Progress 08/01/10 to 07/31/13
Outputs
Progress Report Objectives (from AD-416): 1. Develop cucumber and melon SNP arrays for whole genome scan. We will utilize internal genomic information and public databases to create two SNP arrays: one for cucumber and one for melon. 2. Develop and characterize cucumber and melon populations segregating for fruit size. A set of segregating populations from cucumber will be analyzed for fruit size phenotype, including detailed analyses of ovary and fruit development pre- and post-anthesis. 3. Combine genomic tools, segregating populations, and phenotypic characterization to identify loci associated with fruit size. Genetic analysis using the SNP arrays developed in this project and segregating populations for fruit size will identify QTL associated with fruit size. Approach (from AD-416): 1. SNP identification. Sequencing data will be analyzed using bioinformatics tools to identify SNPs. 2. Microarray printing and validation. The microarray will be self designed and printed using the Agilent eArray platform. 3. Phenotyping segregating populations for fruit size. Three mapping populations will be used for phenotyping of fruit size (RIL and F2:3 families). Phenotypic data will be collected from field trials in two years (2010 and 2011) at two locations. 4. Characterize ovary and fruit development in parental lines. Fruits of three cucumber types: pickling, Chinese Long and hardwickii (PI183967) will be examined for ovary and fruit development. Ovaries will be examined for length, diameter, and presence and number of ovules pre- and post-anthesis The identified key features will be used in combination with segregation analyses and studies of field performance to partition contributions of fruit size QTL identified by WGS experiments. 5. Whole genome scan of different population segregating for fruit size QTL analysis will be performed to establish marker-fruit size trait associations. This project was renumbered from 3655-21000-048-24R to 3655-21000-062-08R. This is the final report, project terminated 07/31/2013. Population development. As a co-PI in this three year project, we developed three mapping populations that were used for linkage mapping of quantitative trait loci (QTL) for fruit sizes (fruit length and diameter). These include 150 recombinant inbred line (RILs) from the cross between Gy14 (US pickle cucumber) and 9930 (China fresh market type), 175 F3 families from a cross between a Chinese landrace (WI 7167) and a plant introduction line from Thailand (WI 7200A), and 500 F2 plants from Gy14 and a wild plant introduction line from India (WI 7221). This work fulfills Objectives 1 and 2. Phenotypic data collection. Replicated trials were conducted at Hancock Experimental Station in 2011, 2012, and 2013 for the Gy14 � 9930 RIL populations. In the 2013 field season, all three populations are growing in the field for data collection. In 2011, the RIL population was also grown in East Lansing, Michigan and Raleigh, North Carolina. The multi- year and multi-location data of the RIL population are being used for QTL mapping with molecular marker data single nucleotide polymorphisms (SNPs) to identify major QTLs that determine fruit length and diameter in cucumber. Data collected from the other two populations are also being used for identifying fruit size QTLs in different genetic backgrounds and validation of QTL identified from the RIL population. This work fulfills objectives 1, 2, and 3 by developing SNP arrays for whole genome scan, developing and characterizing cucumber and melon populations, and combining genomic tools and phenotypic characterization to identify loci associated with fruit size.
Impacts
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Progress 10/01/11 to 09/30/12
Outputs
Progress Report Objectives (from AD-416): 1. Develop cucumber and melon SNP arrays for whole genome scan. We will utilize internal genomic information and public databases to create two SNP arrays: one for cucumber and one for melon. 2. Develop and characterize cucumber and melon populations segregating for fruit size. A set of segregating populations from cucumber will be analyzed for fruit size phenotype, including detailed analyses of ovary and fruit development pre- and post-anthesis. 3. Combine genomic tools, segregating populations, and phenotypic characterization to identify loci associated with fruit size. Genetic analysis using the SNP arrays developed in this project and segregating populations for fruit size will identify QTL associated with fruit size. Approach (from AD-416): 1. SNP identification. Sequencing data will be analyzed using bioinformatics tools to identify SNPs. 2. Microarray printing and validation. The microarray will be self designed and printed using the Agilent eArray platform. 3. Phenotyping segregating populations for fruit size. Three mapping populations will be used for phenotyping of fruit size (RIL and F2:3 families). Phenotypic data will be collected from field trials in two years (2010 and 2011) at two locations. 4. Characterize ovary and fruit development in parental lines. Fruits of three cucumber types: pickling, Chinese Long and hardwickii (PI183967) will be examined for ovary and fruit development. Ovaries will be examined for length, diameter, and presence and number of ovules pre- and post-anthesis The identified key features will be used in combination with segregation analyses and studies of field performance to partition contributions of fruit size QTL identified by WGS experiments. 5. Whole genome scan of different population segregating for fruit size QTL analysis will be performed to establish marker-fruit size trait associations. Development of populations for fruit size quantitative trait loci (QTL) mapping in cucumber. We continued developing a recombinant inbred line (RILs) mapping population for QTL mapping of fruit size in cucumber. Now 145 RILs from the cross between Gy14 and 9930 have been advanced at F7 and F8. A new population was developed for fruit size QTL mapping from XSBN-3 and PI 249561. One hundred and forty five F2 plants were advanced to F3 for fruit size phenotyping. Phenotypic data collection. Replicated trials were conducted in three locations with the Gy14 � 9930 RIL populations. Data for fruit size of F2 plants from XSBN-3 x PI 249561 has been collected. Leaf sample from the Gy14 x 9930 RILs will be collected for DNA extraction. This research relates to Objective 1, Determine the genetic basis of and initiate selection for carrot, onion, cucumber, and melon quality attributes influencing human nutrition and health, disease resistances, and yield and quality components, and stress tolerance in cucurbits, and perform field performance and quality trials; Objective 2, Utilize current biotechnology to discover and evaluate genetic variation and to map agriculturally important traits in Allium, Cucurbit, and Daucus germplasm, and to develop genetic and breeding stocks.
Impacts
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Progress 10/01/10 to 09/30/11
Outputs
Progress Report Objectives (from AD-416) 1. Develop cucumber and melon SNP arrays for whole genome scan. We will utilize internal genomic information and public databases to create two SNP arrays: one for cucumber and one for melon. 2. Develop and characterize cucumber and melon populations segregating for fruit size. A set of segregating populations from cucumber will be analyzed for fruit size phenotype, including detailed analyses of ovary and fruit development pre- and post-anthesis. 3. Combine genomic tools, segregating populations, and phenotypic characterization to identify loci associated with fruit size. Genetic analysis using the SNP arrays developed in this project and segregating populations for fruit size will identify QTL associated with fruit size. Approach (from AD-416) 1. SNP identification. Sequencing data will be analyzed using bioinformatics tools to identify SNPs. 2. Microarray printing and validation. The microarray will be self designed and printed using the Agilent eArray platform. 3. Phenotyping segregating populations for fruit size. Three mapping populations will be used for phenotyping of fruit size (RIL and F2:3 families). Phenotypic data will be collected from field trials in two years (2010 and 2011) at two locations. 4. Characterize ovary and fruit development in parental lines. Fruits of three cucumber types: pickling, Chinese Long and hardwickii (PI183967) will be examined for ovary and fruit development. Ovaries will be examined for length, diameter, and presence and number of ovules pre- and post-anthesis The identified key features will be used in combination with segregation analyses and studies of field performance to partition contributions of fruit size QTL identified by WGS experiments. 5. Whole genome scan of different population segregating for fruit size QTL analysis will be performed to establish marker-fruit size trait associations. Development of populations for fruit size Quantitative Trait Loci (QTL) mapping in cucumber. We are in the process of developing a recombinant inbred line (RIL) mapping population for QTL mapping of fruit size in cucumber. Now 124 RILs from the cross between Gy14 and 9930 have been advanced at F6 and F7. Thirty more RILs are currently at F4 or F5. Within the next 12 months, we will have a minimum of 150 F7 RILs. Another RIL population is Gy14 � PI 183967. Sixty nine F8 RILs are currently available for use. Two additional mapping populations are being developed. One is from cucumber cultivar Rissen Schol � PI 183967, and the other from XSBN � PI 183967. The populations are currently at F2. We plan to develop 150 F2:3 families from each cross for use in this project. Phenotypic data collection. In the 2011 field season, replicated trials were conducted in three locations with the Gy14 � 9930 RIL populations. Another RIL population segregating for fruit size is the Gy14 � PI 183967. Sixty nine RILs were planted in the 2010 field season (3 reps per RIL). Fruit size data were collected for each RIL. Deoxyribonucleic acid (DNA) samples of cucumber line 9930 were prepared and sent for whole genome sequencing for single-nucleotide polymorphism (SNP) identification. Leaf sample from the Gy14 x 9930 RILs have been collected for DNA extraction. Project monitoring is done through e-mail correspondence and conference calls. In January 2011 during the Plant and Animal Genome Meeting, all participants met to review the progress and plan the research.
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