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United States Department of Agriculture

Agricultural Research Service

Research Project: COTTON GENOMICS AND GENETIC ANALYSIS

Location: Crop Germplasm Research

Publications (Clicking on the reprint icon Reprint Icon will take you to the publication reprint.)

Genome sequence of the cultivated cotton Gossypium arboreum - (Peer Reviewed Journal)
Li, F., Fan, G., Wang, K., Sun, F., Yuan, Y., Song, G., Ma, Z., Li, Q., Lu, C., Zou, C., Chen, W., Liang, X., Shang, H., Liu, W., Xiao, G., Gou, C., Ye, W., Xu, X., Zhang, X., Wei, H., Li, Z., Zhang, G., Wang, J., Liu, K., Kohel, R.J., Percy, R.G., Yu, J., Zhu, Y., Wang, J., Yu, S. 2014. Genome sequence of the cultivated cotton Gossypium arboreum. Nature Genetics. 46(6):567-574.
BAC-pool sequencing and analysis of large segments of A12 and D12 homoeologous chromosomes in Upland cotton - (Peer Reviewed Journal)
Buyyarapu, R., Kantety, R.V., Yu, J., Xu, Z., Kohel, R.J., Percy, R.G., Macmil, S., Wiley, G.B., Roe, B.A., Sharma, G.C. 2013. BAC-pool sequencing and analysis of large segments of A12 and D12 homoeologous chromosomes in Upland cotton. PLoS One. 8(10): e76757. doi:10.1371/journal.pone.0076757.
Development of Single Nucleotide Polymorphism Markers via Sequence-based Genotyping in Cotton (Gossypium spp) - (Abstract Only)
(01-Nov-12)
Localization of Allotetraploid Gossypium SNPs Using Physical Mapping Resources - (Abstract Only)
(01-Sep-12)
A comparison of candidate gene-based and genotyping-by-sequencing (GBS) approaches to trait mapping in Gossypium barbadense L - (Abstract Only)
(01-Sep-12)
De novo SNP discovery and development of an interspecific cotton genome map using a simplified genotyping-by-sequencing (GBS) approach - (Abstract Only)
(01-Sep-12)
The draft genome of a diploid cotton Gossypium raimondii - (Peer Reviewed Journal)
Wang, K., Wang, Z., Li, F., Ye, W., Wang, J., Song, G., Yue, Z., Cong, L., Shang, H., Zhu, S., Zou, C., Li, Q., Yuan, Y., Lu, C., Wei, H., Gou, C., Zheng, Z., Yin, Y., Zhang, X., Liu, K., Wang, B., Song, C., Shi, N., Kohel, R.J., Percy, R.G., Yu, J., Zhu, Y., Wang, J., Yu, S. 2012. The draft genome of a diploid cotton Gossypium raimondii. Nature Genetics. 44(10:1098-1103.
Development of a core set of SSR markers for the characterization of Gossypium germplasm - (Peer Reviewed Journal)
Yu, J., Fang, D.D., Kohel, R.J., Ulloa, M., Hinze, L.L., Percy, R.G., Zhang, J., Chee, P., Scheffler, B.E., Jones, D.C. 2012. Development of a core set of SSR markers for the characterization of Gossypium germplasm. Euphytica. 187(2):203-213.
Genome-Wide Gossypium SNP development and validation - (Abstract Only)
(06-Jan-12)
Collaborative development of SNPs for cotton research, introgression, MAS and breeding - (Abstract Only)
(06-Jan-12)
Molecular tools for contemporary cotton breeding - (Abstract Only)
Yu, J., Fang, D.D., Abdurakhmonov, I.Y., Yu, S., Percy, R.G. 2012. Molecular tools for contemporary cotton breeding [abstract]. Proceedings of the Plant and Animal Genome Conference XX, January 14-18, 2012, San Diego, California. W543.
Genome-wide SNP development and validation for allotetraploid Gossypium - (Abstract Only)
Hulse, A.M., Wang, F., Hoegenauer, K.A., Stelly, D.M., Ashrafi, H., Van Deynze, A., Yu, J., Chen, Z., Udall, J., Jones, D.C. 2012. Genome-wide SNP development and validation for allotetraploid Gossypium [abstract]. Proceedings of the Plant and Animal Genome Conference XX, January 14-18, 2012, San Diego, California. P0199.
Development of new candidate gene and EST-based molecular markers for Gossypium species - (Peer Reviewed Journal)
Buyyarapu, R., Kantety, R.V., Yu, J., Saha, S., Sharma, G.C. 2011. Development of new candidate gene and EST-based molecular markers for Gossypium species. International Journal of Plant Genomics. 2011:Article 894598.
A high-density simple sequence repeat and single nucleotide polymorphism genetic map of the tetraploid cotton genome - (Peer Reviewed Journal)
Yu, J., Kohel, R.J., Fang, D.D., Cho, J., Van Deynze, A., Ulloa, M., Hoffman, S.M., Pepper, A.E., Stelly, D.M., Jenkins, J.N., Saha, S., Kumpatla, S.P., Shah, M.R., Hugie, W.V., Percy, R.G. 2012. A high-density simple sequence repeat and single nucleotide polymorphism genetic map of the tetraploid cotton genome. Genes, Genomes, Genetics. 2:43-58.
Development of gene-tagged SNP markers for gland morphogenesis in cotton - (Abstract Only)
(10-Dec-10)
Use of diversity arrays technology markers for integration into a cotton reference map and anchoring to a recombinant inbred line map - (Peer Reviewed Journal)
Reddy, U.K., Rong, J., Heller-Uszynska, K., Nimmakayala, P., Vajja, G., Rahman, M.A., Yu, J., Soliman, K.M., Kilian, A., Paterson, A.H. 2011. Use of diversity arrays technology markers for integration into a cotton reference map and anchoring to a recombinant inbred line map. Genome. 54:349-359.
Polyploidization altered gene functions in cotton (Gossypium spp.) - (Peer Reviewed Journal)
Xu, Z., Yu, J., Cho, J., Yu, J., Kohel, R.J., Percy, R.G. 2010. Polyploidization altered gene functions in cotton (Gossypium spp.). PLoS One. 5(12):e14351. doi:10.1371/journal.pone.0014351.
Development and mapping of gene-tagged SNP markers for gland morphogenesis in cotton - (Peer Reviewed Journal)
Cho, J., Lu, C., Kohel, R.J., Yu, J. 2011. Development and mapping of gene-tagged SNP markers for gland morphogenesis in cotton. Journal of Cotton Science. 15:22-32.
Distribution of fiber development genes and transcription factors between At and Dt subgenomes in tetraploid cotton - (Abstract Only)
(21-Jun-10)
The construction of a tetraploid cotton genome-wide comprehensive reference map and the comparison with cotton physical mapping information - (Abstract Only)
(21-Jun-10)
The construction of a tetraploid cotton genome wide comprehensive reference map - (Peer Reviewed Journal)
Yu, J., Kohel, R.J., Smith, C. 2010. The construction of a tetraploid cotton genome wide comprehensive reference map. Genomics. 95:230-240.
Development of core SSR markers for Gossypium germplasm characterization - (Abstract Only)
Yu, J., Fang, D.D., Ulloa, M., Percy, R.G., Kohel, R.J., Hinze, L.L., Frelichowski, J.E., Cho, J., Campbell, B.T., Chee, P., Zhang, J., Abdurakhmonov, I., Abdukarimov, A., Jones, D.C. 2010. Development of core SSR markers for Gossypium germplasm characterization [abstract]. In: Proceedings of the National Cotton Council Beltwide Cotton Conferences, January 4-7, 2010, New Orleans, Louisiana. p. 811. CDROM.
Portable DNA markers tailored for systematic characterization of Gossypium germplasm - (Abstract Only)
Yu, J., Fang, D.D., Ulloa, M., Percy, R.G., Kohel, R.J., Hinze, L.L., Frelichowski, J.E., Cho, J., Campbell, B.T., Chee, P., Abdurakhmonov, I., Abdukarimov, A., Jones, D.C. 2010. Portable DNA markers tailored for systematic characterization of Gossypium germplasm [abstract]. In: Plant and Animal Genome Conference Proceedings, January 9-13, 2010, San Diego, California. P149.
Sampling nucleotide diversity in cotton - (Peer Reviewed Journal)
Van Deynze, A., Stoffel, K., Lee, M., Wilkins, T.A., Kozik, A., Cantrell, R.G., Yu, J., Kohel, R.J., Stelly, D.M. 2009. Sampling nucleotide diversity in cotton. BMC Plant Biology. 9:Article 125.
CottonDB: A resource for cotton genome research - (Abstract Only)
Yu, J., Kohel, R.J., Hinze, L.L., Frelichowski, J.E., Xu, Z., Yu, J., Percy, R.G. 2009. CottonDB: A resource for cotton genome research [abstract]. In: Proceedings of the Plant and Animal Genome Conference, January 10-14, 2009, San Diego, California. 2009 CDROM.
BAC-pool 454-sequencing: A rapid and efficient approach to sequence complex tetraploid cotton genomes - (Abstract Only)
Buyyarapu, R., Kantety, R., Xu, Z., Yu, J., Kohel, R.J., Percy, J.T., Macmil, S., Wiley, G., Roe, B., Sharma, G. 2009. BAC-pool 454-sequencing: A rapid and efficient approach to sequence complex tetraploid cotton genomes [abstract]. In: Proceedings of the Plant and Animal Genome Conference, January 10-14, 2009, San Diego, California. 2009 CDROM.
Distribution and organization of gene-rich islands for fiber development in the cotton genome - (Abstract Only)
Xu, Z., Kohel, R.J., Song, G., Cho, J., Alabady, M., Yu, J., Koo, P., Chu, J., Yu, S., Wilkins, T.A., Zhu, Y., Yu, J. 2009. Distribution and organization of gene-rich islands for fiber development in the cotton genome [abstract]. In: Proceedings of the Plant and Animal Genome Conference, January 10-14, 2009, San Diego, California. 2009 CDROM.
Molecular diversity and association mapping of fiber quality traits in exotic G. hirsutum L. germplasm - (Peer Reviewed Journal)
Abdurakhmonov, I.Y., Kohel, R.J., Yu, J., Pepper, A.E., Abdullaev, A.A., Kushanov, F.N., Salakhutdinov, I.B., Buriev, Z.T., Saha, S., Scheffler, B.E., Jenkins, J.N., Abdukarimov, A. 2008. Molecular diversity and association mapping of fiber quality traits in exotic G. hirsutum L. germplasm. Genomics. 92:478-487.
Perspectives of the International Cotton Genome Initiative - (Abstract Only)
Yu, J., Percy, R.G. 2008. Perspectives of the International Cotton Genome Initiative [abstract]. In: Proceedings of the International Cotton Genome Initiative Workshop, July 8-11, 2008, Anyang, China. p. 2.
Sequencing of the cultivated tetraploid cotton genome - Gossypium hirsutum - (Abstract Only)
Yu, S., Wang, K., Li, F., Kohel, R.J., Percy, R.G., Yu, J. 2008. Sequencing of the cultivated tetraploid cotton genome - Gossypium hirsutum [abstract]. In: Proceedings of the International Cotton Genome Initiative Workshop, July 8-11, 2008, Anyang, China. p. 4.
An integrated genetic, physical, and transcript map of homoeologous chromosomes 12 and 26 in Upland cotton (Gossypium hirsutum L.) - (Abstract Only)
Xu, Z., Kohel, R.J., Song, G., Cho, J., Yu, J., Yu, S., Tomkins, J., Yu, J. 2008. An integrated genetic, physical, and transcript map of homoeologous chromosomes 12 and 26 in Upland cotton (Gossypium hirsutum L.) [abstract]. In: Proceedings of the International Cotton Genome Initiative Workshop, July 8-11, 2008, Anyang, China. p. 22.
CottonDB enhancement - (Abstract Only)
Yu, J., Kohel, R.J., Hinze, L.L., Frelichowski, J.E., Xu, Z., Yu, J., Percy, R.G. 2008. CottonDB enhancement [abstract]. In: Proceedings of the International Cotton Genome Initiative Workshop, July 8-11, 2008, Anyang, China. p. 120.
Gene-rich islands for fiber development in the cotton genome - (Peer Reviewed Journal)
Xu, Z., Kohel, R.J., Song, G., Cho, J., Alabady, M., Yu, J., Poo, K., Chu, J., Yu, S., Wilkins, T.A., Zhu, Y., Yu, J. 2008. Gene-rich islands for fiber development in the cotton genome. Genomics. 92:173-183.
An integrated genetic and physical map of homoeologous chromosomes 12 and 26 in Upland cotton (G. hirsutum L.) - (Peer Reviewed Journal)
Xu, Z., Kohel, R.J., Song, G., Cho, J., Yu, J., Yu, S., Tomkins, J., Yu, J. 2008. An integrated genetic and physical map of homoeologous chromosomes 12 and 26 in Upland cotton (G. hirsutum L.). BMC Genomics. 9:108.
Assembly and sorting of homologous BAC contigs in allotetraploid cotton genomes - (Abstract Only)
Yu, J., Xu, Z., Kohel, R.J. 2008. Assembly and sorting of homologous BAC contigs in allotetraploid cotton genomes [abstract]. In: Proceedings of the Beltwide Cotton Conferences, January 8-11, 2008, Nashville, Tennessee. 2008 CDROM.
Last Modified: 7/30/2014
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