QTL mapping to identify loci and candidate genes associated with freezing tolerance trait in camelina sativa.

Authors: SHAIKH, TM - Missouri State University; RAHMAN, MUKHLESUR - North Dakota State University; Anderson, James; Sthapit Kandel, Jinita; Vaughn, Justin; Smith, Timothy - Tim; ABERNATHY, BRIAN - University Of Georgia; ONTANO, ANDREW - University Of Georgia; Dobrin, Barbara; Horvath, David; Dorn, Kevin

Submitted to: Industrial Crops and Products
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 8/29/2024
Publication Date: 9/3/2024
Citation: Shaikh, T., Rahman, M., Anderson, J.V., Sthapit Kandel, J., Vaughn, J.N., Smith, T.P., Abernathy, B., Ontano, A., Dobrin, B.H., Horvath, D.P., Dorn, K.M. 2024. QTL mapping to identify loci and candidate genes associated with freezing tolerance trait in camelina sativa.. Industrial Crops and Products. 222:119562. https://doi.org/10.1016/j.indcrop.2024.119562.
DOI: https://doi.org/10.1016/j.indcrop.2024.119562

Interpretive Summary: Understanding the genes and mechanisms underlying freezing tolerance in crops is essential for improving crop performance in northern cropping systems. Camelina sativa is an emerging biofuel crop and potential cash cover-crop suitable for the northern great plains, but spring varieties that can flower without a winter chilling period are susceptible to freezing damage. A cross between a freezing tolerant winter variety and a freezing sensitive spring variety provided a genetic map of the genes associated with freezing tolerance. Five genes that likely play a role in enhanced freezing tolerance from the winter variety were identified. Interestingly, four of those five genes are also known to regulate flowering in response to winter chilling. This work will assist in understanding how flowering genes control freezing tolerance and provide breeders with information needed to improve freezing tolerance in both spring and winter varieties of camelina.

Technical Abstract: Lack of freezing tolerance is a major constraint for the production of agronomically important Brassica species, particularly in the Northern Great Plains (NGP) of the United States and Canada. However, within the Brassicaceae family, winter varieties of camelina have shown excellent freezing tolerance and overwinter potential in the NGPs. Differences in freezing tolerance between a winter variety (Joelle) and the spring variety (CO46) of camelina appear to be controlled by a small number of dominant or co-dominant genes. To unravel the genetic mechanisms for the differences in freezing tolerance, 254 Recombinant Inbred Lines (RILs) were developed using reciprocal crosses between these two camelina varieties. The RIL population was phenotyped at the F7 stage of regeneration for freezing tolerance under controlled conditions and genotyped by whole-genome skim sequencing. A one-way ANOVA test revealed a significant (P < 0.001) difference exists among the RILs for freezing tolerance. A significant and strong correlation (r = 0.60, P < 0.001) was also observed between freezing tolerance and flowering time, indicating that regulation of flowering time might also influence freezing tolerance in camelina. A de novo linkage map was constructed using 4507 SNP markers covering a total of 1208.5 cM map distance with an average of 0.3 cM distances between the markers, which formed 20 linkage groups representing the 20 chromosomes (Chr) of C. sativa. The QTL analyses using three different programs revealed significant loci on Chr 8, 11, 13, 16 and 18 with LOD threshold value of over 3.5 for freezing tolerance. The QTL peaks with the greatest LOD values of 20.7 and 26.8 were observed at Chr 8 and Chr 13 and accounted for 18.3% and 25.3% of the phenotypic variation respectively. A total of 3369 annotated camelina genes were identified within ±50 Kb from a consensus QTL intervals generated from the output of the three mapping programs. Among them, 125 were transcription factors including twelve MIKC_MADS on Chr 8, 11, 13, 16 and 18 and two that annotate as the floral regulators FLC on Chr 8 and 13, an orthologue of FLC (MAF4), or closely related to FLC (MAF3) of arabidopsis on Chr18, and an orthologue of SHORT VEGETATIVE PHASE (SVP) on Chr 16. Although many of the candidate genes identified near the freezing tolerance QTLs have previously been associated with cold responses in plants, further studies are needed to help unravel freezing tolerance mechanisms and improve freezing tolerance in other Brassica crop species.