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ARS Home » Southeast Area » Mississippi State, Mississippi » Crop Science Research Laboratory » Corn Host Plant Resistance Research » Research » Publications at this Location » Publication #321462

Title: Genome-wide association studies of drought related metabolic changes to improve drought tolerance in maize

item ZHANG, XUEHAI - Huazhong Agricultural University
item Warburton, Marilyn
item SETTER, TIM - Cornell University
item XUE, YADONG - Henan Agricultural University
item YANG, NING - Huazhong Agricultural University
item LIU, HAIJUN - Huazhong Agricultural University
item YAN, JIANBING - Huazhong Agricultural University
item XIAO, YINGJIE - Huazhong Agricultural University

Submitted to: Theoretical and Applied Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 4/15/2016
Publication Date: 4/27/2016
Citation: Zhang, X., Warburton, M.L., Setter, T., Xue, Y., Yang, N., Liu, H., Yan, J., Xiao, Y. 2016. Genome-wide association studies of drought related metabolic changes in maize using an enlarged SNP panel. Theoretical and Applied Genetics. 129:1449-1463.

Interpretive Summary: Drought severely limits the yield potential of all crop plants, and is one of the most economically devastating factors faced by corn farmers around the world. The corn plant responds to drought stress by initiating a range of metabolic changes at the cellular level, in an attempt to regulate the damage done to lack of sufficient water. This study used 156,599 Single Nucleotide Polymorphism (SNP) markers to track changes in the DNA sequences of 318 corn inbred lines and correlate these changes with changes in metabolites produced by these corn lines when they were grown under either well watered or water stressed environments. 183 significantly correlated SNPs were identified, which fell within 75 different corn genes. To validate these genes, the most drought tolerant and drought susceptible lines were placed into two pools, creating two groups with very different average yield under drought. Using these two pools, 12 genes were validated from the original list of 75, and three of these encode MYB transcription factors, which are genes known to turn on other genes in sequence, initiating entirely new pathways and provide clues to understanding the basis for drought responses via cellular metabolism. This may lead to faster plant breeding for the genetic improvement of corn varieties with high drought tolerance.

Technical Abstract: Water deficit or drought is the most serious abiotic stress of plant development and greatly reduces crop production, and the plant’s response to this deficit leads to many metabolic changes. To dissect the genetic basis of drought tolerance in maize, we performed a genome-wide association analysis of drought-related traits using 156,599 SNPs in 318 maize inbred lines. In total, 183 significant SNP/trait associations (P = 6.39E-6) involving 75 loci were identified for related metabolic traits in multiple tissues and different environments under two irrigation treatments. The majority of significant loci were specifically detected in well watered or water stress treatment, reflecting the different genetic determinants of metabolic response to the drought stress. To evaluate the potential of use of significant loci in applied hybrid maize breeding, we assembled two groups of hybrid entries with extremely high or low drought tolerance and measured the metabolic traits. Among 12 loci identified by GWAS, six exhibited significantly different allele frequencies between the two groups, and the favorable alleles of these six loci were significantly enriched in hybrids with high drought-tolerance. Notably, three candidate genes were identified in the association panel. GRMZM2G052544 and GRMZM2G170049 encode MYB transcription factors that are involved in secondary metabolism, hormone signal transduction and drought stresses, and GRMZM2G062009 (which was also identified in the hybrid maize test) encodes a NAC domain-containing protein that confers abiotic stress response through the ABA pathway. These results provide clues to understanding the genetic basis for metabolic changes related to drought tolerance, potentially facilitating the genetic improvement of varieties with high drought tolerance in maize breeding programs.