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Collinearity-based marker mining for the fine mapping of Pm6, a powdery mildew resistance gene in wheat

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Abstract

The genome sequences of rice (Oryza sativa L.) and Brachypodium distachyon and the comprehensive Triticeae EST (Expressed Sequence Tag) resources provide invaluable information for comparative genomics analysis. The powdery mildew resistance gene, Pm6, which was introgressed into common wheat from Triticum timopheevii, was previously mapped to the wheat chromosome bin of 2BL [fraction length (FL) 0.50–1.00] with limited DNA markers. In this study, we saturated the Pm6 locus in wheat using the collinearity-based markers by extensively exploiting these genomic resources. All wheat ESTs located in the bin 2BL FL 0.50–1.00 and their corresponding orthologous genes on rice chromosome 4 were firstly used to develop STS (Sequence Tagged Site) markers. Those identified markers that flanked the Pm6 locus were then used to identify the collinear regions in the genomes of rice and Brachypodium. Triticeae ESTs with orthologous genes in these collinear regions were further used to develop new conserved markers for the fine mapping of Pm6. Using two F2 populations derived from crosses of IGVI-465 × Prins and IGVI-466 × Prins, we mapped a total of 29 markers to the Pm6 locus. Among them, 14 markers were co-segregated with Pm6 in the IGVI-466/Prins population. Comparative genome analysis showed that the collinear region of the 29 linked markers covers a ~5.6-Mb region in chromosome 5L of Brachypodium and a ~6.0-Mb region in chromosome 4L of rice. The marker order is conserved between rice and Brachypodium, but re-arrangements are present in wheat. Comparative mapping in the two populations showed that two conserved markers (CINAU123 and CINAU127) flanked the Pm6 locus, and an LRR-receptor-like protein kinase cluster was identified in the collinear regions of Brachypodium and rice. This putative resistance gene cluster provides a potential target site for further fine mapping and cloning of Pm6. Moreover, the newly developed conserved markers closely linked to Pm6 can be used for the marker-assisted selection (MAS) of Pm6 in wheat breeding programs.

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Acknowledgments

This research was supported by grants from the Chinese High Tech Program of China (No. 2006AA10Z1F6), the Natural Science Foundation of Jiangsu Province (No. BK2006720), Important National Science & Technology Specific Projects of Transgenic Research (No. 2009ZX08002-001B) and the Programme of Introducing Talents of Discipline to Universities (No. B08025).

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  1. State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, China

    Bi Qin, Aizhong Cao, Haiyan Wang, Tingting Chen, Yangyang Liu, Jianhui Ji, Dajun Liu, Peidu Chen & Xiu-e Wang

  2. Department of Plant Sciences, University of California, Davis, CA, 95616, USA

    Frank M. You

  3. Genomics and Gene Discovery Research Unit, USDA-ARS, Western Regional Research Center, Albany, CA, 94710, USA

    Frank M. You

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  1. Bi Qin
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  2. Aizhong Cao
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Correspondence to Xiu-e Wang.

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Qin, B., Cao, A., Wang, H. et al. Collinearity-based marker mining for the fine mapping of Pm6, a powdery mildew resistance gene in wheat. Theor Appl Genet 123, 207–218 (2011). https://doi.org/10.1007/s00122-011-1577-9

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