Genomic variation within the maize stiff-stalk heterotic germplasm pool.
Journal
The plant genome
ISSN: 1940-3372
Titre abrégé: Plant Genome
Pays: United States
ID NLM: 101273919
Informations de publication
Date de publication:
11 2021
11 2021
Historique:
received:
14
03
2021
accepted:
06
05
2021
pubmed:
19
7
2021
medline:
29
3
2022
entrez:
18
7
2021
Statut:
ppublish
Résumé
The stiff-stalk heterotic group in Maize (Zea mays L.) is an important source of inbreds used in U.S. commercial hybrid production. Founder inbreds B14, B37, B73, and, to a lesser extent, B84, are found in the pedigrees of a majority of commercial seed parent inbred lines. We created high-quality genome assemblies of B84 and four expired Plant Variety Protection (ex-PVP) lines LH145 representing B14, NKH8431 of mixed descent, PHB47 representing B37, and PHJ40, which is a Pioneer Hi-Bred International (PHI) early stiff-stalk type. Sequence was generated using long-read sequencing achieving highly contiguous assemblies of 2.13-2.18 Gbp with N50 scaffold lengths >200 Mbp. Inbred-specific gene annotations were generated using a core five-tissue gene expression atlas, whereas transposable element (TE) annotation was conducted using de novo and homology-directed methodologies. Compared with the reference inbred B73, synteny analyses revealed extensive collinearity across the five stiff-stalk genomes, although unique components of the maize pangenome were detected. Comparison of this set of stiff-stalk inbreds with the original Iowa Stiff Stalk Synthetic breeding population revealed that these inbreds represent only a proportion of variation in the original stiff-stalk pool and there are highly conserved haplotypes in released public and ex-Plant Variety Protection inbreds. Despite the reduction in variation from the original stiff-stalk population, substantial genetic and genomic variation was identified supporting the potential for continued breeding success in this pool. The assemblies described here represent stiff-stalk inbreds that have historical and commercial relevance and provide further insight into the emerging maize pangenome.
Banques de données
Dryad
['10.5061/dryad.wh70rxwmw']
Types de publication
Journal Article
Research Support, U.S. Gov't, Non-P.H.S.
Langues
eng
Sous-ensembles de citation
IM
Pagination
e20114Informations de copyright
© 2021 The Authors. The Plant Genome published by Wiley Periodicals LLC on behalf of Crop Science Society of America.
Références
Beissinger, T. M., Hirsch, C. N., Vaillancourt, B., Deshpande, S., Barry, K., Buell, C. R., Kaeppler, S. M., Gianola, D., & De Leon, N. (2014). A genome-wide scan for evidence of selection in a maize population under long-term artificial selection for ear number. Genetics, 196, 829-840. https://doi.org/10.1534/genetics.113.160655
Bradbury, P. J., Zhang, Z., Kroon, D. E., Casstevens, T. M., Ramdoss, Y., & Buckler, E. S. (2007). TASSEL: Software for association mapping of complex traits in diverse samples. Bioinformatics, 23, 2633-2635. https://doi.org/10.1093/bioinformatics/btm308
Bray, N. L., Pimentel, H., Melsted, P., & Pachter, L. (2016). Near-optimal probabilistic RNA-seq quantification. Nature Biotechnology, 34, 525-527. https://doi.org/10.1038/nbt.3519
Brohammer, A. B., Kono, T. J. Y., Springer, N. M., Mcgaugh, S. E., & Hirsch, C. N. (2018). The limited role of differential fractionation in genome content variation and function in maize (Zea mays L.) inbred lines. The Plant Journal, 93, 131-141. https://doi.org/10.1111/tpj.13765
Chang, C., Lu, J., Zhang, H. -. P., Ma, C. X., & Sun, G. (2015). Copy number variation of cytokinin oxidase gene Tackx4 associated with grain weight and chlorophyll content of flag leaf in common wheat. PLoS ONE, 10, e0145970. https://doi.org/10.1371/journal.pone.0145970
Chin, C. S., Alexander, D. H., Marks, P., Klammer, A. A., Drake, J., Heiner, C., Clum, A., Copeland, A., Huddleston, J., Eichler, E. E., Turner, S. W., & Korlach, J. (2013). Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data. Nature Methods, 10, 563-569. https://doi.org/10.1038/nmeth.2474
Clark, R. M., Tavaré, S., & Doebley, J. (2005). Estimating a nucleotide substitution rate for maize from polymorphism at a major domestication locus. Molecular Biology and Evolution, 22, 2304-2312. https://doi.org/10.1093/molbev/msi228
Coffman, S. M., Hufford, M. B., Andorf, C. M., & Lübberstedt, T. (2020). Haplotype structure in commercial maize breeding programs in relation to key founder lines. Theoretical and Applied Genetics, 133, 547-561. https://doi.org/10.1007/s00122-019-03486-y
Cook, D. E., Lee, T. G., Guo, X., Melito, S., Wang, K., Bayless, A. M., Wang, J., Hughes, T. J., Willis, D. K., Clemente, T. E., Diers, B. W., Jiang, J., Hudson, M. E., & Bent, A. F. (2012). Copy number variation of multiple genes at Rhg1 mediates nematode resistance in soybean. Science, 338, 1206-1209. https://doi.org/10.1126/science.1228746
Doyle, J. J., & Doyle, J. L. (1987). A rapid DNA isolation procedure for small quantities of fresh leaf tissue. Phytochemical Bulletin, 19, 11-15.
Duvick, D. N. (2005). The contribution of breeding to yield advances in maize (Zea mays L.). Advances in Agronomy, 86, 83-45. https://doi.org/10.1016/S0065-2113(05)86002-X
Emms, D. M., & Kelly, S. (2017). STRIDE: species tree root inference from gene duplication events. Molecular Biology and Evolution, 34, 3267-3278. https://doi.org/10.1093/molbev/msx259
Emms, D. M., & Kelly, S. (2018). STAG: Species tree inference from all genes. bioRxiv 267914. https://doi.org/10.1101/267914
Emms, D. M., & Kelly, S. (2019). OrthoFinder: Phylogenetic orthology inference for comparative genomics. Genome Biology, 20, 238. https://doi.org/10.1186/s13059-019-1832-y
Finn, R. D., Coggill, P., Eberhardt, R. Y., Eddy, S. R., Mistry, J., Mitchell, A. L., Potter, S. C., Punta, M., Qureshi, M., Sangrador-Vegas, A., Salazar, G. A., Tate, J., & Bateman, A. (2016). The Pfam protein families database: Towards a more sustainable future. Nucleic Acids Res., 44, D279-D285. https://doi.org/10.1093/nar/gkv1344
Gage, J. L., Vaillancourt, B., Hamilton, J. P., Manrique-Carpintero, N. C., Gustafson, T. J., Barry, K., Lipzen, A., Tracy, W. F., Mikel, M. A., Kaeppler, S. M., Buell, C. R., & Leon, N. (2019). Multiple maize reference genomes impact the identification of variants by genome-wide association study in a diverse inbred panel. The Plant Genome, 12, 180069. https://doi.org/10.3835/plantgenome2018.09.0069
Gan, X., Stegle, O., Behr, J., Steffen, J. G., Drewe, P., Hildebrand, K. L., Lyngsoe, R., Schultheiss, S. J., Osborne, E. J., Sreedharan, V. T., Kahles, A., Bohnert, R., Jean, G., Derwent, P., Kersey, P., Belfield, E. J., Harberd, N. P., Kemen, E., Toomajian, C., … Mott, R. (2011). Multiple reference genomes and transcriptomes for Arabidopsis thaliana. Nature, 477, 419-423. https://doi.org/10.1038/nature10414
Gao, L., Gonda, I., Sun, H., Ma, Q., Bao, K., Tieman, D. M., Burzynski-Chang, E. A., Fish, T. L., Stromberg, K. A., Sacks, G. L., Thannhauser, T. W., Foolad, M. R., Diez, M. J., Blanca, J., Canizares, J., Xu, Y., Van Der Knaap, E., Huang, S., Klee, H. J., … Fei, Z. (2019). The tomato pan-genome uncovers new genes and a rare allele regulating fruit flavor. Nature Genetics, 51, 1044-1051. https://doi.org/10.1038/s41588-019-0410-2
Gerke, J. P., Edwards, J. W., Guill, K. E., Ross-Ibarra, J., & McMullen, M. D. (2015). The genomic impacts of drift and selection for hybrid performance in maize. Genetics, 201, 1201-1211. https://doi.org/10.1534/genetics.115.182410
Goodman, M. M. (1990). Genetic and germ plasm stocks worth conserving. Journal of Heredity, 81, 11-16. https://doi.org/10.1093/oxfordjournals.jhered.a110919
Gordon, S. P., Contreras-Moreira, B., Woods, D. P., Des Marais, D. L., Burgess, D., Shu, S., Stritt, C., Roulin, A. C., Schackwitz, W., Tyler, L., Martin, J., Lipzen, A., Dochy, N., Phillips, J., Barry, K., Geuten, K., Budak, H., Juenger, T. E., Amasino, R., … Vogel, J. P. (2017). Extensive gene content variation in the Brachypodium distachyon pan-genome correlates with population structure. Nature Communications, 8, 2184. https://doi.org/10.1038/s41467-017-02292-8
Graham, G. I., Wolff, D. W., & Stuber, C. W. (1997). Characterization of a yield quantitative trait locus on chromosome five of maize by fine mapping. Crop Science, 37, 1601-1610. https://doi.org/10.2135/cropsci1997.0011183X003700050033x
Gustafson, T. J., Leon, N., Kaeppler, S. M., & Tracy, W. F. (2018). Genetic analysis of sugarcane mosaic virus resistance in the Wisconsin diversity panel of maize. Crop Science, 58, 1853-1865. https://doi.org/10.2135/cropsci2017.11.0675
Haas, B. J., Wortman, J. R., Ronning, C. M., Hannick, L. I., Smith, R. K., Maiti, R., Chan, A. P., Yu, C., Farzad, M., Wu, D., White, O., & Town, C. D. (2005). Complete reannotation of the Arabidopsis genome: Methods, tools, protocols and the final release. BMC Biology, 3, 7. https://doi.org/10.1186/1741-7007-3-7
Haberer, G., Kamal, N., Bauer, E., Gundlach, H., Fischer, I., Seidel, M. A., Spannagl, M., Marcon, C., Ruban, A., Urbany, C., Nemri, A., Hochholdinger, F., Ouzunova, M., Houben, A., Schön, C. C., & Mayer, K. F. X. (2020). European maize genomes highlight intraspecies variation in repeat and gene content. Nature Genetics, 52, 950-957. https://doi.org/10.1038/s41588-020-0671-9
Hardigan, M. A., Crisovan, E., Hamilton, J. P., Kim, J., Laimbeer, P., Leisner, C. P., Manrique-Carpintero, N. C., Newton, L., Pham, G. M., Vaillancourt, B., Yang, X., Zeng, Z., Douches, D. S., Jiang, J., Veilleux, R. E., & Buell, C. R. (2016). Genome reduction uncovers a large dispensable genome and adaptive role for copy number variation in asexually propagated Solanum tuberosum. Plant Cell, 28, 388-405. https://doi.org/10.1105/tpc.15.00538
Hardigan, M. A., Laimbeer, F. P. E., Newton, L., Crisovan, E., Hamilton, J. P., Vaillancourt, B., Wiegert-Rininger, K., Wood, J. C., Douches, D. S., Farré, E. M., Veilleux, R. E., & Buell, C. R. (2017). Genome diversity of tuber-bearing Solanum uncovers complex evolutionary history and targets of domestication in the cultivated potato. Proceedings of the National Academy of Sciences, 114, E9999-E10008. https://doi.org/10.1073/pnas.1714380114
Hinze, L. L., Kresovich, S., Nason, J. D., & Lamkey, K. R. (2005). Population genetic diversity in a maize reciprocal recurrent selection program. Crop Science, 45, 2435-2442. https://doi.org/10.2135/cropsci2004.0662
Hirsch, C. N., Foerster, J. M., Johnson, J. M., Sekhon, R. S., Muttoni, G., Vaillancourt, B., Peñagaricano, F., Lindquist, E., Pedraza, M. A., Barry, K., De Leon, N., Kaeppler, S. M., & Buell, C. R. (2014). Insights into the maize pan-genome and pan-transcriptome. Plant Cell, 26, 121-135. https://doi.org/10.1105/tpc.113.119982
Hirsch, C. N., Hirsch, C. D., Brohammer, A. B., Bowman, M. J., Soifer, I., Barad, O., Shem-Tov, D., Baruch, K., Lu, F., Hernandez, A. G., Fields, C. J., Wright, C. L., Koehler, K., Springer, N. M., Buckler, E., Buell, C. R., De Leon, N., Kaeppler, S. M., Childs, K. L., & Mikel, M. A. (2016). Draft assembly of elite inbred line PH207 provides insights into genomic and transcriptome diversity in maize. Plant Cell, 28, 2700-2714. https://doi.org/10.1105/tpc.16.00353
Hu, Y., Colantonio, V., Müller, B. S. F., Leach, K. A., Nanni, A., Finegan, C., Wang, B., Baseggio, M., Newton, C. J., Juhl, E. M., Hislop, L., Gonzalez, J. M., Rios, E. F., Hannah, L. C., Swarts, K., Gore, M. A., Hennen-Bierwagen, T. A., Myers, A. M., Settles, A. M., … Resende, M. F. R. (2021). Genome assembly and population genomic analysis provide insights into the evolution of modern sweet corn. Nature Communications, 12, 1227. https://doi.org/10.1038/s41467-021-21380-4
Hufford, M. B., Seetharam, A. S., Woodhouse, M. R., Chougule, K. M., Ou, S., Liu, J., Ricci, W. A., Guo, T., Olson, A., Qiu, Y., Coletta, R. D., Tittes, S., Hudson, A. I., Marand, A. P., Wei, S., Lu, Z., Wang, B., Tello-Ruiz, M. K., Piri, R. D., … Dawe, R. K. (2021). De novo assembly, annotation, and comparative analysis of 26 diverse maize genomes. bioRxiv 2021.01.14.426684. https://doi.org/10.1101/2021.01.14.426684
Jeffares, D. C., Jolly, C., Hoti, M., Speed, D., Shaw, L., Rallis, C., Balloux, F., Dessimoz, C., Bähler, J., & Sedlazeck, F. J. (2017). Transient structural variations have strong effects on quantitative traits and reproductive isolation in fission yeast. Nature Communications, 8, 14061. https://doi.org/10.1038/ncomms14061
Jiao, Y., Peluso, P., Shi, J., Liang, T., Stitzer, M. C., Wang, B., Campbell, M. S., Stein, J. C., Wei, X., Chin, C. S., Guill, K., Regulski, M., Kumari, S., Olson, A., Gent, J., Schneider, K. L., Wolfgruber, T. K., May, M. R., Springer, N. M., … Ware, D. (2017). Improved maize reference genome with single-molecule technologies. Nature, 546, 524-527. https://doi.org/10.1038/nature22971
Kim, D., Paggi, J. M., Park, C., Bennett, C., & Salzberg, S. L. (2019). Graph-based genome alignment and genotyping with HISAT2 and HISAT genotype. Nature Biotechnology, 37, 907-915. https://doi.org/10.1038/s41587-019-0201-4
Kovaka, S., Zimin, A. V., Pertea, G. M., Razaghi, R., Salzberg, S. L., & Pertea, M. (2019). Transcriptome assembly from long-read RNA-seq alignments with StringTie2. Genome Biology, 20, 278. https://doi.org/10.1186/s13059-019-1910-1
Krattinger, S. G., & Keller, B. (2016). Molecular genetics and evolution of disease resistance in cereals. New Phytol., 212, 320-332. https://doi.org/10.1111/nph.14097
Lai, J., Li, R., Xu, X., Jin, W., Xu, M., Zhao, H., Xiang, Z., Song, W., Ying, K., Zhang, M., Jiao, Y., Ni, P., Zhang, J., Li, D., Guo, X., Ye, K., Jian, M., Wang, B., Zheng, H., … Wang, J. (2010). Genome-wide patterns of genetic variation among elite maize inbred lines. Nature Genetics, 42, 1027-1030. https://doi.org/10.1038/ng.684
Larièpe, A., Mangin, B., Jasson, S., Combes, V., Dumas, F., Jamin, P., Lariagon, C., Jolivot, D., Madur, D., Fiévet, J., Gallais, A., Dubreuil, P., Charcosset, A., & Moreau, L. (2012). The genetic basis of heterosis: Multiparental quantitative trait loci mapping reveals contrasted levels of apparent overdominance among traits of agronomical interest in maize (Zea mays L.). Genetics, 190, 795-811. https://doi.org/10.1534/genetics.111.133447
Li, H. (2018). Minimap2: Pairwise alignment for nucleotide sequences. Bioinformatics, 34, 3094-3100. https://doi.org/10.1093/bioinformatics/bty191
Li, H., & Durbin, R. (2009). Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics, 25, 1754-1760. https://doi.org/10.1093/bioinformatics/btp324
Li, H., Handsaker, B., Wysoker, A., Fennell, T., Ruan, J., Homer, N., Marth, G., Abecasis, G., & Durbin, R. (2009). The sequence alignment/map format and SAMtools. Bioinformatics, 25, 2078-2079. https://doi.org/10.1093/bioinformatics/btp352
Li, Z., Zhou, P., Della Coletta, R., Zhang, T., Brohammer, A. B., O'Connor, C., Vaillancourt, B., Lipzen, A., Daum, C., Barry, K., De Leon, N., Hirsch, C. D., Buell, C. R., Kaeppler, S. M., Springer, N. M., & Hirsch, C. N. (2020). Single-parent expression drives dynamic gene expression complementation in maize hybrids. Plant Journal, 105, 93-107. https://doi.org/10.1111/tpj.15042
Liu, J., Seetharam, A. S., Chougule, K., Ou, S., Swentowsky, K. W., Gent, J. I., Llaca, V., Woodhouse, M. R., Manchanda, N., Presting, G. G., Kudrna, D. A., Alabady, M., Hirsch, C. N., Fengler, K. A., Ware, D., Michael, T. P., Hufford, M. B., & Dawe, R. K. (2020). Gapless assembly of maize chromosomes using long-read technologies. Genome Biology, 21, 121. https://doi.org/10.1186/s13059-020-02029-9
Liu, Q., Liu, H., Gong, Y., Tao, Y., Jiang, L., Zuo, W., Yang, Q., Ye, J., Lai, J., Wu, J., Lübberstedt, T., & Xu, M. (2017). An atypical thioredoxin imparts early resistance to sugarcane mosaic virus in maize. Molecular Plant, 10, 483-497. https://doi.org/10.1016/j.molp.2017.02.002
Lu, F., Romay, M. C., Glaubitz, J. C., Bradbury, P. J., Elshire, R. J., Wang, T., Li, Y., Li, Y., Semagn, K., Zhang, X., Hernandez, A. G., Mikel, M. A., Soifer, I., Barad, O., & Buckler, E. S. (2015). High-resolution genetic mapping of maize pan-genome sequence anchors. Nature Communications, 6, 6914. https://doi.org/10.1038/ncomms7914
Martin, M. (2011). Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet.journal, 17, 10-12. https://doi.org/10.14806/ej.17.1.200
Mazaheri, M., Heckwolf, M., Vaillancourt, B., Gage, J. L., Burdo, B., Heckwolf, S., Barry, K., Lipzen, A., Ribeiro, C. B., Kono, T. J. Y., Kaeppler, H. F., Spalding, E. P., Hirsch, C. N., Robin Buell, C., De Leon, N., & Kaeppler, S. M. (2019). Genome-wide association analysis of stalk biomass and anatomical traits in maize. BMC Plant Biology, 19, 45. https://doi.org/10.1186/s12870-019-1653-x
McKenna, A., Hanna, M., Banks, E., Sivachenko, A., Cibulskis, K., Kernytsky, A., Garimella, K., Altshuler, D., Gabriel, S., Daly, M., & Depristo, M. A. (2010). The genome analysis toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data. Genome Research, 20, 1297-1303. https://doi.org/10.1101/gr.107524.110
Michelmore, R. W., Christopoulou, M., & Caldwell, K. S. (2013). Impacts of resistance gene genetics, function, and evolution on a durable future. Annual Review of Phytopathology, 51, 291-319. https://doi.org/10.1146/annurev-phyto-082712-102334
Mikel, M. A. (2011). Genetic composition of contemporary U.S. commercial dent corn germplasm. Crop Science, 51, 592-599. https://doi.org/10.2135/cropsci2010.06.0332
Mistry, J., Finn, R. D., Eddy, S. R., Bateman, A., & Punta, M. (2013). Challenges in homology search: HMMER3 and convergent evolution of coiled-coil regions. Nucleic Acids Res., 41, e121. https://doi.org/10.1093/nar/gkt263
Osuna-Cruz, C. M., Paytuvi-Gallart, A., Di Donato, A., Sundesha, V., Andolfo, G., Aiese Cigliano, R., Sanseverino, W., & Ercolano, M. R. (2018). PRGdb 3.0: A comprehensive platform for prediction and analysis of plant disease resistance genes. Nucleic Acids Research, 46, D1197-D1201. https://doi.org/10.1093/nar/gkx1119
Ou, L., Li, D., Lv, J., Chen, W., Zhang, Z., Li, X., Yang, B., Zhou, S., Yang, S., Li, W., Gao, H., Zeng, Q., Yu, H., Ouyang, B., Li, F., Liu, F., Zheng, J., Liu, Y., Wang, J., … Zou, X. (2018). Pan-genome of cultivated pepper (Capsicum) and its use in gene presence-absence variation analyses. New Phytologist, 220, 360-363. https://doi.org/10.1111/nph.15413
Ou, S., Chen, J., & Jiang, N. (2018). Assessing genome assembly quality using the LTR Assembly Index (LAI). Nucleic Acids Research, 46, e126. https://doi.org/10.1093/nar/gky730
Ou, S., & Jiang, N. (2018). LTR_retriever: A highly accurate and sensitive program for identification of long terminal repeat retrotransposons. Plant Physiology, 176, 1410-1422. https://doi.org/10.1104/pp.17.01310
Ou, S., Liu, J., Chougule, K. M., Fungtammasan, A., Seetharam, A. S., Stein, J. C., Llaca, V., Manchanda, N., Gilbert, A. M., Wei, S., Chin, C. S., Hufnagel, D. E., Pedersen, S., Snodgrass, S. J., Fengler, K., Woodhouse, M., Walenz, B. P., Koren, S., Phillippy, A. M., … Ware, D. (2020). Effect of sequence depth and length in long-read assembly of the maize inbred NC358. Nature Communications, 11, 2288. https://doi.org/10.1038/s41467-020-16037-7
Ou, S., Su, W., Liao, Y., Chougule, K., Agda, J. R. A., Hellinga, A. J., Lugo, C. S. B., Elliott, T. A., Ware, D., Peterson, T., Jiang, N., Hirsch, C. N., & Hufford, M. B. (2019). Benchmarking transposable element annotation methods for creation of a streamlined, comprehensive pipeline. Genome Biology, 20, 275. https://doi.org/10.1186/s13059-019-1905-y
Pertea, G., & Pertea, M. (2020). GFF utilities: GffRead and GffCompare. F1000Res, 9, 304. https://doi.org/10.12688/f1000research.23297.1
Pham, G. M., Hamilton, J. P., Wood, J. C., Burke, J. T., Zhao, H., Vaillancourt, B., Ou, S., Jiang, J., & Buell, C. R. (2020). Construction of a chromosome-scale long-read reference genome assembly for potato. Gigascience, 9, giaa100. https://doi.org/10.1093/gigascience/giaa100
Pucker, B., Holtgräwe, D., Stadermann, K. B., Frey, K., Huettel, B., Reinhardt, R., & Weisshaar, B. (2019). A chromosome-level sequence assembly reveals the structure of the Arabidopsis thaliana Nd-1 genome and its gene set. PLoS ONE, 14, e0216233. https://doi.org/10.1371/journal.pone.0216233
Qi, J., Liu, X., Shen, D., Miao, H., Xie, B., Li, X., Zeng, P., Wang, S., Shang, Y., Gu, X., Du, Y., Li, Y., Lin, T., Yuan, J., Yang, X., Chen, J., Chen, H., Xiong, X., Huang, K., … Huang, S. (2013). A genomic variation map provides insights into the genetic basis of cucumber domestication and diversity. Nature Genetics, 45, 1510-1515. https://doi.org/10.1038/ng.2801
Robinson, J. T., Thorvaldsdóttir, H., Winckler, W., Guttman, M., Lander, E. S., Getz, G., & Mesirov, J. P. (2011). Integrative genomics viewer. Nature Biotechnology, 29, 24-26. https://doi.org/10.1038/nbt.1754
Schnable, P. S., Ware, D., Fulton, R. S., Stein, J. C., Wei, F., Pasternak, S., Liang, C., Zhang, J., Fulton, L., Graves, T. A., Minx, P., Reily, A. D., Courtney, L., Kruchowski, S. S., Tomlinson, C., Strong, C., Delehaunty, K., Fronick, C., Courtney, B., … Wilson, R. K. (2009). The B73 maize genome: Complexity, diversity, and dynamics. Science, 326, 1112-1115. https://doi.org/10.1126/science.1178534
Sedlazeck, F. J., Rescheneder, P., Smolka, M., Fang, H., Nattestad, M., Von Haeseler, A., & Schatz, M. C. (2018). Accurate detection of complex structural variations using single-molecule sequencing. Nature Methods, 15, 461-468. https://doi.org/10.1038/s41592-018-0001-7
Simão, F. A., Waterhouse, R. M., Ioannidis, P., Kriventseva, E. V., & Zdobnov, E. M. (2015). BUSCO: Assessing genome assembly and annotation completeness with single-copy orthologs. Bioinformatics, 31, 3210-3212. https://doi.org/10.1093/bioinformatics/btv351
Song, J. M., Guan, Z., Hu, J., Guo, C., Yang, Z., Wang, S., Liu, D., Wang, B.o, Lu, S., Zhou, R., Xie, W. Z., Cheng, Y., Zhang, Y., Liu, K., Yang, Q. Y., Chen, L. L., & Guo, L. (2020). Eight high-quality genomes reveal pan-genome architecture and ecotype differentiation of Brassica napus. Nature Plants, 6, 34-45. https://doi.org/10.1038/s41477-019-0577-7
Springer, N. M., Anderson, S. N., Andorf, C. M., Ahern, K. R., Bai, F., Barad, O., Barbazuk, W. B., Bass, H. W., Baruch, K., Ben-Zvi, G., Buckler, E. S., Bukowski, R., Campbell, M. S., Cannon, E. K. S., Chomet, P., Dawe, R. K., Davenport, R., Dooner, H. K., Du, L. H., … Brutnell, T. P. (2018). The maize W22 genome provides a foundation for functional genomics and transposon biology. Nature Genetics, 50, 1282-1288. https://doi.org/10.1038/s41588-018-0158-0
Springer, N. M., Ying, K., Fu, Y., Ji, T., Yeh, C. T., Jia, Y., Wu, W., Richmond, T., Kitzman, J., Rosenbaum, H., Iniguez, A. L., Barbazuk, W. B., Jeddeloh, J. A., Nettleton, D., & Schnable, P. S. (2009). Maize inbreds exhibit high levels of copy number variation (CNV) and presence/absence variation (PAV) in genome content. PLoS Genetics, 5, e1000734. https://doi.org/10.1371/journal.pgen.1000734
Stanke, M., Diekhans, M., Baertsch, R., & Haussler, D. (2008). Using native and syntenically mapped cDNA alignments to improve de novo gene finding. Bioinformatics, 24, 637-644. https://doi.org/10.1093/bioinformatics/btn013
Sun, S., Zhou, Y., Chen, J., Shi, J., Zhao, H., Zhao, H., Song, W., Zhang, M., Cui, Y., Dong, X., Liu, H., Ma, X., Jiao, Y., Wang, B., Wei, X., Stein, J. C., Glaubitz, J. C., Lu, F., Yu, G., … Lai, J. (2018). Extensive intraspecific gene order and gene structural variations between Mo17 and other maize genomes. Nature Genetics, 50, 1289-1295. https://doi.org/10.1038/s41588-018-0182-0
Tracy, W. F., & Chandler, M. A. (2006). The historical and biological basis of the concept of heterotic patterns in corn belt dent. In M. K. R. Lamkey & M. Lee, (Eds.), Plant breeding: The Arnel R. Hallauer international symposium (pp. 219-233). Blackwell Publishing. https://doi.org/10.1002/9780470752708.ch16
Troyer, A. F. (1999). Background of U.S. hybrid corn. Crop Science, 39, 601-626. https://doi.org/10.2135/cropsci1999.0011183X003900020001xa
Plant Variety Protection Act, 7 U.S.C. § 2321-2583 (1970). https://uscode.house.gov/view.xhtml?path=/prelim@title7/chapter57&edition=prelim
Wang, W., Mauleon, R., Hu, Z., Chebotarov, D., Tai, S., Wu, Z., Li, M., Zheng, T., Fuentes, R. R., Zhang, F., Mansueto, L., Copetti, D., Sanciangco, M., Palis, K. C., Xu, J., Sun, C., Fu, B., Zhang, H., Gao, Y., … Leung, H. (2018). Genomic variation in 3,010 diverse accessions of Asian cultivated rice. Nature, 557, 43-49. https://doi.org/10.1038/s41586-018-0063-9
Wang, Y., Tang, H., Debarry, J. D., Tan, X., Li, J., Wang, X., Lee, T. H., Jin, H., Marler, B., Guo, H., Kissinger, J. C., & Paterson, A. H. (2012). MCScanX: A toolkit for detection and evolutionary analysis of gene synteny and collinearity. Nucleic Acids Res., 40, e49. https://doi.org/10.1093/nar/gkr1293
Waterhouse, R. M., Seppey, M., Simão, F. A., Manni, M., Ioannidis, P., Klioutchnikov, G., Kriventseva, E. V., & Zdobnov, E. M. (2018). BUSCO applications from quality assessments to gene prediction and phylogenomics. Molecular Biology and Evolution, 35, 543-548. https://doi.org/10.1093/molbev/msx319
Weir, B. S., & Cockerham, . C. C. (1984). Estimating F-statistics for the analysis of population structure. Evolution, 38, 1358-1370.
White, M. R., Mikel, M. A., Leon, N., & Kaeppler, S. M. (2020). Diversity and heterotic patterns in North American proprietary dent maize germplasm. Crop Science, 60, 100-114. https://doi.org/10.1002/csc2.20050
Wu, T. D., & Watanabe, C. K. (2005). GMAP: A genomic mapping and alignment program for mRNA and EST sequences. Bioinformatics, 21, 1859-1875. https://doi.org/10.1093/bioinformatics/bti310
Xiao, C. L., Chen, Y., Xie, S. Q., Chen, K. N., Wang, Y., Han, Y., Luo, F., & Xie, Z. (2017). MECAT: Fast mapping, error correction, and de novo assembly for single-molecule sequencing reads. Nature Methods, 14, 1072-1074. https://doi.org/10.1038/nmeth.4432
Yang, J., Mezmouk, S., Baumgarten, A., Buckler, E. S., Guill, K. E., Mcmullen, M. D., Mumm, R. H., & Ross-Ibarra, J. (2017). Incomplete dominance of deleterious alleles contributes substantially to trait variation and heterosis in maize. PLoS Genetics, 13, e1007019. https://doi.org/10.1371/journal.pgen.1007019
Yang, N., Liu, J., Gao, Q., Gui, S., Chen, L., Yang, L., Huang, J., Deng, T., Luo, J., He, L., Wang, Y., Xu, P., Peng, Y., Shi, Z., Lan, L., Ma, Z., Yang, X., Zhang, Q., Bai, M., … Li, S., Li, W., Liu, L., Jackson, D., & Yan, J. (2019). Genome assembly of a tropical maize inbred line provides insights into structural variation and crop improvement. Nature Genetics, 51, 1052-1059. https://doi.org/10.1038/s41588-019-0427-6
Yang, N., Xu, X. W., Wang, R. R., Peng, W. L., Cai, L., Song, J. M., Li, W., Luo, X., Niu, L., Wang, Y., Jin, M., Chen, L., Luo, J., Deng, M., Wang, L., Pan, Q., Liu, F., Jackson, D., Yang, X., … Yan, J. (2017). Contributions of Zea mays subspecies mexicana haplotypes to modern maize. Nature Communications, 8, 1874. https://doi.org/10.1038/s41467-017-02063-5