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ARS Home » Southeast Area » Stoneville, Mississippi » Genomics and Bioinformatics Research » Research » Publications at this Location » Publication #305923

Research Project: Genomics and Bioinformatics Research in Agriculturally Important Organisms

Location: Genomics and Bioinformatics Research

Title: Sequencing of allotetraploid cotton (Gossypium hirsutum L. acc. TM-1) provides a resource for fiber improvement

Author
item ZHANG, TIANZHEN - Nanjing Agricultural University
item HU, YAN - Nanjing Agricultural University
item JIANG, WENKAI - Novogene Bioinformatics Institue
item FANG, LEI - Nanjing Agricultural University
item GUAN, XUEYING - University Of Texas
item CHEN, JIEDAN - Nanjing Agricultural University
item ZHANG, JINBO - Novogene Bioinformatics Institue
item SASKI, CHRISTOPHER - Clemson University
item Scheffler, Brian
item STELLY, DAVID - Texas A&M University
item HULSE-KEMP, AMANDA - Texas A&M University
item WAN, QUN - Nanjing Agricultural University
item LIU, BINGLIANG - Nanjing Agricultural University
item LIU, CHUNXIAO - Nanjing Agricultural University
item WANG, SEN - Nanjing Agricultural University
item PAN, MENGQIAO - Nanjing Agricultural University
item WANG, YANGKUN - Nanjing Agricultural University
item WANG, DAWEI - Novogene Bioinformatics Institue
item YE, WENXUE - Nanjing Agricultural University
item CHANG, LIJING - Nanjing Agricultural University
item ZHANG, WENPAN - Nanjing Agricultural University
item SONG, QINGXIN - University Of Texas
item KIRKBRIDE, RYAN - University Of Texas
item CHEN, XIAOYA - Chinese Academy Of Sciences
item DENNIS, ELIZABETH - Commonwealth Scientific And Industrial Research Organisation (CSIRO)
item LLEWELLYN, DANNY - Commonwealth Scientific And Industrial Research Organisation (CSIRO)
item PETERSON, DANIEL - Mississippi State University
item THAXTON, PEGGY - Delta Research & Extension Center
item JONES, DON - Cotton, Inc
item WANG, QIONG - Nanjing Agricultural University
item XU, XIAOYANG - Nanjing Agricultural University
item ZHANG, HUA - Nanjing Agricultural University
item WU, HUAITONG - Nanjing Agricultural University
item ZHOU, LEI - Nanjing Agricultural University
item MEI, GAOFU - Nanjing Agricultural University
item CHEN, SHUQI - Nanjing Agricultural University
item TIAN, YUE - Nanjing Agricultural University
item XIANG, DAN - Nanjing Agricultural University
item LI, XINGHE - Nanjing Agricultural University
item DING, JIAN - Nanjing Agricultural University
item ZUO, QIYANG - Novogene Bioinformatics Institue
item TAO, LINNA - Novogene Bioinformatics Institue
item LIU, YUNCHAO - Novogene Bioinformatics Institue
item LI, JI - Novogene Bioinformatics Institue
item LIN, YU - Novogene Bioinformatics Institue
item HUI, YUANYUAN - Novogene Bioinformatics Institue
item CAO, ZHISHENG - Novogene Bioinformatics Institue
item CAI, CAIPING - Nanjing Agricultural University
item ZHU, XIEFEI - Nanjing Agricultural University
item JIANG, ZHI - Novogene Bioinformatics Institue
item ZHOU, BAOLIANG - Nanjing Agricultural University
item GUO, WANGZHEN - Nanjing Agricultural University
item LI, RUIQIANG - Novogene Bioinformatics Institue
item CHEN, Z. JEFFREY - Nanjing Agricultural University

Submitted to: Nature Biotechnology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 3/15/2015
Publication Date: 4/20/2015
Citation: Zhang, T., Hu, Y., Jiang, W., Fang, L., Guan, X., Chen, J., Zhang, J., Saski, C., Scheffler, B.E., Stelly, D.M., Hulse-Kemp, A.M., Wan, Q., Liu, B., Liu, C., Wang, S., Pan, M., Wang, Y., Wang, D., Ye, W., Chang, L., Zhang, W., Song, Q., Kirkbride, R.C., Chen, X., Dennis, E., Llewellyn, D.J., Peterson, D.G., Thaxton, P., Jones, D.C., Wang, Q., Xu, X., Zhang, H., Wu, H., Zhou, L., Mei, G., Chen, S., Tian, Y., Xiang, D., Li, X., Ding, J., Zuo, Q., Tao, L., Liu, Y., Li, J., Lin, Y., Hui, Y., Cao, Z., Cai, C., Zhu, X., Jiang, Z., Zhou, B., Guo, W., Li, R., Chen, Z. 2015. Sequencing of allotetraploid cotton (Gossypium hirsutum L. acc. TM-1) provides a resource for fiber improvement. Nature Biotechnology. 33(5):531-537. doi:10.1038/nbt.3207.

Interpretive Summary: Cotton is the most important natural textile fiber and in some parts of the world is a valuable source of oil and protein. In worldwide production systems, cotton is produced by three different Gossypium species with upland cotton (Gossypium hirsutum) accounting the vast majority of cotton production. Upland cotton is a tetraploid species meaning it has chromosomes from two different diploid cotton species. The exact ancestors of upland cotton are not known but one is closely related to a cotton species that produces low quality fibers and the other ancestor does not produce any significant amount of fiber. However the combined genomes plus evolution and selection overtime has resulted in upland cotton which is produces high quality fiber with significant yields. How upland cotton was achieved and thus can be further improved for fiber traits and yield is an important agricultural question. Working towards this goal, this paper deals with determining the DNA sequence of the upland cotton, which is extremely difficult because it contains the DNA of the two ancestral species. A cost effective method was used to determine the sequence of upland cotton so the final genome assembly while not perfect is a useful tool for exploring important agricultural studies. As such, this paper has determined that in upland cotton certain genes for biotic stress from one ancestral species are more expressed than the other ancestor and the reverse is true for genes associated with fiber production.

Technical Abstract: Cotton is the world’s most important natural textile fibre and a significant oilseed crop. Upland cotton (Gossypium hirsutum L.), an allotetraploid derived from A- and D-genome progenitors, accounts for >95% of world production. Here, we sequenced and assembled 88% of the 2.5-gigabase genome of the genetic standard Upland cotton TM-1 using Illumina whole-genome shotgun and Sanger BAC-end sequencing platforms. Homoeologous chromosome assemblies were assigned using an ultra-dense linkage map containing 5 millions of single nucleotide polymorphisms. The allotetraploid genome consists of 70,478 predicted protein-coding genes, including 32,032 (45%) and 34,402(49%) in the A and D subgenomes, respectively. We showed that the A subgenome expressed more positively selected genes related to fibre development and the D subgenome expressed more stress induced genes, leading to fibre domestication and its wide adaptation. This high-quality genomic resource provides tools for the genetic improvement of cotton and for sequencing other allopolyploid crop genomes.