Abstract
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 indica 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” semi-dwarf 1 (sd1) was most likely the gene controlling the tall plant height in RI92. Sequencing analysis of SD1 revealed that an intragenic recombination occurred between two parental non-functional sd1 alleles and generated a functional SD1 in RI92. Four-fold high recombination rate in SD1 located bins to the genome-wide average was observed in two RIL populations, indicating recombination hotspot in the SD1 region. Intragenic recombination creates new alleles in the progeny distinct from parental alleles and diversifies natural variation.
Highlights
Recombination and mutation are the motivation of evolution
Because of its extraordinary plant height in the recombinant inbred line (RIL) population, it is possible that RI92 contaminated by alien pollen from uncertain genotypes
We proved that the genetic constitution is the mixture of both parents Zhenshan 97 (ZS97) and Minhui 63 (MH63), and no alien genotypes using 221 restriction fragment length polymorphism (RFLP) and SSR markers [27], we compared its genome constitution with both parents by lowgenome coverage re-sequencing [28]
Summary
Recombination is critical for repairing DNA lesions and for chromosomal pairing and exchange during meiosis [1]. The well-studied yeast meiotic recombination revealed that non-uniformity of recombination is observed when the frame of reference is an entire chromosome, a multi-gene region, a pair of genes, or a small region upstream of a gene [2]. The ratio of genetic distance, measured by meiotic recombination frequencies, to physical distance, measured by molecular markers, is used for evaluating recombination rate and varies within different species and genome regions. The genome regions with higher recombination rate than the genome average is called recombination hotspots, which enhance the resolution of gene mapping and help introduce the excellent alleles into breeding lines by broken linkage. Intragenic recombination, the recombination among different varying sites within the same gene locus, can create novel alleles with more
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