Allele-specific marker-based assessment revealed that the rice blast resistance genes Pi2 and Pi9 have not been widely deployed in Chinese indica rice cultivars

Abstract

BackgroundThe most sustainable approach to control rice blast disease is to develop durably resistant cultivars. In molecular breeding for rice blast resistance, markers developed based on polymorphisms between functional and non-functional alleles of resistance genes, can provide precise and accurate selection of resistant genotypes without the need for difficult, laborious and time-consuming phenotyping. The Pi2 and Pi9 genes confer broad-spectrum resistance against diverse blast isolates. Development of allele-specific markers for Pi2 and Pi9 would facilitate breeding of blast resistant rice by using the two blast resistance genes.ResultIn this work, we developed two new markers, named Pi9-Pro and Pi2-LRR respectively, targeting the unique polymorphisms of the resistant and susceptible alleles of Pi2 and of Pi9. The InDel marker Pi9-Pro differentiates three different genotypes corresponding to the Pi2/Piz-t, Pi9 and non-Pi2/Piz-t/Pi9 alleles, and the CAPS marker Pi2-LRR differentiates the Pi2 allele from the non-Pi2 allele. Based on the two newly developed markers and two available markers Pi2SNP and Pi9SNP, the presence of Pi2 and Pi9 was assessed in a set of 434 rice accessions consisting of 377 Chinese indica cultivars/breeding materials and 57 Chinese japonica cultivars/breeding materials. Of the 434 accessions tested, while one indica restorer line Huazhan was identified harboring the Pi2 resistance allele, no other rice line was identified harboring the Pi2 or Pi9 resistance alleles.ConclusionsAllele-specific marker-based assessment revealed that Pi2 and Pi9 have not been widely incorporated into diverse Chinese indica rice cultivars. Thus, the two blast resistance genes can be new gene sources for developing blast resistant rice, especially indica rice, in China. The two newly developed markers should be highly useful for using Pi2 and Pi9 in marker-assisted selection (MAS) breeding programs.Electronic supplementary materialThe online version of this article (doi:10.1186/s12284-016-0091-8) contains supplementary material, which is available to authorized users.

Exploring Key Blast and Bacterial Blight Resistance Genes in Genetically Diverse Rice Accessions through Molecular and Phenotypic Evaluation

“…The employed marker details such as primer sequences and distance to target gene are provided in Table 1 Blast is the most dangerous fungal disease. Tian et al (2016) assessed a set of 434 Chinese rice cultivars and breeding materials for the Pi9 gene and found that none of the screened rice materials had Pi9, which is in close agreement with the present study. More than 100 blast resistance genes have been reported and, among them, Pi9, Piz-t, and Pib are a few of the important genes that provide resistance to a wide range of M. grisea isolates (Wang et al, 1999;Qu et al, 2006;Zhou et al, 2006).…”

Improving of Rice Blast Resistances in Japonica by Pyramiding Major R Genes

“…Pyramiding rice blast resistance genes has been becoming an effective strategy to develop a new variety with long lasting resistance. Currently, several broad-spectrum resistance genes such as Pi9 , Pi2 , Pizt , and Pi54 , have already been cloned, but their distribution frequencies in elite parents of Chinese indica and japonica rice were low (Huang et al, 2015; Wu et al, 2015; Tian et al, 2016). Moreover, research in levels of resistances to leaf and panicle blasts of rice plants pyramiding either Pi9 or Pizt , and Pi54 hasn’t yet been reported.…”

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.…”

“…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 ).…”