Development of markers for identification and maker-assisted breeding of Xa7 gene in rice (Oryza sativa L.)

Utilization of resistance (R) genes to breed resistant cultivars is one of the most effective and economical approach to control rice bacterial blight (BB). Xa7, a dominant, broad-spectrum and durable BB-resistant gene, is an ideal gene resource to improve the resistance of rice varieties to bacterial blight, and this well-known gene with important breeding value has been cloned in our recent study. The isolation of Xa7 will facilitate its application in rice breeding by molecular maker-assisted selection (MAS). In this study, based on the specific sequences in the promoter of Xa7, a functional marker, named as MX7, was developed, which can effectively distinguish the dominant BB-resistant Xa7, the recessive BB-susceptible xa7 and the null allele from different rice varieties. Since MX7 is a dominant marker, it can't tell homozygous from heterozygous, a co-dominant marker closely linked to Xa7, named as M6, was developed simultaneously. After verified by amplification in numerous rice varieties and sequence alignment in RICE 3 K database, it is proved that marker M6 is co-segregated with the Xa7 locus. In addition, the effectiveness and accuracy of the two markers were further validated by two F-2 populations. Finally, the designed makers were effectively applied in MAS breeding to improve the BB-resistance of a susceptible variety. This study not only provides reliable functional markers for the identification of Xa7 gene in different rice materials, but also will contribute to the application of Xa7 gene in marker-assisted selection to breed rice varieties with durable disease resistance.

Automated summary

This study developed functional marker MX7 and co-dominant marker M6 based on specific sequences in the promoter of Xa7, effectively distinguishing Xa7, xa7, and null allele in different rice varieties. The effectiveness and accuracy of the markers were validated, and they were successfully applied in MAS breeding to improve disease resistance in susceptible rice varieties. This provides reliable tools for the identification and application of Xa7 gene in breeding programs.