{"id":1119725,"date":"2023-11-30T20:35:15","date_gmt":"2023-12-01T01:35:15","guid":{"rendered":"https:\/\/www.euvolution.com\/prometheism-transhumanism-posthumanism\/uncategorized\/pangenome-analysis-reveals-genomic-variations-associated-with-domestication-traits-in-broomcorn-millet-nature-com\/"},"modified":"2023-11-30T20:35:15","modified_gmt":"2023-12-01T01:35:15","slug":"pangenome-analysis-reveals-genomic-variations-associated-with-domestication-traits-in-broomcorn-millet-nature-com","status":"publish","type":"post","link":"https:\/\/www.euvolution.com\/prometheism-transhumanism-posthumanism\/transhuman-news-blog\/genome\/pangenome-analysis-reveals-genomic-variations-associated-with-domestication-traits-in-broomcorn-millet-nature-com\/","title":{"rendered":"Pangenome analysis reveals genomic variations associated with domestication traits in broomcorn millet &#8211; Nature.com"},"content":{"rendered":"<p><p>        Lemmon, Z. H. et al. Rapid improvement of domestication        traits in an orphan crop by genome editing. Nat.        Plants 4, 766770 (2018).      <\/p>\n<p>        Article        CAS PubMed                Google Scholar      <\/p>\n<p>        Ye, C. Y. & Fan, L. Orphan crops and their wild relatives        in the genomic era. Mol. Plant 14, 2739        (2021).      <\/p>\n<p>        Article        CAS PubMed                Google Scholar      <\/p>\n<p>        Cullis, C. & Kunert, K. J. Unlocking the potential of        orphan legumes. J. Exp. Bot. 68, 18951903        (2017).      <\/p>\n<p>        CAS PubMed                Google Scholar      <\/p>\n<p>        Tadele, Z. Orphan crops: their importance and the urgency        of improvement. Planta 250, 677694 (2019).      <\/p>\n<p>        Article        CAS PubMed                Google Scholar      <\/p>\n<p>        Chiurugwi, T., Kemp, S., Powell, W. & Hickey, L. T. Speed        breeding orphan crops. Theor. Appl. Genet.        132, 607616 (2019).      <\/p>\n<p>        Article        PubMed                Google Scholar      <\/p>\n<p>        Shi, J. et al. Chromosome conformation capture resolved        near complete genome assembly of broomcorn millet. Nat.        Commun. 10, 464 (2019).      <\/p>\n<p>        Article        CAS PubMed        PubMed        Central         Google Scholar      <\/p>\n<p>        Zou, C. et al. The genome of broomcorn millet. Nat.        Commun. 10, 436 (2019).      <\/p>\n<p>        Article        CAS PubMed        PubMed        Central         Google Scholar      <\/p>\n<p>        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).      <\/p>\n<p>        Article CAS PubMed        PubMed        Central         Google Scholar      <\/p>\n<p>        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).      <\/p>\n<p>        Article CAS PubMed        PubMed        Central         Google Scholar      <\/p>\n<p>        Wang, C.-C. et al. Genomic insights into the formation of        human populations in East Asia. Nature 591,        413419 (2021).      <\/p>\n<p>        Article        CAS PubMed        PubMed        Central         Google Scholar      <\/p>\n<p>        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).      <\/p>\n<p>        Article                Google Scholar      <\/p>\n<p>        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).      <\/p>\n<p>        Article        PubMed        PubMed        Central         Google Scholar      <\/p>\n<p>        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).      <\/p>\n<p>        Article        CAS PubMed        PubMed        Central         Google Scholar      <\/p>\n<p>        Santra, D. K., Khound, R. & Das, S. Proso Millet        (Panicum miliaceum L.) Breeding: Progress, Challenges and        Opportunities (Springer, 2019).      <\/p>\n<p>        Singh, M. & Sood, S. Millets and Pseudo Cereals: Genetic        Resources and Breeding Advancements (Woodhead        Publishing, 2020).      <\/p>\n<p>        United States Department of Agriculture (USDA) & National        Agricultural Statistics Service. 2021 Crop        Production (USDA, 2022).      <\/p>\n<p>        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).      <\/p>\n<p>        Article PubMed        PubMed        Central         Google Scholar      <\/p>\n<p>        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).      <\/p>\n<p>        Article CAS         Google Scholar      <\/p>\n<p>        Hunt, H. V. et al. Genetic diversity and phylogeography of        broomcorn millet (Panicum miliaceum L.) across        Eurasia. Mol. Ecol. 20, 47564771 (2011).      <\/p>\n<p>        Article        PubMed        PubMed        Central         Google Scholar      <\/p>\n<p>        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).      <\/p>\n<p>        Article        CAS PubMed        PubMed        Central         Google Scholar      <\/p>\n<p>        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).      <\/p>\n<p>        Article PubMed        PubMed        Central         Google Scholar      <\/p>\n<p>        Hellmann, I. et al. Population genetic analysis of shotgun        assemblies of genomic sequences from multiple individuals.        Genome Res. 18, 10201029 (2008).      <\/p>\n<p>        Article CAS PubMed        PubMed        Central         Google Scholar      <\/p>\n<p>        Gore, M. A. et al. A first-generation haplotype map of        maize. Science 326, 11151117 (2009).      <\/p>\n<p>        Article CAS PubMed                Google Scholar      <\/p>\n<p>        Alexander, D. H., Novembre, J. & Lange, K. Fast model-based        estimation of ancestry in unrelated individuals. Genome        Res. 19, 16551664 (2009).      <\/p>\n<p>        Article CAS PubMed        PubMed        Central         Google Scholar      <\/p>\n<p>        Pritchard, J. K., Stephens, M. & Donnelly, P. Inference of        population structure using multilocus genotype data.        Genetics 155, 945959 (2000).      <\/p>\n<p>        Article        CAS PubMed        PubMed        Central         Google Scholar      <\/p>\n<p>        Raj, A., Stephens, M. & Pritchard, J. K. fastSTRUCTURE:        variational inference of population structure in large SNP        data sets. Genetics 197, 573589 (2014).      <\/p>\n<p>        Article        PubMed        PubMed        Central         Google Scholar      <\/p>\n<p>        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).      <\/p>\n<p>        Article PubMed        PubMed        Central         Google Scholar      <\/p>\n<p>        Huang, X. et al. A map of rice genome variation reveals the        origin of cultivated rice. Nature 490,        497501 (2012).      <\/p>\n<p>        Article CAS PubMed        PubMed        Central         Google Scholar      <\/p>\n<p>        Zhou, Z. et al. Resequencing 302 wild and cultivated        accessions identifies genes related to domestication and        improvement in soybean. Nat. Biotechnol. 33,        408414 (2015).      <\/p>\n<p>        Article CAS PubMed                Google Scholar      <\/p>\n<p>        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).      <\/p>\n<p>        Article                Google Scholar      <\/p>\n<p>        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).      <\/p>\n<p>        Article        CAS PubMed        PubMed        Central         Google Scholar      <\/p>\n<p>        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).      <\/p>\n<p>        Article CAS PubMed        PubMed        Central         Google Scholar      <\/p>\n<p>        Ou, S., Chen, J. & Jiang, N. Assessing genome assembly        quality using the LTR Assembly Index (LAI). Nucleic        Acids Res. 46, e126 (2018).      <\/p>\n<p>        PubMed        PubMed        Central         Google Scholar      <\/p>\n<p>        Holt, C. & Yandell, M. MAKER2: an annotation pipeline and        genome-database management tool for second-generation        genome projects. BMC Bioinformatics 12, 491        (2011).      <\/p>\n<p>        Article PubMed        PubMed        Central         Google Scholar      <\/p>\n<p>        Liu, Y. et al. Pan-genome of wild and cultivated soybeans.        Cell 182, 162176 (2020).      <\/p>\n<p>        Article        CAS PubMed                Google Scholar      <\/p>\n<p>        Hufford, M. B. et al. De novo assembly, annotation,        and comparative analysis of 26 diverse maize genomes.        Science 373, 655662 (2021).      <\/p>\n<p>        Article CAS PubMed        PubMed        Central         Google Scholar      <\/p>\n<p>        Qin, P. et al. Pan-genome analysis of 33 genetically        diverse rice accessions reveals hidden genomic variations.        Cell 184, 35423558 (2021).      <\/p>\n<p>        Article        CAS PubMed                Google Scholar      <\/p>\n<p>        Kou, Y. et al. Evolutionary genomics of structural        variation in Asian rice (Oryza sativa)        domestication. Mol. Biol. Evol. 37, 35073524        (2020).      <\/p>\n<p>        Article CAS PubMed        PubMed        Central         Google Scholar      <\/p>\n<p>        Garrison, E. et al. Variation graph toolkit improves read        mapping by representing genetic variation in the reference.        Nat. Biotechnol. 36, 875879 (2018).      <\/p>\n<p>        Article CAS PubMed        PubMed        Central         Google Scholar      <\/p>\n<p>        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).      <\/p>\n<p>        Article        CAS PubMed        PubMed        Central         Google Scholar      <\/p>\n<p>        Chen, H., Patterson, N. & Reich, D. Population        differentiation as a test for selective sweeps. Genome        Res. 20, 393402 (2010).      <\/p>\n<p>        Article CAS PubMed        PubMed        Central         Google Scholar      <\/p>\n<p>        Sun, Y. et al. Biased mutations and gene losses underlying        diploidization of the tetraploid broomcorn millet genome.        Plant J. 113, 787801 (2023).      <\/p>\n<p>        Article CAS PubMed                Google Scholar      <\/p>\n<p>        Tamaki, S., Matsuo, S., Wong, H. L., Yokoi, S. & Shimamoto,        K. Hd3a protein is a mobile flowering signal in rice.        Science 316, 10331036 (2007).      <\/p>\n<p>        Article CAS PubMed                Google Scholar      <\/p>\n<p>        Li, P. et al. LAZY1 controls rice shoot gravitropism        through regulating polar auxin transport. Cell Res.        17, 402410 (2007).      <\/p>\n<p>        Article CAS PubMed                Google Scholar      <\/p>\n<p>        Zhou, Y. et al. Graph pangenome captures missing        heritability and empowers tomato breeding. Nature        606, 527534 (2022).      <\/p>\n<p>        Article        CAS PubMed        PubMed        Central         Google Scholar      <\/p>\n<p>        Doebley, J. F., Gaut, B. S. & Smith, B. D. The molecular        genetics of crop domestication. Cell 127,        13091321 (2006).      <\/p>\n<p>        Article        CAS PubMed                Google Scholar      <\/p>\n<p>        Lin, Z. et al. Parallel domestication of the        Shattering1 genes in cereals. Nat. Genet.        44, 720724 (2012).      <\/p>\n<p>        Article CAS PubMed        PubMed        Central         Google Scholar      <\/p>\n<p>        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).      <\/p>\n<p>        Article CAS PubMed        PubMed        Central         Google Scholar      <\/p>\n<p>        Jiang, L. et al. The APETALA2-like transcription factor        SUPERNUMERARY BRACT controls rice seed shattering and seed        size. Plant Cell 31, 1736 (2019).      <\/p>\n<p>        Article CAS PubMed        PubMed        Central         Google Scholar      <\/p>\n<p>        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).      <\/p>\n<p>        Article CAS PubMed                Google Scholar      <\/p>\n<p>        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).      <\/p>\n<p>        Article PubMed        PubMed        Central         Google Scholar      <\/p>\n<p>        Sweeney, M. T. et al. Global dissemination of a single        mutation conferring white pericarp in rice. PLoS        Genet. 3, e133 (2007).      <\/p>\n<p><!-- Auto Generated --><\/p>\n<p>Read more from the original source:<br \/>\n<a target=\"_blank\" href=\"https:\/\/www.nature.com\/articles\/s41588-023-01571-z\" title=\"Pangenome analysis reveals genomic variations associated with domestication traits in broomcorn millet - Nature.com\" rel=\"noopener\">Pangenome analysis reveals genomic variations associated with domestication traits in broomcorn millet - Nature.com<\/a><\/p>\n","protected":false},"excerpt":{"rendered":"<p> Lemmon, Z. H <a href=\"https:\/\/www.euvolution.com\/prometheism-transhumanism-posthumanism\/transhuman-news-blog\/genome\/pangenome-analysis-reveals-genomic-variations-associated-with-domestication-traits-in-broomcorn-millet-nature-com\/\">Continue reading <span class=\"meta-nav\">&rarr;<\/span><\/a><\/p>\n","protected":false},"author":1,"featured_media":0,"comment_status":"closed","ping_status":"closed","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[25],"tags":[],"class_list":["post-1119725","post","type-post","status-publish","format-standard","hentry","category-genome"],"_links":{"self":[{"href":"https:\/\/www.euvolution.com\/prometheism-transhumanism-posthumanism\/wp-json\/wp\/v2\/posts\/1119725"}],"collection":[{"href":"https:\/\/www.euvolution.com\/prometheism-transhumanism-posthumanism\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/www.euvolution.com\/prometheism-transhumanism-posthumanism\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/www.euvolution.com\/prometheism-transhumanism-posthumanism\/wp-json\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/www.euvolution.com\/prometheism-transhumanism-posthumanism\/wp-json\/wp\/v2\/comments?post=1119725"}],"version-history":[{"count":0,"href":"https:\/\/www.euvolution.com\/prometheism-transhumanism-posthumanism\/wp-json\/wp\/v2\/posts\/1119725\/revisions"}],"wp:attachment":[{"href":"https:\/\/www.euvolution.com\/prometheism-transhumanism-posthumanism\/wp-json\/wp\/v2\/media?parent=1119725"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.euvolution.com\/prometheism-transhumanism-posthumanism\/wp-json\/wp\/v2\/categories?post=1119725"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.euvolution.com\/prometheism-transhumanism-posthumanism\/wp-json\/wp\/v2\/tags?post=1119725"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}