Research Project: Advanced Genomic and Bioinformatic Tools for Accelerated Cotton Genetic Improvement

Location: Crop Germplasm Research

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

Dual domestication, diversity, and differential introgression in Old World cotton diploids - (Peer Reviewed Journal)
Grover, C.E., Arick II, M.A., Thrash, A., Sharbrough, J., Hu, G., Yuan, D., Miller, E.R., Ramaraj, T., Peterson, D.G., Udall, J.A., Wendell, J.F. 2022. Dual domestication, diversity, and differential introgression in Old World cotton diploids. Genome Biology and Evolution. 14(12). https://doi.org/10.1093/gbe/evac170.

The Gossypium herbaceum L. Wagad genome as a resource for understanding cotton domestication - (Peer Reviewed Journal)
Ramaraj, T., Grover, C.E., Azalea, M., Arick II, M.A., Jareczek, J., Leach, A., Peterson, D., Wendel, J.F., Udall, J.A. 2022. The Gossypium herbaceum L. Wagad genome as a resource for understanding cotton domestication. G3, Genes/Genomes/Genetics. 13(2). https://doi.org/10.1093/g3journal/jkac308.

Insight between the epigenetics and transcription responding of cotton hypocotyl cellular elongation under salt-alkaline stress - (Peer Reviewed Journal)
Rui, C., Zhang, Y., Fan, Y., Han, M., Dai, M., Wang, Q., Chen, X., Lu, X., Wang, D., Wang, S., Gao, W., Yu, J., Ye, W. 2021. Insight between the epigenetics and transcription responding of cotton hypocotyl cellular elongation under salt-alkaline stress. Frontiers in Plant Science. 12. Article 772123. https://doi.org/10.3389/fpls.2021.772123.

The Gossypium anomalum genome as a resource for cotton improvement and evolutionary analysis of hybrid incompatibility - (Peer Reviewed Journal)
Grover, C.E., Yuan, D., Arick, M.A., Miller, E.R., Hu, G., Peterson, D.G., Wendel, J.F., Udall, J.A. 2021. The Gossypium anomalum genome as a resource for cotton improvement and evolutionary analysis of hybrid incompatibility. Genes, Genomes, Genetics. Article jkab319. https://doi.org/10.1093/g3journal/jkab319.

The Gossypium stocksii genome as a novel resource for cotton improvement - (Peer Reviewed Journal)
Grover, C.E., Yuan, D., Arick, M.A., Miller, E.R., Hu, G., Peterson, D.G., Wendel, J.F., Udall, J.A. 2021. The Gossypium stocksii genome as a novel resource for cotton improvement. G3, Genes/Genomes/Genetics. 11(7). Article jkab125. https://doi.org/10.1093/g3journal/jkab125.

The power of cotton genomics - (Proceedings)
Yu, J. 2021. The power of cotton genomics. Proceedings of World Cotton Research Conference Proceedings. Cotton Innovations Newsletter. 1(3):6-7.

The mystery solved: A-genome origin of cultivated diploid and tetraploid cottons - (Proceedings)
Yu, J. 2021. The mystery solved: A-genome origin of cultivated diploid and tetraploid cottons. In: Proceedings of the National Cotton Council Beltwide Cotton Conference, January 5-7, 2021, Virtual. p. 126.

Cotton transcriptome analysis reveals novel biological pathways that eliminate reactive oxygen species (ROS) under sodium bicarbonate (NaHCO3) alkaline stress - (Peer Reviewed Journal)
Fan, Y., Lu, X., Chen, X., Wang, J., Wang, D., Wang, S., Guo, L., Rui, C., Zhang, Y., Cui, R., Wang, Q., Yu, J., Ye, W. 2021. Cotton transcriptome analysis reveals novel biological pathways that eliminate reactive oxygen species (ROS) under sodium bicarbonate (NaHCO3) alkaline stress. Genomics. 113(3):1157-1169. https://doi.org/10.1016/j.ygeno.2021.02.022.

Improved reconstruction and comparative analysis of chromosome 12 to rectify mis-assemblies in Gossypium arboreum - (Peer Reviewed Journal)
Ashraf, J., Zuo, D., Cheng, H., Malik, W., Wang, Q., Zhang, Y., Abid, M., Yang, Q., Feng, X., Yu, J., Song, G. 2020. Improved reconstruction and comparative analysis of chromosome 12 to rectify mis-assemblies in Gossypium arboreum. Biomed Central (BMC) Genomics. 21. Article 470. https://doi.org/10.1186/s12864-020-06814-5.

Genome sequence of Gossypium herbaceum and genome updates of Gossypium arboreum and Gossypium hirsutum provide insights into cotton A-genome evolution - (Peer Reviewed Journal)
Huang, G., Wu, Z., Percy, R.G., Bai, M., Li, Y., Frelichowski, J.E., Hu, J., Wang, K., Yu, J., Zhu, Y. 2020. Genome sequence of Gossypium herbaceum and genome updates of Gossypium arboreum and Gossypium hirsutum provide insights into cotton A-genome evolution. Nature Genetics. https://doi.org/10.1038/s41588-020-0607-4.

The Gossypium longicalyx genome as a resource for cotton breeding and evolution - (Peer Reviewed Journal)
Grover, C.E., Pan, M., Yuan, D., Arick, M.A., Hu, G., Brase, L., Stelly, D.M., Lu, Z., Schmitz, R.J., Peterson, D.G., Wendel, J.F., Udall, J.A. 2020. The Gossypium longicalyx genome as a resource for cotton breeding and evolution. Genes, Genomes, Genetics. 10:1457-1467. https://doi.org/10.1534/g3.120.401050.

Cotton roots are the major source of gossypol biosynthesis and accumulation - (Peer Reviewed Journal)
Zhao, T., Xie, Q., Li, C., Li, C., Mei, L., Yu, J., Chen, J., Zhu, S. 2020. Cotton roots are the major source of gossypol biosynthesis and accumulation. Biomed Central (BMC) Plant Biology. 20:88. https://doi.org/10.1186/s12870-020-2294-9.

Exploiting genetic variation of Gossypium gene pools for cotton improvement - (Abstract Only)
Yu, J., Frelichowski, J.E., Hinze, L.L., Udall, J.A. 2020. Exploiting genetic variation of Gossypium gene pools for cotton improvement [abstract]. Plant and Animal Genome Conference, January 11-15, 2020, San Diego, California. W820.

The genome sequence of Gossypioides kirkii illustrates a descending dysploidy in plants - (Peer Reviewed Journal)
Udall, J.A., Long, E., Ramaraj, T., Conover, J.L., Yuan, D., Grover, C.E., Gong, L., Arick, M.A., Masonbrink, R.E., Peterson, D.G., Wendel, J.F. 2019. The genome sequence of Gossypioides kirkii illustrates a descending dysploidy in plants. Frontiers in Plant Science. 10:1541. https://doi.org/10.3389/fpls.2019.01541.

De novo genome assemblies of Gossypium raimondii and G. turneri - (Peer Reviewed Journal)
Udall, J.A., Long, E., Hanson, C., Yuan, D., Ramaraj, T., Conover, J.L., Gong, L., Arick, M.A., Grover, C.E., Peterson, D.G., Wendel, J.F. 2019. De novo genome assemblies of Gossypium raimondii and G. turneri. G3, Genes/Genomes/Genetics. 9(10):3079-3085. https://doi.org/10.1534/g3.119.400392.

Transcriptome analysis reveals cotton (Gossypium hirsutum) genes that are differentially expressed in cadmium (Cd) stress tolerance - (Peer Reviewed Journal)
Han, M., Lu, X., Yu, J., Chen, X., Wang, X., Malik, W., Wang, J., Wang, D., Wang, S., Guo, L., Chen, C., Cui, R., Yang, X., Ye, W. 2019. Transcriptome analysis reveals cotton (Gossypium hirsutum) genes that are differentially expressed in cadmium (Cd) stress tolerance. International Journal of Molecular Sciences. 20(6):1479. https://doi.org/10.3390/ijms20061479.

Genomic analysis of marker-associated fiber development genes in Upland cotton (Gossypium hirsutum L) - (Peer Reviewed Journal)
Yu, J., Gervers, K. 2019. Genomic analysis of marker-associated fiber development genes in Upland cotton (Gossypium hirsutum L). Euphytica. 215:74. https://doi.org/10.1007/s10681-019-2388-3.