Plant & Animal Genomes XIV Conference

January 14-18, 2006
Town & Country Convention Center
San Diego, CA

Integration Of Expression And QTL Analyses Reveals New Candidate Genes Contributing To Quantitative Resistance Against Rice Blast

Bin Liu^1,3 , Kouji Satoh² , Ramil Mauleon¹ , Shaohong Zhang³ , Xiaoyuan Zhu³ , Jianyuan Yang³ , Qiyun Yang³ , Shangzhong Wu³ , Scot Hulbert⁴ , Jan Leach⁵ , Shoshi Kikuchi² , Hei Leung¹

¹  International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines

²  National Institute of Agrobiological Sciences, 2-1-2 Kan-nondai Tsukuba Ibaraki 305-8602, Japan

³  Guangdong Academy of Agricultural Sciences, Wushan, Guangzhou 510640, P.R. China

⁴  Kansas State University, Manhattan 66506-5502, U.S.A

⁵  Colorado State University, Fort Collins, Colorado 80523-1177, USA

To identify genes contributing to blast resistance in Sanhuangzhan 2 (SHZ-2, an indica variety from South China), we correlated gene expression polymorphism in the resistant SHZ-2 and susceptible Lijiangxintuanheigu (LTH) parents with genomic variations in recombinant inbred (RI) and backcross (BC) lines. Gene expression analysis of SHZ-2 and LTH using the 22K Rice Oligo Microarray (Agilent Technologies) revealed 422 and 372 genes showing differential expression (with 222 genes in common) at 48h and 96h after blast challenge, respectively. Contrasts between LTH and SHZ-2 showed 24 genes with significant differential expression (P<0.01). Polymorphic SSR markers flanking these genes were tested for association with quantitative resistance in RI and BC lines. Eleven of the 24 (46%) genes showed different levels of association with quantitative blast resistance. Five genes were mapped in the intervals of previously identified QTLs. The other six genes were mapped on different chromosomes, suggesting new QTL positions not detected by conventional mapping. Interestingly, three genes (encoding cytochrome 450, far-red impaired response protein, and an unknown protein) contributing major effects (R2 values of 20-27%, P< 0.0001) were clustered around a region on chromosome 8 that is rich in disease resistance QTL. Whole-genome genotyping of two highly resistant BC3 lines, BC10 and BC116, showed 13 and 11 introgressed segments from SHZ-2, respectively, with seven chromosomal segments in common. Significant association between the locations of the differentially expressed genes and introgressed regions was observed in BC116. Thus, expression data can be used in conjunction with advanced breeding lines to identify new candidate genes contributing to the target phenotypes.