Genome-wide association study identifies acyl-lipid metabolism candidate genes involved in the genetic control of natural variation for seed fatty acid traits in Brassica napus L.

Authors: GAZAVE, ELIODE - Cornell University; Tassone, Erica; BASWGGIO, MATHEUS - Cornell University; CYDER, MICHELLE - US Department Of Agriculture (USDA); BYREL, KELLI - US Department Of Agriculture (USDA); Oblath, Emily; Lueschow-Guijosa, Shiloh; Poss, David; Hardy, Cody; WINGERSON, MEGAN - University Of Idaho; JAMES, DAVID - University Of Idaho; Abdel-Haleem, Hussein; Grant, David; Hatfield, Jerry; Isbell, Terry; Vigil, Merle; Dyer, John; JENKS, MATTHEW - University Of Arizona; BROWN, JACK - University Of Idaho; GORE, MICHAEL - Cornell University; PAULI, DUKE - University Of Arizona

Submitted to: Industrial Crops and Products
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 12/29/2019
Publication Date: 1/6/2020
Publication URL: https://handle.nal.usda.gov/10113/6800326
Citation: Gazave, E., Tassone, E.E., Baswggio, M., Cyder, M., Byrel, K., Oblath, E.A., Lueschow, S.R., Poss, D.J., Hardy, C.D., Wingerson, M., James, D.B., Abdel-Haleem, H.A., Grant, D.M., Hatfield, J.L., Isbell, T., Vigil, M.F., Dyer, J.M., Jenks, M.A., Brown, J., Gore, M.A., Pauli, D. 2020. Genome-wide association study identifies acyl-lipid metabolism candidate genes involved in the genetic control of natural variation for seed fatty acid traits in Brassica napus L. Industrial Crops and Products. 145. https://doi.org/10.1016/j.indcrop.2019.112080.
DOI: https://doi.org/10.1016/j.indcrop.2019.112080

Interpretive Summary: Finding environmentally responsible solutions for the production of hydrotreated renewable fuels, also known as “renewable diesel fuel,” is an alternative path for securing sustainable, carbon-based energy production. However, to meet market and user demands, current bioenergy feed stocks, such as vegetable oil produced from B. napus, must be optimized with respect to end-product composition and quality before these biofuels can be utilized for large-scale energy production. While seed oil content and composition can be readily altered using transgenic approaches, high regulatory costs and low public acceptance have increased the need to develop non-transgenic methods for oil modification that leverage existing genetic resources. In light of this, a spring-type panel of B. napus accessions was evaluated in four different environments across multiple years to identify candidate genes, via Genome Wide Association Studies (GWAS), within the acyl lipid biosynthetic pathway responsible for fatty acid (FA) synthesis. These candidate genes, which control the various enzymatic steps in FA synthesis, could serve as precise targets for genomics-assisted breeding to directly alter seed oil composition and quality to meet market criteria. To further expand on the utility of genomics with respect to breeding, we investigated the efficacy of whole-genome prediction to assess how practical this method would be for implementing genomic selection in breeding programs focused on seed oil traits. The outcomes from these two lines of inquiry provide information on how genomics can be leveraged to enhance the speed and effectiveness of B. napus cultivar development for biofuel production.

Technical Abstract: Brassica napus L. represents a potential plant feedstock for the sustainable production of hydrotreated renewable fuels needed to support carbon-based energy production. However, to increase the use of plant-derived oils for energy needs, breeding efforts are required to optimize the amount and profile of fatty acids (FAs) contained in the oil extracted from B. napus seed to meet demands of the various market categories. To this end, we analyzed the genetic basis of FA content and composition of seed from a diverse panel of spring-type B. napus accessions evaluated at four US locations across multiple years. The extent of phenotypic variations for total oil content, nine FA compounds, and 14 derivative traits were found, in general, to be highly heritable. A genome-wide association study (GWAS) was conducted that detected 53 SNPs significantly associated with one or more of the 24 FA seed traits, resulting in the implicated genetic role of 12 candidate genes, four of which had two homologs each, from the acyl-lipid pathway. To our knowledge, the two detected homologs of 3-Ketoacyl-CoA thiolase (KAT), have never been associated with seed oil traits in B. napus. Through the application of whole-genome prediction, the 24 FA seed traits were generally found to have moderately high predictive abilities (70% of traits with abilities > 0.70), suggesting that these traits are highly amenable to genomic selection. Overall, our results contribute to the expanding body of knowledge regarding key enzymes in the acyl-lipid pathway at the quantitative genetic level and illustrate how genomics-assisted breeding could be leveraged to genetically improve FA seed traits in B. napus.