Latest genomic studies of wheat sheds new light on crop adaptation and domestication

Mar. 25, 2013 ? The advanced online publication version of Nature today presents two manuscripts that provide an unprecedented glimpse into the adaptation and domestication of wheat. The two projects sequenced and analyzed two ancestral wheat genomes of Triticum urartu and Aegilops tauschii, respectively, throwing light on the biology of the world's primary staple crop and providing valuable new resource for the genetic improvement of wheat.

Wheat is a globally important crop due to its enhanced adaptability to a wide range of climates and improved grain quality for the production of baker's flour. Major efforts are underway worldwide to increase its yield and quality by increasing genetic diversity and analyzing key traits related to its resistance to cold, drought and disease. However, the extremely large size and polyploid complexity of the wheat genome has to date been a substantial barrier for researchers to gain insight into its biology and evolution.

These achievements are the results of joint efforts led by the Institute of Genetics and Developmental Biology (IGDB), Chinese Academy of Sciences, Chinese Academy of Agricultural Sciences (CAAS), and BGI.

The first manuscript, led by teams at IGDB and BGI, presents the genome of Bread wheat (T. aestivum, AABBDD), the progenitor of the Wheat A genome. Using a whole-genome shotgun strategy and Next-generation sequencing (NGS), researchers identified a large set of gene models (34,879) and abundant genetic markers with the potential to provide a valuable resource for accelerating deeper and more systematic genomic and breeding studies. For example, they found the T. urartu homolog of OsGASR7 might be a useful candidate for improving wheat yield. The discovery of 2,989,540 SNPs (single nucleotide polymorphisms) is useful for the future development and characterization of genetic markers. The researchers also reported genomic evidence of the role of repeat expansion in the enlargement of genome size during the evolution of the Triticeae tribe of grasses.

Ae. tauschii (DD), also known as Tausch's goatgrass, is a diploid goat grass species which has contributed the D genome of common wheat. Around 8,000 years ago in the Fertile Crescent, it crossed with the tetraploid wheat T. turgidum (AABB) in rare hybridization events that resulted in the hexaploid wheat T. aestivum. However, the modern strategy of breeding for hybrid vigor has been accompanied by marked changes in patterns of gene expression.

The second manuscript, led by teams at CAAS and BGI, focuses on the genome sequencing and analysis of the wild diploid grass Ae. tauschii. They found that more than 65.9% of the Ae. tauschii genome was composed of 410 different transposable element (TE) families, and the expansion of the Ae. tauschii genome was relatively recent and coincided with the abrupt climate change that occurred during the Pliocene Epoch. They also found the expansion of the micro-RNA miR2275 family may contribute to Ae. Tauschii' s enhanced disease resistance. Remarkably, a higher number of genes for the cytochrome P450 family were identified in Ae. tauschii (485) than sorghum (365), rice (333), Brachypodium (262) and maize (261). This family of genes has been found to be important for abiotic stress response, especially in biosynthetic and detoxification pathways.

Shancen Zhao, Project Manager of BGI, said, "Genetic improvement of crops is the key output of breeding research. The genomic data provides a valuable resource for botanists and breeders to comprehensively understand wheat's genetic diversity and evolutionary history.The two studies also represent a major step forward for improving this vital crop in the face of global climate change, growing human population, and bio-energy. " Providing the global agricultural community with these resources new resources for crop improvement and in keeping with the scientific community's goals of making all data fully and freely available, the huge amounts of data (1.5 terabytes) are available in the GigaScience database, GigaDB, in a citable format (see: http://dx.doi.org/10.5524/100050 and http://dx.doi.org/10.5524/100054), and are available as raw reads in the NCBI SRA database (Accession # SRP005973 and SRP005974).

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The above story is reprinted from materials provided by BGI Shenzhen.

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Journal References:

1. Jizeng Jia, Shancen Zhao, Xiuying Kong, Yingrui Li, Guangyao Zhao, Weiming He, Rudi Appels, Matthias Pfeifer, Yong Tao, Xueyong Zhang, Ruilian Jing, Chi Zhang, Youzhi Ma, Lifeng Gao, Chuan Gao, Manuel Spannagl, Klaus F. X. Mayer, Dong Li, Shengkai Pan, Fengya Zheng, Qun Hu, Xianchun Xia, Jianwen Li, Qinsi Liang, Jie Chen, Thomas Wicker, Caiyun Gou, Hanhui Kuang, Genyun He, Yadan Luo, Beat Keller, Qiuju Xia, Peng Lu, Junyi Wang, Hongfeng Zou, Rongzhi Zhang, Junyang Xu, Jinlong Gao, Christopher Middleton, Zhiwu Quan, Guangming Liu, Jian Wang, Huanming Yang, Xu Liu, Zhonghu He, Long Mao, Jun Wang. Aegilops tauschii draft genome sequence reveals a gene repertoire for wheat adaptation. Nature, 2013; DOI: 10.1038/nature12028
2. Hong-Qing Ling, Shancen Zhao, Dongcheng Liu, Junyi Wang, Hua Sun, Chi Zhang, Huajie Fan, Dong Li, Lingli Dong, Yong Tao, Chuan Gao, Huilan Wu, Yiwen Li, Yan Cui, Xiaosen Guo, Shusong Zheng, Biao Wang, Kang Yu, Qinsi Liang, Wenlong Yang, Xueyuan Lou, Jie Chen, Mingji Feng, Jianbo Jian, Xiaofei Zhang, Guangbin Luo, Ying Jiang, Junjie Liu, Zhaobao Wang, Yuhui Sha, Bairu Zhang, Huajun Wu, Dingzhong Tang, Qianhua Shen, Pengya Xue, Shenhao Zou, Xiujie Wang, Xin Liu, Famin Wang, Yanping Yang, Xueli An, Zhenying Dong, Kunpu Zhang, Xiangqi Zhang, Ming-Cheng Luo, Jan Dvorak, Yiping Tong, Jian Wang, Huanming Yang, Zhensheng Li, Daowen Wang, Aimin Zhang, Jun Wang. Draft genome of the wheat A-genome progenitor Triticum urartu. Nature, 2013; DOI: 10.1038/nature11997

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Source: http://feeds.sciencedaily.com/~r/sciencedaily/top_news/top_environment/~3/wDyDhBmn6bc/130326112310.htm

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