A natural allele of the transcription factor gene TaMYB-D7b is a genetic signature for phosphorus deficiency in wheat.

Phosphorus (P) and nitrogen (N) deficiencies are major yield-limiting factors for wheat (Triticum aestivum) production worldwide, particularly in the acidic soils of the southern Great Plains of North America. In this study, we report that the transcription factor gene TaMYB-D7 is responsible for a major quantitative trait locus controlling purple leaf color. The wheat cultivar "2174" showed purple coleoptiles regardless of P status, whereas "Jagger" did not, even under P limitation. The 2 cultivars differed by 1 amino acid in TaMYB-D7: Gly-50 in TaMYB-D7b (encoded by the 2174 allele) and Ser-50 in TaMYB-D7a (encoded by the Jagger allele). We used genome editing to inactivate all 3 TaMYB7 homoeologs in cv. 2174. The resulting edited wheat plants did not accumulate purple pigments throughout their life cycle, validating the functions of TaMYB-7Db associated with the purple phenotype. In the TaMYB7-edited plants, chalcone synthase 2-like (TaCHSL2), which may be involved in anthocyanidin biosynthesis and metabolism, was dramatically downregulated, suggesting that TaMYB7 induces its transcription. We also discovered that the expression of TaMYB7 and TaCHSL2 was upregulated by P but downregulated by N. Lastly, we developed a Kompetitive Allele Specific PCR (KASP) marker to facilitate the genotyping of TaMYB-D7b, which can be used for marker-assisted breeding. Our results provide insight into nutrient use efficiency in wheat.