Internode length of NIL, ZS97 and RI92.

<p>Internode length of NIL, ZS97 and RI92.</p

GA3 and PBZ treatment of homozygote <i>sd1</i>/<i>sd1</i> and <i>SD1/SD1</i> plants.

<p>GA3 and PBZ treatment of homozygote <i>sd1</i>/<i>sd1</i> and <i>SD1/SD1</i> plants.</p

Plant height (cm) of RI92 and its NIL and parents at seedling and maturation stages.

<p>Plant height (cm) of RI92 and its NIL and parents at seedling and maturation stages.</p

Intragenic recombination between two non-functional <i>semi-dwarf 1</i> alleles produced a functional <i>SD1</i> allele in a tall recombinant inbred line in rice

<div><p>Intragenic recombination is one of the most important sources of genetic variability. In our previous study, RI92 a tall line (160 cm of plant height) was observed in the cross progeny between two semi-dwarf <i>indica</i> cultivars Zhenshan 97 and Minghui 63. Genome-wide genotyping and sequencing indicated that the genome constitution of RI92 was completely from both parents. Bulk segregant analysis in a BC₃F₂ population revealed that “green revolution gene” <i>semi-dwarf 1</i> (<i>sd1</i>) was most likely the gene controlling the tall plant height in RI92. Sequencing analysis of <i>SD1</i> revealed that an intragenic recombination occurred between two parental non-functional <i>sd1</i> alleles and generated a functional <i>SD1</i> in RI92. Four-fold high recombination rate in <i>SD1</i> located bins to the genome-wide average was observed in two RIL populations, indicating recombination hotspot in the <i>SD1</i> region. Intragenic recombination creates new alleles in the progeny distinct from parental alleles and diversifies natural variation.</p></div

The genetic effects of <i>sd1</i> on grain yield related traits in the BC₃F₂ population.

<p>The genetic effects of <i>sd1</i> on grain yield related traits in the BC₃F₂ population.</p

The construction of near isogenic line population used for mapping plant height.

<p>The construction of near isogenic line population used for mapping plant height.</p

Comparison of the allele sequences of <i>SD1</i> among ZS97, MH63 and RI92.

<p>(A) Bulk segregant analysis of 10 tall and dwarf plants in BC₃F₂ population. The red arrows indicate the target band for ZS97 and MH63 genotypes, respectively (B) Comparison of <i>SD1</i> sequences between ZS97 and MH63 alleles. (C) The intragenic recombination of <i>sd1</i>, (D) and the same 2-bp insertion in MH63 and RI92.</p

The genetic constitute of RI92.

<p>The genetic constitute of RI92.</p

Frequency distribution of seedling height (A) and plant height (B) in the random BC₃F₂ population.

<p>The red, blue and green bars mean the homozygotes of <i>SD1/SD1</i> and <i>sd1/sd1</i> types and heterozygote identified by the functional SNP (FNP) in the third exon of <i>SD1</i>.</p