Quantitative Trait Loci Analysis of Low Temperature Responses in Grapevine F2 Population

Freezing injury, caused by freezing temperatures in the late fall, midwinter, or early spring, can result in significant loss to grape growers. The damage may range from the partial damage of parts of the plants to the total death of the plant, and may vary between years. Freezing tolerance is a multi-genetic, complex quantitative trait that involves many related traits like dormancy induction, growth cessation, acclimation, deacclimation and bud break. Developing an understanding of the genetics behind the complex trait requires connecting the phenotype with the genotype to enable discovering the underlying genes that can contribute to quantifiable differences between individuals. The objective of this thesis is to detect the genomic location(s) underlying genetic variation in low-temperature response traits like freezing tolerance and bud break using quantitative trait loci analysis (QTL). An F2 population developed by selfing a single F1 from a cross between American species Vitis riparia and a hybrid grapevine Seyval, was used to conduct QTL analysis for subzero temperature tolerance. The low temperature exotherms (LTE) obtained from differential thermal analysis (DTA) were used as phenotype data for the QTL analysis. The phenotyping was conducted in multiple months and dormant seasons. LTE results when the supercooled water inside the bud freezes and identifies the temperature at which buds are killed. Best linear unbiased predictors (BLUP) was also calculated using the LTEs to calculate random genetic effects. Composite interval mapping (CIM) was conducted using either the average LTEs or BLUP values in R/QTL with 1000 permutations and error rate of 5%. The LTEs for individual genotypes varied in the different months. QTLs were identified using either average LTEs or BLUP values for all the months and dormant seasons. QTLs appeared on Chromosome 1, 5, 9, 13 and 16 in different months or dormant seasons. Many potential candidate genes associated with calcium signaling, ethylene signaling, ABA signaling, cellular metabolism and dehydration response were found underlying the 1.5 LOD interval of these QTLs. The bud break phenology was studied at three chilling periods to identify bud break related QTL. Bud break occurs upon the exposure to optimal growth conditions, after the chilling requirement fulfillment transitions the bud from endodormancy to ecodormancy. Three one node cuttings of the grapevines were forced at 13 hours of daylength and 25⁰C/20⁰C thermoperiod in the growth chamber for four weeks. Each week the growth stage of the cuttings was scored using Modified Eichhorn-Lorenz (Modified E-L) phenology scale. This was repeated in multiple dormant seasons and months. The bud break data was ordinal, monotonic and based on repeated measurements, thus similar to data in disease epidemiological studies in which disease severity is scored repeatedly over a time period. Therefore, the concept of area under the curve (AUC) was applied to the bud break data. The area under the bud break progression curve (AUBPC) was calculated for the bud break data of each individual for an individual month. CIM was conducted with the average week 3 phenology score data or AUBPC data in R/qtl using 1000 permutations. Both data processing approaches provided similar QTL results on chromosome 3, 7, 8, 9, 13, 18 and 19. These QTLs encompassed candidate genes involved in calcium signaling, auxin signaling, ethylene signaling, circadian clock signaling, cellular metabolism, primary and secondary metabolism, dehydration stress response, drought stress response, fruit ripening and many transcription factors. The results from this study can be useful in developing low temperature response trait markers that can be applied in marker-assisted breeding and selection to develop the grapevine cultivars suitable for northern continental climates where freezing temperatures are common. This will enhance the sustainability of cold climate grape production and promote expansion of grape growing regions.