Abstract
The recessive mutation of the XANTHA gene (XNT) transforms seedlings and plants into a yellow color, visually distinguishable from normal (green) rice. Thus, it has been introduced into male sterile lines as a distinct marker for rapidly testing and efficiently increasing varietal purity in seed and paddy production of hybrid rice. To identify closely linked markers and eventually isolate the XNT gene, two mapping populations were developed by crossing the xantha mutant line Huangyu B (indica) with two wild type japonica varieties; a total of 1,720 mutant type F2 individuals were analyzed for fine mapping using polymorphic InDel markers and high dense microsatellite markers. The XNT gene was mapped on chromosome 11, within in a fragment of ~100 kb, where 13 genes are annotated. The NP_001067671.1 gene within the delimited region is likely to be a candidate XNT gene, since it encodes ATP-dependent chloroplast protease ATP-binding subunit clp A. However, no sequence differences were observed between the mutant and its parent. Bioinformatics analysis demonstrated that four chlorophyll deficient mutations that were previously mapped on the same chromosome are located outside the XNT region, indicating XNT is a new gene. The results provide useful DNA markers not only for marker assisted selection of the xantha trait but also its eventual cloning.
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Acknowledgements
We thank Dr. X. Y. Guo (Zhejiang University, China) for helping us identify the InDel markers. We are grateful to Mr. Z. D. Yu and Mr. B. Yang (China Jiliang University) for their technical assistance. The assistance of Drs. H.W. Fu, Q.L. Liu and Mr. Y.C. Jin in the development and phenotyping of the mapping populations is sincerely acknowledged.
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Chi, XF., Zhou, XS. & Shu, QY. Fine mapping of a Xantha mutation in rice (Oryza sativa L.). Euphytica 172, 215–220 (2010). https://doi.org/10.1007/s10681-009-0048-8
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DOI: https://doi.org/10.1007/s10681-009-0048-8