Silent-site nucleotide diversity (usage-based) of 12 genes around the <i>Ma</i>_<i>3</i> gene.

<p>a: Locus name from <i>Sorghum bicolor</i>1.4,</p><p>b: Locus name from <i>Sorghum bicolor</i>2.1</p><p>Silent-site nucleotide diversity (usage-based) of 12 genes around the <i>Ma</i>_<i>3</i> gene.</p

Association tests for <i>Ma</i>_<i>3</i>.

<p><b>Red dot – supposed synthetic association site; blue dashed line – 5% significance threshold.</b> Arrow bar—promoter region; thick line—the gene region from the start codon ATG to the stop codon TGA; thin line—the 3’ flanking region from the stop codon TGA to the black box.</p

Molecular Evolution of the Sorghum Maturity Gene <i>Ma₃</i>

<div><p>Time to maturity is a critical trait in sorghum (<i>Sorghum bicolor</i>) breeding, as it determines whether a variety can be grown in a particular cropping system or ecosystem. Understanding the nucleotide variation and the mechanisms of molecular evolution of the maturity genes would be helpful for breeding programs. In this study, we analyzed the nucleotide diversity of <i>Ma₃</i>, an important maturity gene in sorghum, using 252 cultivated and wild sorghum materials from all over the world. The nucleotide variation and diversity were analyzed based both on race- and usage-based groups. We also sequenced 12 genes around the <i>Ma₃</i> gene in 185 of these materials to search for a selective sweep and found that purifying selection was the strongest force on <i>Ma₃</i>, as low nucleotide diversity and low-frequency amino acid variants were observed. However, a very special mutation, described as <i>ma₃^R</i>, seemed to be under positive selection, as indicated by dramatically reduced nucleotide variation not only at the loci but also in the surrounding regions among individuals carrying the mutations. In addition, in an association study using the <i>Ma₃</i> nucleotide variations, we detected 3 significant SNPs for the heading date at a high-latitude environment (Beijing) and 17 at a low-latitude environment (Hainan). The results of this study increases our understanding of the evolutionary mechanisms of the maturity genes in sorghum and will be useful in sorghum breeding.</p></div

Sliding-window analysis of silent-site nucleotide diversity (π value) for the entire <i>Ma</i>_<i>3</i> region.

<p>Window length: 200; Step size: 100. Introns are indicated as thin lines, and exons are indicated as filled boxes. C: cultivated sorghum; W: wild sorghum.</p

Silent-site nucleotide diversity (race-based) of 12 genes around the <i>Ma</i>_<i>3</i> gene.

<p>a: Locus name from <i>Sorghum bicolor</i>1.4,</p><p>b: Locus name from <i>Sorghum bicolor</i>2.1</p><p>Silent-site nucleotide diversity (race-based) of 12 genes around the <i>Ma</i>_<i>3</i> gene.</p

Nucleotide variations across the <i>Ma</i>_<i>3</i> genomic region of <i>Sorghum bicolor</i>.

<p>Numbers along the vertical axis indicate the ratios of the silent-site π values of cultivated sorghum and wild sorghum. Labels along the horizontal axis indicate the genomic locations of the 12 flanking genes and the <i>Ma</i>_{<b><i>3</i></b>} gene.</p

The phenotype of the mutant.

<p>A: the phenotype of the mutant and wild type, M is mutant <i>lf1132</i>; WT is Zhonghua 11. B: the panicle length and internode length for mutants and wild type. 15 total plants were investigated from five repeats containing three individuals. C: The heading-date of the wild type and mutant on different sowing-dates. Wild type and mutant were planted in the CNRRI experimental field, Zhejiang province on six sowing-dates from 15, May to 21, July 2007. D: The change in photoperiod during different sowing-dates. E: The change in temperature (mean value of everyday temperature) during different sowing-dates. Red box indicates the temperature of the heading period at the last sowing-date, 21, July.</p

The effect of different photoperiods and temperatures on heading-date.

<p>Notes: Zhonghua 11 and <i>lf1132</i> were grown in phytotrons with four different treatments. Heading-date was investigated at least 10 plants for each treatment.</p

<i>Hd1</i> expression under different photoperiods and temperatures.

<p>Leaves were harvested from 33 day old plants at the indicated times (once every 4 h for 24 h) in phytotrons, and real-time PCR was carried out for analysis of <i>Hd1</i>. M is <i>lf1132</i>; WT is Zhonghua 11.</p

The heading-date of the mutant and wild type for different photoperiod and temperature treatments.

<p><i>lf1132</i> and wild type plants were planted in the CNRRI experimental fields, and two week old seedlings were transferred to phytotrons with different photoperiod and temperature treatments. The heading-date for each treatment was observed and recorded for at least 10 plants. Four phytotrons were used: LD, 27°C phytotron; LD, 23°C phytotron; SD, 27°C phytotron; SD, 23°C phytotron; A: the heading-date under different photoperiods and temperatures; B: The velocity ratio of leaf growth (VRL) for the mutant and wild type under different photoperiods (SD and LD) and temperatures (27°C, 23°C). LD treatment: 14.5 h light and 9.5 h dark; SD treatment: 11.5 h light and 12.5 h dark.</p