Pan-genome inversion index reveals evolutionary insights into the subpopulation structure of Asian rice

Nature Communications, Journal Year: 2023, Volume and Issue: 14(1)

Published: March 21, 2023

Understanding and exploiting genetic diversity is a key factor for the productive stable production of rice. Here, we utilize 73 high-quality genomes that encompass subpopulation structure Asian rice (Oryza sativa), plus two wild relatives (O. rufipogon O. punctata), to build pan-genome inversion index 1769 non-redundant inversions span an average ~29% sativa cv. Nipponbare reference genome sequence. Using this index, estimate rate ~700 per million years in rice, which 16 50 times higher than previously estimated plants. Detailed analyses these show evidence their effects on gene expression, recombination rate, linkage disequilibrium. Our study uncovers prevalence scale large (≥100 bp) across hints at largely unexplored role functional biology crop performance.

Language: Английский

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Genome structure variation analyses of peach reveal population dynamics and a 1.67 Mb causal inversion for fruit shape

Genome biology, Journal Year: 2021, Volume and Issue: 22(1)

Published: Jan. 5, 2021

Abstract Background Structural variations (SVs), a major resource of genomic variation, can have profound consequences on phenotypic yet the impacts SVs remain largely unexplored in crops. Results Here, we generate high-quality de novo genome assembly for flat-fruit peach cultivar and produce comprehensive SV map peach, as high proportion sequence is occupied by heterozygous genome. We conduct population-level analyses that indicate undergone strong purifying selection during domestication, find evidence positive selection, with significant preference upstream intronic regions later improvement. perform SV-based GWAS identifies large 1.67-Mb inversion segregates perfectly shape. Mechanistically, this derived allele alters expression PpOFP2 gene positioned near proximal breakpoint inversion, confirm transgenic tomatoes causal Conclusions Thus, beyond introducing new genomics resources research, our study illustrates how focusing data drive basic functional discoveries plant science.

Language: Английский

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Population genomics of apricots unravels domestication history and adaptive events

Nature Communications, Journal Year: 2021, Volume and Issue: 12(1)

Published: June 25, 2021

Abstract Among crop fruit trees, the apricot ( Prunus armeniaca ) provides an excellent model to study divergence and adaptation processes. Here, we obtain nearly 600 Armeniaca genomes four high-quality assemblies anchored on genetic maps. Chinese European apricots form two differentiated gene pools with high diversity, resulting from independent domestication events distinct wild Central Asian populations, subsequent flow. A relatively low proportion of genome is affected by selection. Different genomic regions show footprints selection in cultivated apricots, despite convergent phenotypic traits, predicted functions both groups involved perennial life cycle, quality disease resistance. Selection appear more abundant a hotspot chromosome 4, while admixture pervasive apricots. Our clues biology selected traits targets for tree research breeding.

Language: Английский

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A donor-DNA-free CRISPR/Cas-based approach to gene knock-up in rice

Nature Plants, Journal Year: 2021, Volume and Issue: 7(11), P. 1445 - 1452

Published: Nov. 15, 2021

Language: Английский

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A multi‐omics framework reveals strawberry flavor genes and their regulatory elements

New Phytologist, Journal Year: 2022, Volume and Issue: 236(3), P. 1089 - 1107

Published: Aug. 2, 2022

Summary Flavor is essential to consumer preference of foods and an increasing focus plant breeding programs. In fruit crops, identifying genes underlying volatile organic compounds has great promise accelerate flavor improvement, but polyploidy heterozygosity in many species have slowed progress. Here we use octoploid cultivated strawberry demonstrate how genomic heterozygosity, transcriptomic intricacy metabolomic diversity can be treated as strengths leveraged uncover their regulatory elements. Multi‐omics datasets were generated including expression quantitative trait loci map with 196 diverse lines, haplotype‐phased genomes a highly‐flavored selection, genome‐wide structural variant using five haplotypes, association study (GWAS) > 300 individuals. Overlaying elements, variants GWAS‐linked allele‐specific numerous variation important flavor. one example, the functional role anthranilate synthase alpha subunit 1 methyl biosynthesis was supported via transient gene assays. These results framework for discovery crops pathway molecular cultivars complex desirable

Language: Английский

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A chromosome‐level genome assembly of radish (Raphanus sativus L.) reveals insights into genome adaptation and differential bolting regulation

Plant Biotechnology Journal, Journal Year: 2023, Volume and Issue: 21(5), P. 990 - 1004

Published: Jan. 17, 2023

Summary High‐quality radish ( Raphanus sativus ) genome represents a valuable resource for agronomical trait improvements and understanding evolution among Brassicaceae species. However, existing assembly remains fragmentary, which greatly hampered functional genomics research genome‐assisted breeding. Here, using NAU‐LB inbred line, we generated reference of 476.32 Mb with scaffold N50 56.88 by incorporating Illumina, PacBio BioNano optical mapping techniques. Utilizing Hi‐C data, 448.12 (94.08%) the assembled sequences were anchored to nine chromosomes 40 306 protein‐coding genes annotated. In total, 249.14 (52.31%) comprised repetitive sequences, long terminal repeats (LTRs, 30.31%) most abundant class. Beyond confirming whole‐genome triplication (WGT) event in R. lineage, found several tandem arrayed involved stress response process, may account distinctive phenotype high disease resistance . By comparing against Xin‐li‐mei genome, total 2 108 573 SNPs, 7740 large insertions, 7757 deletions 84 inversions identified. Interestingly, 647‐bp insertion promoter RsVRN1 gene can be directly bound DOF transcription repressor RsCDF3 , resulting into its low activity late‐bolting cultivar. Importantly, introgression this allele, In‐536 early‐bolting genotype could contribute delayed bolting time, indicating that it is potential genetic Together, provides information facilitate comparative genomic analysis accelerate genome‐guided breeding improvement radish.

Language: Английский

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Graph pangenome reveals the regulation of malate content in blood-fleshed peach by NAC transcription factors

Genome biology, Journal Year: 2025, Volume and Issue: 26(1)

Published: Jan. 9, 2025

Abstract Background Fruit acidity and color are important quality attributes in peaches. Although there some exceptions, blood-fleshed peaches typically have a sour taste. However, little is known about the genetic variations linking organic acid regulation Results Here, we report peach graph-based pangenome constructed from sixteen individual genome assemblies, capturing abundant structural 82.3 Mb of sequences absent reference genome. Pangenome analysis reveals long terminal repeat retrotransposon insertion promoter NAC transcription factor (TF) PpBL peaches, which enhances expression . Genome-wide association study identifies significant between malate content. Silencing fruit ectopic overexpression tomatoes confirm that positive regulator accumulation. Furthermore, demonstrate works synergistically with another TF, PpNAC1, to activate aluminum-activated transporter PpALMT4 , leading increased Conclusions These findings, along previous research showing PpNAC1 also regulate anthocyanin accumulation, explain red coloration taste fruits.

Language: Английский

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Population-scale peach genome analyses unravel selection patterns and biochemical basis underlying fruit flavor

Nature Communications, Journal Year: 2021, Volume and Issue: 12(1)

Published: June 14, 2021

Abstract A narrow genetic basis in modern cultivars and strong linkage disequilibrium peach ( Prunus persica ) has restricted resolution power for association studies this model fruit species, thereby limiting our understanding of economically important quality traits including flavor. Here, we present a high-quality genome assembly Chinese landrace, Longhua Shui Mi (LHSM), representative the Cling peaches that have been central global improvement. We also map resequencing data 564 accessions to LHSM at an average depth 26.34× per accession. Population genomic analyses reveal fascinating history convergent selection sweetness yet divergent acidity eastern vs. western cultivars. Molecular-genetics biochemical establish PpALMT1 (aluminum-activated malate transporter 1) contributes their difference content increases fructose accounts increased fruits, as regulated by PpERDL16 (early response dehydration 6-like 16). Our study illustrates utility genomics resources both basic applied efforts understand exploit peach.

Language: Английский

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Genomic analyses of rice bean landraces reveal adaptation and yield related loci to accelerate breeding

Nature Communications, Journal Year: 2022, Volume and Issue: 13(1)

Published: Sept. 29, 2022

Rice bean (Vigna umbellata) is an underexploited domesticated legume crop consumed for dietary protein in Asia, yet little known about the genetic diversity of this species. Here, we present a high-quality reference genome rice landrace (FF25) built using PacBio long-read data and Hi-C chromatin interaction map, assess phylogenetic position speciation time within Vigna genus. We sequence 440 landraces (two core collections), GWAS based on growth sites at three widely divergent latitudes reveal loci associated with flowering yield. Loci harboring orthologs FUL (FRUITFULL), FT (FLOWERING LOCUS T), PRR3 (PSEUDO-RESPONSE REGULATOR 3) contribute to adaptation from its low latitude center origin towards higher latitudes, which pyramid early-flowering alleles these display maximally short times. also demonstrate that copy-number-variation VumCYP78A6 can regulate seed-yield traits. Intriguingly, 32 collected mountainous region South-Central China harbor recently acquired InDel TFL1 (TERMINAL FLOWER1) affecting stem determinacy; materials have exceptionally high values multiple human-desired traits could therefore substantially advance breeding efforts improve bean.

Language: Английский

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Chromosome-level genome assemblies of four wild peach species provide insights into genome evolution and genetic basis of stress resistance

BMC Biology, Journal Year: 2022, Volume and Issue: 20(1)

Published: June 13, 2022

Abstract Background Peach ( Prunus persica) is an economically important stone fruit crop in Rosaceae and widely cultivated temperate subtropical regions, emerging as excellent material to study the interaction between plant environment. During its genus, there are four wild species of peach, all living harsh environments. For example, one species, P. mira , originates from Qinghai-Tibet Plateau (QTP) exhibits strong cold/ultraviolet ray environmental adaptations. Although remarkable progresses gene discovery quality-related traits peach using previous assembled genome were obtained, genomic basis response these different geographical environments remains unclear. Results To uncover key genes regulating adaptability analyze role genetic variations resistance formation, we performed de novo assembling relatives persica ), davidiana kansuensis ferganensis resequenced 175 varieties. The phylogenetic tree showed that divergence time other was 11.5 million years ago, which consistent with drastic crustal movement QTP. Abundant identified when compared results plant-pathogen pathways enriched containing small insertions deletions copy number peach. Then, data used identify new resistance. presence/absence result a hybridization event occurred dulcis enhanced their putative hybrid, . Using bulked segregant analysis, located nematode locus chromosome 2. Within mapping region, deletion promoter NBS-LRR found involve by expression. Furthermore, combined RNA-seq selective sweeps proposed CBF essential for high-altitude adaptation through increasing low temperature. Conclusions In general, reference genomes facilitate our understanding mechanism perennial crops, provide valuable resources future breeding improvement.

Language: Английский

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