Grant, V. Plant Speciation (Columbia Univ. Press, 1981).
J. Masterson Stomatal size in fossil plants: evidence for polyploidy in majority of angiosperms Science 264 421 424 1:STN:280:DC%2BC3cvlvVSgtQ%3D%3D 17836906
L. Cui et al. Widespread genome duplications throughout the history of flowering plants Genome Res. 16 738 749 1:CAS:528:DC%2BD28XlvVeiurY%3D 16702410 1479859
K.S. Dinesh Babu et al. A short review on sugarcane: its domestication, molecular manipulations and future perspectives Genet. Resour. Crop Evol. 69 2623 2643 36159774 9483297
A.L. Healey et al. The complex polyploid genome architecture of sugarcane Nature 628 804 810 1:CAS:528:DC%2BB2cXmvFersLY%3D 38538783 11041754
The International Wheat Genome Sequencing Consortium (IWGSC). A chromosome-based draft sequence of the hexaploid bread wheat (Triticum aestivum) genome. Science345, 1251788 (2014).
E. Stokstad The new potato Science 363 574 577 1:CAS:528:DC%2BC1MXhsVOhurbL 30733400
M.C. Sattler C.R. Carvalho W.R. Clarindo The polyploidy and its key role in plant breeding Planta 243 281 296 1:CAS:528:DC%2BC2MXitV2rsbvM 26715561
K.A. Bird R. VanBuren J.R. Puzey P.P. Edger The causes and consequences of subgenome dominance in hybrids and recent polyploids N. Phytol. 220 87 93
M.R. Woodhouse et al. Origin, inheritance, and gene regulatory consequences of genome dominance in polyploids Proc. Natl Acad. Sci. USA 111 5283 5288 1:CAS:528:DC%2BC2cXkslGlt70%3D 24706847 3986174
Q. Lian et al. Acquisition of deleterious mutations during potato polyploidization J. Integr. Plant Biol. 61 7 11 1:CAS:528:DC%2BC1MXhsFynt74%3D 30474354
J.L. Conover J.F. Wendel Deleterious mutations accumulate faster in allopolyploid than diploid cotton (Gossypium) and unequally between subgenomes Mol. Biol. Evol. 39 msac024 1:CAS:528:DC%2BB38XhvVait7zP 35099532 8841602
Stebbins, G. L. in Advances in Genetics Vol. 1 (ed. Demerec, M.) 403–429 (Elsevier, 1947).
J.P. Spoelhof P.S. Soltis D.E. Soltis Pure polyploidy: closing the gaps in autopolyploid research J. Syst. Evol. 55 340 352
Y. Song et al. Phased gap-free genome assembly of octoploid cultivated strawberry illustrates the genetic and epigenetic divergence among subgenomes Hortic. Res. 11 uhad252 1:CAS:528:DC%2BB2MXjtlyqs7o%3D 38269295
X. Jin et al. Haplotype-resolved genomes of wild octoploid progenitors illuminate genomic diversifications from wild relatives to cultivated strawberry Nat. Plants 9 1252 1266 1:CAS:528:DC%2BB3sXhslShs7rL 37537397
B. Chalhoub et al. Early allopolyploid evolution in the post-Neolithic Brassica napus oilseed genome Science 345 950 953 1:CAS:528:DC%2BC2cXhtlOmsr%2FK 25146293
F. Li et al. Genome sequence of cultivated Upland cotton (Gossypium hirsutum TM-1) provides insights into genome evolution Nat. Biotechnol. 33 524 530 25893780
H. Cheng G.T. Concepcion X. Feng H. Zhang H. Li Haplotype-resolved de novo assembly using phased assembly graphs with hifiasm Nat. Methods 18 170 175 1:CAS:528:DC%2BB3MXis1OntL0%3D 33526886 7961889
S. Nurk et al. HiCanu: accurate assembly of segmental duplications, satellites, and allelic variants from high-fidelity long reads Genome Res. 30 1291 1305 1:CAS:528:DC%2BB3MXltl2isw%3D%3D 32801147 7545148
H. Sun et al. Chromosome-scale and haplotype-resolved genome assembly of a tetraploid potato cultivar Nat. Genet. 54 342 348 1:CAS:528:DC%2BB38XmtVehsbc%3D 35241824 8920897
G. Hoopes et al. Phased, chromosome-scale genome assemblies of tetraploid potato reveal a complex genome, transcriptome, and predicted proteome landscape underpinning genetic diversity Mol. Plant 15 520 536 1:CAS:528:DC%2BB38XktVGkur4%3D 35026436
P.P. Edger et al. Origin and evolution of the octoploid strawberry genome Nat. Genet. 51 541 547 1:CAS:528:DC%2BC1MXmsVyqsLw%3D 30804557 6882729
Y. Zheng et al. Allele-aware chromosome-scale assembly of the allopolyploid genome of hexaploid Ma bamboo (Dendrocalamus latiflorus Munro) J. Integr. Plant Biol. 64 649 670 1:CAS:528:DC%2BB38XhtFyjs7zO 34990066
T. Marcussen et al. Ancient hybridizations among the ancestral genomes of bread wheat Science 345 1250092 25035499
T. Zhang et al. Sequencing of allotetraploid cotton (Gossypium hirsutum L. acc. TM-1) provides a resource for fiber improvement Nat. Biotechnol. 33 531 537 1:CAS:528:DC%2BC2MXhtFemtrnK 25893781
D.J. Bertioli et al. The genome sequence of segmental allotetraploid peanut Arachis hypogaea Nat. Genet. 51 877 884 1:CAS:528:DC%2BC1MXoslKqtro%3D 31043755
R. VanBuren et al. Exceptional subgenome stability and functional divergence in the allotetraploid Ethiopian cereal teff Nat. Commun. 11 1:CAS:528:DC%2BB3cXkvFajsrw%3D 32060277 7021729 884
J. Miao et al. Chromosome-scale assembly and analysis of biomass crop Miscanthus lutarioriparius genome Nat. Commun. 12 1:CAS:528:DC%2BB3MXpvFartb4%3D 33911077 8080599 2458
T. Mitros et al. Genome biology of the paleotetraploid perennial biomass crop Miscanthus Nat. Commun. 11 1:CAS:528:DC%2BB3cXit1Ojur7J 33116128 7595124 5442
H. Chen et al. A chromosome-scale genome assembly of Artemisia argyi reveals unbiased subgenome evolution and key contributions of gene duplication to volatile terpenoid diversity Plant Commun. 4 100516 1:CAS:528:DC%2BB3sXis1Wjtbk%3D 36597358 10203441
Y. Miao et al. Genome sequencing reveals chromosome fusion and extensive expansion of genes related to secondary metabolism in Artemisia argyi Plant Biotechnol. J. 20 1902 1915 1:CAS:528:DC%2BB38XitVelsrfM 35689517 9491451
A. Song et al. Analyses of a chromosome-scale genome assembly reveal the origin and evolution of cultivated chrysanthemum Nat. Commun. 14 1:CAS:528:DC%2BB3sXnslajs78%3D 37037808 10085997 2021
J. Yang et al. Haplotype-resolved sweet potato genome traces back its hexaploidization history Nat. Plants 3 696 703 1:CAS:528:DC%2BC1cXktVGqtL8%3D 28827752
X. Zhang S. Zhang Q. Zhao R. Ming H. Tang Assembly of allele-aware, chromosomal-scale autopolyploid genomes based on Hi-C data Nat. Plants 5 833 845 1:CAS:528:DC%2BC1MXhsFCmsr3O 31383970
J. Zhang et al. Allele-defined genome of the autopolyploid sugarcane Saccharum spontaneum L Nat. Genet. 50 1565 1573 1:CAS:528:DC%2BC1cXitVCitL3F 30297971
H. Chen et al. Allele-aware chromosome-level genome assembly and efficient transgene-free genome editing for the autotetraploid cultivated alfalfa Nat. Commun. 11 1:CAS:528:DC%2BB3cXpvF2lt7w%3D 32427850 7237683 2494
R. Long et al. Genome assembly of alfalfa cultivar Zhongmu-4 and identification of SNPs associated with agronomic traits Genom. Proteom. Bioinform. 20 14 28 1:CAS:528:DC%2BB3sXhvFKrsLvM
F. Wang et al. The autotetraploid potato genome provides insights into highly heterozygous species Plant Biotechnol. J. 20 1996 2005 1:CAS:528:DC%2BB38XitVelsLnM 35767385 9491450
H. Zhang et al. The haplotype-resolved genome assembly of autotetraploid rhubarb Rheum officinale provides insights into its genome evolution and massive accumulation of anthraquinones Plant Commun. 5 100677 1:CAS:528:DC%2BB3sXitFKlsbfI 37634079
S. Wang et al. Haplotype-resolved chromosome-level genome of hexaploid Jerusalem artichoke provides insights into its origin, evolution, and inulin metabolism Plant Commun. 5 100767 1:CAS:528:DC%2BB2cXhtlKkuw%3D%3D 37974403
X. Zeng et al. Chromosome-level scaffolding of haplotype-resolved assemblies using Hi-C data without reference genomes Nat. Plants 10 1184 1120 1:CAS:528:DC%2BB2cXhslWrsLfM 39103456
Z. Bao et al. Genome architecture and tetrasomic inheritance of autotetraploid potato Mol. Plant 15 1211 1226 1:CAS:528:DC%2BB38Xhs1SmtL%2FN 35733345
R. Serra Mari et al. Haplotype-resolved assembly of a tetraploid potato genome using long reads and low-depth offspring data Genome Biol. 25 1:CAS:528:DC%2BB2cXhvF2muro%3D 38243222 10797741 26
H. Cheng M. Asri J. Lucas S. Koren H. Li Scalable telomere-to-telomere assembly for diploid and polyploid genomes with double graph Nat. Methods 21 967 970 1:CAS:528:DC%2BB2cXhtVCku7rI 38730258 11214949
Y. Bao et al. A chromosomal-scale genome assembly of modern cultivated hybrid sugarcane provides insights into origination and evolution Nat. Commun. 15 1:CAS:528:DC%2BB2cXpt12js7s%3D 38589412 11001919 3041
A.S. Deshpande et al. Identifying synergistic high-order 3D chromatin conformations from genome-scale nanopore concatemer sequencing Nat. Biotechnol. 40 1488 1499 1:CAS:528:DC%2BB38XhsVWjsLnJ 35637420
Z. Zhang et al. Haplotype-resolved genome assembly and resequencing provide insights into the origin and breeding of modern rose Nat. Plants 10 1659 1671 1:CAS:528:DC%2BB2cXit1alsL3N 39394508
L. Gabriel et al. BRAKER3: fully automated genome annotation using RNA-seq and protein evidence with GeneMark-ETP, AUGUSTUS, and TSEBRA Genome Res. 34 769 777 1:CAS:528:DC%2BB2cXitFyktb3F 38866550 11216308
R. Zhang et al. A high-resolution single-molecule sequencing-based Arabidopsis transcriptome using novel methods of Iso-seq analysis Genome Biol. 23 1:CAS:528:DC%2BB38XitVGgs7rM 35799267 9264592 149
N.D. Olson et al. Variant calling and benchmarking in an era of complete human genome sequences Nat. Rev. Genet. 24 464 483 1:CAS:528:DC%2BB3sXnvFems7o%3D 37059810
P.W. Hook W. Timp Beyond assembly: the increasing flexibility of single-molecule sequencing technology Nat. Rev. Genet. 24 627 641 1:CAS:528:DC%2BB3sXpsl2jsLc%3D 37161088
B. Wang et al. Variant phasing and haplotypic expression from long-read sequencing in maize Commun. Biol. 3 78 32071408 7028979
J. Wu S. Mukhopadhyay E. Pérez-López Sr Resistance gene enrichment sequencing refines the Brassica napus NLRome Plant Physiol. 197 kiae631 1:CAS:528:DC%2BB2MXhtFahtLfK 39603796
Holst, F. et al. Helixer—de novo prediction of primary eukaryotic gene models combining deep learning and a hidden Markov model. Preprint at bioRxivhttps://doi.org/10.1101/2023.02.06.527280 (2023).
L. Gabriel F. Becker K.J. Hoff M. Stanke Tiberius: end-to-end deep learning with an HMM for gene prediction Bioinformatics 40 btae685 1:CAS:528:DC%2BB2MXisVKrtLw%3D 39558581 11645249
Zhai, J. et al. Cross-species modeling of plant genomes at single nucleotide resolution using a pre-trained DNA language model. Proc. Natl Acad. Sci. USA122, e2421738122 (2025).
G. Benegas S.S. Batra Y.S. Song DNA language models are powerful predictors of genome-wide variant effects Proc. Natl Acad. Sci. USA 120 e2311219120 1:CAS:528:DC%2BB3sXisVylsLvF 37883436 10622914
L. Comai The advantages and disadvantages of being polyploid Nat. Rev. Genet. 6 836 846 1:CAS:528:DC%2BD2MXhtFygt7%2FO 16304599
F. Cheng et al. Gene retention, fractionation and subgenome differences in polyploid plants Nat. Plants 4 258 268 1:CAS:528:DC%2BC1cXpsVWgs7g%3D 29725103
J. Yuan et al. Dynamic and reversible DNA methylation changes induced by genome separation and merger of polyploid wheat BMC Biol. 18 1:CAS:528:DC%2BB3cXis1yht7rJ 33218336 7679994 171
R.H. Ramírez-González et al. The transcriptional landscape of polyploid wheat Science 361 eaar6089 30115782
P.M. Bourke R.E. Voorrips R.G. Visser C. Maliepaard The double-reduction landscape in tetraploid potato as revealed by a high-density linkage map Genetics 201 853 863 26377683 4649655
B. Julier et al. Construction of two genetic linkage maps in cultivated tetraploid alfalfa (Medicago sativa) using microsatellite and AFLP markers BMC Plant Biol. 3 14683527 324403 9
B. Hurgobin et al. Homoeologous exchange is a major cause of gene presence/absence variation in the amphidiploid Brassica napus Plant Biotechnol. J. 16 1265 1274 1:CAS:528:DC%2BC1cXhtFKhtL%2FP 29205771 5999312
Z. Zhang et al. Homoeologous exchanges occur through intragenic recombination generating novel transcripts and proteins in wheat and other polyploids Proc. Natl Acad. Sci. USA 117 14561 14571 1:CAS:528:DC%2BB3cXhsVCgsrbI 32518116 7321986
C. Fan et al. The KL system in wheat permits homoeologous crossing over between closely related chromosomes Crop J. 11 808 816
G. Hu et al. Evolutionary dynamics of chromatin structure and duplicate gene expression in diploid and allopolyploid cotton Mol. Biol. Evol. 41 msae095 1:CAS:528:DC%2BB2MXitFSqsLs%3D 38758089 11140268
Y. Wu et al. Phylogenomic discovery of deleterious mutations facilitates hybrid potato breeding Cell 186 2313 2328.e15 1:CAS:528:DC%2BB3sXptlWnt7c%3D 37146612
T. Herben J. Suda J. Klimešová Polyploid species rely on vegetative reproduction more than diploids: a re-examination of the old hypothesis Ann. Bot. 120 341 349 28334206 5737615
S. Walkowiak et al. Multiple wheat genomes reveal global variation in modern breeding Nature 588 277 283 1:CAS:528:DC%2BB3cXisVeqtr3P 33239791 7759465
J. Li et al. Convergence and divergence of diploid and tetraploid cotton genomes Nat. Genet. 56 2562 2573 1:CAS:528:DC%2BB2cXitlKgtbvK 39472693
H. Hu et al. Plant pangenomics, current practice and future direction Agric. Commun. 2 100039
M. Schreiber M. Jayakodi N. Stein M. Mascher Plant pangenomes for crop improvement, biodiversity and evolution Nat. Rev. Genet. 25 563 577 1:CAS:528:DC%2BB2cXktVyjsLo%3D 38378816 7616794
J. Shi Z. Tian J. Lai X. Huang Plant pan-genomics and its applications Mol. Plant 16 168 186 1:CAS:528:DC%2BB38XjtFylu7bP 36523157
Y. Li et al. De novo assembly of soybean wild relatives for pan-genome analysis of diversity and agronomic traits Nat. Biotechnol. 32 1045 1052 1:CAS:528:DC%2BC2cXhsFOlt7jF 25218520
Q. Zhao et al. Pan-genome analysis highlights the extent of genomic variation in cultivated and wild rice Nat. Genet. 50 278 284 1:CAS:528:DC%2BC1cXkslGitbc%3D 29335547
C.N. Hirsch et al. Insights into the maize pan-genome and pan-transcriptome Plant Cell 26 121 135 1:CAS:528:DC%2BC2cXks1Sgur8%3D 24488960 3963563
M. Jayakodi et al. The barley pan-genome reveals the hidden legacy of mutation breeding Nature 588 284 289 1:CAS:528:DC%2BB3cXisVeqtr3K 33239781 7759462
M. Jayakodi et al. Structural variation in the pangenome of wild and domesticated barley Nature 636 654 662 1:CAS:528:DC%2BB2cXisV2nu77J 39537924 11655362
J. Chen et al. Pangenome analysis reveals genomic variations associated with domestication traits in broomcorn millet Nat. Genet. 55 2243 2254 1:CAS:528:DC%2BB3sXisFSlsr7O 38036791 10703678
G. Hickey et al. Genotyping structural variants in pangenome graphs using the vg toolkit Genome Biol. 21 32051000 7017486 35
T.R. MacNish et al. Brassica Panache: a multi-species graph pangenome representing presence absence variation across forty-one Brassica genomes Plant Genome 18 1:CAS:528:DC%2BB2cXisl2jsbjI 39648684 e20535
Y. Zhang et al. Structural variation reshapes population gene expression and trait variation in 2,105 Brassica napus accessions Nat. Genet. 56 2538 2550 1:CAS:528:DC%2BB2cXisVaqsbzE 39501128 11549052
H. Sun et al. The phased pan-genome of tetraploid European potato Nature 642 389 397 1:CAS:528:DC%2BB2MXhtlGis73P 40240601 12158759
G. Nieto Feliner J. Casacuberta J.F. Wendel Genomics of evolutionary novelty in hybrids and polyploids Front. Genet. 11 792 32849797 7399645
M.R. Brown R.J. Abbott A.D. Twyford The emerging importance of cross‐ploidy hybridisation and introgression Mol. Ecol. 33 e17315 38501394
G.M. Douglas et al. Hybrid origins and the earliest stages of diploidization in the highly successful recent polyploid Capsella bursa-pastoris Proc. Natl Acad. Sci. USA 112 2806 2811 1:CAS:528:DC%2BC2MXivFWqtbk%3D 25691747 4352811
Z. Wang et al. Dispersed emergence and protracted domestication of polyploid wheat uncovered by mosaic ancestral haploblock inference Nat. Commun. 13 1:CAS:528:DC%2BB38Xhslent7nL 35794156 9259585 3891
X. Zhao et al. Population genomics unravels the Holocene history of bread wheat and its relatives Nat. Plants 9 403 419 36928772
T. Wang et al. Interploidy introgression shaped adaptation during the origin and domestication history of Brassica napus Mol. Biol. Evol. 40 msad199 1:CAS:528:DC%2BB2cXhsVentLo%3D 37707440 10504873
M.A. Hardigan et al. Genome diversity of tuber-bearing Solanum uncovers complex evolutionary history and targets of domestication in the cultivated potato Proc. Natl Acad. Sci. USA 114 E9999 1:CAS:528:DC%2BC2sXhslemsrzL 29087343 5699086
C. Shen et al. The chromosome-level genome sequence of the autotetraploid alfalfa and resequencing of core germplasms provide genomic resources for alfalfa research Mol. Plant 13 1250 1261 1:CAS:528:DC%2BB3cXhs1GrtLrI 32673760
P. Monnahan et al. Pervasive population genomic consequences of genome duplication in Arabidopsis arenosa Nat. Ecol. Evol. 3 457 468 30804518
Y. Zhou et al. Triticum population sequencing provides insights into wheat adaptation Nat. Genet. 52 1412 1422 1:CAS:528:DC%2BB3cXitFKlu7zJ 33106631
N. Kamal et al. The mosaic oat genome gives insights into a uniquely healthy cereal crop Nature 606 113 119 1:CAS:528:DC%2BB38Xhtlajtr3I 35585233 9159951
K. Lu et al. Whole-genome resequencing reveals Brassica napus origin and genetic loci involved in its improvement Nat. Commun. 10 30858362 6411957 1154
M. Wang et al. Asymmetric subgenome selection and cis-regulatory divergence during cotton domestication Nat. Genet. 49 579 587 1:CAS:528:DC%2BC2sXltVWgu74%3D 28263319
S. Wang et al. Characterization of polyploid wheat genomic diversity using a high‐density 90,000 single nucleotide polymorphism array Plant Biotechnol. J. 12 787 796 1:CAS:528:DC%2BC2cXht1Wmsr%2FI 24646323
C. Sun et al. The Wheat 660K SNP array demonstrates great potential for marker‐assisted selection in polyploid wheat Plant Biotechnol. J. 18 1354 1360 1:CAS:528:DC%2BB3cXoslOksrc%3D 32065714 7206996
M.O. Winfield et al. High‐density SNP genotyping array for hexaploid wheat and its secondary and tertiary gene pool Plant Biotechnol. J. 14 1195 1206 1:CAS:528:DC%2BC28XlvV2jsbw%3D 26466852
K.J. Felcher et al. Integration of two diploid potato linkage maps with the potato genome sequence PLoS ONE 7 e36347 1:CAS:528:DC%2BC38Xnt1Cruro%3D 22558443 3338666
Q. You et al. Development of an Axiom Sugarcane100K SNP array for genetic map construction and QTL identification Theor. Appl. Genet. 132 2829 2845 1:CAS:528:DC%2BC1MXhsVajsr%2FM 31321474
L. Meng H. Li L. Zhang J. Wang QTL IciMapping: integrated software for genetic linkage map construction and quantitative trait locus mapping in biparental populations Crop J. 3 269 283
S.K. Deb P.P. Edger J.C. Pires M.R. McKain Patterns, mechanisms, and consequences of homoeologous exchange in allopolyploid angiosperms: a genomic and epigenomic perspective N. Phytol. 238 2284 2304 1:CAS:528:DC%2BB3sXptVKhsr0%3D
Y. Wu et al. Genomic mosaicism due to homoeologous exchange generates extensive phenotypic diversity in nascent allopolyploids Natl Sci. Rev. 8 nwaa277 1:CAS:528:DC%2BB3MXitVSmsbrO 34691642
A. Stein et al. Mapping of homoeologous chromosome exchanges influencing quantitative trait variation in Brassica napus Plant Biotechnol. J. 15 1478 1489 1:CAS:528:DC%2BC2sXhs1egsr7E 28370938 5633767
L. Jiang X. Ren R. Wu Computational characterization of double reduction in autotetraploid natural populations Plant J. 105 1703 1709 1:CAS:528:DC%2BB3MXhsVCmsbk%3D 33295001
N.C. Manrique-Carpintero et al. Genome reduction in tetraploid potato reveals genetic load, haplotype variation, and loci associated with agronomic traits Front. Plant Sci. 9 944 30018631 6037889
S.P. Otto The evolutionary consequences of polyploidy Cell 131 452 462 1:CAS:528:DC%2BD2sXhtlWitr%2FJ 17981114
P.M. Bourke et al. Partial preferential chromosome pairing is genotype dependent in tetraploid rose Plant J. 90 330 343 1:CAS:528:DC%2BC2sXksV2kt7o%3D 28142191
P.A. Wadl et al. Genetic diversity and population structure of the USDA sweetpotato (Ipomoea batatas) germplasm collections using GBSpoly Front. Plant Sci. 9 1166 30186293 6111789
M. Mollinari et al. Unraveling the hexaploid sweetpotato inheritance using ultra-dense multilocus mapping G3 10 281 292 31732504
C.A. Hackett B. Boskamp A. Vogogias K.F. Preedy I. Milne TetraploidSNPMap: software for linkage analysis and QTL mapping in autotetraploid populations using SNP dosage data J. Hered. 108 438 442 1:CAS:528:DC%2BC1MXjtVaqu70%3D
H. Takagi et al. QTL ‐seq: rapid mapping of quantitative trait loci in rice by whole genome resequencing of DNA from two bulked populations Plant J. 74 174 183 1:CAS:528:DC%2BC3sXktFOnsrs%3D 23289725
J. Chen et al. A tetrasomic inheritance model and likelihood‐based method for mapping quantitative trait loci in autotetraploid species N. Phytol. 230 387 398 1:CAS:528:DC%2BB3MXotFWju78%3D
Z. Ma et al. Resequencing a core collection of upland cotton identifies genomic variation and loci influencing fiber quality and yield Nat. Genet. 50 803 813 1:CAS:528:DC%2BC1cXpt1GksrY%3D 29736016
Q. Lu et al. A genomic variation map provides insights into peanut diversity in China and associations with 28 agronomic traits Nat. Genet. 56 530 540 1:CAS:528:DC%2BB2cXktVyjtrg%3D 38378864
J.-M. Song et al. Eight high-quality genomes reveal pan-genome architecture and ecotype differentiation of Brassica napus Nat. Plants 6 34 45 1:CAS:528:DC%2BB3cXhtVOru7c%3D 31932676 6965005
S. Jin et al. Structural variation (SV)-based pan-genome and GWAS reveal the impacts of SVs on the speciation and diversification of allotetraploid cottons Mol. Plant 16 678 693 1:CAS:528:DC%2BB3sXjvFCjs7k%3D 36760124
S.L. Dwivedi P. Heslop‐Harrison J. Amas R. Ortiz D. Edwards Epistasis and pleiotropy‐induced variation for plant breeding Plant Biotechnol. J. 22 2788 2807 1:CAS:528:DC%2BB2cXhtlemu77K 38875130 11536456
J. Jia et al. Genome resources for the elite bread wheat cultivar Aikang 58 and mining of elite homeologous haplotypes for accelerating wheat improvement Mol. Plant 16 1893 1910 1:CAS:528:DC%2BB3sXisVamsLrM 37897037
S.K. Sharma et al. Linkage disequilibrium and evaluation of genome-wide association mapping models in tetraploid potato G3 8 3185 3202 1:CAS:528:DC%2BC1MXhvFSgsr7L 30082329 6169395
E. Haque et al. Polyploid GWAS reveals the basis of molecular marker development for complex breeding traits including starch content in the storage roots of sweet potato Front. Plant Sci. 14 1181909 37342138 10277646
M. Chen et al. Genome-wide identification of agronomically important genes in outcrossing crops using OutcrossSeq Mol. Plant 14 556 570 1:CAS:528:DC%2BB3MXjtVSrsLk%3D 33429094
B. Huang D.M. Spooner Q. Liang Genome diversity of the potato Proc. Natl Acad. Sci. USA 115 E6392 1:CAS:528:DC%2BC1cXitlWru7jL 29934399 6048492
D.P. Cooke D.C. Wedge G. Lunter Benchmarking small-variant genotyping in polyploids Genome Res. 32 403 408 1:CAS:528:DC%2BB2cXit1CmsLjP 34965940 8805713
W.-W. Liao et al. A draft human pangenome reference Nature 617 312 324 1:CAS:528:DC%2BB3sXpvVansLk%3D 37165242 10172123
C. Groza et al. Pangenome graphs improve the analysis of structural variants in rare genetic diseases Nat. Commun. 15 1:CAS:528:DC%2BB2cXivVWhs7Y%3D 38253606 10803329 657
Y. Dong Y.-Z. Wang Seed shattering: from models to crops Front. Plant Sci. 6 476 26157453 4478375
J. Van Dam P.L. Kooman P.C. Struik Effects of temperature and photoperiod on early growth and final number of tubers in potato (Solanum tuberosum L.) Potato Res. 39 51 62
J.F. Martínez-García J.L. García-Martínez J. Bou S. Prat The interaction of gibberellins and photoperiod in the control of potato tuberization J. Plant Growth Regul. 20 377 386 11986763
T. Johns Detoxification function of geophagy and domestication of the potato J. Chem. Ecol. 12 635 646 1:CAS:528:DyaL28XhvVGjsrY%3D 24306904
Y. Shang et al. Biosynthesis, regulation, and domestication of bitterness in cucumber Science 346 1084 1088 1:CAS:528:DC%2BC2cXhvFKqtb7N 25430763
R. Avni et al. Wild emmer genome architecture and diversity elucidate wheat evolution and domestication Science 357 93 97 1:CAS:528:DC%2BC2sXhtFans7fP 28684525
J. Jia et al. Aegilops tauschii draft genome sequence reveals a gene repertoire for wheat adaptation Nature 496 91 95 1:CAS:528:DC%2BC3sXkvFOqt70%3D 23535592
Z. Zheng et al. Chloroplast and whole-genome sequencing shed light on the evolutionary history and phenotypic diversification of peanuts Nat. Genet. 56 1975 1984 1:CAS:528:DC%2BB2cXhvVSks7bK 39138385 11387195
Z.A. Desta R. Ortiz Genomic selection: genome-wide prediction in plant improvement Trends Plant Sci. 19 592 601 1:CAS:528:DC%2BC2cXhtFans7rJ 24970707
T. Meuwissen B. Hayes M. Goddard Accelerating improvement of livestock with genomic selection Annu. Rev. Anim. Biosci. 1 221 237 25387018
L.G. Batista V.H. Mello A.P. Souza G.R. Margarido Genomic prediction with allele dosage information in highly polyploid species Theor. Appl. Genet. 135 723 739 1:CAS:528:DC%2BB38XotlCktL4%3D 34800132
S. Yadav et al. Accelerating genetic gain in sugarcane breeding using genomic selection Agronomy 10 585 1:CAS:528:DC%2BB3cXitFSrtbvO
M. Gouy et al. Experimental assessment of the accuracy of genomic selection in sugarcane Theor. Appl. Genet. 126 2575 2586 1:STN:280:DC%2BC3sflvFGrtA%3D%3D 23907359
D. Bonnett et al. Response to early generation genomic selection for yield in wheat Front. Plant Sci. 12 718611 35087542 8787636
J. Pandey D.C. Scheuring J.W. Koym J.B. Endelman M.I. Vales Genomic selection and genome-wide association studies in tetraploid chipping potatoes Plant Genome 16 e20297 1:CAS:528:DC%2BB3sXhsVSgtbY%3D 36651146
Y. Wang et al. Simultaneous editing of three homoeoalleles in hexaploid bread wheat confers heritable resistance to powdery mildew Nat. Biotechnol. 32 947 951 1:CAS:528:DC%2BC2cXhtFygs7jJ 25038773
I.E. Johansen et al. High efficacy full allelic CRISPR/Cas9 gene editing in tetraploid potato Sci. Rep. 9 31776399 6881354 17715
J. Li X. Yu C. Zhang N. Li J. Zhao The application of CRISPR/Cas technologies to Brassica crops: current progress and future perspectives aBIOTECH 3 146 161 36304520 9590542
A.K. Mall et al. CRISPR/Cas-mediated genome editing for sugarcane improvement Sugar Tech. 27 1 13
K. Vondracek F. Altpeter T. Liu S. Lee Advances in genomics and genome editing for improving strawberry (Fragaria × ananassa) Front. Genet. 15 1382445 1:CAS:528:DC%2BB2cXhtV2rsLrN 38706796 11066249
L. Tripathi V.O. Ntui J.N. Tripathi CRISPR/Cas9-based genome editing of banana for disease resistance Curr. Opin. Plant Biol. 56 118 126 1:CAS:528:DC%2BB3cXhtFKisrfJ 32604025
Y. Liu et al. Targeted mutagenesis in tetraploid switchgrass (Panicum virgatum L.) using CRISPR/Cas9 Plant Biotechnol. J. 16 381 393 1:CAS:528:DC%2BC1cXitVWgs7w%3D 28640964
H. Tang et al. Fertility recovery of wheat male sterility controlled by Ms2 using CRISPR/Cas9 Plant Biotechnol. J. 19 224 226 1:CAS:528:DC%2BB3MXns1Ohur8%3D 32970905
H. Zhu C. Li C. Gao Applications of CRISPR–Cas in agriculture and plant biotechnology Nat. Rev. Mol. Cell Biol. 21 661 677 1:CAS:528:DC%2BB3cXhvFWmurfM 32973356
Y. Zhang et al. Efficient and transgene-free genome editing in wheat through transient expression of CRISPR/Cas9 DNA or RNA Nat. Commun. 7 1:CAS:528:DC%2BC28XhsVChtrfO 27558837 5007326 12617
J. Li Y. Li L. Ma Recent advances in CRISPR/Cas9 and applications for wheat functional genomics and breeding aBIOTECH 2 375 385 1:CAS:528:DC%2BB38XnsFemurg%3D 36304421 9590522
Q.U. Zaman C. Li H. Cheng Q. Hu Genome editing opens a new era of genetic improvement in polyploid crops Crop J. 7 141 150
A.A. Levy M. Feldman Evolution and origin of bread wheat Plant Cell 34 2549 2567 35512194 9252504
U. Rosyara et al. Genetic contribution of synthetic hexaploid wheat to CIMMYT’s spring bread wheat breeding germplasm Sci. Rep. 9 31451719 6710277 12355
H. Yu et al. A route to de novo domestication of wild allotetraploid rice Cell 5 1156 1170
L. Cheng et al. Leveraging a phased pangenome for haplotype design of hybrid potato Nature 640 408 417 1:CAS:528:DC%2BB2MXhvFyjsb8%3D 39843749 11981936
M. Ye et al. Generation of self-compatible diploid potato by knockout of S-RNase Nat. Plants 4 651 654 1:CAS:528:DC%2BC1cXhsFSqtb%2FM 30104651
C. Zhang et al. The genetic basis of inbreeding depression in potato Nat. Genet. 51 374 378 1:CAS:528:DC%2BC1MXlvFSgtbk%3D 30643248
C. Zhang et al. Genome design of hybrid potato Cell 184 3873 3883 1:CAS:528:DC%2BB3MXhsVWhtbjO 34171306
J.D. Washburn J.A. Birchler Polyploids as a “model system” for the study of heterosis Plant Reprod. 27 1 5 24202960
D. Mieulet et al. Turning rice meiosis into mitosis Cell Res. 26 1242 1254 1:CAS:528:DC%2BC28XhslGgs7nJ 27767093 5099866
Y. Wang et al. Harnessing clonal gametes in hybrid crops to engineer polyploid genomes Nat. Genet. 56 1075 1079 1:CAS:528:DC%2BB2cXhtVGrs7bL 38741016 11176054
S. Liu et al. A telomere-to-telomere genome assembly coupled with multi-omic data provides insights into the evolution of hexaploid bread wheat Nat. Genet. 57 1008 1020 1:CAS:528:DC%2BB2MXoslSisbY%3D 40195562 11985340
Z. Wang et al. Near-complete assembly and comprehensive annotation of the wheat Chinese Spring genome Mol. Plant 18 892 907 1:CAS:528:DC%2BB2MXltFantLg%3D 39949061
N. Athiyannan et al. Long-read genome sequencing of bread wheat facilitates disease resistance gene cloning Nat. Genet. 54 227 231 1:CAS:528:DC%2BB38XntFCjtbY%3D 35288708 8920886
K.-H. Jia et al. SubPhaser: a robust allopolyploid subgenome phasing method based on subgenome-specific k-mers N. Phytol. 235 801 809 1:CAS:528:DC%2BB38XhvVeiurjM
J.T. Lovell et al. Genomic mechanisms of climate adaptation in polyploid bioenergy switchgrass Nature 590 438 444 1:CAS:528:DC%2BB3MXitlSmsr0%3D 33505029 7886653
H. Yan et al. Post-polyploidization centromere evolution in cotton Nat. Genet. 57 1021 1030 1:CAS:528:DC%2BB2MXoslSisLo%3D 40033059
G. Hu et al. A telomere-to-telomere genome assembly of cotton provides insights into centromere evolution and short-season adaptation Nat. Genet. 57 1031 1043 1:CAS:528:DC%2BB2MXoslSitrw%3D 40097785
A. Sreedasyam et al. Genome resources for three modern cotton lines guide future breeding efforts Nat. Plants 10 1039 1051 38816498 11208153
B. Li et al. A gap-free reference genome reveals structural variations associated with flowering time in rapeseed (Brassica napus) Hortic. Res. 10 uhad171 1:CAS:528:DC%2BB2cXhtlelur%2FM 37841499 10569240
C. Zhao et al. Chromosome-scale genome assembly-assisted identification of Brassica napus BnDCPA1 for improvement of plant architecture and yield heterosis Plant Commun. 5 100854 1:CAS:528:DC%2BB2cXhtVaqsbzI 38419333 11287117
S. Gao et al. The centromere landscapes of four karyotypically diverse Papaver species provide insights into chromosome evolution and speciation Cell Genom. 4 100626 1:CAS:528:DC%2BB2cXhs1GlsLvI 39084227 11406182
X. Yang et al. Three chromosome-scale Papaver genomes reveal punctuated patchwork evolution of the morphinan and noscapine biosynthesis pathway Nat. Commun. 12 1:CAS:528:DC%2BB3MXit1Glsb7O 34654815 8521590 6030
S. Kumar et al. TimeTree 5: an expanded resource for species divergence times Mol. Biol. Evol. 39 msac174 1:CAS:528:DC%2BB3sXhsVCjtb4%3D 35932227 9400175
J.W. Clark P.C. Donoghue Whole-genome duplication and plant macroevolution Trends Plant Sci. 23 933 945 1:CAS:528:DC%2BC1cXhsVSmtrnP 30122372
J.M. Kreiner P. Kron B.C. Husband Evolutionary dynamics of unreduced gametes Trends Genet. 33 583 593 1:CAS:528:DC%2BC2sXhtFCgs7fP 28732599
J. Ramsey D.W. Schemske Pathways, mechanisms, and rates of polyploid formation in flowering plants Annu. Rev. Ecol. Syst. 29 467 501
Z.J. Chen et al. Genomic diversifications of five Gossypium allopolyploid species and their impact on cotton improvement Nat. Genet. 52 525 533 1:CAS:528:DC%2BB3cXnsFSnur4%3D 32313247 7203012
D. Dai et al. Unzipped chromosome-level genomes reveal allopolyploid nematode origin pattern as unreduced gamete hybridization Nat. Commun. 14 1:CAS:528:DC%2BB3sXitlaqsLjP 37935661 10630426 7156
