Exploring Phenotypic Diversity and Quantitative Trait Loci Mapping for Root Architecture, Freezing Tolerance, Chilling Fulfillment, and Photoperiod Traits in Grapevine Populations
Dissertation - Open Access
Doctor of Philosophy (PhD)
Department / School
Agronomy, Horticulture, and Plant Science
Chilling fulfillment, Freezing tolerance, Grapevine, QTL mapping, Root system architecture, Vitis riparia
Grapevine (Vitis species) is one of the most valuable fruit crops widely cultivated throughout the United States of America (USA). Grape and wine industries in the northern USA have been expanding rapidly with the demand for quality wine grapes that can be grown in Northern cold climate regions. As most popular cultivars are freezing sensitive, the development of new cultivars for the region continues through breeding. In this study, we evaluated grapevine root system architecture, freezing tolerance, and bud break in different genetic backgrounds in natural or controlled environments. The dissertation research objectives were to explore trait phenotypic variation and identify quantitative trait loci (QTL). A mapping population of 266 F2 genotypes a self of a F1 (16_9_2) from a cross between V. riparia ‘Manitoba 37’ and ‘Seyval’ cross was grown in the greenhouse for the root study. Sixteen root system architecture (RSA) traits were measured to study natural variations of F2 root morphology. Several trait-specific significant phenotype-genotype associations were identified. Forty-two QTLs were detected for root system architecture with hotspots on chromosomes 1, 9, 11, 13, and 19. Enriched pathways identified common (Cell division) and specific (lateral root development) genetic mechanisms suggesting complex genetic control encompassing morphology traits. Freezing tolerance, identified by low temperature exotherms, of field grown F2 grapevine was evaluated using digital thermal analysis for six winter seasons. Significant correlation was detected between freezing tolerance and monthly temperature. Eight significant QTLs were identified for freezing tolerance traits, one each on chromosomes 4 and 8 and two QTLs on chromosomes 2, 13, and 14. QTLs on chromosomes 4 and 14 were associated with enriched genetic pathways for grapevine freezing tolerance. Colocation of freezing tolerance and long-term winter endurance QTLs was detected on chromosome (chr) 14 suggesting interrelated genetic control. An enriched circadian pathway under freezing tolerance QTL on chr13 indicates the potential impact of photoperiod on initiation of freezing tolerance of grapevine. Chilling fulfillment was measured in F2 grapevine buds after different amounts of natural chilling in the field. Bud break was measured for four weeks under optimal forcing conditions in the laboratory after sampling. Chilling fulfillment, measured over six winter seasons, was associated with 53 QTLs across 14 chromosomes. Colocalization of chilling fulfillment QTLs were identified on chromosomes 3, 8, and 18. A pattern of QTL emerging with chilling fulfillment was identified suggesting that biochemical pathways related to meristem activation were initiated during chilling fulfillment and dormancy release. A total of 143 genotypes in a Riesling × Cabernet Sauvignon F1 grapevine population was studied under 12 chilling (168 to 2016 by 168 chilling hours) and two photoperiod treatments (13 hours (h) and 24h). Increased chilling and chilling fulfillment increase the rate of bud break and reduce the time for initiation of bud break. Longer (24h) photoperiod increased the rate of bud break and replaced the insufficient chilling. QTL mapping identified 55 QTL (26 and 29 QTLs for the 13h and 24h photoperiods respectively). Two major QTL were observed on chr2 (for 13h and 24h photoperiods) and chr10 (for 24h photoperiod). Root system architecture, freezing tolerance and chilling fulfillment studies identified several QTLs with significantly enriched pathways within the loci. These enriched pathways provide candidate genes that may be used to further dissect the mechanisms underlying root system characters and winter sustainability in grapevine.
Library of Congress Subject Headings
Grapes -- Genome mapping.
Grapes -- Genetics.
Grapes -- Roots.
Grapes -- Effect of freezes on.
Grapes -- Frost resistance.
Number of Pages
South Dakota State University
Alahakoon, Dilmini, "Exploring Phenotypic Diversity and Quantitative Trait Loci Mapping for Root Architecture, Freezing Tolerance, Chilling Fulfillment, and Photoperiod Traits in Grapevine Populations" (2020). Electronic Theses and Dissertations. 4855.