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ARS Home » Pacific West Area » Albany, California » Western Regional Research Center » Crop Improvement and Genetics Research » Research » Publications at this Location » Publication #330405

Research Project: Enhancement of Wheat through Genomic and Molecular Approaches

Location: Crop Improvement and Genetics Research

Title: Sequencing and comparative analyses of Aegilops tauschii chromosome arm 3DS revealed rapid evolution of Triticeae genome

Author
item XIE, J - China Agricultural University
item HUO, X - University Of California
item ZHOU, S - China Agricultural University
item WANG, Y - University Of California
item GUO, G - China Agricultural University
item DEAL, K - University Of California
item OUYANG, S - China Agricultural University
item LIANG, Y - China Agricultural University
item WANG, Z - China Agricultural University
item XIAO, L - University Of California
item ZHU, T - University Of California
item HU, G - Henan Institute Of Science And Technology
item TIWARI, V - Kansas State University
item ZHANG, J - University Of Arizona
item LI, H - Northwest Agricultural & Forestry University
item NI, Z - China Agricultural University
item YAO, Y - China Agricultural University
item PENG, H - China Agricultural University
item ZHANG, S - Henan Institute Of Science And Technology
item Anderson, Olin
item MCGUIRE, P - University Of California
item DVORAK, J - University Of California
item LUO, M - University Of California
item LIU, Y - China Agricultural University
item Gu, Yong
item SUN, Q - China Agricultural University

Submitted to: Journal of Genetics and Genomics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 9/27/2016
Publication Date: 2/3/2017
Citation: Xie, J., Huo, X., Zhou, S., Wang, Y., Guo, G., Deal, K., Ouyang, S., Liang, Y., Wang, Z., Xiao, L., Zhu, T., Hu, G., Tiwari, V., Zhang, J., Li, H., Ni, Z., Yao, Y., Peng, H., Zhang, S., Anderson, O.D., McGuire, P., Dvorak, J., Luo, M., Liu, Y., Gu, Y.Q., Sun, Q. 2017. Sequencing and comparative analyses of Aegilops tauschii chromosome arm 3DS revealed rapid evolution of Triticeae genome. Journal of Genetics and Genomics. 44:51-61.

Interpretive Summary: Wheat (Triticum aestivum) accounts for approximately 30% of global cereal consumption. Modern bread wheat has three different genomes called A, B and D. One of the factors limiting progress in wheat breeding is a lack of genetic variation in genes in the wheat D genome. Aegilops tauschii (Tausch’s goatgrass), the wild ancestor of the modern wheat D genome, is a geographically widespread and genetically diverse species, and is a logical source for broadening genetic diversity in the wheat D genome. Ae. tauschii has also served as an exceptional source of genes for resistance to various wheat diseases, including wheat rust diseases. A high-quality reference genome sequence for Ae. tauschii will greatly facilitate wheat improvement research. In this research report, we employed a novel sequencing strategy to sequence the DNA from the shorter arm of Ae. tauschii chromosome 3 (At3DS). When the resulting high-quality sequence was compared with the equivalent regions of chromosomes of other grass species such as rice and sorghum, we found that Ae. tauschii have gained 38% more genes, suggesting its fast genome evolution. Our results also indicate that genes from Ae. tauschii share high sequence identities (99%) with those from the D genome of bread wheat. Therefore, the high-quality ordered At3DS DNA sequence provides a useful resource for cloning important genes for improvement of wheat and other grass crops.

Technical Abstract: Bread wheat (Triticum aestivum, AABBDD) is an allohexaploid species derived from multiple rounds of interspecific hybridizations. A high-quality genome assembly of diploid Ae. tauschii, the donor of the wheat D genome, will provide a useful platform to study polyploid wheat evolution. A combinational approach of BAC pooling and next-generation sequencing technology was employed to sequence the minimal tiling path (MTP) of 3,337 BAC clones from the short arm of Ae. tauschii chromosome 3 (At3DS). The final assembly of 135 super-scaffolds with N50 of 4.2 Mb was used to build a 247-Mb pseudomolecule with an estimated coverage of 90% and a total of 2,124 predicted genes. At3DS contains 38% more genes compared to the orthologous regions of rice, Brachypodium, and sorghum. We estimate that 48% of these At3DS non-syntenic genes resulted from inter-chromosomal gene duplications and 21% from intra-chromosomal gene duplications. The 85-Mb larger size of wheat Ta3BS compared to At3DS is primarily due to the expansion of the non-centromeric region, suggesting transposable element (TE) bursts in Ta3B likely occurred in the non-centromeric region. The size increase of Ta3B appears to be proportional to its increase in gene number. We show that major gene loss (less that 0.27%) did not occur in the Ta3DS genes after polyploidization. Genes in Ta3DS are under purifying selection with an overall Ks/Ka of 0.33. Our study reveals divergent evolution of grass genomes and provides new insights into sequence changes in the polyploid wheat genome. The high-quality At3DS assembly provides a useful resource for cloning important genes for crop improvement.