substantial differences. A broad array genetic genomic tools has helped identify QTLs candidate genes biosynthesis phenolic flavonoids. The aim this review was synthesize available information making it easily researchers breeders. phenylpropanoid pathway is tightly regulated by structural genes, which conserved across species, along a complex network regulatory elements like transcription factors, especially MYB family, cellular transporters. Moreover, compounds accumulate tissue-specific developmental-dependent ways, different paths metabolic activated/deactivated development. We retrieved 104 annotated putative orthologues encoding key enzymes tomato (37), (29) (38) compiled 267 (217 tomato, 16 34 pepper) linked acids, total phenolics content. Combining molecular variability, through both conventional engineering strategies, feasible approach improve content pepper. Finally, although biosynthetic well-studied Solanaceae, more research needed on identification behind many QTLs, interactions other genes.

Language: Английский

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Fruity, sticky, stinky, spicy, bitter, addictive, and deadly: evolutionary signatures of metabolic complexity in the Solanaceae

Natural Product Reports, Journal Year: 2022, Volume and Issue: 39(7), P. 1438 - 1464

Published: Jan. 1, 2022

Covering: 2000-2022Plants collectively synthesize a huge repertoire of metabolites. General metabolites, also referred to as primary are conserved across the plant kingdom and required for processes essential growth development. These include amino acids, sugars, lipids, organic acids. In contrast, specialized historically termed secondary structurally diverse, exhibit lineage-specific distribution provide selective advantage host species facilitate reproduction environmental adaptation. Due their potent bioactivities, metabolites attract considerable attention use flavorings, fragrances, pharmaceuticals, bio-pesticides. The Solanaceae (Nightshade family) consists approximately 2700 includes crops significant economic, cultural, scientific importance: these potato, tomato, pepper, eggplant, tobacco, petunia. has emerged model family studying biochemical evolution metabolism multiple examples exist that influence senses physiology commensal harmful organisms, including humans. include, alcohols, phenylpropanoids, carotenoids contribute fruit aroma color in tomato (

Language: Английский

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Genome–Wide Identification and Functional Characterization of Auxin Response Factor (ARF) Genes in Eggplant

International Journal of Molecular Sciences, Journal Year: 2022, Volume and Issue: 23(11), P. 6219 - 6219

Published: June 1, 2022

Auxin response factors (ARFs) are important plant transcription that differentially expressed in to auxin and various abiotic stresses. ARFs play roles mediating growth stress responses; however, these have not been studied eggplants. In this study, genome-wide identification the functional analysis of ARF gene family eggplants (Solanum melongena L.) were performed. A total 20 (SmARF) genes identified phylogenetically classified into three groups. Our revealed four domains 10 motifs proteins. Subcellular localization showed SmARFs localized nucleus. To investigate biological functions under 2,4-D salt treatments, quantitative real-time RT-PCR (qRT-PCR) was conducted. Most SmARF exhibited changes expression treatments flowers, especially SmARF4 7B. All quickly responded stress, except SmARF17 19 leaves, SmARF1A 7B roots, SmARF2A, SmARF7B, SmARF16B stems. These results helped elucidate role signaling

Language: Английский

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