Progress 10/01/14 to 09/30/15
Outputs
Target Audience:Students, Watermelon seed companies, companies interested in marker assisted selection tools Changes/Problems:
Nothing Reported
What opportunities for training and professional development has the project provided?Two students submitted their thesis in watermelon breeding and genomic research. One student identified fruit specific DNA markers and other student performed GWAS for trichome features in watermelon. Three undergraduate students were recruited in this project and we imparted genomics, genetic and plant breeding training to them. How have the results been disseminated to communities of interest?Five new publications are published in peer reviewed and high impact journals. We shared improved watermelon lines with breeding community to introgress novel genes into culitvars. We presented our results in International Plant Genome Conferrence and 1890 ARD Conference. What do you plan to do during the next reporting period to accomplish the goals?
Nothing Reported
Impacts
What was accomplished under these goals?
We generated tetraploids and characterized various genetic factors that can be used to improve fruit quality in watermelon. Whole genome level transcriptome was characterized for tetraploids, diploids and derivative triploids. We identified 8000 new SNP markers for use in watermelon genomics. We characterized several traits at molecular level and identified DNA markers. Our research is published in five peer reviewed high impact genomics and genetics journals. We presented our results in intenational conferences.
Publications
- Type:
Journal Articles
Status:
Published
Year Published:
2014
Citation:
1. Reddy UK, Abburi L, Abburi VL, Saminathan T, Cantrell R, Vajja VG, Reddy R, Tomason YR, Levi A, Wehner TC, Nimmakayala P (2014) A Genome-Wide Scan of Selective Sweeps and Association Mapping of Fruit Traits Using Microsatellite Markers in Watermelon. Journal of Heredity. doi:10.1093/jhered/esu077
2. Saminathan T, Nimmakayala P, Manohar S, Malkaram S, Almeida A, Cantrell R, Tomason Y, Abburi L, Rahman MA, Vajja VG, Khachane A, Kumar B, Rajasimha HK, Levi A, Wehner T, Reddy UK (2014) Differential gene expression and alternative splicing between diploid and tetraploid watermelon. Journal of Experimental Botany. doi:10.1093/jxb/eru486
3. Padma Nimmakayala, Amnon Levi, Lavanya Abburi, Venkata Lakshmi Abburi, Yan R. Tomason, Thangasamy Saminathan, Venkata Gopinath Vajja, Sridhar Malkaram, Rishi Reddy, Todd C. Wehner, and Umesh K. Reddy 2014. Single nucleotide polymorphisms generated by genotyping by sequencing used to characterize genome-wide diversity, linkage disequilibrium and selection sweep for worldwide cultivated watermelon. BMC Genomics 2014, 15:767 (Highly accessed)
4. Nimmakayala P, Abburi V, Bhandary A, Abburi L, Vajja V, Reddy R, Malkaram S, Venkatramana P, Wijeratne A, Tomason Y, Levi A, Wehner T, Reddy U (2014) Use of VeraCode 384-plex assays for watermelon diversity analysis and integrated genetic map of watermelon with single nucleotide polymorphisms and simple sequence repeats. Mol Breeding 34 (2):537-548. doi:10.1007/s11032-014-0056-9
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Progress 10/01/13 to 09/30/14
Outputs
Target Audience: Graduate and undergraduate students, watermelon growers, Watermelon Geneticists and Plant breeders Changes/Problems:
Nothing Reported
What opportunities for training and professional development has the project provided? Two graduate students submitted their thesis research. Four undergraduate students worked in the project. How have the results been disseminated to communities of interest? Conference presentations and peer reviewed publications What do you plan to do during the next reporting period to accomplish the goals? We plan to estimate various important metabolites like lycopene, citrulline and vitamin C across the diversity panel and perform GWAS for identifying respective genes that are important for these traits.
Impacts
What was accomplished under these goals?
We have generated large set of SNP markers using Genotyping By Sequencing (GBS) technology, for 180 diverse watermelon accessions.We subjected entire panel for SNP genotyping and generated 10,000 SNPs that have minor allele frequency above 0.05. Diversity analysis indicated that cultivated watermelons originated from West Africa. Accessions of Africa were grouped into three major clusters, out of which one of the cluster relates entire world watermelon cultivars. Population structure analysis resolved the genetic differentiation of Asian and American ecotypes. We used 250 genome-wide microsatellites and used them to resolve selection sweeps across the genome.A high resolution genetic map was constructed consisting 10,480 SNPs.
Publications
- Type:
Journal Articles
Status:
Accepted
Year Published:
2014
Citation:
Reddy UK, Nimmakayala P, Levi A, Abburi VL, Saminathan T, Tomason YR, Vajja G, Reddy R, Abburi L, Wehner TC, Ronin Y, Karol A. 2014 High-Resolution Genetic Map for Understanding the Effect of Genome-Wide Recombination Rate on Nucleotide Diversity in Watermelon. G3: Genes|Genomes|Genetics, 4:2219-2230.
- Type:
Journal Articles
Status:
Accepted
Year Published:
2014
Citation:
Nimmakayala, P., Abburi VL, Bhandari A, Abburi L, Vajja VG, Reddy R, Malkaram S, Venkatramana P, Wijeratne A, Tomason YR, Levi A, Wehner T and Reddy UK. 2014. Use of VeraCode 384-plex assays for watermelon diversity analysis and integrated genetic map of watermelon with single nucleotide polymorphisms and simple sequence repeats. Molecular Breeding, 34(2): 537-548
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Progress 10/01/12 to 09/30/13
Outputs
Target Audience: Local farmers Graduate and undergraduate students Plant breeders and Geneticists Changes/Problems:
Nothing Reported
What opportunities for training and professional development has the project provided? Two graduate students submitted their thesis. One graduate student is currently working. Three undergrads, two technicians and one postdoctoral research associate worked in the project. Most importantly, a melon breeder, Dr. Bharathi visited from India to learn marker assisted selection. One high school teacher and students worked to understand genetics of trichomes in watermelons. How have the results been disseminated to communities of interest? To incorporate disease resistance in watermelons, we need to diversify genetic base. We identified diverse lines (PI 32137, PI 525084 and PI 482248) and several seed companies and public breeders are interested in these pre-breeding material. We are also in process of developing tetraploids for breeding seedless watermelons. A presentation was made at the International Plant Genome Conference. A manuscript is currently in press. The project results have been disseminated through emails, conference presentations and peer reviewed publications. What do you plan to do during the next reporting period to accomplish the goals? We plan to develop markers for the genes in carotenoid pathway and citrulline pathways and pre-breeding materal for value added watermelons.
Impacts
What was accomplished under these goals?
We developed a SNP assay containing 384 markers that was suitable for high resolution genetic mapping and resolving genetic diversity among cultivated watermelon. Most SNP-containing sequences were found to have catalytic and binding activities and included a large number of hydrolases, kinases and transferases. Other abundant assignments were abiotic and biotic stress-response along with the other signal transduction, transport and transcriptional regulations. The genetic map we developed consisted of all 11 chromosomes spanning 924.72cM. As compared with the physical and genetic map positions of various SNPs, we noted many disagreements, which may have occurred because our mapping population was derived from a cross of C. lanatus var. lanatus x C. lanatus var. citroides, which are known to produce genome-wide distortions. From our analysis of only cultivated forms or edible watermelons, we support published findings of the narrow genetic diversity among American watermelon accessions. Using these SNPs, we identified markers for fruit length, weight, sucrose percent and seedling traits. Our diversity study revealed that 134 SNPs were polymorphic among our cultivar collection. Overall genetic similarity was 0.95% among the cultivars, so edible watermelons of world collections maintain 5% genetic diversity among them. However, when African red-fleshed watermelons were analyzed separately, PI 32137, PI 525084 and PI 482248 were distinctly different and were separated by 7%, 8.5% and 11% genetic distance, respectively, from the remaining types indicating these lines will be of immense use for diversifying watermelon varieties that belong to the USA.
Publications
- Type:
Journal Articles
Status:
Accepted
Year Published:
2014
Citation:
Nimmakayala P, Abburi VL, Tomason Y, Wehner T, Levi A and Reddy UK. 2014.Use of VeraCode 384-plex assays for
watermelon diversity analysis and integrated genetic map of watermelon with single nucleotide polymorphisms and simple
sequence repeats (Molecular Breeding)
Nimmakayala P, Abburi VL, Tomason Y, Wehner T, Levi A and Reddy UK. 2014. Genome-wide Association Mapping of
Fruit Traits in Watermelon. International Plant & Animal Genome XXII. Conference. January 12-16, 2014
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Progress 01/01/12 to 09/30/12
Outputs
Target Audience: Local farmers Graduate and undergraduate students Plant breeders and Geneticists Changes/Problems:
Nothing Reported
What opportunities for training and professional development has the project provided? Two graduate students submitted their thesis. One graduate student is currently working. Three undergrads, two technicians and one postdoctoral research associate worked in the project. Most importantly, a melon breeder, Dr. Bharathi visited from India to learn marker assisted selection. One high school teacher and students worked to understand genetics of trichomes in watermelons. How have the results been disseminated to communities of interest? To incorporate disease resistance in watermelons, we need to diversify genetic base. We identified diverse lines (PI 32137, PI 525084 and PI 482248) and several seed companies and public breeders are interested in these pre-breeding material. We are also in process of developing tetraploids for breeding seedless watermelons. A presentationwas made at the International Plant Genome Conference. A manuscript is currently in press. The project results have been disseminated through emails, conference presentations and peer reviewed publications. What do you plan to do during the next reporting period to accomplish the goals? We plan to develop markers for the genes in carotenoid pathway and citrulline pathways and pre-breeding materal for value added watermelons.
Impacts
What was accomplished under these goals?
We developed a SNP assay containing 384 markers that was suitable for high resolution genetic mapping and resolving genetic diversity among cultivated watermelon. Most SNP-containing sequences were found to have catalytic and binding activities and included a large number of hydrolases, kinases and transferases. Other abundant assignments were abiotic and biotic stress-response along with the other signal transduction, transport and transcriptional regulations. The genetic map we developed consisted of all 11 chromosomes spanning 924.72cM. As compared with the physical and genetic map positions of various SNPs, we noted many disagreements, which may have occurred because our mapping population was derived from a cross of C. lanatus var. lanatus x C. lanatus var. citroides, which are known to produce genome-wide distortions. From our analysis of only cultivated forms or edible watermelons, we support published findings of the narrow genetic diversity among American watermelon accessions. Using these SNPs, we identified markers for fruit length, weight, sucrose percent and seedling traits. Our diversity study revealed that 134 SNPs were polymorphic among our cultivar collection. Overall genetic similarity was 0.95% among the cultivars, so edible watermelons of world collections maintain 5% genetic diversity among them. However, when African red-fleshed watermelons were analyzed separately, PI 32137, PI 525084 and PI 482248 were distinctly different and were separated by 7%, 8.5% and 11% genetic distance, respectively, from the remaining types indicating these lines will be of immense use for diversifying watermelon varieties that belong to the USA.
Publications
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Progress 01/01/11 to 12/31/11
Outputs
OUTPUTS: Implementing Single Nucleotide Polymorphism (SNP) marker technology in watermelon breeding and germplasm evaluation programs holds a key to improve horticulturally important traits. Next-generation sequencing strategies coupled with the high density genotyping platforms offer an opportunity to discover SNP markers and use them in routine genotyping projects in a cost effective manner. We discovered a large number of SNPs (>10,000) using Restriction site Associated DNA (RAD) protocol and Illumina/Solexa paired-end sequencing. Genomic DNAs of mapping parents (PI 244018 of var. citroides and PI270306 of var. lanatus) were used for SNP discovery. A subset of 384 SNPs with high ADT(Assay Design Tool) design scores were identified for Illumina golden gate genotyping. Genotyping experiments were carried using the Illumina BeadExpress platform on the genomic DNAs of a mapping population (94 progenies) and 288 genbank accessions containing 273, 9 and 6 accessions of var. lanatus (Citrullus lanatus var. lanatus), citroides (Citrullus lanatus var. citroides) and colocynthis (Citrullus colocynthis) respectively. A genetic map was constructed by integrating SNP data with the previously mapped 120 microsatellite markers. Molecular diversity data was further used to analyze the population structure and LD blocks. We identified SNP haplotypes within the cultivated watermelon. Fruit quality data obtained from the field evaluation of 40 cultivated watermelons provided preliminary insights into the use of SNP data for association mapping strategies. PARTICIPANTS: At WVSU total of four students were involved, out of which one is undergraduate and three MS students. Undergraduate student carried out independent experiments using microsatellite markers and also recorded observations on plant morphology including fruit traits for genetic mapping studies. Graduates students were involved in northern blotting and RT PCR of genes across various species. TARGET AUDIENCES: Graduate students, Geneticists, watermelon Breeders, and seed companies. PROJECT MODIFICATIONS: Nothing significant to report during this reporting period.
Impacts
SNP markers, maps, genome sequences and SNP platforms developed in this study using Solexa sequencing technologies will have immense impact to speed up watermelon breeding goals. Genetic map with the whole genome coverage will facilitate the identification and genetic mapping of putative SNPs that will be useful in future studies to enhance disease and pest resistance in watermelon cultivars. Watermelons are the important vegetable crops, grown in 44 states in the United States. We found that although watermelon crop cultivars are widely diverse in their fruit shape, size, color, and quality, they share a narrow genetic base. This narrow genetic base is a result of many years of cultivation and selection for varieties with desirable fruit qualities. As a result, the American cultivars are susceptible to a large number of diseases and pests, and there is a continuous need to improve them and make them more resistant to diseases and pests. In this study, we have collaborated with the scientists at USDA-ARS on conducting experiments aiming to elucidate the molecular events that control the genes affecting the quality of watermelon. The knowledge gained in this study should be useful for researchers and plant breeders interested in understanding and the genetic and biological mechanisms that produce the differences among watermelon crop cultivars, and in utilizing these mechanisms to improve quality suitable to consumer needs. Through this project support, we have created a million dollar worth SNP markers spanning across the watermelon genome. These resources led to identification of disease resistant genes and genes for fruit quality and yield. Resistant varieties for diseases esp. powdery mildew and seedless watermelon technology collectively can impact up to $1 million dollar worth income for the watermelon producers per year.
Publications
- Reddy UK, Nischit A, Nurul Islam-Faridi, Tomason YR, Levi A, and Nimmakayala P. 2011. Cytomolecular characterization of rDNA distribution and copy number variation among various Citrullus species using fluorescent in situ hybridization. Genetica (in review)
- Nimmakayala P, Tomason YR, Levi A, Reddy UK. 2011. SNP marker distribution and LD pattern across the watermelon genome. BMC Genomics (in preparation)
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