AUTHOR=Nishio Sogo , Shirasawa Kenta , Nishimura Ryotaro , Takeuchi Yukie , Imai Atsushi , Mase Nobuko , Takada Norio 

TITLE=A self-compatible pear mutant derived from γ-irradiated pollen carries an 11-Mb duplication in chromosome 17

JOURNAL=Frontiers in Plant Science

VOLUME=15

YEAR=2024

URL=https://www.frontiersin.org/journals/plant-science/articles/10.3389/fpls.2024.1360185

DOI=10.3389/fpls.2024.1360185

ISSN=1664-462X

ABSTRACT=<p>Self-compatibility is a highly desirable trait for pear breeding programs. Our breeding program previously developed a novel self-compatible pollen-part Japanese pear mutant (<italic>Pyrus pyrifolia</italic> Nakai), ‘415-1’, by using γ-irradiated pollen. ‘415-1’ carries the <italic>S</italic>-genotype <italic>S<sub>4</sub>dS<sub>5</sub>S<sub>5</sub></italic>, with “<italic>d</italic>” indicating a duplication of <italic>S</italic><sub>5</sub> responsible for breakdown of self-incompatibility. Until now, the size and inheritance of the duplicated segment was undetermined, and a reliable detection method was lacking. Here, we examined genome duplications and their inheritance in 140 F<sub>1</sub> seedlings resulting from a cross between ‘515-20’ (<italic>S<sub>1</sub>S<sub>3</sub></italic>) and ‘415-1’. Amplicon sequencing of <italic>S-RNase</italic> and <italic>SFBB18</italic> clearly detected <italic>S</italic>-haplotype duplications in the seedlings. Intriguingly, 30 partially triploid seedlings including genotypes <italic>S<sub>1</sub>S<sub>4</sub>dS<sub>5</sub></italic>, <italic>S<sub>3</sub>S<sub>4</sub>dS<sub>5</sub></italic>, <italic>S<sub>1</sub>S<sub>5</sub>dS<sub>5</sub></italic>, <italic>S<sub>3</sub>S<sub>5</sub>dS<sub>5</sub></italic>, and <italic>S<sub>3</sub>S<sub>4</sub>dS<sub>4</sub></italic> were detected among the 140 seedlings. Depth-of-coverage analysis using ddRAD-seq showed that the duplications in those individuals were limited to chromosome 17. Further analysis through resequencing confirmed an 11-Mb chromosome duplication spanning the middle to the end of chromosome 17. The duplicated segment remained consistent in size across generations. The presence of an <italic>S<sub>3</sub>S<sub>4</sub>dS<sub>4</sub></italic> seedling provided evidence for recombination between the duplicated <italic>S<sub>5</sub></italic> segment and the original <italic>S<sub>4</sub></italic>haplotype, suggesting that the duplicated segment can pair with other parts of chromosome 17. This research provides valuable insights for improving pear breeding programs using partially triploid individuals.</p>