Genome-wide association study (GWAS) analysis of camelina seedling germination under salt stress condition

Authors: Luo, Zinan; Szczepanek, Aaron; Abdel-Haleem, Hussein

Submitted to: Agronomy
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 9/19/2020
Publication Date: 9/22/2020
Publication URL: https://handle.nal.usda.gov/10113/7115947
Citation: Luo, Z., Szczepanek, A.E., Abdel-Haleem, H.A. 2020. Genome-wide association study (GWAS) analysis of camelina seedling germination under salt stress condition. Agronomy. 10(9). Article 1444. https://doi.org/10.3390/agronomy10091444.
DOI: https://doi.org/10.3390/agronomy10091444

Interpretive Summary: Camelina is an important renewable oilseed crop for biofuel and feedstock that can relieve the reliance on petroleum-derived oils and reduce greenhouse gases and waste solids resulted from petroleum-derived oils consumption. Carmelina molecular mechanisms affected by salinity stress has yet unknown. this study, we screened 211 camelina accessions that were germinated under 100mM NaCl concentration. Seedling germination traits, including germination rate at two stages (5- and 9-day seedling stages), germination index, dry and fresh weight, and dry/fresh ratio, were recorded. Significant correlations were found between germination rate at two stages as well as plant biomass traits. A total of 17 significant trait-associated molecular markers were identified to be related to germination rate at the two stages and dry weight. These markers are located on the putative candidate genes controlling plant root development and indirectly related to salt stress resistance . These identified markers could provide a foundation for future molecular breeding efforts aiming to improve salt tolerance in Carmelina.

Technical Abstract: Camelina sativa is an important renewable oilseed crop for biofuel and feedstock that can relieve the reliance on petroleum-derived oils and reduce greenhouse gases and waste solids resulting from petroleum-derived oils consumption. C. sativa has recently seen revived attention due to its high oil content, high omega-3 unsaturated fatty acids, short life cycle, broader regional adaptation, and low-input agronomic requirements. However, abiotic stress such as salinity stress has imposed threatens on plant photosynthesis and growth by reducing water availability or osmotic stress, ion (Na+ and Cl-) toxicity, nutritional disorders and oxidative stress yield. There still remains much to know for the molecular mechanisms underlying these effects. In this study, a preliminary study applying 10 C. sativa cultivars to be treated under a gradient NaCl concentrations ranging from 0-250mM and found that 100mM was the optimal NaCl concentration to effectively differentiate phenotypic performance among different genotypes. Then a spring panel consisting of 211 C. sativa accessions were germinated under 100mM NaCl concentration. Six seedling germination traits, including germination rate at two stages (5- and 9-day seedling stages), germination index, dry and fresh weight, and dry/fresh ratio, were measured. Significant correlations were found between germination rate at two stages as well as plant biomass traits. Combining the phenotypic data and previously obtained genotypic data, a total of 17 significant trait-associated SNPs for germination rate at the two stages and dry weight were identified from genome-wide association analysis (GWAS). These SNPs are located on putative candidate genes controlling plant root development by synergistically mediating phosphate metabolism, signal transduction and cell membrane activities. These identified SNPs could provide a foundation for future molecular breeding efforts aimed at improved salt tolerance in C. sativa.