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ARS Home » Pacific West Area » Davis, California » Crops Pathology and Genetics Research » Research » Publications at this Location » Publication #286295
Title: High resolution genotyping by restriction enzyme-phased sequencing of advanced backcross lines of rice exhibiting differential cold stress recovery

Author
item KIM, SANG-IC - University Of California
item Tai, Thomas

Submitted to: Euphytica
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 2/15/2013
Publication Date: 3/6/2013
Citation: Kim, S., Tai, T. 2013. High resolution genotyping by restriction enzyme-phased sequencing of advanced backcross lines of rice exhibiting differential cold stress recovery. Euphytica. 192(1):107-115.

Interpretive Summary: Two very closely related rice lines that were developed from the same parents show different abilities to withstand low temperatures. One line called MIb 6885-2 is able to resume growing after cold treatment much more rapidly and with overall greater growth than its sibling line MIb 4853-9. Using a very high resolution DNA fingerprinting technique, the differences at the DNA level between these two lines were identified. One or more of these DNA differences are behind the different growth responses of these two lines after cold stress.

Technical Abstract: Advanced backcross rice lines MIb 4853-9 and 6885-2 harbor major seedling cold tolerance QTL qCTS4 and qCTS12 from the temperate japonica M202 in the genetic background of the indica IR50. Previous studies have shown that these lines exhibit the same tolerance, based on visual ratings, under constant and intermittent exposure to cold stress. However, some differences between the MIb lines with regard to physiological stress indicators are observed under constant exposure and a clear difference is detected using a cold stress recovery assay. Genotyping with over 120 SSR markers did not detect any polymorphisms. Here we report using a reduced representation sequencing method called Restriction Enzyme Site Comparative Analysis to identify M202 introgressions unique to each MIb line as candidate loci for the cold stress recovery trait.