Research Project: Trait Discovery, Genetics, and Enhancement of Allium, Cucumis, and Daucus Germplasm

Location: Vegetable Crops Research

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

Population genomics identifies genetic signatures of carrot domestication and improvement and uncovers the origin of high-carotenoid orange carrots - (Peer Reviewed Journal)
Coe, K., Bostan, H., Rolling, W.R., Turner-Hissong, S., Macko-Podgorni, A., Senalik, D.A., Liu, S., Seth, R., Curaba, J., Fentie Mengist, M., Grzebelus, D., Van Deynze, A., Dawson, J., Ellison, S., Simon, P.W., Iorizzo, M. 2023. Population genomics identifies genetic signatures of carrot domestication and improvement and uncovers the origin of high-carotenoid orange carrots. Nature Plants. 9:1643–1658. https://doi.org/10.1038/s41477-023-01526-6.

Novel players in organogenesis of and flavonoid biosynthesis in cucumber glandular trichomes - (Peer Reviewed Journal)
Feng, Z., Sun, L., Dong, M., Fan, S., Xi, K., Wang, W., Song, L., Weng, Y., Liu, X., Ren, H. 2023. Novel players in organogenesis of and flavonoid biosynthesis in cucumber glandular trichomes. Plant Physiology. 192 (4), 2723-2736. https://doi.org/10.1093/plphys/kiad236.

Characterization of purple carrot germplasm for antioxidant capacity and root concentration of anthocyanins, phenolics, and carotenoids - (Peer Reviewed Journal)
Perez, M.B., Carvajal, S., Beretta, V., Bannoud, F., Fangio, M.F., Berli, F., Fontana, A., Salomon, M.V., Gozalez, R., Valerga, L., Altamirano, J.C., Yildiz, M., Iorizzo, M., Simon, P.W., Cavagnaro, P.C. 2023. Characterization of purple carrot germplasm for antioxidant capacity and root concentration of anthocyanins, phenolics, and carotenoids. Plants. 12(9). Article 1796. https://doi.org/10.3390/plants12091796.

Improving Agrobacterium tumefaciens-mediated genetic transformation for gene function studies and mutagenesis in cucumber (Cucumis sativus) - (Peer Reviewed Journal)
Liu, H., Zhao, J., Chen, F., Wu, Z., Tan, J., Nguyen, N., Cheng, Z., Weng, Y. 2023. Improving Agrobacterium tumefaciens-mediated genetic transformation for gene function studies and mutagenesis in cucumber (Cucumis sativus). Genes. 14(3), 601. https://doi.org/10.3390/genes14030601.

Carrot genotypes differentially alter soil microbial communities and scavenge nitrogen from organic materials in soil - (Peer Reviewed Journal)
Trivino, N., Rodriguez-Sanchez, A., Filley, T., Camberato, J., Colley, M., Simon, P.W., Hoagland, L. 2023. Carrot genotypes differentially alter soil microbial communities and scavenge nitrogen from organic materials in soil. Frontiers in Plant Science. Article (the author) 2023. https://doi.org/10.1007/s11104-023-05892-0.

LTR retrotransposon insertion inside CsERECTA for a LRR receptor-like Serine/threonine-protein kinase results in compact (cp) plant architecture in cucumber - (Peer Reviewed Journal)
Chen, F., Yong, J., Zhang, G., Liu, M., Wang, Q., Zhong, H., Pan, Y., Chen, P., Weng, Y., Li, Y. 2023. LTR retrotransposon insertion inside CsERECTA for a LRR receptor-like Serine/threonine-protein kinase results in compact (cp) plant architecture in cucumber. Journal of Theoretical and Applied Genetics. Article number 31. https://doi.org/10.1007/s00122-023-04273-6.

Natural Variation in CRABS CLAW contributes to fruit length divergence in cucumber - (Peer Reviewed Journal)
Che, G., Pan, Y., Liu, X., Li, M., Zhao, J., Yan, S., Yuting, H., Wang, Z., Cheng, Z., Song, W., Zhou, Z., Wu, T., Weng, Y., Zhang, X. 2022. Natural Variation in CRABS CLAW contributes to fruit length divergence in cucumber. The Plant Cell. 35(2). https://doi.org/10.1093/plcell/koac335.

Phytochrome-interacting factor PIF3 integrates phytochrome B and UVB signaling pathways to regulate gibberellin- and auxin-dependent growth in cucumber hypocotyls - (Peer Reviewed Journal)
Zhao, J., Bo, K., Pan, Y., Li, Y., Yu, D., Li, C., Chang, J., Wu, S., Wang, Z., Zhang, X., Gu, X., Weng, Y. 2022. Phytochrome-interacting factor PIF3 integrates phytochrome B and UVB signaling pathways to regulate gibberellin- and auxin-dependent growth in cucumber hypocotyls. Journal of Experimental Botany. 74(15):4520-4539. https://doi.org/10.1093/plcell/koac335.

Variation in seed germination and amylase activity of diverse carrot [daucus carota (L.)] germplasm under simulated drought stress - (Peer Reviewed Journal)
Nijabat, A., Manzoor, S., Faiz, S., Naveed, N., Bolton, A., Khan, B., Ali, A., Simon, P.W. 2023. Variation in seed germination and amylase activity of diverse carrot [daucus carota (L.)] germplasm under simulated drought stress. HortScience. 58(2):205-214. https://doi.org/10.21273/HORTSCI16806-22.

Sigma factor binding protein 1 (CsSIB1) is a putative candidate of the major-effect QTL dm5.3 for downy mildew resistance in cucumber (Cucumis sativus) - (Peer Reviewed Journal)
Tan, J., Wang, Y., Dymerski, R.D., Wu, Z., Weng, Y. 2022. Sigma factor binding protein 1 (CsSIB1) is a putative candidate of the major-effect QTL dm5.3 for downy mildew resistance in cucumber (Cucumis sativus). Theoretical and Applied Genetics. 135:4197–4215. https://doi.org/10.1007/s00122-022-04212-x.

The fruit glossiness locus, dull fruit (D) encodes a C2H2 type zinc finger transcription factor CsDULL in cucumber (Cucumis sativus L.) - (Peer Reviewed Journal)
Zhai, X., Wu, H., Wang, Y., Zhang, Z., Shan, L., Zhao, X., Wang, R., Liu, C., Weng, Y., Wang, Y., Liu, X., Ren, H. 2022. The fruit glossiness locus, dull fruit (D) encodes a C2H2 type zinc finger transcription factor CsDULL in cucumber (Cucumis sativus L.). Horticulture Research. 2022, 9: uhac146. https://doi.org/10.1093/hr/uhac146.

EPIDERMAL PATTERNING FACTOR 2-like (McEPFL2) gene is a putative candidate for the continuous ridge (cr) fruit skin locus in bitter gourd (Momordica charantia L.) - (Peer Reviewed Journal)
Yang, J., Weng, Y., Li, H., Kong, Q., Wang, W., Yan, C., Wang, L. 2022. EPIDERMAL PATTERNING FACTOR 2-like (McEPFL2) gene is a putative candidate for the continuous ridge (cr) fruit skin locus in bitter gourd (Momordica charantia L.). Genes. 2022, 13(7), 1148. https://doi.org/10.3390/genes13071148.

Functional Copy Number Variation of CsSHINE1 is Associated with Fruit Skin Netting Intensity in Cucumber, Cucumis sativus - (Peer Reviewed Journal)
Zhang, H., Wang, Y., Tan, J., Weng, Y. 2022. Functional copy number variation of CsSHINE1 is associated with fruit skin netting intensity in cucumber, cucumis sativus. Journal of Theoretical and Applied Genetics. 135, pages2101–2119. https://doi.org/10.1007/s00122-022-04100-4.

Sensory profiles of 10 cucumber varieties using a panel trained with chemical references - (Peer Reviewed Journal)
Williams, C., Weng, Y., Du, X. 2022. Sensory profiles of 10 cucumber varieties using a panel trained with chemical references. ACS Food Science and Technology. 2:815-824. https://doi.org/10.1021/acsfoodscitech.1c00453.

Fresh cucumber fruit physicochemical properties, consumer acceptance, and impact of variety and harvest date - (Peer Reviewed Journal)
Du, X., Davila, M., Williams, C., Weng, Y. 2022. Fresh cucumber fruit physicochemical properties, consumer acceptance, and impact of variety and harvest date. Journal of the Science of Food and Agriculture. 2, 616-629. https://doi.org/10.1021/acsfoodscitech.1c00433.

Current progress in genetic and genomics-aided breeding for stress resistance in cucumber (Cucumis sativus L.) - (Peer Reviewed Journal)
Das, A., Singh, S., Islam, Z., Munsh, A., Behera, T., Dutta, S., Weng, Y., Dey, S. 2022. Current progress in genetic and genomics-aided breeding for stress resistance in cucumber (Cucumis sativus L.). Scientia Horticulturae. 300, 111059. https://doi.org/10.1016/j.scienta.2022.111059.

Promoter variation in a homeobox gene, CpDll, is associated with deeply lobed leaf in Cucurbita pepo L - (Peer Reviewed Journal)
Bo, K., Duan, Y., Qiu, X., Zhang, M., Shu, Q., Sun, Y., He, Y., Shi, Y., Weng, Y., Wang, C. 2022. Promoter variation in a homeobox gene, CpDll, is associated with deeply lobed leaf in Cucurbita pepo L. Theoretical and Applied Genetics. 135:1223–1234. https://doi.org/10.1007/s00122-021-04026-3.

Genetic analyses and mapping of resistance to fusarium basal rot in onion - (Peer Reviewed Journal)
Straley, E., Marzu, J., Havey, M.J. 2021. Genetic analyses and mapping of resistance to fusarium basal rot in onion. Journal of the American Society for Horticultural Science. 7,538. https://doi.org/10.3390/horticulturae7120538.

Development of carrot nutraceutical products as an alternative supplement for the prevention of disease - (Peer Reviewed Journal)
Riaz, N., Yousaf, Z., Yasmin, Z., Munawar, M., Younas, A., Rashid, M., Aftab, A., Shamsheer, H., Yasin, H., Najeebullah, M., Simon, P.W. 2022. Development of carrot nutraceutical products as an alternative supplement for the prevention of disease. Frontiers in Nutrition. 8:787351. https://doi.org/10.3389/fnut.2021.787351.

Genetic characterization of carrot root shape and size using genome-wide association analysis and genomic-estimated breeding values. - (Peer Reviewed Journal)
Brainard, S., Ellison, S., Simon, P.W., Dawson, J., Goldman, I. 2021. Genetic characterization of carrot root shape and size using genome-wide association analysis and genomic-estimated breeding values.. Theoretical and Applied Genetics. 135:605–622. https://doi.org/10.1007/s00122-021-03988-8.

CarrotOmics: a genetics and comparative genomics database for carrot (Daucus carota) - (Peer Reviewed Journal)
Rolling, W.R., Senalik, D.A., Iorizzo, M., Ellison, S., Van Deynze, A., Simon, P.W. 2022. CarrotOmics: a genetics and comparative genomics database for carrot (Daucus carota). Horticulture Research. 2022, 1-8. https://doi.org/10.1093/database/baac079.

Identification of bacterial wilt (erwinia tracheiphila) resistances in USDA melon collection - (Peer Reviewed Journal)
Acharya, B., Mackasmiel, L., Taheri, A., Ondzighi-Assoume, C.A., Weng, Y., Dumenyo, C.K. 2021. Identification of bacterial wilt (erwinia tracheiphila) resistances in USDA melon collection. Plants. 10(9), 1972. https://doi.org/10.3390/plants10091972.

Genetic and transcription profile analysis of tissue-specific anthocyanin pigmentation in the carrot root phloem - (Peer Reviewed Journal)
Bannoud, F., Carvajal, S., Ellison, S., Senalik, D.A., Gomez Talquenca, S., Massimo, I., Simon, P.W., Cavagnaro, P. 2021. Genetic and transcription profile analysis of tissue-specific anthocyanin pigmentation in the carrot root phloem. Genes. 12(10), 1464. https://doi.org/10.3390/genes12101464.

Genetic resources and vulnerabilities of major cucurbit crops - (Peer Reviewed Journal)
Grumet, R., Mccreight, J.D., Mcgregor, C., Weng, Y., Mazourek, M., Reitsma, K., Labate, J.A., Davis, A., Fei, Z. 2021. Genetic resources and vulnerabilities of major cucurbit crops. Gene. genes12 081222. https://doi.org/10.3390/genes12081222.

The influence of the Or and Carotene Hydroxylase genes on carotenoid accumulation in orange carrots [Daucus carota (L.)] - (Peer Reviewed Journal)
Coe, K., Ellison, S., Senalik, D.A., Dawson, J., Simon, P.W. 2021. The influence of the Or and Carotene Hydroxylase genes on carotenoid accumulation in orange carrots [Daucus carota (L.)]. Theoretical and Applied Genetics. 134:3351–3362. https://doi.org/10.1007/s00122-021-03901-3.

Genetic analysis of mitochondrial sorting from the MSC3 mosaic mutant of cucumber - (Peer Reviewed Journal)
Wallace, L.T., Havey, M.J. 2021. Genetic analysis of mitochondrial sorting from the MSC3 mosaic mutant of cucumber. Journal of the American Society for Horticultural Science. 146(5):346-350. https://doi.org/10.21273/JASHS05075-21.

Transcriptomic and histological analyses of the response of susceptible and resistant cucumbers to root-knot nematode infection reveal complex resistance via multiple signaling pathways - (Peer Reviewed Journal)
Li, X., Sun, Y., Yang, Y., Yang, X., Xue, W., Wu, M., Chen, P., Weng, Y., Chen, S. 2021. Transcriptomic and histological analyses of the response of susceptible and resistant cucumbers to root-knot nematode infection reveal complex resistance via multiple signalling pathways. Frontiers in Plant Science. 12. Article 675429. https://doi.org/10.3389/fpls.2021.675429.

A mutation in CsHY2 encoding a phytochromobilin (PFB) synthase leads to a deficiency in phytochrome system and elongated hypocotyl 1(elh1) phenotype in cucumber (Cucumis sativus L.) - (Peer Reviewed Journal)
Liangliang, H., Zhuoshuai, J., Peng, L., Jing, S., Weng, Y., Peng, C., Shenli, D., Aiming, W., Yuhong, L. 2021. A mutation in CsHY2 encoding a phytochromobilin (PFB) synthase leads to a deficiency in phytochrome system and elongated hypocotyl 1(elh1) phenotype in cucumber (Cucumis sativus L.). Theoretical and Applied Genetics. 134:2639-2652. https://doi.org/10.1007/s00122-021-03849-4.

CsKTN1 for a katanin p60 subunit is associated with the regulation of fruit elongation in cucumber (Cucumis sativus L.) - (Peer Reviewed Journal)
Hul, W., Jing, S., Fang, Y., Weng, Y., Peng, C., Shenli, D., Aiming, W., Yuhong, L. 2021. CsKTN1 for a katanin p60 subunit is associated with the regulation of fruit elongation in cucumber (Cucumis sativus L.). Theoretical and Applied Genetics. 134:2429-2441. https://doi.org/10.1007/s00122-021-03833-y.

Molecular, morphological and palynological assessment of hemerocallis core collection - (Peer Reviewed Journal)
Li, S., Ji, F., Hou, F., Shi, Q., Xing, G., Chen, H., Weng, Y., Kang, X. 2021. Molecular, morphological and palynological assessment of hemerocallis core collection. Scientia Horticulturae. 285. Article 110181. https://doi.org/10.1016/j.scienta.2021.110181.

Potential for managing onion thrips (Thrips tabaci) in organic onion production using multiple IPM tactics - (Peer Reviewed Journal)
Iglesias, L., Havey, M.J., Nault, B.A. 2021. Potential for managing onion thrips (Thrips tabaci) in organic onion production using multiple IPM tactics. Insects. 12(3). Article 207. https://doi.org/10.3390/insects12030207.

Genetic analysis of the unique epicuticular-wax profile of ‘Odourless Greenleaf’ onion - (Peer Reviewed Journal)
Havey, M.J., Hunsaker, D.J., Munaiz, E.D. 2021. Genetic analysis of the unique epicuticular-wax profile of ‘Odourless Greenleaf’ onion. Journal of the American Society for Horticultural Science. 146(2):118-124. https://doi.org/10.21273/JASHS05024-20.

Editorial: translational research for cucurbit molecular breeding: traits, markers, and genes - (Peer Reviewed Journal)
Weng, Y., Garcia-Mas, J., Levi, A., Luan, F. 2020. Editorial: translational research for cucurbit molecular breeding: traits, markers, and genes. Frontiers in Plant Science. 11. Article 615346. https://doi.org/10.3389/fpls.2020.615346.

Genetic linkage mapping and QTL identification for morphology and fruit quality related traits of melon by SNP based CAPS markers - (Peer Reviewed Journal)
Amanullah, S., Gao, P., Agyei, B., Osaeab, A., Yang, T., Liu, S., Weng, Y., Luan, F. 2021. Genetic linkage mapping and QTL identification for morphology and fruit quality related traits of melon by SNP based CAPS markers. Scientia Horticulturae. 278(27 February 2021). Article 109849. https://doi.org/10.1016/j.scienta.2020.109849.

Identities of and Phenotypic Variation for Epicuticular Waxes among Leaves and Plants from Inbred Onion Populations - (Peer Reviewed Journal)
Khosa, J.S., Hunsaker, D.J., Havey, M.J. 2020. Identities of and Phenotypic Variation for Epicuticular Waxes among Leaves and Plants from Inbred Onion Populations. HortScience. 55(12):2008–2010. 2020. https://doi.org/10.21273/HORTSCI15414-20.

Quantitative Trait Loci for Horticulturally Important Traits Defining the Sikkim Cucumber, Cucumis sativus var. sikkimensis - (Peer Reviewed Journal)
Wang, Y., Jihang, B., Dymerski, R., Xu, X., Weng, Y. 2020. Quantitative Trait Loci for Horticulturally Important Traits Defining the Sikkim Cucumber, Cucumis sativus var. sikkimensis. Theoretical and Applied Genetics. (2021) 134:229–247. https://doi.org/10.1007/s00122-020-03693-y.

WUSCHEL-Related Homeobox1 (WOX1) regulates vein patterning and leaf size in Cucumis sativus - (Peer Reviewed Journal)
Wang, H., Niu, H., Li, C., Shen, G., Liu, X., Weng, Y., Wu, T., Li, Z. 2020. WUSCHEL-Related Homeobox1 (WOX1) regulates vein patterning and leaf size in Cucumis sativus. Horticulture Research. (2020) 7:182. https://doi.org/10.1038/s41438-020-00404-y.

Tapping into wild carrot diversity for new sources of abiotic stress tolerance to strengthen carrot pre-breeding in Bangladesh and Pakistan - (Peer Reviewed Journal)
Simon, P.W., Rolling, W.R., Senalik, D.A., Bolton, A., Rahim, M.A., Mannan, M., Islam, F., Ali, A., Nijabat, A., Naveed, N.H., Hussain, R., Ijaz, A. 2021. Tapping into wild carrot diversity for new sources of abiotic stress tolerance to strengthen carrot pre-breeding in Bangladesh and Pakistan. Crop Science. 61(1):163-176. https://doi.org/10.1002/csc2.20333.

Melon short internode (CmSi) encodes an erecta-like receptor kinase regulating stem elongation through auxin signaling - (Peer Reviewed Journal)
Yang, S., Zhang, K., Zhu, H., Zhang, X., Yan, W., Liu, D., Hu, J., Wu, Y., Weng, Y., Yang, L. 2020. Melon short internode (CmSi) encodes an erecta-like receptor kinase regulating stem elongation through auxin signaling. Horticulture Research. 7. Article 202. https://doi.org/10.1038/s41438-020-00426-6.

Carrots and related Apiaceae crops, 2nd edition - (Book / Chapter)
Geoffriau, E., Simon, P.W. (editors). 2021. Carrots and related Apiaceae crops, 2nd edition. Boston: CAB International. 346 p.

Carrot anthocyanins genetics and genomics: Status and perspectives to optimize its application for the food colorant industry - (Peer Reviewed Journal)
Iorizzo, M., Curaba, J., Pottorff, M., Ferruzzi, M., Simon, P.W., Cavagnaro, P. 2020. Carrot anthocyanins genetics and genomics: Status and perspectives to optimize its application for the food colorant industry. Genes. 11(8). Article 906. https://doi.org/10.3390/genes11080906.

Changes in the core endophytic mycobiome of carrot taproots in response to crop management and genotype - (Peer Reviewed Journal)
Abdelrazek, S., Choudhari, S., Thimmapuram, J., Simon, P.W., Colley, M., Mengiste, T., Hoagland, L. 2020. Changes in the core endophytic mycobiome of carrot taproots in response to crop management and genotype. Scientific Reports. 10. Article 13685. https://doi.org/10.1038/s41598-020-70683-x.

Reflectance spectroscopy for QTL mapping of amounts and types of epicuticular waxes on onion leaves - (Peer Reviewed Journal)
Munaiz, E.D., Townsend, P.A., Havey, M.J. 2020. Reflectance spectroscopy for QTL mapping of amounts and types of epicuticular waxes on onion leaves. Molecules. 2020, 25(15), 3454. https://doi.org/10.3390/molecules25153454.

Cucumis sativus: Chromosome evolution, domestication, and genetic diversity: Implications for cucumber breeding - (Peer Reviewed Journal)
Weng, Y. 2021. Cucumis sativus: Chromosome evolution, domestication, and genetic diversity: Implications for cucumber breeding. In: Goldman, I., editor. Plant Breeding Reviews, Volume 44. Wiley Online Library. p. 79-111. https://doi.org/10.1002/9781119717003.ch4.

Cell membrane stability and relative cell injury in response to heat stress during early and late seedling stages of diverse carrot (Daucus carota L.) germplasm - (Peer Reviewed Journal)
Nijabat, A., Bolton, A., Mahmood-Ur-Rehman, M., Ijaz Shah, A., Hussain, R., Naveed, N., Ali, A., Simon, P.W. 2020. Cell membrane stability and relative cell injury in response to heat stress during early and late seedling stages of diverse carrot (Daucus carota L.) germplasm. Hortscience Proceedings. 55(9):1446-1452. https://doi.org/10.21273/HORTSCI15058-20.

Domestication and improvement history of melon from selection signal and genome-wide association analyses in 297 resequenced accessions - (Peer Reviewed Journal)
Liu, S., Gao, P., Zhu, Q., Zhu, Z., Liu, H., Wang, X., Weng, Y., Gao, M., Luan, F. 2020. Domestication and improvement history of melon from selection signal and genome-wide association analyses in 297 resequenced accessions. Plant Biotechnology Journal. (2020), pp. 1–14. https://doi.org/10.1111/pbi.13434.

Mining for candidate genes controlling secondary growth of the carrot storage root - (Peer Reviewed Journal)
Macko-Podgórni, A., Stelmach, K., Kwolek, K., Machaj, G., Ellison, S., Senalik, D.A., Simon, P.W., Grzebelus, D. 2020. Mining for candidate genes controlling secondary growth of the carrot storage root. International Journal of Molecular Sciences. 21(12). Article 4263. https://doi.org/10.3390/ijms21124263.

Carrot endophytes: role of crop management system and genotype on composition and antagonistic activity towards Alternaria dauci - (Peer Reviewed Journal)
Abdelrazek, S., Simon, P.W., Colley, M., Aime, C., Mengiste, T., Hoagland, L. 2020. Carrot endophytes: role of crop management system and genotype on composition and antagonistic activity towards Alternaria dauci. PLoS ONE. 15(6). Article e0233783. https://doi.org/10.1371/journal.pone.0233783.

Carrot endophytes: role of crop management system and genotype on composition and antagonistic activity towards Alternaria dauci - (Peer Reviewed Journal)
Abdelrazazek, S., Simon, P.W., Colley, M., Aime, C., Mengiste, T., Hoagland, L. 2020. Carrot endophytes: role of crop management system and genotype on composition and antagonistic activity towards Alternaria dauci. PLoS One. 1/26 (2020). https://doi.org/10.1371/journal.pone.0233783.

Overlapping vitamin A interventions with provitamin A carotenoids and preformed vitamin A fortificant cause high liver retinol stores in male mongolian gerbils - (Peer Reviewed Journal)
Sowa, M., Mourao, L., Sheftel, J., Kaeppler, M., Simons, G., Davis, C.R., Simon, P.W., Pixley, K.V., Tanumihardjo, S.A. 2020. Overlapping vitamin A interventions with provitamin A carotenoids and preformed vitamin A fortificant cause high liver retinol stores in male mongolian gerbils. Journal of Nutrition. 150(11):2912-2923. https://doi.org/10.1093/jn/nxaa142.

Subspecies variation of Daucus carota coastal (“gummifer”) morphotypes using genotyping-by-sequencing - (Peer Reviewed Journal)
Flores, F.M., Crespo, M.B., Simon, P.W., Ruess, H.M., Reitsma, K., Geoffriau, E., Allender, C., Mezghani, N., Spooner, D.M. 2020. Subspecies variation of Daucus carota coastal (“gummifer”) morphotypes using genotyping-by-sequencing. Systematic Botany. Volume 45, Number 3, September 2020, pp. 688-702(15). https://doi.org/10.1600/036364420X15935294613527.

Gene regulatory network of carpel number variation in cucumber - (Peer Reviewed Journal)
Che, G., Gu, R., Zhao, J., Liu, X., Cheng, Z., Wang, Z., Liu, R., Yan, L., Weng, Y., Zhang, X., Zi, H., Song, X., Shen, J. 2020. Gene regulatory network of carpel number variation in cucumber. Development. 147(7). https://doi.org/10.1242/dev.184788.

QTL for horticulturally important traits associated with pleiotropic andromonoecy and carpel number loci, and a paracentric inversion in cucumber - (Peer Reviewed Journal)
Pan, Y., Wen, C., Han, Y., Wang, Y., Li, Y., Li, S., Cheng, X., Weng, Y. 2020. QTL for horticulturally important traits associated with pleiotropic andromonoecy and carpel number loci, and a paracentric inversion in cucumber. Journal of Theoretical and Applied Genetics. 133:2271-2290. https://doi.org/10.1007/s00122-020-03596-y.

First generation genome editing in potato using hairy root transformation - (Peer Reviewed Journal)
Butler, N.M., Jansky, S.H., Jiang, J. 2020. First generation genome editing in potato using hairy root transformation. Plant Biotechnology Journal. p.1-9. https://doi.org/10.1111/pbi.13376.

Gynoecy instability in cucumber (Cucumis sativus L.) is due to unequal crossover at the copy number variation-dependent femaleness (F) locus - (Peer Reviewed Journal)
Li, Z., Han, Y., Niu, H., Wang, Y., Jiang, B., Weng, Y. 2020. Gynoecy instability in cucumber (Cucumis sativus L.) is due to unequal crossover at the copy number variation-dependent femaleness (F) locus. Horticulture Research. 7:32. https://doi.org/10.1038/s41438-020-0251-2.

Variable penetrance among different sources of the male-fertility-restoration allele of onion - (Peer Reviewed Journal)
Lee, H., Havey, M.J. 2020. Variable penetrance among different sources of the male fertility restoration allele of onion. HortScience. 55(4):543-546. https://doi.org/10.21273/HORTSCI14709-19.

90 years of USDA onion breeding for resistance to onion thrips - (Trade Journal)
Havey, M.J. 2020. 90 years of USDA onion breeding for resistance to onion thrips. Onion World. 36:8-9.

Identification of an SCPL gene controlling anthocyanin acylation in carrot (Daucus carota L.) root - (Peer Reviewed Journal)
Curaba, J., Bostan, H., Cavagnaro, P., Senalik, D.A., Mengist, M., Zhao, Y., Simon, P.W., Iorizzo, M. 2020. Identification of an SCPL gene controlling anthocyanin acylation in carrot (Daucus carota L.) root. Frontiers in Plant Science. 10(1770):1-17. https://doi.org/10.3389/fpls.2019.01770.

Genetic mapping of chartreuse bulb color in onion - (Peer Reviewed Journal)
Havey, M.J. 2020. Genetic mapping of chartreuse bulb color in onion. Journal of the American Society for Horticultural Science. 145(2):110-119. https://doi.org/10.21273/JASHS04861-20.

Molecularly tagged genes and quantitative trait loci in cucumber - and recommendation of controlled vocabulary for QTL mapping - (Peer Reviewed Journal)
Wang, Y., Bo, K., Gu, X., Pan, J., Li, Y., Chen, J., Wen, C., Ren, Z., Ren, H., Chen, X., Grumet, R., Weng, Y. 2020. Molecularly tagged genes and quantitative trait loci in cucumber with recommendations for QTL nomenclature. Horticulture Research. 7:3. https://doi.org/10.1038/s41438-019-0226-3.

Genetic Architecture of Fruit Size Variation in Cucurbits: a comparative perspective - (Peer Reviewed Journal)
Pan, Y., Wang, Y., McGregor, C., Liu, S., Luan, F., Meiling, G., Weng, Y. 2019. Genetic architecture of fruit size and shape variation in cucurbits: a comparative perspective. Theoretical and Applied Genetics. 133:1-21. https://doi.org/10.1007/s00122-019-03481-3.

Genetic analyses of epicuticular waxes associated with the glossy foliage of ‘White Persian’ onion - (Peer Reviewed Journal)
Munaiz, E.D., Havey, M.J. 2019. Genetic analyses of epicuticular waxes associated with the glossy foliage of ‘White Persian’ onion. Journal of the American Society for Horticultural Science. 145(1):67-72. https://doi.org/10.21273/JASHS04840-19.

QTL and transcriptomic analyses implicate cuticle transcription factor SHINE as a source of natural variation for epidermal traits in cucumber fruit - (Peer Reviewed Journal)
Rett-Cadman, S., Colle, M., Mansfeld, B.N., Barry, C., Wang, Y., Weng, Y., Gao, L., Fei, Z., Grumet, R. 2019. QTL and transcriptomic analyses implicate cuticle transcription factor SHINE as a source of natural variation for epidermal traits in cucumber fruit. Frontiers in Plant Science. 10:1536. https://doi.org/10.3389/fpls.2019.01536.

Investigating Carrot Colors to Produce Healthier Crops - (Literature Review)
Simon, P.W. 2019. Investigating Carrot Colors to Produce Healthier Crops . Scientia Global. https://doi.org/10.33548/SCIENTIA433.

Genetic analyses and mapping of pink-root resistance in onion - (Peer Reviewed Journal)
Colcol Marzu, J., Straley, E., Havey, M.J. 2019. Genetic analyses and mapping of pink-root resistance in onion. Journal of the American Society for Horticultural Science. 143(6):503-507. https://doi.org/10.21273/JASHS04509-18.

Amounts and types of epicuticular leaf waxes among onion accessions selected for reduced damage by onion thrips - (Peer Reviewed Journal)
Munaiz, E.D., Groves, R.L., Havey, M.J. 2019. Amounts and types of epicuticular leaf waxes among onion accessions selected for reduced damage by onion thrips. Journal of the American Society for Horticultural Science. Volume 145: Issue 1,page 30-35. https://doi.org/10.21273/JASHS04773-19.

Amounts and types of epicuticular leaf waxes among onion accessions selected for reduced damage by onion thrips - (Peer Reviewed Journal)
Munaiz, E.D., Groves, R.L., Havey, M.J. 2019. Amounts and types of epicuticular leaf waxes among onion accessions selected for reduced damage by onion thrips. Journal of the American Society for Horticultural Science. 145(1):30-35. https://doi.org/10.21273/JASHS04773-19.

Improving the health benefits of snap bean: Genome wide association studies of total phenolic content - (Peer Reviewed Journal)
Myers, J.R., Wallace, L.T., Moghaddam, S.M., Kleintop, A.E., Echeverria, D., Thompson, H.J., Brick, M.A., Lee, R., McClean, P.E. 2019. Improving the health benefits of snap bean: Genome- wide association studies of total phenolic content. Nutrients. 11(10):2509. https://doi.org/10.3390/nu11102509.

Quantitative trait loci for fruit size and flowering time-related traits under domestication and diversifying selection in cucumber (Cucumis sativus) - (Peer Reviewed Journal)
Sheng, Y., Pan, Y., Yuhong, L., Yang, L., Weng, Y. 2019. Quantitative trait loci for fruit size and flowering time-related traits under domestication and diversifying selection in cucumber (Cucumis sativus). John Wiley Journal. 139:176-191. https://doi.org/10.1111/pbr.12754.

Identification of resistance to Fusarium basal rot and improved seedling vigour through the creation and characterisation of a novel onion diversity set - (Peer Reviewed Journal)
Taylor, A., Teakle, G.R., Walley, P.G., Finsh-Savage, W., Jackson, A.C., Jones, J.E., Hand, P., Thomas, B., Havey, M.J., Pink, D.A., Clarkson, J.P. 2019. Identification of resistance to Fusarium basal rot and improved seedling vigour through the creation and characterisation of a novel onion diversity set. Frontiers in Plant Science. 132:3245–3264. https://doi.org/10.1007/s00122-019-03422-0.

CsTFL1 inhibits determinate growth through interaction with CsNOT2 and CsFDP in cucumber (Cucumis sativus L.) - (Peer Reviewed Journal)
Wen, C., Zhao, W., Liu, W., Yang, L., Wang, Y., Liu, X., Xu, Y., Ren, H., Guo, Y., Li, G., Li, J., Weng, Y., Zhang, X. 2019. CsTFL1 inhibits determinate growth through interaction with CsNOT2 and CsFDP in cucumber (Cucumis sativus L.). Development. 146(14):1-12. https://doi.org/10.1242/dev.180166.

Changes in copy numbers of mitochondrial genes during melon leaf development reveals fewer genes than mitochondria - (Peer Reviewed Journal)
Shen, J., Zhang, Y., Havey, M.J., Shou, W. 2019. Changes in copy numbers of mitochondrial genes during melon leaf development reveals fewer genes than mitochondria. Horticulture Research. 6(1):1-9. https://doi.org/10.1038/s41438-019-0177-8.

The carrot genome - (Book / Chapter)
Simon, P.W., Iorizzo, M., Grzebelus, D., Baranski, R. 2019. The carrot genome. Cham, Switzerland:Springer Nature Switzerland AG. 372 p. https://doi.org/10.1007/978-3-030-03389-7.

Variation for heat tolerance during seed germination in diverse carrot [Daucus carota (L.)] germplasm - (Peer Reviewed Journal)
Bolton, A., Nijabat, A., Mahmood-Ur-Rehman, M., Naveed, N., Mannan, A., Ali, A., Rahim, M., Simon, P.W. 2019. Variation for heat tolerance during seed germination in diverse carrot [Daucus carota (L.)] germplasm. HortScience. 54(9):1470–1476. https://doi.org/10.21273/HORTSCI14144-19.

Dissecting the genetic control of root and leaf tissue-specific anthocyanin pigmentation in carrot (Daucus carota L.) - (Peer Reviewed Journal)
Bannoud, F., Ellison, S., Paolinelli, M., Horejsi, T.F., Senalik, D.A., Fanzone, M., Iorizzo, M., Simon, P.W., Cavagnaro, P. 2019. Dissecting the genetic control of root and leaf tissue-specific anthocyanin pigmentation in carrot (Daucus carota L.). Theoretical and Applied Genetics. 132:2485–2507. https://doi.org/10.1007/s00122-019-03366-5.

Molecular breeding research in USDA-ARS cucumber improvement program - past, present and future - (Literature Review)
Weng, Y. 2019. Molecular breeding research in USDA-ARS cucumber improvement program - past, present and future. Journal of Tianjin Agricultural Sciences. 25(6):6-18.

A functional allele of CsFUL1 regulates fruit length through repressing CsSUP and inhibiting auxin transport in cucumber - (Peer Reviewed Journal)
Zhao, J., Jiang, L., Che, G., Li, Y., Pan, Y., Zhao, W., Zhong, Y., Ding, Y., Yan, S., Sun, C., Weng, Y., Zhang, X. 2019. A functional allele of CsFUL1 regulates fruit length through repressing CsSUP and inhibiting auxin transport in cucumber. The Plant Cell. 31:1289–1307. https://doi.org/10.1105/tpc.18.00905.

QTL mapping of low temperature germination ability in cucumber - (Peer Reviewed Journal)
Yagcioglu, M., Jiang, B., Wang, P., Wang, Y., Ellialtioglu, S.S., Weng, Y. 2019. QTL mapping of low temperature germination ability in cucumber. Euphytica. 215:84.

Cytological evaluations of advanced generations of interspecific hybrids between Allium cepa and Allium fistulosum Showing resistance to stemphylium vesicarium - (Peer Reviewed Journal)
Kudryavtseva, N., Havey, M.J., Black, L., Hanson, P., Sokolov, P., Odintsov, S., Divashuk, M., Khrustaleva, L. 2019. Cytological evaluations of advanced generations of interspecific hybrids between Allium cepa and Allium fistulosum Showing resistance to stemphylium vesicarium. Horticulturae. 10(3):195. https://doi.org/10.3390/genes10030195.

Carrot leaves maintain liver vitamin A concentrations in mongolian gerbils regardless of the alpha- to beta-carotene ratio when beta-carotene equivalents are equalized - (Peer Reviewed Journal)
Titcomb, T.J., Kaeppler, M.S., Sandoval Cates, S.B., Shannon, J.M., Simon, P.W., Tanumihardjo, S.A. 2019. Carrot leaves maintain liver vitamin A concentrations in male mongolian gerbils regardless of the ratio of alpha- to beta-carotene when beta-carotene equivalents are equalized. Journal of Nutrition. 149(6):951-958. https://doi.org/10.1093/jn/nxz036.

Rare maternal and bi-parental transmission of the cucumber mitochondrial DNA reveals sorting of polymorphisms among progenies - (Peer Reviewed Journal)
Shen, J., Shou, W., Zhang, Y., Yuan, G., Zhao, Y., Chen, J., Havey, M.J. 2019. Rare maternal and bi-parental transmission of the cucumber mitochondrial DNA reveals sorting of polymorphisms among progenies. Theoretical and Applied Genetics. 132(4):1223-1233. https://doi.org/10.1007/s00122-018-03274-0.

Comparison of representative and custom methods of generating core subsets of a carrot germplasm collection - (Peer Reviewed Journal)
Corak, K.E., Ellison, S.L., Simon, P.W., Spooner, D.M., Dawson, J.C. 2019. Comparison of representative and custom methods of generating core subsets of a carrot germplasm collection. Crop Science. 59(3):1107-1121. https://doi.org/10.2135/cropsci2018.09.0602.

A cluster of MYB transcription factors regulates anthocyanin biosynthesis in carrot (Daucus carota L.) root and petiole - (Peer Reviewed Journal)
Iorizzo, M., Cavagnaro, P.F., Bostan, H., Zhao, Y., Zhang, J., Simon, P.W. 2019. A cluster of MYB transcription factors regulates anthocyanin biosynthesis in carrot (Daucus carota L.) root and petiole. Frontiers in Plant Science. 9:1927. https://doi.org/10.3389/fpls.2018.01927.

Rare maternal and bi-parental transmission of the cucumber mitochondrial DNA reveals sorting of polymorphisms among progenies - (Abstract Only)
Shen, J., Shou, W., Zhang, Y., Yuan, G., Zhao, Y., Chen, J., Havey, M.J. 2019. Rare maternal and bi-parental transmission of the cucumber mitochondrial DNA reveals sorting of polymorphisms among progenies. Meeting Abstract. 132:1223-1233. https://doi.org/10.1007/s00122-018-03274-0.

An automated, high-throughput image analysis pipeline enables genetic studies of shoot and root morphology in carrot (Daucus carota L.) - (Peer Reviewed Journal)
Turner, S.D., Ellison, S.L., Senalik, D.A., Simon, P.W., Spalding, E.P., Miller, N.D. 2018. An automated, high-throughput image analysis pipeline enables genetic studies of shoot and root morphology in carrot (Daucus carota L.). Frontiers in Plant Science. 9(1703):1-17. https://doi.org/10.3389/fpls.2018.01703.

Cucurbit Genomics Database (CuGenDB): a central portal for comparative and functional genomics of cucurbit crops - (Peer Reviewed Journal)
Zheng, Y., Wu, S., Bai, Y., Sun, H., Jiao, C., Guo, S., Zhao, K., Blanca, J., Zhang, Z., Huang, S., Xu, Y., Weng, Y., Mazourek, M., Reddy, U.K., Ando, K., Mccreight, J.D., Schaffer, A., Burger, J., Tadmor, Y., Katzir, N., Tang, Z., Liu, Y., Giovannoni, J.J., Ling, K., Wechter, P.W., Levi, A., Garcia-Mas, J., Grumet, R., Fei, Z. 2018. Cucurbit Genomics Database (CuGenDB): a central portal for comparative and functional genomics of cucurbit crops. Nucleic Acids Research. (2019): Vol. 4747(D1):D1128-D1136.. https://doi.org/10.1093/nar/gky944.

A mutation in class III homeodomain-leucine zipper (HD-ZIP III) transcription factor results in curly leaf (cl) in cucumber (Cucumis sativus L.) - (Peer Reviewed Journal)
Rong, F., Chen, F., Hunag, L., Zhang, J., Cheng, Z., Hou, D., Weng, Y., Chen, P., Li, Y. 2018. A mutation in class III homeodomain-leucine zipper (HD-ZIP III) transcription factor results in curly leaf (cl) in cucumber (Cucumis sativus L.). Journal of Theoretical and Applied Genetics. 132:113-123.

Cucurbit Genomics Database (CuGenDB): a central portal for comparative and functional genomics of cucurbit crops - (Peer Reviewed Journal)
Zheng, Y., Wu, S., Bai, Y., Sun, H., Jiao, C., Guo, S., Zhao, K., Blanca, J., Zhang, Z., Huang, S., Xu, Y., Weng, Y., Mazourek, M., Reddy, U., Ando, K., McCreight, J.D., Schaffer, A.A., Burger, J., Tadmor, Y., Katzir, N., Tang, X., Liu, Y., Giovannoni, J.J., Ling, K., Wechter, W.P., Levi, A., Garcia-Mas, J., Grumet, R., Fei, Z. 2018. Cucurbit Genomics Database (CuGenDB): a central portal for comparative and functional genomics of cucurbit crops. Nucleic Acids Research. 47(D1):1128-1136. https://doi.org/10.1093/nar/gky944.

Variation for salinity tolerance during seed germination in diverse carrot [Daucus carota (L.)] germplasm - (Peer Reviewed Journal)
Bolton, A., Simon, P.W. 2019. Variation for salinity tolerance during seed germination in diverse carrot [Daucus carota (L.)] germplasm. HortScience. 54(1):38-44. https://doi.org/10.21273/HORTSCI13333-18.

Classification of fruit trichomes in cucumber and effects of plant hormones on type II fruit trichome development - (Peer Reviewed Journal)
Xue, S., Dong, M., Liu, X., Xu, S., Pang, J., Zhang, W., Weng, Y., Ren, H. 2018. Classification of fruit trichomes in cucumber and effects of plant hormones on type II fruit trichome development. Planta. 249:407-416. https://doi.org/10.1007/s00425-018-3004-9.

Confirmation of significant parent-of-origin effects in cucumber - (Abstract Only)
Olberg, M., Havey, M.J. 2018. Confirmation of significant parent-of-origin effects in cucumber. Meeting Abstract. pp. 29. Available: http://cucurbit2018.ucdavis.edu/wp-content/uploads/2018/10/2018_Cucurbits_Abstracts_Book.pdf

The USDA cucumber (Cucumis sativus L.) collection: genetic diversity, population structure, genome-wide association studies and core collection development - (Peer Reviewed Journal)
Wang, X., Bao, K., Reddy, U.K., Bai, Y., Hammar, S.A., Jiao, C., Wehner, T.C., Madera, A.R., Weng, Y., Grumet, R., Fei, Z.J. 2018. The USDA cucumber (Cucumis sativus L.) collection: genetic diversity, population structure, genome-wide association studies and core collection development. Horticulture Research. 5(64):1-13. https://doi.org/10.1038/s41438-018-0080-8.

STAYGREEN, STAY HEALTHY: a loss-of-susceptibility mutation in the STAYGREEN gene provides durable, broad-spectrum disease resistances for over 50 years of U.S. cucumber production - (Peer Reviewed Journal)
Wang, Y., Tan, J., Wu, Z., Vandenlangenberg, K., Wehner, T., Wen, C., Zheng, X., Owens, K., Thornton, A., Bang, H., Hoeft, E., Kraan, P., Suelmann, J., Pan, J., Weng, Y. 2018. STAYGREEN, STAY HEALTHY: a loss-of-susceptibility mutation in the STAYGREEN gene provides durable, broad-spectrum disease resistances for over 50 years of U.S. cucumber production. New Phytologist. 221:415-430. https://doi.org/10.1111/nph.15353.