Nan Jiang1,2,3, Jun Fu3, Qin Zeng2, Yi Liang1,2, Yanlong Shi2, Zhouwei Li2, Youlun Xiao4, Zhizhou He2, Yuntian Wu2, Yu Long2, Kai Wang3, Yuanzhu Yang3, Xionglun Liu5, Junhua Peng6,7. 1. Southern Regional Collaborative Innovation Center for Grain and Oil Crops and College of Agronomy, Hunan Agricultural University, Changsha, China. 2. Huazhi Bio-Tech Company Ltd., Changsha, China. 3. Key Laboratory of Southern Rice Innovation and Improvement, Ministry of Agriculture and Rural Affairs, Hunan Engineering Laboratory of Disease and Pest Resistant Rice Breeding, Yuan Longping High-Tech Agriculture Company Ltd., Changsha, China. 4. Institute of Plant Protection, Hunan Academy of Agricultural Sciences, Changsha, China. 5. Southern Regional Collaborative Innovation Center for Grain and Oil Crops and College of Agronomy, Hunan Agricultural University, Changsha, China. xionglun@hunau.edu.cn. 6. Southern Regional Collaborative Innovation Center for Grain and Oil Crops and College of Agronomy, Hunan Agricultural University, Changsha, China. junhuapeng@yahoo.com. 7. Huazhi Bio-Tech Company Ltd., Changsha, China. junhuapeng@yahoo.com.
Abstract
MAIN CONCLUSION: Using genome-wide SNP association mapping, a total of 77 and 7 loci were identified for rice bacterial blight and bacterial leaf streak resistance, respectively, which may facilitate rice resistance improvement. Bacterial blight (BB) and bacterial leaf streak (BLS) caused by Gram-negative bacteria Xanthomonas oryzae pv. oryzae (Xoo) and X. oryzae pv. oryzicola (Xoc), respectively, are two economically important diseases negatively affecting rice production. To mine new sources of resistance, a set of rice germplasm collection consisting of 895 re-sequenced accessions from the 3000 Rice Genomes Project (3 K RGP) were screened for BB and BLS resistance under field conditions. Higher levels of BB resistance were observed in aus/boro subgroup, whereas the japonica, temperate japonica and tropical japonica subgroups possessed comparatively high levels of resistance to BLS. A genome-wide association study (GWAS) mined 77 genomic loci significantly associated with BB and 7 with BLS resistance. The phenotypic variance (R2) explained by these loci ranged from 0.4 to 30.2%. Among the loci, 7 for BB resistance were co-localized with known BB resistance genes and one for BLS resistance overlapped with a previously reported BLS resistance QTL. A search for the candidates in other novel loci revealed several defense-related genes that may be involved in resistance to BB and BLS. High levels of phenotypic resistance to BB or BLS could be attributed to the accumulation of the resistance (R) alleles at the associated loci, indicating their potential value in rice resistance breeding via gene pyramiding. The GWAS analysis validated the known genes underlying BB and BLS resistance and identified novel loci that could enrich the current resistance gene pool. The resources with strong resistance and significant SNPs identified in this study are potentially useful in breeding for BB and BLS resistance.
MAIN CONCLUSION: Using genome-wide SNP association mapping, a total of 77 and 7 loci were identified for rice bacterial blight and bacterial leaf streak resistance, respectively, which may facilitate rice resistance improvement. Bacterial blight (BB) and bacterial leaf streak (BLS) caused by Gram-negative bacteria Xanthomonas oryzae pv. oryzae (Xoo) and X. oryzae pv. oryzicola (Xoc), respectively, are two economically important diseases negatively affecting rice production. To mine new sources of resistance, a set of rice germplasm collection consisting of 895 re-sequenced accessions from the 3000 Rice Genomes Project (3 K RGP) were screened for BB and BLS resistance under field conditions. Higher levels of BB resistance were observed in aus/boro subgroup, whereas the japonica, temperate japonica and tropical japonica subgroups possessed comparatively high levels of resistance to BLS. A genome-wide association study (GWAS) mined 77 genomic loci significantly associated with BB and 7 with BLS resistance. The phenotypic variance (R2) explained by these loci ranged from 0.4 to 30.2%. Among the loci, 7 for BB resistance were co-localized with known BB resistance genes and one for BLS resistance overlapped with a previously reported BLS resistance QTL. A search for the candidates in other novel loci revealed several defense-related genes that may be involved in resistance to BB and BLS. High levels of phenotypic resistance to BB or BLS could be attributed to the accumulation of the resistance (R) alleles at the associated loci, indicating their potential value in rice resistance breeding via gene pyramiding. The GWAS analysis validated the known genes underlying BB and BLS resistance and identified novel loci that could enrich the current resistance gene pool. The resources with strong resistance and significant SNPs identified in this study are potentially useful in breeding for BB and BLS resistance.
Authors: Di Wu; Dan Wu; Hui Feng; Lingfeng Duan; Guoxing Dai; Xiao Liu; Kang Wang; Peng Yang; Guoxing Chen; Alan P Gay; John H Doonan; Zhiyou Niu; Lizhong Xiong; Wanneng Yang Journal: Plant Commun Date: 2021-01-29