Identification of aPi9-Containing Rice Germplasm with a Newly Developed Robust Marker

Abstract

The Pi9 gene in rice, originating from Oryza minuta, is an effective resistance gene for controlling rice blast disease. However, currently available linked DNA markers do not accurately identify the function of Pi9, thus hindering its efficient incorporation into new cultivars through marker-assisted selection (MAS). In addition, no known Pi9-containing rice germplasm is available to breeders. In the present study, DNA sequence variation of Pi9 alleles and their family members was analyzed in 40 diverse rice germplasm accessions from the AA genome to develop a robust Pi9 marker. In total, 29 DNA primers of 20 to 23 nucleotides were designed and each possible combination of primer pairs was used to detect Pi9. Only one combination of DNA primers, KS28/KS6, was identified to specifically detect Pi9 in the monogenic line IRBL9-W. The presence of Pi9 was verified with the predicted Pi9-specific blast reaction. Subsequently, 201 genetically diverse mini-core rice accessions from 114 countries were screened with KS28/KS6. One germplasm, IR 9660-48-1-1-2, was identified to carry Pi9 and the function of Pi9 was verified with pathogenicity assays. This robust Pi9 marker and a rice germplasm, IR9660-48-1-1-2 (GSOR310687), carrying Pi9 can be used to improve blast resistance with a MAS approach.

Marker‐assisted selection for rice blast resistance genes Pi2 and Pi9 through high‐resolution melting of a gene‐targeted amplicon

“…Recently, Tian et al. () reported the development of an InDel marker and a CAPS marker for genotyping of Pi2 and Pi9 targeting the Pi2/Pi9 locus; Scheuermann and Jia () also developed a dominant marker to identify Pi9 ‐containing rice germplasm. In the study, we report on the development of a gene‐targeted and codominant marker for discriminating the Pi2 and Pi9 genes.…”

“…The Pi2 and Pi9 in rice were two well-known R genes showing very broad-spectrum resistance to most of M. oryzae isolates collected from 13 countries (Liu et al 2002). Recently, Tian et al (2016) reported the development of an InDel marker and a CAPS marker for genotyping of Pi2 and Pi9 targeting the Pi2/Pi9 locus; Scheuermann and Jia (2016) also developed a dominant marker to identify Pi9-containing rice germplasm. In the study, we report on the development of a gene-targeted and codominant marker for discriminating the Pi2 and Pi9 genes.…”

“…These four allelic R genes, Pi2 , Piz‐t and Pi50 were isolated from Oryza sativa , while the Pi9 was originated from Oryza minuta . Though they had been characterized for years, the R genes Pi2 and Pi9 have not yet been widely deployed in rice breeding programmes (Tian et al , Scheuermann and Jia ).…”

“…The improvement of blast resistance through markerassisted introgression of the Pi2 or Pi9 has been reported, while these studies were based on linked markers flanking the target gene (Singh et al 2012, Ni et al 2015. Recently, Tian et al (2016) reported the development of an InDel marker and a CAPS marker for genotyping of Pi2 and Pi9 that derived from the polymorphisms within the Pi2/Pi9 locus; Scheuermann and Jia (2016) also developed a dominant marker to identify Pi9containing rice germplasm. Here, we report on the development of a robust and specific marker for Pi2 and Pi9 based upon HRM analysis of SNPs within the target gene, as well as its use in developing improved rice lines with enhanced blast resistance.…”

A Toolbox for Managing Blast and Sheath Blight Diseases of Rice in the United States of America

“…The genetic markers linked or derived from the cloned R genes were developed to predict resistance function and to monitor the existence of each of the R genes [31][32][33][44][45][46][47][48][49][50][51][52]. Differential blast races were identified ( Table 2) and have been used to validate their predicted resistance efficacies.…”