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Evolutionary analysis of RB/Rpi-blb1 locus in the Solanaceae family

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Abstract

Late blight caused by the oomycete Phytophthora infestans is one of the most severe threats to potato production worldwide. Numerous studies suggest that the most effective protective strategy against the disease would be to provide potato cultivars with durable resistance (R) genes. However, little is known about the origin and evolutional history of these durable R-genes in potato. Addressing this might foster better understanding of the dynamics of these genes in nature and provide clues for identifying potential candidate R-genes. Here, a systematic survey was executed at RB/Rpi-blb1 locus, an exclusive broad-spectrum R-gene locus in potato. As indicated by synteny analysis, RB/Rpi-blb1 homologs were identified in all tested genomes, including potato, tomato, pepper, and Nicotiana, suggesting that the RB/Rpi-blb1 locus has an ancient origin. Two evolutionary patterns, similar to those reported on RGC2 in Lactuca, and Pi2/9 in rice, were detected at this locus. Type I RB/Rpi-blb1 homologs have frequent copy number variations and sequence exchanges, obscured orthologous relationships, considerable nucleotide divergence, and high non-synonymous to synonymous substitutions (Ka/Ks) between or within species, suggesting rapid diversification and balancing selection in response to rapid changes in the oomycete pathogen genomes. These characteristics may serve as signatures for cloning of late blight resistance genes.

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Acknowledgments

This work was supported by the National Natural Science Foundation of China (91331205, J1103512, and J1210026), NSFC of Jiangsu Province (BK2011015), Program for Changjiang Scholars and Innovative Research Team in University (IRT_14R27). We would like to thank Sveriges Lantbruksuniversitet, Department of Plant Protection Biology of the Swedish University of Agricultural Sciences for offering Sarpo Mira (harvested on May 9, 2012) for testing (Ali et al. 2007).

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    1. State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210093, China

      Zhengqing Xie, Weina Si, Rongchao Gao, Xiaohui Zhang & Sihai Yang

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    Communicated by C. Gebhardt.

    Z. Xie and W. Si contributed equally to this work.

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    Xie, Z., Si, W., Gao, R. et al. Evolutionary analysis of RB/Rpi-blb1 locus in the Solanaceae family. Mol Genet Genomics 290, 2173–2186 (2015). https://doi.org/10.1007/s00438-015-1068-9

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