A Trial for the Identification of Brown Planthopper (Nilaparvata lugens Stal) Resistance Alleles in Two Rice Lines, Norin-PL3 and Norin-PL4, Using Next-generation Sequencing and Simple Graphical Genotyping Methods

Norin-PL3 and Norin-PL4 are rice (Oryza sativa L.) breeding lines that carry a brown planthopper ( BPH) resistance gene. Norin-PL3 was bred by introgressing BPH1 derived from the Indica Group variety Mudgo into Japonica Group rice, whereas Norin-PL4 was bred by introgressing BPH2 derived from the Indica Group variety IR 1154-243 into Japonica Group rice. To detect the alleles derived from resistance donor varieties in these lines, we developed a simple method to create graphical genotypes using a part of the InDel information obtained by a short-read next-generation sequencing system. In Norin-PL3, chromosomal regions derived from Mudgo were found on chromosome 12 and two other locations on the short arm of chromosome 1. In Norin-PL4, the chromosomal regions derived from IR 1145-243 were found on chromosomes 5 and 12, the short arm of chromosome 4, and chromosome 8. Among these regions derived from resistant donors, chromosomal regions contributing to resistance were identified. This method could also assist in creating graphical genotypes of the other rice lines with both Japonica Group and Indica Group varieties as parents. Moreover, the results of the graphical genotype and DNA marker information of Norin-PL3 and Norin-PL4 will be useful for rice breeding research on BPH resistance.

Automated summary

Norin-PL3 and Norin-PL4 are rice breeding lines carrying brown planthopper (BPH) resistance genes derived from different indica rice varieties. A method was developed to detect alleles from resistant donor varieties in these lines using InDel information from short-read next-generation sequencing data, identifying chromosomal regions contributing to resistance. This method can also be applied to create graphical genotypes of other rice lines with both japonica and indica variety parents, and the results will be beneficial for rice breeding research on BPH resistance.