TaCKXgene family, at large, is associated with thousand-grain weight and plant height in common wheat

摘要

Key message We used SMRT sequencing and explored the haplotypes ofTaCKXgenes, linked with thousand-grain weight and plant height, and developed the functionally validated markers, which can be used in the marker-assisted breeding program. Cytokinin oxidase/dehydrogenase (CKX) enzymes catalyze the permanent degradation of cytokinins. Identification of theTaCKXalleles associated with yield traits and the development of functional markers is the first step in using these alleles in marker-assisted breeding program. To identify the alleles, we sequenced the genome fragments, containingTaCKXgenes from 48 wheat genotypes, by PacBio(R)sequencing. Six out of 22TaCKXgenes were found polymorphic, forming 14 distinct haplotypes. Functional markers were developed and validated for all the polymorphicTaCKXgenes. Four specific haplotypes, i.e.,TaCKX2A_2,TaCKX4A_2,TaCKX5A_3, andTaCKX9A_2,were found significantly associated with high thousand-grain weight (TGW) and short plant height (PH) in Chinese wheat micro-core collection (MCC) and GWAS open population (GWAS-OP), whereasTaCKX1B_2in GWAS-OP andTaCKX11A_3in MCC were significantly associated with high TGW and short PH. The mean values of TGW and PH for cumulative favorable haplotypes from chromosome 3A, i.e.,TaCKX2A_2,TaCKX4A_2,andTaCKX5A_3, were significantly higher as compared to the cumulative unfavored haplotypes, and the change was additive in manner. Frequency distribution analysis revealed that since the 1960s, the frequency of the favorable haplotypes and TGW has gradually increased in Chinese wheat cultivars. Expression profiling in the seed tissue excised at 2, 4, 6, and 8 days after anthesis depicted that the favorable haplotypes are significantly less expressive as compared to the unfavored haplotypes. We conclude that the functional markers developed in this study can be used to select the favorable haplotypes ofTaCKXgenes in wheat marker-assisted breeding programs.