Genetic Characterization of Universal Differential Variety Sets Developed Under the IRRI-Japan Collaborative Research Project

Abstract

The IRRI-Japan Collaborative Research Project has developed four universal differential variety sets, monogenic lines (MLs) with a Japonica-type variety Lijianxintuanheigu (LTH) genetic background, and near-isogenic lines (NILs) with three different genetic backgrounds, LTH, an Indica type variety CO39, and a universal susceptible line, US-2. These lines targeted 24 resistance genes:Pia, Pib, Pii, Pik, Pik-h, Pik-m, Pik-p, Pik-s, Pish, Pita(Pi4), Pita-2, Pit, Piz, Piz-5(Pi-2), Piz-t, Pi1, Pi3, Pi5(t), Pi7(t), Pi9, Pi11(t), Pi12(t), Pi19 and Pi20(t). The MLs have been distributed to more than 15 countries. To characterize these genetic components and confirm the introgression of chromosome segments harboring resistance genes, the graphical genotypes were determined using 162 simple sequence repeat (SSR) markers distributed throughout the rice genome. The genotypes of the three sets of NILs were more uniform than those of MLs. Several introgression segments, which corresponded to the locations of blast resistance genes, were also confirmed. The genome restoration rates of 31 MLs to LTH ranged from 50 to 90.0%, averaging 77.3%. All LTH, CO39, and US-2 NILs were developed by backcrossing six times with each recurrent parent. The genome restoration rates of the parent in 34 LTH NILs ranged from 75.6 to 96.9% with an average of 90.6%, lower than the theoretical value of 99%. The 31 CO39 NILs showed greater than 90% genome restoration rate compared to the recurrent parent with an average of 97.3%. The genomic restoration rate of the 16 US-2 NILs closely resembled those of the recurrent parent, with frequencies ranging from 88.9 to 98.8% with an average of 94.6%. Genetic characterization of four universal differential variety sets was carried out using DNA markers. This information will be linked with resistance genes that are potentially very useful for marker-assisted selection (MAS) in rice breeding programs, since the differential varieties can be applied as genetic sources.