A Self-compatible Pear Mutant Derived from γ-irradiated Pollen Carries an 11-Mb Duplication in Chromosome 17

Overview

Journal Front Plant Sci

Date 2024 Mar 20

PMID 38504898

Authors

Sogo Nishio

Kenta Shirasawa

Ryotaro Nishimura

Yukie Takeuchi

Atsushi Imai

Nobuko Mase

Norio Takada

Affiliations

Soon will be listed here.

Abstract

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 ( Nakai), '415-1', by using γ-irradiated pollen. '415-1' carries the -genotype , with "" indicating a duplication of 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 seedlings resulting from a cross between '515-20' () and '415-1'. Amplicon sequencing of and clearly detected -haplotype duplications in the seedlings. Intriguingly, 30 partially triploid seedlings including genotypes , , , , and 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 seedling provided evidence for recombination between the duplicated segment and the original 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.

Citing Articles

The importance of genotyping within the climate-smart plant breeding value chain - integrative tools for genetic enhancement programs.

Garcia-Oliveira A, Ortiz R, Sarsu F, Rasmussen S, Agre P, Asfaw A Front Plant Sci. 2025; 15:1518123.

PMID: 39980758 PMC: 11839310. DOI: 10.3389/fpls.2024.1518123.

References

Li H, Durbin R . Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics. 2009; 25(14):1754-60. PMC: 2705234. DOI: 10.1093/bioinformatics/btp324. View

Gabay G, Dahan Y, Izhaki Y, Faigenboim A, Ben-Ari G, Elkind Y . High-resolution genetic linkage map of European pear (Pyrus communis) and QTL fine-mapping of vegetative budbreak time. BMC Plant Biol. 2018; 18(1):175. PMC: 6117884. DOI: 10.1186/s12870-018-1386-2. View

Magoc T, Salzberg S . FLASH: fast length adjustment of short reads to improve genome assemblies. Bioinformatics. 2011; 27(21):2957-63. PMC: 3198573. DOI: 10.1093/bioinformatics/btr507. View

Shirasawa K, Tanaka M, Takahata Y, Ma D, Cao Q, Liu Q . A high-density SNP genetic map consisting of a complete set of homologous groups in autohexaploid sweetpotato (Ipomoea batatas). Sci Rep. 2017; 7:44207. PMC: 5345071. DOI: 10.1038/srep44207. View

Danecek P, Auton A, Abecasis G, Albers C, Banks E, DePristo M . The variant call format and VCFtools. Bioinformatics. 2011; 27(15):2156-8. PMC: 3137218. DOI: 10.1093/bioinformatics/btr330. View

Komura S, Jinno H, Sonoda T, Oono Y, Handa H, Takumi S . Genome sequencing-based coverage analyses facilitate high-resolution detection of deletions linked to phenotypes of gamma-irradiated wheat mutants. BMC Genomics. 2022; 23(1):111. PMC: 8827196. DOI: 10.1186/s12864-022-08344-8. View

Knaus B, Grunwald N . vcfr: a package to manipulate and visualize variant call format data in R. Mol Ecol Resour. 2016; 17(1):44-53. DOI: 10.1111/1755-0998.12549. View

Shirasawa K, Itai A, Isobe S . Chromosome-scale genome assembly of Japanese pear (Pyrus pyrifolia) variety 'Nijisseiki'. DNA Res. 2021; 28(2). PMC: 8092371. DOI: 10.1093/dnares/dsab001. View

Sumitomo K, Shirasawa K, Isobe S, Hirakawa H, Hisamatsu T, Nakano Y . Genome-wide association study overcomes the genome complexity in autohexaploid chrysanthemum and tags SNP markers onto the flower color genes. Sci Rep. 2019; 9(1):13947. PMC: 6763435. DOI: 10.1038/s41598-019-50028-z. View

10.

Yamakawa H, Haque E, Tanaka M, Takagi H, Asano K, Shimosaka E . Polyploid QTL-seq towards rapid development of tightly linked DNA markers for potato and sweetpotato breeding through whole-genome resequencing. Plant Biotechnol J. 2021; 19(10):2040-2051. PMC: 8486255. DOI: 10.1111/pbi.13633. View

11.

Pele A, Rousseau-Gueutin M, Chevre A . Speciation Success of Polyploid Plants Closely Relates to the Regulation of Meiotic Recombination. Front Plant Sci. 2018; 9:907. PMC: 6031745. DOI: 10.3389/fpls.2018.00907. View

12.

Sassa H . Molecular mechanism of the S-RNase-based gametophytic self-incompatibility in fruit trees of Rosaceae. Breed Sci. 2016; 66(1):116-21. PMC: 4780795. DOI: 10.1270/jsbbs.66.116. View

13.

Shirasawa K, Hirakawa H, Isobe S . Analytical workflow of double-digest restriction site-associated DNA sequencing based on empirical and in silico optimization in tomato. DNA Res. 2016; 23(2):145-53. PMC: 4833422. DOI: 10.1093/dnares/dsw004. View

14.

Linsmith G, Rombauts S, Montanari S, Deng C, Celton J, Guerif P . Pseudo-chromosome-length genome assembly of a double haploid "Bartlett" pear (Pyrus communis L.). Gigascience. 2019; 8(12). PMC: 6901071. DOI: 10.1093/gigascience/giz138. View

15.

Mase N, Sawamura Y, Yamamoto T, Takada N, Nishio S, Saito T . A segmental duplication encompassing -haplotype triggers pollen-part self-compatibility in Japanese pear (). Mol Breed. 2014; 33:117-128. PMC: 3890579. DOI: 10.1007/s11032-013-9938-5. View

16.

Bolger A, Lohse M, Usadel B . Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics. 2014; 30(15):2114-20. PMC: 4103590. DOI: 10.1093/bioinformatics/btu170. View

17.

Kakui H, Tsuzuki T, Koba T, Sassa H . Polymorphism of SFBB-gamma and its use for S genotyping in Japanese pear (Pyrus pyrifolia). Plant Cell Rep. 2007; 26(9):1619-25. DOI: 10.1007/s00299-007-0386-8. View

18.

Hase Y, Satoh K, Kitamura S . Comparative analysis of seed and seedling irradiation with gamma rays and carbon ions for mutation induction in Arabidopsis. Front Plant Sci. 2023; 14:1149083. PMC: 10117944. DOI: 10.3389/fpls.2023.1149083. View

19.

McClure B . S-RNase and SLF determine S-haplotype-specific pollen recognition and rejection. Plant Cell. 2004; 16(11):2840-7. PMC: 527184. DOI: 10.1105/tpc.104.161130. View

20.

Okada K, Tonaka N, Moriya Y, Norioka N, Sawamura Y, Matsumoto T . Deletion of a 236 kb region around S 4-RNase in a stylar-part mutant S 4sm-haplotype of Japanese pear. Plant Mol Biol. 2008; 66(4):389-400. DOI: 10.1007/s11103-007-9277-1. View