Browsing by Author "Bryon Sosinski, Committee Co-Chair"

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    AFLP-based Genetic Diversity Assessment of Global Sweetpotato (Ipomoea batatas (L.) Lam.) Germplasm Resources: Progress Toward The Development of a Sweetpotato Core Collection.
    (2004-11-15) Bruckner, Adam Wesley; Jenny Xiang, Committee Member; Craig Yencho, Committee Co-Chair; Bryon Sosinski, Committee Co-Chair
    Sweetpotato (Ipomoea batatas (L.) Lam) is an extremely diverse and important crop ranking seventh in terms of global production. It is grown throughout the world as a staple crop, and is particularly important in tropical developing countries due to its wide adaptability as well as its enormous potential for preventing malnutrition. The International Potato Center (CIP) in Lima, Peru and the USDA-ARS Plant Genetic Resources Conservation unit (PGRCU) in Griffin, Georgia are the most important sweetpotato gene banks worldwide. Roughly 7,000 and 750 accessions are present in each, respectively. Both collections have been characterized for many phenotypic traits of economic importance, and they are very important in terms of germplasm conservation, as they represent a vital resource for breeders seeking future genetic improvement of sweetpotato. The molecular genetic diversity present in each collection, however, is poorly understood. In this study, 775 accessions from the PGRCU collected from various countries were sampled and fingerprinted using AFLP markers derived from 10 primer pair combinations. A total of 183 polymorphic and clearly scorable bands were generated. Using polymorphisms and phylogenetic software (PAUP and NTSysPC), we were able to clearly distinguish a different banding pattern for each of the 775 accessions. A Neighbor-Joining phylogram was constructed and revealed 6 base clades with no region specificity. Analysis of molecular variance (AMOVA) was carried out using the software program Arlequin. The within-region variation at 97.94% was the major source of molecular variance. Pairwise genetic distances between regions were calculated and the smallest distance was between the Caribbean and Central America and the greatest distance was between the Pacific Islands and South America. Principle coordinate analysis (PCO) was performed by NTSysPC and several clusters of germplasm were noted. This research indicates that there is an abundance of genetic diversity present in sweetpotato.
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    Development of a Genetic Linkage Map and QTL Analysis in Sweetpotato
    (2007-08-01) Cervantes-Flores, Jim Carlos; Bryon Sosinski, Committee Co-Chair; Craig Yencho, Committee Co-Chair; William Thompson, Committee Member; Zhao-Bang Zeng, Committee Member
    Despite its worldwide importance, sweetpotato [Ipomoea batatas (L.) Lam] genetic research lags behind that of other major crops. To address this issue, we developed a genetic linkage mapping population consisting of 240 individuals of a cross between 'Beauregard' (a leading orange-fleshed US sweetpotato cultivar) and 'Tanzania' (a cream-fleshed African landrace). A total of 1751 ('Beauregard') and 1944 ('Tanzania') AFLP markers were located and framework maps consisting of 726 and 947 single-dose AFLP markers were ordered into 90 and 86 linkage groups for 'Beauregard' and 'Tanzania', respectively. Multiple-dose markers were used to identify homologous groups, allowing the assignment of the linkage groups to 15 homologous groups for each parental map. Only few linkage groups remained unassigned. The mapping population was phenotyped and quantitative trait loci (QTL) identified for important traits using single-point and interval mapping procedures. Resistance to root-knot nematode [Meloidogyne incognita (Kofoid & White) Chitwood], a worldwide pest, in the progeny was assessed. QTL analyses revealed seven significant QTL in 'Tanzania' and two in 'Beauregard'. In 'Tanzania', QTL with negative and positive effects on resistance were observed, each explaining approximately 20% of the observed variation. In 'Beauregard', two QTL that increased resistance explained approximately 6% of the observed variation. Based on molecular and phenotypic data, RKN resistance is hypothesized to be conferred by several genes, but at least nine loci (7 from 'Tanzania' and 2 from 'Beauregard') had the biggest effect. Genetic analyses of dry-matter, starch, and beta-carotene content and storage root yield were also conducted. Several QTL ranging from 8 (beta-carotene) to 18 (yield) were identified that affected these traits, and their importance in their inheritance is discussed. Strong correlations were observed between carotene and starch content in the storage roots, and also between starch and dry-matter content. To our knowledge, this is the most complete genetic linkage map of sweetpotato available, and we report the first QTL mapping studies in sweetpotato for storage root quality traits. We anticipate that this research will have a great impact for the sweetpotato breeding community, providing a foundation for the use of molecular techniques in sweetpotato breeding.
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    Genetic and Quantitative Analysis of Red Raspberry (Rubus idaeus) for Heat Tolerance and Longer Chilling Requirement
    (2009-12-04) Molina Bravo, Ramon; Bryon Sosinski, Committee Co-Chair; James Ballington, Committee Member; Gina Fernandez, Committee Co-Chair; James Holland, Committee Member
    Despite the high level of interest for growing red raspberries (Rubus ideaus) in the southeastern US, production is limited by the lack of adapted, high quality cultivars. Breeding efforts are underway for increasing cultivar availability for this region, however breeding improvements in Rubus are slow and time-consuming. In order to expedite the slow, but effective, breeding process, more molecular breeding tools should be developed. Cultivars adapted to the southeastern US need to tolerate warm summers, and winters with temperature fluctuations. To address this issue, we have developed a genetic linkage mapping population from a cross that segregates for the tolerance of both conditions, (R. parvifolius × ‘Tulameen’) × ‘Qualicum’. This population was used for the construction of a genetic linkage map and for quantitative trait loci (QTL) analysis of heat tolerance, and chilling requirement for tolerance to fluctuating winter temperatures. As expected, seven linkage groups were created and were similar to the already published map. Because heat tolerance is a difficult trait to measure, a protocol was developed using chlorophyll fluorescence to assess heat tolerance. This protocol was used to measure tolerance in the population, and after QTL analysis, 3 QTL explained ~35% of the variation. Chilling requirements in the population were estimated by measuring bud break under greenhouse conditions. Quantitative analysis was performed on these estimates, and 3 QTL were found in two separate season evaluations, and in most cases co-localization occurred in the same region on the map. These regions explained the majority of the variation in the trait (100-64.5%). In summary, this research has established a protocol that measures heat tolerance in red raspberry, without relying on visual assessment, and has mapped important QTL for further molecular studies. Future research should focus on these regions to develop closely linked molecular markers for marker assisted breeding.
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    Sinks Above and Sinks Below - Physical Mapping of Fruit-derived ESTs in Peach, a Model Species for Prunus and Rosaceae Structural Genomics, and Identification of Amplified Fragment Length Polymorphism (AFLP) Markers Associated with Internal Heat Necrosis (IHN) in 4x-2x Solanum tuberosum x S. phureja-S. stenotomum hybrids
    (2005-07-26) McCord, Per Hilding; Craig Yencho, Committee Co-Chair; Bryon Sosinski, Committee Co-Chair; Rebecca Boston, Committee Member
    Peach (Prunus persica (L.) Batsch) has been proposed as a model organism for structural genomics in the family Rosaceae. Several resources have been or are currently being developed to study the structural genomics of the species. A highly saturated genetic linkage map has been developed from an interspecific 'Texas' almond X 'Earligold' peach cross (T X E), and two peach BAC libraries from the cultivars 'Nemared' and 'Lovell' have been generated for the creation of a physical mapping resource. A framework map has been generated by the hybridization of markers from the T X E and other Prunus maps to the 'Nemared' library. In addition, peach and almond unigenes are being hybridized to the library in order to generate an anchored transcript map, identify contigs for overall map construction, and provide information on genome organization. A subgroup of the Prunus unigene set comprising 942 ESTs derived from peach fruit mesocarp was hybridized to the 44,150-clone 'Nemared' library. Eight hundred ninety-nine of these ESTs successfully hybridized to the library, identifying 3475 BACs, of which 2725 were unique. Seventy-six of these ESTs are now anchored to the reference map by hybridization to genetically anchored BAC clones or contigs. Twenty-six of these ESTs mapped near loci for important agronomic traits, including flesh acidity, fruit skin pubescence, and almond shell hardness. Unanchored ESTs generated contigs of 2 to 44 clones, which are being fingerprinted and integrated into the growing peach physical map in preparation for sequencing of the peach genome. Internal heat necrosis (IHN) is a physiological disorder of potato tubers resulting in the discoloration of parenchymal tissue. Environmental conditions and the large acreage of the IHN-susceptible cultivar 'Atlantic' result in significant losses due to the disorder in the mid-Atlantic states and Florida. A combination of bulked segregant analysis and AFLP marker technology was used to search for molecular markers for IHN in a population of tetraploid 4x-2x S. tuberosum x S. phureja-S. stenotomum (tub x phu-stn) hybrids. These clones are being used to breed an IHN-resistant, high specific-gravity replacement for 'Atlantic'. One marker, potPCR13-HindIII-R, was identified in two small test populations and was strongly associated with resistance to IHN, explaining 69.9% and 64 % of the observed variation for IHN incidence and severity, respectively. This marker showed strong sequence homology to calcium-dependent protein kinases (CDPKs), reinforcing prior evidence of the importance of calcium to the manifestation of IHN. When tested on a different set of clones from a combining ability study for IHN, this marker was no longer significant. However, a second putative marker from the BSA-AFLP screen (potPCR31-A) that was not statistically significant in the small populations, was significantly associated with IHN susceptibility in this second population, and the regression models of potPCR-31-A on IHN severity and incidence explained 17.8% and 18.6% of the phenotypic variation, respectively. This marker showed homology to plastid terminal oxidases (PTOXs), which are involved in desaturation of carotenoids, and may have a role in protecting biomolecules under oxidative stress. The small sample sizes used in marker development and initial testing may have resulted in these markers being significant predictors only in certain populations. It is also possible that, given the quantitative nature of IHN, only a subset of all IHN-associated loci may be necessary for the disorder to be manifest. This research is the first molecular marker study of the genetics of IHN, and has set a foundation for future studies.