Identification of a Novel Allele of <i>TaCKX6a02</i> Associated with Grain Size, Filling Rate and Weight of Common Wheat

<div><p>Cytokinin oxidase (CKX) plays a crucial role in plant growth and development by reversibly inactivating cytokinin (CTK). Twenty-four primer pairs, designed from ESTs of the <i>TaCKX</i> genes family of common wheat, were used to identify their allelic variations associated with grain size, weight, and filling rate in 169 recombinant inbred lines (RIL) derived from Jing 411 × Hongmangchun 21. <i>TaCKX6a02</i>, a member of <i>TaCKX</i> gene family, amplified by primer pair <i>T31–32</i>, showed a close association with grain traits in this RIL population. Statistical analysis indicated that allelic variation of <i>TaCKX6a02</i> had significant correlation with grain size, weight, and filling rate (GFR; <i>P</i> < 0.001) under varied environments. The <i>TaCKX6a02-D1a</i> allele from Jing411 significantly increased grain size, weight and grain filling rate, compared with <i>TaCKX6a02-D1b</i> from Hongmangchun 21. <i>TaCKX6a02</i> was located on chromosome 3DS in the interval of <i>Xbarc1119</i> and <i>Xbarc1162</i>, with a genetic distance of 1.4 cM. The location was further confirmed using Chinese Spring nulli–tetrasomic lines. A major QTL (quantitative trait locus) tightly linked to <i>TaCKX6a02</i> was detected in the RIL population, explaining 17.1~38.2% of phenotype variations for grain size, weight, GFRmax and GFRmean in different environments. In addition, significant effects of variations of <i>TaCKX6a02</i> on grain weight and GFR were further validated by association analysis among 102 wheat varieties in two cropping seasons. 12.8~35.1% of phenotypic variations were estimated for these genotypes. A novel 29-bp InDel behind the stop codon was detected by DNA sequence analysis between the two alleles of <i>TaCKX6a02-D1</i>. The gene-specific marker, <i>TKX3D</i>, was designed according to the novel variation, and can be used in marker-assisted selection (MAS) for grain size, weight, and GFR in common wheat.</p>