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ARS Home » Southeast Area » Charleston, South Carolina » Vegetable Research » Research » Research Project #425105

Research Project: Genetic Enhancement of Watermelon, Broccoli, and Leafy Brassicas for Economically Important Traits

Location: Vegetable Research

Publications (Clicking on the reprint icon Reprint Icon will take you to the publication reprint.)

QTL mapping of resistance to Fusarium oxysporum f. sp. niveum race 2 and Papaya ringspot virus in Citrullus amarus Reprint Icon - (Peer Reviewed Journal)
Branham, S., Wechter, W.P., Ling, K., Chanda, B., Massey, L.M., Zhao, G., Guner, N., Bello, M., Kabelka, E., Fei, Z., Levi, A. 2019. QTL mapping of resistance to Fusarium oxysporum f. sp. niveum race 2 and Papaya ringspot virus in Citrullus amarus. Theoretical and Applied Genetics. 133:677-687. https://doi.org/10.1007/s00122-019-03500-3.

The CucCap project: Leveraging applied genomics to improve disease in cucurbit crops - (Proceedings)
Grumet, R., Fei, Z., Levi, A., Mazourek, M., Mccreight, J.D., Schultheis, J., Weng, Y., Hausbeck, M., Kousik, C.S., Ling, K., Linares-Ramirez, A., Mcgregor, C., Quesada-Ocampo, L., Reddy, U., Smart, C., Wechter, W.P., Wehner, T., Wessel-Beaver, L., Wintermantel, W.M. 2019. The CucCap project: Leveraging applied genomics to improve disease in cucurbit crops. International Symposium on Cucurbits Proceedings. https://doi.org/364300.

Identification of heat tolerance loci in broccoli through bulked segregant analysis using whole genome resequencing - (Peer Reviewed Journal)
Branham, S., Farnham, M.W. 2019. Identification of heat tolerance loci in broccoli through bulked segregant analysis using whole genome resequencing. Euphytica. 215:34.

QTL-seq and marker development for resistance to Fusarium oxysporum f. sp. niveum race 1 in cultivated watermelon - (Peer Reviewed Journal)
Branham, S., Wechter, W.P., Lambel, S., Massey, L.M., Ma, M., Fauve, J., Farnham, M.W., Levi, A. 2018. QTL-seq and marker development for resistance to Fusarium oxysporum f. sp. niveum race 1 in cultivated watermelon. Molecular Breeding. 38:139.

NMR analysis reveals a wealth of metabolites in root-knot nematode resistant roots of Citrullus amarus watermelon plants Reprint Icon - (Peer Reviewed Journal)
Kantor, M., Levi, A., Thies, J.A., Guner, N., Kantor, C., Parnham, S., Boroujerdi, A. 2018. NMR analysis reveals a wealth of metabolites in root-knot nematode resistant roots of Citrullus amarus watermelon plants. Journal of Nematology. 50(3)303-316. https://doi.org/10.21307/jofnem-2018-030.

Utilizing genetic resources and precision agriculture to enhance resistance to biotic and abiotic stress in watermelon - (Literature Review)
Kantor, M., A. Levi. 2018. Utilizing genetic resources and precision agriculture to enhance resistance to biotic and abiotic stress in watermelon. Notulae Scientia Biologicae. 10:2067-3205. https://doi.org/351346.

Metagenomic and metatranscriptomic analysis of the microbiome of watermelon fruits Reprint Icon - (Peer Reviewed Journal)
Saminathan, T., Garacia, M., Ghimire, B., Lopez, C., Bodunrin, A., Balagurusamy, N., Nimmakayala, P., Huber, D., Levi, A., Reddy, K. 2018. Metagenomic and metatranscriptomic analysis of the microbiome of watermelon fruits. Frontiers in Plant Science. 9:1-4. https://doi.org/10.3389/fpls.2018.00004.

QTL-seq analysis of heat tolerance in broccoli - (Abstract Only)
Branham, S., Farnham, M.W. 2018. QTL-seq analysis of heat tolerance in broccoli. Plant and Animal Genome Conference Proceedings. p.0568.

Genetic mapping of a major co-dominant QTL associated with B-carotene accumulation in watermelon Reprint Icon - (Peer Reviewed Journal)
Branham, S., Vexler, L., Meir, A., Tzuri, G., Frieman, Z., Levi, A., Wechter, W.P., Tadmor, Y., Gur, A. 2017. Genetic mapping of a major co-dominant QTL associated with B-carotene accumulation in watermelon. Molecular Breeding. 37:146. https://doi.org/10.1007/s11032-017-0747-0.

A tonoplast sugar transporter underlies a sugar accumulation QTL in watermelon Reprint Icon - (Peer Reviewed Journal)
Ren, Y., Guo, S., Zhang, J., He, H., Sun, H., Tian, S., Gong, G., Zhang, H., Levi, A., Tadmor, Y., Xu, Y. 2017. A tonoplast sugar transporter underlies a sugar accumulation QTL in watermelon. Plant Physiology. 176(1):836-850. https://doi:10.1104/pp.17.01290.

Use of a quality trait index to increase the reliability of phenotypic evaluations in broccoli Reprint Icon - (Peer Reviewed Journal)
Stansell, Z., Bjorkman, T., Branham, S., Couillard, D.M., Farnham, M.W. 2017. Use of a quality trait index to increase the reliability of phenotypic evaluations in broccoli. HortScience. 52(11):1490-1495. https://doi:10.21273/HORTSCI12202-17.

USVL-380, A zucchini yellow mosaic virus resistant watermelon breeding line Reprint Icon - (Peer Reviewed Journal)
Levi, A., Ling, K. 2017. USVL-380, A zucchini yellow mosaic virus resistant watermelon breeding line. HortScience. 52(10):1448-1450. https://doi:10.21273/HORTSCI12292-17.

Genetic mapping and identification of quantitative trait loci associated with resistance to Fusarium oxysporum f. sp. niveum races 1 and 2 in watermelon - (Abstract Only)

Genotyping-by-sequencing of waxy and glossy near-isogenic broccoli lines - (Peer Reviewed Journal)
Branham, S., Farnham, M.W. 2017. Genotyping-by-sequencing of waxy and glossy near-isogenic broccoli lines. Euphytica. 213:84-89.

Genetic Resources of Watermelon Reprint Icon - (Book / Chapter)
Levi, A., Jarret, R.L., Kousik, C.S., Wechter, W.P., Nimmakayala, P., Reddy, U. 2017. Genetic Resources of Watermelon. In: Grumet R., Garcia-Mas J., and Katzir N., editors. Genetics and Genomics of Cucurbitaceae. Springer International Publishing AG 2016. p. 87-110. https://doi:10.1007/7397_2016_34.

Comparative Genomics of the Cucurbitaceae Reprint Icon - (Book / Chapter)
Nimmakayala, P., Saminathan, T., Abburi, V.L., Yadav, L.K., Tomason, Y., Levi, A., Weng, Y., Reddy, K.U. 2017. Comparative Genomics of the Cucurbitaceae. In: Grumet, R., Katzir, N., Garcia-Mas, J, editors. Plant Genetics and Genomics: Crops and Models. Springer International Publishing AG. 20:p. 229-240. https://doi:10.1007/7397_2017_2.

Genetic diversity in the desert watermelon Citrullus colocynthis and its relationship with Citrullus species as determined by high-frequency oligonucleotides-targeting active gene markers - (Peer Reviewed Journal)
Levi, A., Simmons, A.M., Massey, L.M., Coffey, J., Wechter, W.P., Jarret, R.L., Tadmor, Y., Nimmakayala, P., Reddy, U. 2017. Genetic diversity in the desert watermelon Citrullus colocynthis and its relationship with Citrullus species as determined by high-frequency oligonucleotides-targeting active gene markers. Journal of the American Society for Horticultural Science. 142(1):47–56. doi:10.21273/JASHS03834-16.

Quantitative trait loci mapping of heat tolerance in broccoli (Brassica oleracea var. italica) using genotyping-by-sequencing - (Peer Reviewed Journal)
Branham, S., Stansell, Z.J., Couillard, D.M., Farnham, M.W. 2017. Quantitative trait loci mapping of heat tolerance in broccoli (Brassica oleracea var. italica) using genotyping-by-sequencing. Theoretical and Applied Genetics. 130(3):529-538.

Genome-wide differentiation of various melon horticultural groups for use in genome wide association study for fruit firmness and construction of a high resolution genetic map - (Peer Reviewed Journal)
Nimmakayala, P., Tomasson, Y., Abburi, V.K., Saminathan, T., Rodrigguez, A.G., Vajja, V.G., Salazar, G., Girish, P., Levi, A., Wechter, W.P., McCreight, J.D., Korol, A., Ronin, Y., Garcia-Mas, J., Reddy, U. 2016. Genome-wide differentiation of various melon horticultural groups for use in genome wide association study for fruit firmness and construction of a high resolution genetic map. Frontiers in Plant Science. 7:1437. doi:org/10.3389/fpls.2016.01437.

Utilizing genetic diversity in the desert watermelon citrullus colocynthis for enhancing watermelon cultivars for resistance to biotic and abiotic stress - (Proceedings)
Levi, A., Simmons, A.M., Ling, K., Tadmor, Y., Nimmakayala, P., Reddy, U. 2016. Utilizing genetic diversity in the desert watermelon citrullus colocynthis for enhancing watermelon cultivars for resistance to biotic and abiotic stress. In Kozik EU and Paris HS (eds.). Cucurbitaceae 2016, XIth EUCARPIA Meeting on Genetics and Breeding of Cucurbitaceae, July 24-28, 2016, Warsaw, Poland. p. 105-108.

Using genotyping-by-sequencing to develop broccoli markers for construction of a high-density linkage map and to identify quantitative trait loci associated with heat tolerance - (Abstract Only)
Branham, S., Stansell, Z.J., Couillard, D.M., Farnham, M.W. 2016. Using genotyping-by-sequencing to develop broccoli markers for construction of a high-density linkage map and to identify quantitative trait loci associated with heat tolerance. HortScience. 51(9):S191-S192.

Genotyping-by-sequencing of glossy mutants - (Abstract Only)
Branham, S., Farnham, M.W. 2016. Genotyping-by-sequencing of glossy mutants. HortScience. 51(9):S269.

Suppression of bacterial blight on mustard greens with host plant resistance and Acibenzolar-S-Methyl - (Peer Reviewed Journal)
Keinath, A.P., Wechter, W.P., Farnham, M.W. 2016. Suppression of bacterial blight on mustard greens with host plant resistance and Acibenzolar-S-Methyl. Plant Disease. 100:1921-1926.

Genome-wide association study in arabidopsis thaliana of natural variation in seed oil melting point, a widespread adaptive trait in plants - (Peer Reviewed Journal)
Branham, S., Reba, A., Wright, S.J., Linder, C.R. 2016. Genome-wide association study in arabidopsis thaliana of natural variation in seed oil melting point, a widespread adaptive trait in plants. Journal of Heredity. doi: 10.1093/jhered/esw008.

Quantitative trait loci mapping of heat tolerance in a doubled haploid population of broccoli using genotyping-by-sequencing - (Abstract Only)
Branham, S., Couillard, D.M., Stansell, Z.J., Farnham, M.W. 2016. Quantitative trait loci mapping of heat tolerance in a doubled haploid population of broccoli using genotyping-by-sequencing. Plant and Animal Genome Conference. P0950.

Genome-wide association study of Arabidopsis thaliana identifies determinants of natural variation in seed oil composition - (Peer Reviewed Journal)
Branham, S., Reba, A., Wright, S.J., Linder, C.R. 2015. Genome-wide association study of Arabidopsis thaliana identifies determinants of natural variation in seed oil composition. Journal of Heredity. doi:10.1093/jhered/esv100.

Genetic relationships in the desert watermelon citrullus colocynthis as viewed with high-frequency, oligonucleotide–targeting active gene (HFO–TAG) markers - (Abstract Only)
Levi, A., Simmons, A.M., Massey, L.M., Coffey, J., Wechter, W.P., Tadmor, Y., Nimakayala, P., Reddt, U. 2016. Genetic relationships in the desert watermelon citrullus colocynthis as viewed with high-frequency, oligonucleotide–targeting active gene (HFO–TAG) markers. Annual International Plant & Animal Genome Conference XXIV. p1154.

Glucoraphanin and other glucosinolates in heads of broccoli cultivars - (Book / Chapter)
Farnham, M.W., Branham, S. 2016. Glucoraphanin and other glucosinolates in heads of broccoli cultivars. Broccoli: Cultivation, Nutritional Properties and Effects on Health. B.H.J. Juurlink (Ed.). Nova Science Publishers. New York, NY. 342 p.

USVL-370, A zucchini yellow mosaic virus resistant watermelon breeding line - (Peer Reviewed Journal)
Levi, A., Harris-Shultz, K.R., Ling, K. 2016. USVL-370, A zucchini yellow mosaic virus resistant watermelon breeding line. HortScience. 51:107-109.

Resistance to papaya ringspot virus-watermelon strain (PRSV-W) in the desert watermelon Citrullus colocynthis - (Peer Reviewed Journal)
Levi, A., Coffey, J., Massey, L.M., Guner, N., Oren, E., Tadmor, Y., Ling, K. 2016. Resistance to papaya ringspot virus-watermelon strain (PRSV-W) in the desert watermelon Citrullus colocynthis. HortScience. 51:4-7.

Genetic diversity and population structure of collard landraces and their relationship to other Brassica oleracea crops - (Peer Reviewed Journal)
Branham, S., Couillard, D.M., Stansell, Z.J., Farnham, M.W. 2015. Genetic diversity and population structure of collard landraces and their relationship to other Brassica oleracea crops. The Plant Genome. 8(3):1-11.

Evaluation of consumer acceptance of west coast versus east coast-produced broccoli through sensory analysis of quality rating factors and nutritionally important metabolites - (Abstract Only)
Sams, C.E., Penfield, M., Kopsell, D., Gomez, M., Bjorkman, T., Farnham, M.W. 2015. Evaluation of consumer acceptance of west coast versus east coast-produced broccoli through sensory analysis of quality rating factors and nutritionally important metabolites. HortScience. 50:S267.

Development of ZYMV-resistant lines using genomic tools - (Abstract Only)
Levi, A., Ling, K. 2015. Development of ZYMV-resistant lines using genomic tools. International Symposium on Cucurbits Proceedings. 41. https://www.verticesur.es/congresos/CUCURBITS2015/programme.php

Sequence-characterized amplified polymorphism markers for selecting rind stripe pattern in watermelon (Citrullus lanatus var. lanatus) - (Peer Reviewed Journal)
Kim, H., Han, D., Kang, J., Choi, Y., Levi, A., Park, Y. 2015. Sequence-characterized amplified polymorphism markers for selecting rind stripe pattern in watermelon (Citrullus lanatus var. lanatus). Journal of Horticulture, Environment and Biotechnology. 56:341-349.

Genetic diversity and population structure of collard landraces collected in the Southeast - (Abstract Only)
Pelc, S., Farnham, M.W., Couillard, D.M., Stansell, Z.J. 2015. Genetic diversity and population structure of collard landraces collected in the Southeast. HortScience. 50:S391.

Using weighted trait indices to select the best performing broccoli hybrids in multi-site and multi-year trials - (Abstract Only)
Stansell, Z.J., Farnham, M.W., Pelc, S., Couillard, D.M., Bjorkman, T. 2015. Using weighted trait indices to select the best performing broccoli hybrids in multi-site and multi-year trials. HortScience. 50:S171.

Increasing plant density in eastern United States broccoli production systems to maximize marketable head yields - (Peer Reviewed Journal)
Ward, B., Smith, P., James, S., Stansell, Z.J., Farnham, M.W. 2015. Increasing plant density in eastern United States broccoli production systems to maximize marketable head yields. HortTechnology. 25:330-334.

Collard land races are novel sources of glucoraphanin and other aliphatic glucosinolates - (Peer Reviewed Journal)
Stansell, Z.J., Cory, W., Couillard, D.M., Farnham, M.W. 2015. Collard land races are novel sources of glucoraphanin and other aliphatic glucosinolates. Plant Breeding. 134:350-355.

Genetic diversity and population structure of collard landraces - (Abstract Only)
Pelc, S., Couillard, D.M., Stansell, Z.J., Farnham, M.W. 2015. Genetic diversity and population structure of collard landraces. HortScience. 50:S40.

Genetic relationships in Cucurbita pepo (pumpkin, squash, gourd) as viewed with high frequency oligonucleotide–targeting active gene (HFO–TAG) markers - (Peer Reviewed Journal)
Paris, H., Faigenboim, A., Reddy, U., Donahoo, R.S., Levi, A. 2015. Genetic relationships in Cucurbita pepo (pumpkin, squash, gourd) as viewed with high frequency oligonucleotide–targeting active gene (HFO–TAG) markers. Genetic Resources and Crop Evolution. 62:1095-1111.

Establishing an eastern broccoli industry: where are we and where do we need to go? - (Proceedings)
Farnham, M.W. 2014. Establishing an eastern broccoli industry: where are we and where do we need to go?. Southeast Vegetable and Fruit Expo. North Carolina Vegetable Growers Association Yearbook. p43-44.

Differential gene expression and alternative splicing between diploid and tetraploid watermelon lines - (Peer Reviewed Journal)

Using genomic data for enhancing disease and pest resistance in watermelon cultivars - (Proceedings)
Levi, A., Massey, L.M., Donahoo, R.S., Jarret, R.L., Wechter, W.P., Thies, J.A., Kousik, C.S., Ling, K., Reddy, U.K., Nimmakayala, P., Fei, Z. 2014. Using genomic data for enhancing disease and pest resistance in watermelon cultivars. Cucurbitaceae Proceedings. 161-163.

Utilizing Citrullus lanatus var. citroides germplasm for developing tetraploid lines useful as rootstocks and in breeding programs of seedless watermelon lines - (Abstract Only)
Levi, A., Thies, J.A., Wechter, W.P., Kousik, C.S., Harrison Jr, H.F., Weng, Y., Hassell, R. 2014. Utilizing Citrullus lanatus var. citroides germplasm for developing tetraploid lines useful as rootstocks and in breeding programs of seedless watermelon lines. Cucurbitaceae Proceedings. 27:A48.

High-resolution genetic map for understanding the effect of genome-wide recombination rate, selection sweep and linkage disequilibrium on nucleotide diversity in watermelon - (Peer Reviewed Journal)
Reddy, U., Nimmakayala, P., Levi, A., Abburi, V.L., Saminathan, T., Tomasson, Y., Vajja, V.G., Reddy, R., Abburi, L., Wehner, T., Ronin, Y. 2014. High-resolution genetic map for understanding the effect of genome-wide recombination rate, selection sweep and linkage disequilibrium on nucleotide diversity in watermelon. Genes, Genomes, Genetics. 4:2219-2230.

Emergence timing and fitness consequences of variation in seed oil composition in Arabidopsis thaliana Reprint Icon - (Peer Reviewed Journal)
Pelc, S., Linder, C.R. 2015. Emergence timing and fitness consequences of variation in seed oil composition in Arabidopsis thaliana. Ecology and Evolution. 5(1): 164–171.

Scanning genomic areas under selection sweep and association mapping as tools to identify horticultural important genes in watermelon - (Peer Reviewed Journal)
Reddy, U., Abburi, L., Abburi, V., Reddy, R., Saminathan, T., Tomasson, Y., Wehner, T., Levi, A., Wehner, T., Nimmakayala, P. 2014. Scanning genomic areas under selection sweep and association mapping as tools to identify horticultural important genes in watermelon. Journal of Heredity. 106:166-176.

Single nucleotide polymorphisms generated by genotyping by sequencing to characterize genome-wide diversity, linkage disequilibrium, and selective sweeps in cultivated watermelon Reprint Icon - (Peer Reviewed Journal)
Nimmakayala, P., Levi, A., Abburi, L., Abburi, V.L., Tomason, Y.R., Saminathan, T., Vajja, V.G., Reddy, R., Wehner, T.C., Mitchell, S.E., Reddy, U.K. 2014. Single nucleotide polymorphisms generated by genotyping by sequencing to characterize genome-wide diversity, linkage disequilibrium, and selective sweeps in cultivated watermelon. Biomed Central (BMC) Genomics. 15:767.

A major QTL associated with Fusarium oxysporum race 1 resistance identified in genetic populations derived from closely related watermelon lines using selective genotyping and genotyping-by-sequencing for SNP discovery - (Peer Reviewed Journal)
Lambel, S., Lanini, B., Vivoda, E., Fauve, J., Wechter, W.P., Harris-Shultz, K.R., Massey, L.M., Levi, A. 2014. A major QTL associated with Fusarium oxysporum race 1 resistance identified in genetic populations derived from closely related watermelon lines using selective genotyping and genotyping-by-sequencing for SNP discovery. Theoretical and Applied Genetics. 127:2105-2115.

A major quantitative trait locus is associated with Fusarium Wilt Race 1 resistance in watermelon - (Abstract Only)
Lambel, S., Lanini, B., Vivoda, E., Fauve, J., Wechter, W.P., Harris-Shultz, K.R., Massey, L.M., Levi, A. 2014. A major quantitative trait locus is associated with Fusarium Wilt Race 1 resistance in watermelon. Annual International Plant & Animal Genome Conference. 127:2105-2115.

Using regional broccoli trial data to select experimental hybrids for input into advanced yield trials - (Abstract Only)
Farnham, M.W., Stansell, Z.J., Griffiths, P.D., Davis, J.M., Hutton, M., Bjorkman, T. 2014. Using regional broccoli trial data to select experimental hybrids for input into advanced yield trials. HortScience. 49(9):S242-S243.

Collard Landraces are novel sources of Glucoraphanin and other Aliphatic Glucosinolates - (Abstract Only)
Stansell, Z.J., Farnham, M.W., Cory, W. 2014. Collard Landraces are novel sources of Glucoraphanin and other Aliphatic Glucosinolates. HortScience. 49(9):S336.

Maximizing plant density affects broccoli yield and quality - (Abstract Only)
Ward, B., Farnham, M.W., Smith, P., Stansell, Z.J., James, S. 2014. Maximizing plant density affects broccoli yield and quality. HortScience. 49(9):S211.

An integrated genetic linkage map of watermelon and genetic diversity based on single nucleotide polymorphism (SNP) and simple sequence repeat (SSR) markers - (Peer Reviewed Journal)

USVL-360, a novel watermelon tetraploid germplasm line - (Peer Reviewed Journal)
Levi, A., Thies, J.A., Wechter, W.P., Farnham, M.W., Weng, Y., Hassel, R. 2013. USVL-360, a novel watermelon tetraploid germplasm line. HortScience. 49:354-357.

Gene sequences present in Citrullus sp. having been lost during domestication of watermelon - (Abstract Only)
Levi, A., Wechter, W.P., Massey, L.M., Donahoo, R.S., Jarret, R.L., Nimmakayala, P., Reddy, U.K., Fei, Z. 2014. Gene sequences present in Citrullus sp. having been lost during domestication of watermelon. Molecular Breeding. P450.

Assessing nutritional changes in a vegetable over time: issues and considerations - (Peer Reviewed Journal)
Farnham, M.W., Grusak, M.A. 2014. Assessing nutritional changes in a vegetable over time: issues and considerations. HortScience. 49:128-132.

Response to the Letter to the Editor of Crop Science from Donald R. Davis regarding our research article published in Crop Science (2011: 51:2721-2727) - (Other)
Farnham, M.W., Keinath, A.P., Grusak, M.A. 2013. Response to the Letter to the Editor of Crop Science from Donald R. Davis regarding our research article entitled "Mineral Concentration of Broccoli Florets in relation to year of cultivar release" published in Crop Science (2011: 51:2721-2727). Crop Science. 53:1830-1831.