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ARS Home » Plains Area » Lubbock, Texas » Cropping Systems Research Laboratory » Plant Stress and Germplasm Development Research » Research » Publications at this Location » Publication #330414

Title: Genome wide association analysis for seedling response traits to thermal stress in sorghum germplasm

item Chopra, Ratan
item Burow, Gloria
item Burke, John
item Xin, Zhanguo
item Gladman, Nicholas

Submitted to: BMC Plant Biology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 12/21/2016
Publication Date: 1/12/2017
Citation: Chopra, R., Burow, G.B., Burke, J.J., Xin, Z., Gladman, N. 2017. Genome wide association analysis for seedling response traits to thermal stress in sorghum germplasm. Biomed Central (BMC) Plant Biology. 17:12. doi:10.1186/s12870-016-0966-2.

Interpretive Summary: Climate variability due to fluctuation in temperature is a worldwide concern that imperils crop production. The need to understand how the genomes of major crops can be utilized to aid in discovering and developing germplasm that can withstand and adapt to temperature fluctuations is more than ever necessary. Here, we analyzed the genetic variation associated with responses extreme thermal stresses in a sorghum association panel (SAP) representing major races and working groups to identify polymorphisms (SNPs) that could be associated with resilience to temperature stress in a major cereal crop. A combined investigation involving physiological and biochemical analyses, aided by genomics based platforms, identified a number of key associations and their complex network of genes underlying the response to cold and heat stresses were examined. Many of the associated SNPs with seedling traits were within the gene or in close proximity of the gene, as compared to the previous GWAS for other gene to trait association studies in sorghum. The haplotype differences between the tolerant and susceptible genotypes for the trait linked markers could serve as a tool for molecular breeding and enhancement of tolerance to thermal stress in germplasm. The differential responses upon thermal stress of the genes tagged by the confirmed haplotypes could help in understanding the role of these genes through molecular characterization while the expression network analysis highlighted one of the possible pathways to use genome wide association data to explore mechanisms of cold tolerance in sorghum.

Technical Abstract: The sorghum association panel exhibited extensive variation for seedling traits under cold and heat stress. Genome-wide analyses identified thirty single nucleotide polymorphisms (SNPs) that were strongly associated with traits measured at seedling stage under cold stress and tagged genes that act as regulators of anthocyanin expression and soluble carbohydrate metabolism. Meanwhile, twelve SNPs were found significantly associated with seedling traits under heat stress and these SNPs tagged genes that function also in sugar metabolism, and ion transport pathways. Evaluation of co-expression networks for genes tagged by significant SNPs indicated complex gene interactions for cold and heat stresses in sorghum. We focused and validated the expression of four genes in the network of Sb06g025040, a bHLH transcription factor that regulates seedling leaf anthocyanin and observed that genes in this network were upregulated during cold stress treatment in a moderately tolerant lines or germplasm as compared to the sensitive lines. In summary, specific genetic regions associated with variation in thermal stress response at seedling stage in sorghum were identified. This study provided foundation for characterization of genes and their networks responsible for adaptation to thermal stress and use of haplotypes for development of temperature resilient sorghum cultivars. Knowledge on the stress networks from this research can be further extended to the other cereal crops for tackling the temperature fluctuations during plant developmental stages.