Pangenome analysis reveals genomic variations associated with domestication traits in broomcorn millet – Nature.com

Lemmon, Z. H. et al. Rapid improvement of domestication traits in an orphan crop by genome editing. Nat. Plants 4, 766770 (2018).

Article CAS PubMed Google Scholar

Ye, C. Y. & Fan, L. Orphan crops and their wild relatives in the genomic era. Mol. Plant 14, 2739 (2021).

Article CAS PubMed Google Scholar

Cullis, C. & Kunert, K. J. Unlocking the potential of orphan legumes. J. Exp. Bot. 68, 18951903 (2017).

CAS PubMed Google Scholar

Tadele, Z. Orphan crops: their importance and the urgency of improvement. Planta 250, 677694 (2019).

Article CAS PubMed Google Scholar

Chiurugwi, T., Kemp, S., Powell, W. & Hickey, L. T. Speed breeding orphan crops. Theor. Appl. Genet. 132, 607616 (2019).

Article PubMed Google Scholar

Shi, J. et al. Chromosome conformation capture resolved near complete genome assembly of broomcorn millet. Nat. Commun. 10, 464 (2019).

Article CAS PubMed PubMed Central Google Scholar

Zou, C. et al. The genome of broomcorn millet. Nat. Commun. 10, 436 (2019).

Article CAS PubMed PubMed Central Google Scholar

Leipe, C., Long, T., Sergusheva, E. A., Wagner, M. & Tarasov, P. E. Discontinuous spread of millet agriculture in eastern Asia and prehistoric population dynamics. Sci. Adv. 5, eaax6225 (2019).

Article CAS PubMed PubMed Central Google Scholar

Lu, H. et al. Earliest domestication of common millet (Panicum miliaceum) in East Asia extended to 10,000 years ago. Proc. Natl Acad. Sci. USA 106, 73677372 (2009).

Article CAS PubMed PubMed Central Google Scholar

Wang, C.-C. et al. Genomic insights into the formation of human populations in East Asia. Nature 591, 413419 (2021).

Article CAS PubMed PubMed Central Google Scholar

Dal Corso, M. et al. Between cereal agriculture and animal husbandry: millet in the early economy of the North Pontic region. J. World Prehist. 35, 321374 (2022).

Article Google Scholar

Filipovi, D. et al. New AMS 14C dates track the arrival and spread of broomcorn millet cultivation and agricultural change in prehistoric Europe. Sci. Rep. 10, 13698 (2020).

Article PubMed PubMed Central Google Scholar

Martin, L. et al. The place of millet in food globalization during Late Prehistory as evidenced by new bioarchaeological data from the Caucasus. Sci. Rep. 11, 13124 (2021).

Article CAS PubMed PubMed Central Google Scholar

Santra, D. K., Khound, R. & Das, S. Proso Millet (Panicum miliaceum L.) Breeding: Progress, Challenges and Opportunities (Springer, 2019).

Singh, M. & Sood, S. Millets and Pseudo Cereals: Genetic Resources and Breeding Advancements (Woodhead Publishing, 2020).

United States Department of Agriculture (USDA) & National Agricultural Statistics Service. 2021 Crop Production (USDA, 2022).

Habiyaremye, C. et al. Proso millet (Panicum miliaceum L.) and its potential for cultivation in the Pacific Northwest, U.S.: a review. Front. Plant Sci. 7, 1961 (2017).

Article PubMed PubMed Central Google Scholar

Xu, Y. et al. Domestication and spread of broomcorn millet (Panicum miliaceum L.) revealed by phylogeography of cultivated and weedy populations. Agronomy 9, 835 (2019).

Article CAS Google Scholar

Hunt, H. V. et al. Genetic diversity and phylogeography of broomcorn millet (Panicum miliaceum L.) across Eurasia. Mol. Ecol. 20, 47564771 (2011).

Article PubMed PubMed Central Google Scholar

Boukail, S. et al. Genome wide association study of agronomic and seed traits in a world collection of proso millet (Panicum miliaceum L.). BMC Plant Biol. 21, 330 (2021).

Article CAS PubMed PubMed Central Google Scholar

Li, C. et al. Genetic divergence and population structure in weedy and cultivated broomcorn millets (Panicum miliaceum L.) revealed by specific-locus amplified fragment sequencing (SLAF-Seq). Front. Plant Sci. 12, 688444 (2021).

Article PubMed PubMed Central Google Scholar

Hellmann, I. et al. Population genetic analysis of shotgun assemblies of genomic sequences from multiple individuals. Genome Res. 18, 10201029 (2008).

Article CAS PubMed PubMed Central Google Scholar

Gore, M. A. et al. A first-generation haplotype map of maize. Science 326, 11151117 (2009).

Article CAS PubMed Google Scholar

Alexander, D. H., Novembre, J. & Lange, K. Fast model-based estimation of ancestry in unrelated individuals. Genome Res. 19, 16551664 (2009).

Article CAS PubMed PubMed Central Google Scholar

Pritchard, J. K., Stephens, M. & Donnelly, P. Inference of population structure using multilocus genotype data. Genetics 155, 945959 (2000).

Article CAS PubMed PubMed Central Google Scholar

Raj, A., Stephens, M. & Pritchard, J. K. fastSTRUCTURE: variational inference of population structure in large SNP data sets. Genetics 197, 573589 (2014).

Article PubMed PubMed Central Google Scholar

Jombart, T., Devillard, S. & Balloux, F. Discriminant analysis of principal components: a new method for the analysis of genetically structured populations. BMC Genet. 11, 94 (2010).

Article PubMed PubMed Central Google Scholar

Huang, X. et al. A map of rice genome variation reveals the origin of cultivated rice. Nature 490, 497501 (2012).

Article CAS PubMed PubMed Central Google Scholar

Zhou, Z. et al. Resequencing 302 wild and cultivated accessions identifies genes related to domestication and improvement in soybean. Nat. Biotechnol. 33, 408414 (2015).

Article CAS PubMed Google Scholar

Stevens, C. J., Shelach-Lavi, G., Zhang, H., Teng, M. & Fuller, D. Q. A model for the domestication of Panicum miliaceum (common, proso or broomcorn millet) in China. Veg. Hist. Archaeobot. 30, 2133 (2021).

Article Google Scholar

Cheng, H., Concepcion, G. T., Feng, X., Zhang, H. & Li, H. Haplotype-resolved de novo assembly using phased assembly graphs with hifiasm. Nat. Methods 18, 170175 (2021).

Article CAS PubMed PubMed Central Google Scholar

Manni, M., Berkeley, M. R., Seppey, M., Simo, F. A. & Zdobnov, E. M. BUSCO update: novel and streamlined workflows along with broader and deeper phylogenetic coverage for scoring of eukaryotic, prokaryotic, and viral genomes. Mol. Biol. Evol. 38, 46474654 (2021).

Article CAS PubMed PubMed Central Google Scholar

Ou, S., Chen, J. & Jiang, N. Assessing genome assembly quality using the LTR Assembly Index (LAI). Nucleic Acids Res. 46, e126 (2018).

PubMed PubMed Central Google Scholar

Holt, C. & Yandell, M. MAKER2: an annotation pipeline and genome-database management tool for second-generation genome projects. BMC Bioinformatics 12, 491 (2011).

Article PubMed PubMed Central Google Scholar

Liu, Y. et al. Pan-genome of wild and cultivated soybeans. Cell 182, 162176 (2020).

Article CAS PubMed Google Scholar

Hufford, M. B. et al. De novo assembly, annotation, and comparative analysis of 26 diverse maize genomes. Science 373, 655662 (2021).

Article CAS PubMed PubMed Central Google Scholar

Qin, P. et al. Pan-genome analysis of 33 genetically diverse rice accessions reveals hidden genomic variations. Cell 184, 35423558 (2021).

Article CAS PubMed Google Scholar

Kou, Y. et al. Evolutionary genomics of structural variation in Asian rice (Oryza sativa) domestication. Mol. Biol. Evol. 37, 35073524 (2020).

Article CAS PubMed PubMed Central Google Scholar

Garrison, E. et al. Variation graph toolkit improves read mapping by representing genetic variation in the reference. Nat. Biotechnol. 36, 875879 (2018).

Article CAS PubMed PubMed Central Google Scholar

Tang, D., Ade, J., Frye, C. A. & Innes, R. W. Regulation of plant defense responses in Arabidopsis by EDR2, a PH and START domain-containing protein. Plant J. 44, 245257 (2005).

Article CAS PubMed PubMed Central Google Scholar

Chen, H., Patterson, N. & Reich, D. Population differentiation as a test for selective sweeps. Genome Res. 20, 393402 (2010).

Article CAS PubMed PubMed Central Google Scholar

Sun, Y. et al. Biased mutations and gene losses underlying diploidization of the tetraploid broomcorn millet genome. Plant J. 113, 787801 (2023).

Article CAS PubMed Google Scholar

Tamaki, S., Matsuo, S., Wong, H. L., Yokoi, S. & Shimamoto, K. Hd3a protein is a mobile flowering signal in rice. Science 316, 10331036 (2007).

Article CAS PubMed Google Scholar

Li, P. et al. LAZY1 controls rice shoot gravitropism through regulating polar auxin transport. Cell Res. 17, 402410 (2007).

Article CAS PubMed Google Scholar

Zhou, Y. et al. Graph pangenome captures missing heritability and empowers tomato breeding. Nature 606, 527534 (2022).

Article CAS PubMed PubMed Central Google Scholar

Doebley, J. F., Gaut, B. S. & Smith, B. D. The molecular genetics of crop domestication. Cell 127, 13091321 (2006).

Article CAS PubMed Google Scholar

Lin, Z. et al. Parallel domestication of the Shattering1 genes in cereals. Nat. Genet. 44, 720724 (2012).

Article CAS PubMed PubMed Central Google Scholar

Yoon, J., Cho, L.-H., Antt, H. W., Koh, H.-J. & An, G. KNOX protein OSH15 induces grain shattering by repressing lignin biosynthesis genes. Plant Physiol. 174, 312325 (2017).

Article CAS PubMed PubMed Central Google Scholar

Jiang, L. et al. The APETALA2-like transcription factor SUPERNUMERARY BRACT controls rice seed shattering and seed size. Plant Cell 31, 1736 (2019).

Article CAS PubMed PubMed Central Google Scholar

Niederhuth, C. E., Cho, S. K., Seitz, K. & Walker, J. C. Letting go is never easy: abscission and receptor-like protein kinases. J. Integr. Plant Biol. 55, 12511263 (2013).

Article CAS PubMed Google Scholar

Roongsattham, P. et al. Cellular and pectin dynamics during abscission zone development and ripe fruit abscission of the monocot oil palm. Front. Plant Sci. 7, 540 (2016).

Article PubMed PubMed Central Google Scholar

Sweeney, M. T. et al. Global dissemination of a single mutation conferring white pericarp in rice. PLoS Genet. 3, e133 (2007).

Read more from the original source:
Pangenome analysis reveals genomic variations associated with domestication traits in broomcorn millet - Nature.com