Searching for the Genetic Basis of Cold Tolerance in Maize's Sister Genus Tripsacum.

Grass species in the two genera Tripsacum and Zea differ in their ability to withstand freezing temperatures. Even though both genera originated in the tropics, Tripsacum from northern climates can overwinter in a dormant state, while freezing temperatures kill maize leaves. The Tripsacum genus diverged from the Zea genus fewer than 1.2 million years ago, and the two genera share an ancestral allopolyploid event (Ross-Ibarra et al., 2009; Chia et al., 2012). Tripsacum and maize share most of their gene content, yet the basis for freezing tolerance in Tripsacum and freezing sensitivity in maize remains unknown. As a first step toward finding cold tolerance genes in Tripsacum, we developed genomic resources for the Tripsacum dactyloides cultivar “Pete”, which is adapted to the northern United States, and Tripsacum floridanum, which is adapted to subtropical and tropical climates. The genome of T. dactyloides “Pete” was sequenced at 40X coverage, and mRNA-seq was also performed on several tissues of T. dactyloides “Pete” and T. floridanum. We searched for sequence variation in known cold tolerance genes between these two species with predicted differences in freezing tolerance. Additionally, we performed a preliminary freezing tolerance screen using 161 Tripsacum offspring from crosses between Tripsacum accessions from the northern and southern United States. Leaf mRNA-seq revealed gene expression dynamics during chilling and freezing stress. A pedigree-based kinship matrix explained 14.5% of the total variation in RNA degradation scores three days after freezing stress, indicating that genetic variation within the population partly explains differing levels of freezing tolerance. Identifying genes that confer freezing tolerance in Tripsacum could enable the genetic engineering of a freezing-tolerant, high-yielding maize variety. Freezing-tolerant maize could be planted earlier in the spring or could be developed into an overwintering line tailored to the southern United States.