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ARS Home » Southeast Area » Stuttgart, Arkansas » Dale Bumpers National Rice Research Center » Research » Publications at this Location » Publication #296773
Title: Application of resistance gene analog markers to analysis of genetic structure and diversity in rice

Author
item REN, JUANSHENG - Sichuan University
item YU, YUCHAO - Sichuan University
item GAO, FANGYUAN - Sichuan University
item ZENG, LIHUA - Sichuan University
item LU, XIANJUN - Sichuan University
item WU, XIANTING - Sichuan University
item Yan, Wengui
item REN, GUANGJUN - Sichuan University

Submitted to: Genome
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 5/30/2013
Publication Date: 7/1/2013
Publication URL: http://handle.nal.usda.gov/10113/57888
Citation: Ren, J., Yu, Y., Gao, F., Zeng, L., Lu, X., Wu, X., Yan, W., Ren, G. 2013. Application of resistance gene analog markers to analysis of genetic structure and diversity in rice. Genome. 56(7):377-387.

Interpretive Summary: Plant disease resistance (R) genes play an important role for the plant to defend itself from attack of fungi, bacteria and viruses pests. A certain degree of genetic variation among R genes is important for a plant to be able to adapt to changes in the environment. Plant disease resistance gene analogs (RGA) are genetic signatures commonly associated with disease resistance genes. We used 472 RGA markers distributed throughout the rice genome to evaluate 178 diverse cultivars from the USDA rice core collection. The results were agreeable with those previously reported using genome-wide microsatellite markers. These results suggest that RGA markers are useful for analyses of genetic structure and diversity in rice, in addition to their use in studying resistance genes.

Technical Abstract: Plant disease resistance gene analog (RGA) markers were designed according to the conserved sequence of known resistance gene analogs and were used to map resistance genes. We used genome-wide RGA markers for analysis of genetic structure and diversity in a global rice germplasm collection. In total, 472 RGA markers were applied to 178 entries selected from the USDA rice core collection. Results from the RGA markers were similar between two analysis methods, UPGMA and STRUCTURE. Additionally, the results from RGA markers in our study were agreeable with those previously reported using SSR markers, including cluster analysis of ancestral classification, genetic diversity estimates, genetic relatedness, and cluster according to geographic origins. These results suggest that RGA markers are applicable for analysis of genetic structure and diversity in rice. However, the RGA markers failed to differentiate temperate japonica, tropical japonica and aromatic subgroups in our study unlike SSR markers. The restricted method for developing RGA markers using the exon sequence might limit the polymorphism of RGA markers in the genome, and thus limit the discriminatory power in comparison with SSR markers.