Graph pangenome captures missing heritability and empowers tomato breeding

Nature, Journal Year: 2022, Volume and Issue: 606(7914), P. 527 - 534

Published: June 8, 2022

Missing heritability in genome-wide association studies defines a major problem genetic analyses of complex biological traits1,2. The solution to this is identify all causal variants and measure their individual contributions3,4. Here we report graph pangenome tomato constructed by precisely cataloguing more than 19 million from 838 genomes, including 32 new reference-level genome assemblies. This was used for study estimation 20,323 gene-expression metabolite traits. average estimated trait 0.41 compared with 0.33 when using the single linear reference genome. 24% increase largely due resolving incomplete linkage disequilibrium through inclusion additional structural identified pangenome. Moreover, allelic locus heterogeneity, improve power factors underlying agronomically important traits leading to, example, identification two genes potentially contributing soluble solid content. newly will facilitate improvement both marker-assisted selection genomic selection. Our advances understanding demonstrates crop breeding.

Language: Английский

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Genome evolution and diversity of wild and cultivated potatoes

Nature, Journal Year: 2022, Volume and Issue: 606(7914), P. 535 - 541

Published: June 8, 2022

Potato (Solanum tuberosum L.) is the world's most important non-cereal food crop, and vast majority of commercially grown cultivars are highly heterozygous tetraploids. Advances in diploid hybrid breeding based on true seeds have potential to revolutionize future potato production1-4. So far, relatively few studies examined genome evolution diversity wild cultivated landrace potatoes, which limits application their breeding. Here we assemble 44 high-quality genomes from 24 20 accessions that representative Solanum section Petota, tuber-bearing clade, as well 2 neighbouring section, Etuberosum. Extensive discordance phylogenomic relationships suggests complexity evolution. We find substantially expanded its repertoire disease-resistance genes when compared with closely related seed-propagated solanaceous crops, indicative effect tuber-based propagation strategies genome. discover a transcription factor determines tuber identity interacts mobile tuberization inductive signal SP6A. also identify 561,433 high-confidence structural variants construct map large inversions, provides insights for improving inbred lines precluding linkage drag, exemplified by 5.8-Mb inversion associated carotenoid content tubers. This study will accelerate enrich our understanding biology global staple crop.

Language: Английский

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Construction of a chromosome-scale long-read reference genome assembly for potato

GigaScience, Journal Year: 2020, Volume and Issue: 9(9)

Published: Sept. 1, 2020

Worldwide, the cultivated potato, Solanum tuberosum L., is No. 1 vegetable crop and a critical food security crop. The genome sequence of DM1-3 516 R44, doubled monoploid clone S. Group Phureja, was published in 2011 using whole-genome shotgun sequencing approach with short-read data. Current advanced technologies now permit generation near-complete, high-quality chromosome-scale assemblies at minimal cost.Here, we present an updated version R44 (v6.1) Oxford Nanopore Technologies long reads coupled proximity-by-ligation scaffolding (Hi-C), yielding assembly. new assembly represents 741.6 Mb (87.8%) estimated 844 genome, which 741.5 non-gapped 731.2 anchored to 12 chromosomes. Use full-length complementary DNA enabled annotation 32,917 high-confidence protein-coding genes encoding 44,851 gene models that had significantly improved representation conserved orthologs compared previous annotation. has contiguity 595-fold increase N50 contig size, 99% reduction number contigs, 44-fold scaffold LTR Assembly Index score 13.56, placing it category reference quality. also permitted centromeres via alignment derived from CENH3 nucleosomes.Access software high-quality, long-read, dataset for genotype potato will facilitate research aimed improving agronomic traits understanding evolution.

Language: Английский

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Chromosome-scale and haplotype-resolved genome assembly of a tetraploid potato cultivar

Nature Genetics, Journal Year: 2022, Volume and Issue: 54(3), P. 342 - 348

Published: March 1, 2022

Abstract Potato is the most widely produced tuber crop worldwide. However, reconstructing four haplotypes of its autotetraploid genome remained an unsolved challenge. Here, we report 3.1 Gb haplotype-resolved (at 99.6% precision), chromosome-scale assembly potato cultivar ‘Otava’ based on high-quality long reads, single-cell sequencing 717 pollen genomes and Hi-C data. Unexpectedly, ~50% was identical-by-descent due to recent inbreeding, which contrasted by highly abundant structural rearrangements involving ~20% genome. Among 38,214 genes, only 54% were present in all with average 3.2 copies per gene. Taking leaf transcriptome as example, 11% genes differently expressed at least one haplotype, where 25% them likely regulated through allele-specific DNA methylation. Our work sheds light breeding history potato, functional organization tetraploid has potential strengthen future genomics-assisted breeding.

Language: Английский

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Phased, chromosome-scale genome assemblies of tetraploid potato reveal a complex genome, transcriptome, and predicted proteome landscape underpinning genetic diversity

Molecular Plant, Journal Year: 2022, Volume and Issue: 15(3), P. 520 - 536

Published: Jan. 10, 2022

Cultivated potato is a clonally propagated autotetraploid species with highly heterogeneous genome. Phased assemblies of six cultivars including two chromosome-scale phased genome revealed extensive allelic diversity, altered coding and transcript sequences, preferential allele expression, structural variation that collectively result in complex transcriptome predicted proteome, which are distributed across the homologous chromosomes. Wild contribute to diversity tetraploid cultivars, demonstrating ancestral introgressions predating modern breeding efforts. As undergoes limited meiosis, dysfunctional deleterious alleles not purged potato. Nearly quarter loci bore mutations have high negative impact on protein function, complicating breeder's efforts reduce genetic load. The StCDF1 locus controls maturity, analysis genomes 12 variants correlated maturity dosage-dependent manner. Knowledge complexity its rampant embedded will be key only implementing precision but also construction homozygous, diploid germplasm containing favorable capitalize heterosis F1 hybrids.

Language: Английский

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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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Leveraging a phased pangenome for haplotype design of hybrid potato

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

Published: Jan. 22, 2025

Language: Английский

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Genome architecture and tetrasomic inheritance of autotetraploid potato

Molecular Plant, Journal Year: 2022, Volume and Issue: 15(7), P. 1211 - 1226

Published: June 22, 2022

Potato (Solanum tuberosum) is the most consumed non-cereal food crop. Most commercial potato cultivars are autotetraploids with highly heterozygous genomes, severely hampering genetic analyses and improvement. By leveraging state-of-the-art sequencing technologies polyploid graph binning, we achieved a chromosome-scale, haplotype-resolved genome assembly of cultivated potato, Cooperation-88 (C88). Intra-haplotype comparative revealed extensive sequence expression differences in this tetraploid genome. We identified haplotype-specific pericentromeres on chromosomes, suggesting distinct evolutionary trajectory homologous centromeres. Furthermore, detected double reduction events that unevenly distributed haplotypes 1021 1034 selfing progeny, feature autopolyploid inheritance. distinguishing maternal paternal haplotype sets C88, simulated origin heterosis survey 3110 tetra-allelic loci deleterious mutations, which were masked condition by two parents. This study provides insights into genomic architecture autopolyploids will guide their breeding.

Language: Английский

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The gap-free potato genome assembly reveals large tandem gene clusters of agronomical importance in highly repeated genomic regions

Molecular Plant, Journal Year: 2022, Volume and Issue: 16(2), P. 314 - 317

Published: Dec. 17, 2022

Potato is a vital food security crop and ranked as the world's third most important after rice wheat. In 2011, first genome assembly of doubled monoploid potato DM1-3 516 R44 (DM) was released (Potato Genome Sequencing Consortium, 2011Potato ConsortiumGenome sequence analysis tuber potato.Nature. 2011; 475: 189-195Crossref PubMed Scopus (1511) Google Scholar), which has been widely used one popular reference genomes in last decade served valuable resource plant genomics genetics community (Leisner et al., 2018Leisner C.P. Hamilton J.P. Crisovan E. Manrique-Carpintero N.C. Marand A.P. Newton L. Pham G.M. Jiang J. Douches D.S. Jansky S.H. al.Genome M6, diploid inbred clone high-glycoalkaloid-producing tuber-bearing species Solanum chacoense, reveals residual heterozygosity.Plant 2018; 94: 562-570Crossref (91) Scholar; Yang 2020Yang X. Y. Ling Guan Guo Dong D. Jin Huang S. Liu Li G. A high-throughput BAC end protocol (BAC-anchor) for profiling physical mapping.Plant Biotechnol. 2020; 18: 364-372Crossref (3) Zheng 2020Zheng Xiong Exogenous SA initiated defense response multi-signaling pathway tetraploid SD20.Horticultural Plant Journal. 6: 99-110Crossref (16) Scholar). The latest version DM (v6.1) (Pham 2020Pham Wood J.C. Burke J.T. Zhao H. Vaillancourt B. Ou Buell C.R. Construction chromosome-scale long-read potato.GigaScience. 9: giaa100-giaa111Crossref (96) Scholar) good quality control studies potatoes (Zhou 2020Zhou Q. Tang W. Z. Zhang Visser R.G.F. Bachem C.W.B. Robin C. al.Haplotype-resolved analyses heterozygous potato.Nat. Genet. 52: 1018-1023Crossref Bao 2022Bao Wang P. Peng Cheng architecture tetrasomic inheritance autotetraploid potato.Mol. Plant. 2022; 15: 1211-1226Abstract Full Text PDF (11) Hoopes 2022Hoopes Meng Achakkagari S.R. de Alves Freitas Guesdes F. Bolger M.E. Coombs J.J. Esselink Kaiser N.R. Kodde al.Phased, assemblies reveal complex genome, transcriptome, predicted proteome landscape underpinning genetic diversity.Mol. 520-536Abstract (42) Sun 2022Sun Jiao W.B. Krause K. Campoy J.A. Goel M. Folz-Donahue Kukat Huettel Schneeberger Chromosome-scale haplotype-resolved cultivar.Nat. 54: 342-348Crossref (45) 2022Tang Jia Feng Zhu evolution diversity wild cultivated potatoes.Nature. 606: 535-541Crossref (62) However, 161 gaps remain DM6.1 (v6.1), centromere telomere structures are incomplete. Considering importance genomics, genetics, breeding studies, generating complete great importance. this study, telomere-to-telomere gap-free (DM8.1) (Figure 1A) assembled through combining Oxford Nanopore Technologies (ONT) ultra-long reads sequencing (119.81× coverage) Hi-C (130.57×) (Supplemental Table 1), well being assisted by multiple gap-closing strategies coupled with high fidelity (HIFI) from circular consensus sequencing. total 179 contigs summed size 773.36 Mb contig N50 59.72 were obtained initial assembly, polishing, decontamination. further anchored 37 into 12 chromosomes Figure 1; Supplemental 2), accounting 95.53% (738.82 Mb) we named it preDM8. For 142 (34.53 unanchored contigs, over 98% short sequences (<1 Mb), all could be aligned to similarity, indicating that these repetitive or redundant sequences. preDM8 better contiguous than pan-genome (Tang 2). there 25 Three methods adopted close 3A; 3). First, ONT preDM8, mapped on flanking regions collected assembled, successfully closed 14 gaps. Second, based syntenic homologous fragments between DM6.1, three consecutive covered Third, target amplification experiments 3B) HIFI performed, remaining eight Figures 3C 4). Finally, generated DM8.1 1A; To verify investigated reliability corresponded DM6.1. We randomly selected 50 designed 100 pairs primers 5) both sides PCR Sanger Both 5′ 3′ boundary obtained, indicated accuracy DM8.1. Meanwhile, achieved BUSCO value 98.70%, an extremely mapping rate (>99.90%) Illumina long reads; (35.85) Merqury analysis; improvement terminal repeat (LTR)-retrotransposon completeness (DM8.1: LAI = 12.92, LTR length 388.58 Mb; DM6.1: 12.75, 375.91 supporting Tables 6 7). 40 155 protein-coding genes 6), among 33 972 (84.60%) functionally annotated 24 362 expressed, estimated 10 mRNA datasets. Further found 1117 mis-annotated gene incorrectly two. These errors revealed individual read (mRNA sequencing) covering linking two neighbor genes, suggesting they transcript 956 349 transposable elements (TEs) predicted, 60.31% (465.81 8; 8). Additionally, 4676 small RNAs 9). All detected using seven-base telomeric sub-telomeric repeats CL14 CL34, identified CENH3 1A). Sequence composition showed contained more Gypsy-type LTRs (49.25%), while harbored unknown TEs filled similar TE contents facilitated identification large tandem clusters functional 181 newly sequences, corresponding gap Of (>15 copies) duplicated found, including 21 patatin (Figures 1B), 31 terpene synthase 18 cupin 10). Among them, much higher expression levels tubers other organs 1C). Intriguingly, under absolute dosage selection, because continuously expanded during evolution, domestication, 1D–1E). family Solanaceae, only largely bit wolfberry (seven keeping fewer copies others even completely lost Physalis tobacco 1E). Etuberosum, sister group potato, four five Etuberosum 1D). This indicates expansion associated speciation may play role formation enlarged potato. Furthermore, reported pan-genomes tomato Zhou 2022Zhou Lyu Zan Wu Fang al.Graph pangenome captures missing heritability empowers breeding.Nature. 527-534Crossref (60) locus maintained population but significantly candolleanum, landraces average copy number growing 5.9 7 14.6, respectively 1D), clearly domestication Moreover, strong positive selection (Ka/Ks > especially domesticated 11), differentiation expansion, associate development, production, tubers. findings together suggest possible breed cultivars yields manipulating dosage, i.e., level, patatin. There have continuous efforts improve DM, scientific research programs DM8.1, serve future function work supported National Natural Science Foundation China (32072119 31801421); Breeding Program Shandong Province, (2020LZGC003); Agriculture Technology Major Program, (NK20220904); Agricultural Research System (CARS-9); Central Public-interest Scientific Institution Basal Fund (Y2022PT23); Innovation Chinese Academy Sciences (CAAS-ASTIP-IVFCAAS).

Language: Английский

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Pangenome analyses reveal impact of transposable elements and ploidy on the evolution of potato species

Proceedings of the National Academy of Sciences, Journal Year: 2023, Volume and Issue: 120(31)

Published: July 24, 2023

Potato (Solanum sp., family Solanaceae) is the most important noncereal food crop globally. It has over 100 wild relatives in Solanum section Petota, which features species with both sexual and asexual reproduction varying ploidy levels. A pangenome of Petota composed 296 accessions was constructed including diploids polyploids compared via presence/absence variation (PAV). The core (genes shared by at least 97% accessions) shell genomes (shared 3 to 97%) are enriched basic molecular cellular functions, while cloud genome present less than 3% member showed enrichment transposable elements (TEs). Comparison PAV domesticated vs. made, a phylogenetic tree based on PAVs, grouping into different clades, similar previous phylogenies produced using DNA markers. cladewise approach identified abiotic stress response among genes clade 1+2 3, flowering/tuberization 4. TE content differed between 1+2, from North Central America reproductive isolation other having much lower clades. In contrast, vitro propagation history were found have high levels TEs. Results indicate role for TEs adaptation new environments, natural artificial, Petota.

Language: Английский

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