Homozygosity mapping identified loci and candidate genes responsible for freezing tolerance in Camelina sativa

Authors: SHAIKH, TM - North Dakota State University; RAHMAN, MUKHLESUR - North Dakota State University; Horvath, David; Smith, Timothy - Tim; Anderson, James; Chao, Wun

Submitted to: The Plant Genome
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 2/5/2023
Publication Date: 3/9/2023
Citation: Shaikh, T., Rahman, M., Horvath, D.P., Smith, T.P., Anderson, J.V., Chao, W.S. 2023. Homozygosity mapping identified loci and candidate genes responsible for freezing tolerance in Camelina sativa. The Plant Genome. 16(2). Article e20318. https://doi.org/10.1002/tpg2.20318.
DOI: https://doi.org/10.1002/tpg2.20318

Interpretive Summary: Having crops that can survive freezing conditions is critical for developing new cover-crops such as camelina that can survive the harsh winter conditions of the Northern Great Plains. We have refined a new technique to identify genes that are critical for freezing tolerance from a cross between a freezing tolerant cultivar and a freezing susceptible cultivar of camelina. Two genes were identified that were not only tightly associated with freezing tolerance, but were also turned on only in the freezing susceptible cultivar. This information will allow researchers to test if turning these genes off allows the plants to survive freezing. This could help breeders improve the freezing tolerance in varieties that have already been bred to have many good agronomic characteristics but which are currently too freezing sensitive to survive winters in the Northern Great Plains.

Technical Abstract: Homozygosity mapping has been used as an effective tool for detecting genomic regions fixed (homozygous) for a given trait in the F2 generation from a bi-parental cross between divergent parents when phenotype is controlled by a limited number of dominant or co-dominant loci. Freezing tolerance is a major attribute in agricultural crops and camelina exhibits moderately high freezing tolerance compared to other brassica crops. However, few major genes segregating for freezing tolerance in camelina breeding populations have been identified by association mapping schemes. Previous studies indicated that freezing tolerance differences between a tolerant (Joelle) and susceptible (CO46) variety of camelina were controlled by a small number of dominant or co-dominant genes. Hence, whole genome homozygosity mapping was performed to identify molecular markers and candidate genes responsible for freezing tolerance difference in these two camelina varieties. Using full genome Illumina sequencing, 28 F3 RILs were sequenced to ~30X coverage, and the parental lines were sequenced to >30X-40X coverage with PacBio HiFi technology and 60X coverage using Illumina whole genome sequencing. Overall, ~126k homozygous SNP markers were identified that differentiate both parents and 617 of these markers were also homozygous in F3 families fixed for freezing tolerance/susceptibility. These markers all mapped to 2 contigs that formed a contiguous stretch of chromosome 11 in the reference camelina genome. The homozygosity mapping detected 21 homozygous blocks among the selected markers and identified 65 candidate genes with strong similarity to regions in or near (within ±50kb) the homozygous blocks. Among them, 15 genes were previously shown to be differentially expressed during cold acclimation in camelina. The largest block contained sequence with strong homology to several cold-induced cysteine-rich RLK genes and a cold-induced receptor serine/threonine kinase gene and one or more of these genes may be primarily responsible for freezing tolerance differences in camelina varieties.