Linkage map of <i>Tackx4</i> on chromosome 3A of wheat.

<p>The four shaded boxes represented the four traits (C5, C10, C15 and TGW, respectively).</p

Homology analysis of <i>Tackx4</i> from wheat (<i>Tackx4-1</i>, <i>Tackx4-2</i> and <i>Tackx4-3</i>), <i>Hvckx4a</i> from barley, and <i>Osckx4</i> from rice.

<p>The percentages indicated the sequence identity among them.</p

Amplified patterns of <i>Tackx4</i> from Chinese Spring nullisomic—tetrasomics using <i>T19-20</i> primer pair.

<p>Lanes 1–14: 1, Jing411; 2, Yumai 8679; 3, Yongchuanbaikemai (Chinese landrace); 4, Chinese spring; 5, Yongchuanbaimaizi (Chinese landrace); 6, Wanxianbaizi (Chinese landrace); 7, Heshangmai; 8, N3BT3A; 9, N3DT3A; 10, N3BT3D; 11, N3AT3D; 12, N3AT3B; 13,Yangmai 158; 14, Y6 (<i>Aegilops tauschii</i>, DD). The genotype-A (<i>Tackx4-1</i> and <i>Tackx4-2</i>) and genotype-C (<i>Tackx4-2</i> and <i>Tackx4-3</i>) are marked with A and C, respectively.</p

Amplification patterns of <i>Tackx4</i> gene for 12 of the 102 wheat varieties using <i>T19-20</i> primer pair.

<p>Lanes 1–12: 1, Jing411; 2, Yumai 8679; 3, Jimai 20; 4, Zhongmai 9; 5, Zheng 9023; 6, Hongmangchun 21; 7, Wanxianbaimaizi; 8, Wangshuibai; 9, Shan 225; 10, Shan 160; 11, Yumai 8679; 12, Xiaobingmai 33.</p

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></div

Linkage map of <i>TaCKX6a02</i> on chromosome 3DS of wheat.

<p>The six shaded boxes represent the six traits of TGW, GW, GL, GT, GFRmax, and GFRmean, respectively.</p

Allelic variation of <i>TaCKX6a02</i> in the RIL population of Jing 411/Hongmangchun 21.

<p>Lane Nos. (1) Jing 411; (2) JH1; (3) Hongmangchun 21; (4) JH19; (5) JH31; (6) JH38; (7) JH2; (8) JH3; (9) JH4; (10) JH5; (11) JH73; (12) JH9; (13) JH10; (14) JH12; (15) JH75; (16) JH79; (17) JH81; (18) JH103; (19) JH105; (20) JH13; (21) JH107; (22) JH113; (23) JH15; (24) JH118; (25) JH120; (26) JH125; (27) JH129; and (28) JH130. In the figure, JH1, JH19, JH31, JH38, etc., represent individual names of the RIL population. Two types of alleles, <i>TaCKX6a02-D1a</i> (Jing 411) and <i>TaCKX6a02-D1b</i> (Hongmangchun 21) are marked with the letters “A” and “B”, respectively.</p

Sequence alignment between <i>TaCKX6a02</i> and <i>TaCKX2</i>.<i>1</i>, <i>TaCKX2</i>.<i>2</i>, <i>TaCKX2</i>.<i>3</i>.<i>1</i>, <i>TaCKX2</i>.<i>3</i>.<i>2</i>, and <i>TaCKX6-D1b</i>.

<p>Two alleles sequences of <i>Tackx6a02</i>, <i>TaCKX6a02-D1a</i>) and <i>TaCKX6a02-D1b</i> were obtained from the reverse-complement sequences of PCR fragments of Jing 411 and Hongmangchun 21. The primer pair and stop codon are marked with arrows in the figure. The InDel sequence is boxed.</p

Genome-wide association study for grain yield and related traits in elite wheat varieties and advanced lines using SNP markers

<div><p>Genetic improvement of grain yield is always an important objective in wheat breeding. Here, a genome-wide association study was conducted to parse the complex genetic composition of yield-related traits of 105 elite wheat varieties (lines) using the Wheat 90K Illumina iSelect SNP array. Nine yield-related traits, including maximum number of shoots per square meter (MSN), effective number of spikes per square meter (ESN), percentage of effective spike (PES), number of kernels per spike (KPS), thousand-kernel weight (TKW), the ratio of kernel length/kernel width (RLW), leaf-area index (LAI), plant height (PH), and grain yield (GY), were evaluated across four environments. Twenty four highly significant marker-trait associations (MTAs) (<i>P</i> < 0.001) were identified for nine yield-related traits on chromosomes 1A, 1D, 2A (2), 3B, 4A (2), 4B, 5A (4), 5B (4), 5D, 6B (2), 7A (2), and 7B (3), explaining 10.86–20.27% of the phenotypic variations. Of these, four major loci were identified in more than three environments, including one locus for RLW (6B), one locus for TKW (7A), and two loci for PH (7B). A cleaved amplified polymorphic sequence (CAPS) marker <i>Td99211</i> for TKW on chromosome 5A was developed and validated in both a natural population composed of 372 wheat varieties (lines) and a RIL population derived from the cross of Yangxiaomai × Zhongyou 9507. The CAPS marker developed can be directly used for marker-assisted selection in wheat breeding, and the major MTAs identified can provide useful information for fine-mapping of the target genes in future studies.</p></div

Details regarding the significant marker–trait associations (<i>P</i> < 0.001) for grain yield and related traits.

<p>Details regarding the significant marker–trait associations (<i>P</i> < 0.001) for grain yield and related traits.</p