Garg, S. Computational methods for chromosome-scale haplotype reconstruction. Genome Biol. 22, 101 (2021).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Leitwein, M., Duranton, M., Rougemont, Q., Gagnaire, P.-A. & Bernatchez, L. Using haplotype information for conservation genomics. Trends Ecol. Evo. 35, 245–258 (2020).

Article  Google Scholar 

Browning, B. L. & Browning, S. R. A unified approach to genotype imputation and haplotype-phase inference for large data sets of trios and unrelated individuals. Am. J. Hum. Genet. 84, 210–223 (2009).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Marchini, J. & Howie, B. Genotype imputation for genome-wide association studies. Nat. Rev. Genet. 11, 499–511 (2010).

Article  CAS  PubMed  Google Scholar 

Bhat, J. A., Yu, D., Bohra, A., Ganie, S. A. & Varshney, R. K. Features and applications of haplotypes in crop breeding. Commun. Biol. 4, 1266 (2021).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Vonholdt, B. M. et al. Genome-wide SNP and haplotype analyses reveal a rich history underlying dog domestication. Nature 464, 898–902 (2010).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Zhao, J., Sauvage, C., Bitton, F. & Causse, M. Multiple haplotype-based analyses provide genetic and evolutionary insights into tomato fruit weight and composition. Horticul. Res. 9, uhab009 (2022).

Article  CAS  Google Scholar 

Blanca, J. et al. Haplotype analyses reveal novel insights into tomato history and domestication driven by long-distance migrations and latitudinal adaptations. Hortic. Res. 9, uhac030 (2022).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Yang, J. et al. Haplotype-resolved sweet potato genome traces back its hexaploidization history. Nat. Plants 3, 696–703 (2017).

Article  CAS  PubMed  Google Scholar 

Yan, M. et al. Haplotype-based phylogenetic analysis and population genomics uncover the origin and domestication of sweetpotato. Mol. Plant 17, 277–296 (2024).

Article  CAS  PubMed  Google Scholar 

Todesco, M. et al. Massive haplotypes underlie ecotypic differentiation in sunflowers. Nature 584, 602–607 (2020).

Article  CAS  PubMed  Google Scholar 

Zhang, F. et al. The landscape of gene–CDS–haplotype diversity in rice: Properties, population organization, footprints of domestication and breeding, and implications for genetic improvement. Mol., Plant 14, 787–804 (2021).

Article  CAS  PubMed  Google Scholar 

Naj, A. C. Genotype imputation in genome‐wide association studies. Curr. Protoc. Hum. Genet. 102, e84 (2019).

Article  PubMed  Google Scholar 

Liu, F., Jiang, Y., Zhao, Y., Schulthess, A. W. & Reif, J. C. Haplotype-based genome-wide association increases the predictability of leaf rust (Puccinia triticina) resistance in wheat. J. Exp. Bot. 71, 6958–6968 (2020).

Article  CAS  PubMed  Google Scholar 

Wu, X. et al. Prioritized candidate causal haplotype blocks in plant genome-wide association studies. PLoS Genet. 18, e1010437 (2022).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Dong, X. et al. Dynamic and antagonistic allele-specific epigenetic modifications controlling the expression of imprinted genes in maize endosperm. Mol. Plant 10, 442–455 (2017).

Article  CAS  PubMed  Google Scholar 

Shao, L. et al. Patterns of genome-wide allele-specific expression in hybrid rice and the implications on the genetic basis of heterosis. Proc. Natl Acad. Sci. USA 116, 5653–5658 (2019).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Guk, J. Y., Jang, M. J., Choi, J. W., Lee, Y. M. & Kim, S. De novo phasing resolves haplotype sequences in complex plant genomes. Plant Biotechnol. J. 20, 1031–1041 (2022).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Mansfeld, B. N. et al. A haplotype resolved chromosome‐scale assembly of North American wild apple Malus fusca and comparative genomics of the fire blight Mfu10 locus. Plant J. 116, 989–1002 (2023).

Article  CAS  PubMed  Google Scholar 

Han, X. et al. Two haplotype-resolved, gap-free genome assemblies for Actinidia latifolia and Actinidia chinensis shed light on the regulatory mechanisms of vitamin C and sucrose metabolism in kiwifruit. Mol. Plant 16, 452–470 (2023).

Article  CAS  PubMed  Google Scholar 

Rhie, A., Walenz, B. P., Koren, S. & Phillippy, A. M. Merqury: reference-free quality, completeness, and phasing assessment for genome assemblies. Genome Biol. 21, 245 (2020).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Browning, S. R. & Browning, B. L. Haplotype phasing: existing methods and new developments. Nat. Rev. Genet. 12, 703–714 (2011).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Schrinner, S. D. et al. Haplotype threading: accurate polyploid phasing from long reads. Genome Biol. 21, 252 (2020).

Article  PubMed  PubMed Central  Google Scholar 

Kuleshov, V. et al. Whole-genome haplotyping using long reads and statistical methods. Nat. Biotechnol. 32, 261–266 (2014).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Howie, B. N., Donnelly, P. & Marchini, J. A flexible and accurate genotype imputation method for the next generation of genome-wide association studies. PLoS Genet. 5, e1000529 (2009).

Article  PubMed  PubMed Central  Google Scholar 

Browning, B. L., Tian, X., Zhou, Y. & Browning, S. R. Fast two-stage phasing of large-scale sequence data. Am. J. Hum. Genet. 108, 1880–1890 (2021).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Zhang, W. et al. A phased genome based on single sperm sequencing reveals crossover pattern and complex relatedness in tea plants. Plant J. l 105, 197–208 (2021).

Article  CAS  Google Scholar 

Martin, M. et al. WhatsHap: weighted haplotype assembly for future-generation sequencing reads. J. Comput. Biol. 22, 498–509 (2015).

Article  Google Scholar 

Duan, H. et al. Physical separation of haplotypes in dikaryons allows benchmarking of phasing accuracy in Nanopore and HiFi assemblies with Hi-C data. Genome Biol. 23, 84 (2022).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Kronenberg, Z. N. et al. Extended haplotype-phasing of long-read de novo genome assemblies using Hi-C. Nat. Commun. 12, 935 (2021).

Article  Google Scholar 

Cheng, H. et al. Haplotype-resolved assembly of diploid genomes without parental data. Nat. Biotechnol. 40, 1332–1335 (2022).

Article  CAS  PubMed  Google Scholar 

Zhang, X., Zhang, S., Zhao, Q., Ming, R. & Tang, H. Assembly of allele-aware, chromosomal-scale autopolyploid genomes based on Hi-C data. Nat. Plants 5, 833–845 (2019).