Progress 03/12/13 to 03/11/18
Outputs
Progress Report Objectives (from AD-416): Objective 1: Evaluate Allium, Cucumis, and Daucus germplasm for genetic diversity in superior horticultural and product quality traits, including: resistance to diseases and pests; growth habit that reduces weed competition; processing quality for pickling cucumbers; postharvest storage capacity for long-storing onions; flavor and nutritional qualities; and provide all relevant information to GRIN. Objective 2: Identify genetic markers and construct detailed maps of genes and quantitative trait loci associated with disease and pest resistance, abiotic stress tolerance, end product quality, and yield components in onion, cucumber, and carrot. Objective 3: Determine the genetic basis and select for pigment, phytonutrient, and flavor content in onion, cucumber, and carrot, disease and pest resistances, and field components of yield, stress tolerance and market quality. Objective 4: Develop genetic stocks and genomic resources for onion, cucumber, and carrot using recurrent inbred lines, haploids, mutant stocks, and dense maps to capture new genetic variation for desired traits, and distribute them to researchers and commercial breeders. Approach (from AD-416): The long-term potential for improving a crop is only as great as the breadth of diversity that breeders utilize. Objective 1 targets evaluation of carrot, onion, and cucumber germplasm for traits important to growers and consumers. Discovery Goal 1: Identify unique phenotypic variation in germplasm collections and breeding stocks to improve nutritional and processing quality, disease resistance, stress tolerance, and yield of Allium, Cucumis, and Daucus vegetables, characterize observed variation and initiate genetic incorporation of these phenotypes into elite germplasm. Dense genetic maps are useful to improve the efficiency of crop improvement. For Objective 2 we will identify DNA polymorphisms in elite onion, cucumber, and carrot germplasm to construct genetic maps for marker-facilitated selection of major horticultural traits. Discovery Goal 2: Identify DNA polymorphisms in elite onion, cucumber, and carrot germplasm and construct detailed genetic maps for marker- facilitated selection of major horticultural traits. Efficient plant breeding depends on knowledge of the genetic basis of traits under selection. Objective 3 targets evaluation and genetic characterization of carrot, onion, and cucumber germplasm for traits important to growers and consumers. Discovery Goal 3: Develop populations to determine the patterns of inheritance of unique phenotypic variation in germplasm collections and breeding stocks to improve nutritional and processing quality, disease resistance, stress tolerance, and yield of Allium, Cucumis, and Daucus vegetables, phenotype observed variation among individuals in populations, and develop genetic models to explain observed genetic patterns. Information from germplasm evaluation and genetic analysis is useful and sets the stage for developing genetic and breeding stocks, and for establishing information resources for stakeholders. Objective 4 targets deployment of germplasm and resources. Discovery Goal 4: Incorporate valuable traits described in Discovery Goal 3 into elite germplasm and genetic stocks using marker-assisted selection and provide stakeholders with germplasm and databases including maps. This is the final report, project terminated March 11, 2018. Carrot provides 12-13% of the dietary vitamin A for U.S. consumers. New breeding populations with higher nutritional value and novel colors were identified and advanced to increase seed production and expand testing. Experimental hybrid carrots from the USDA program performed very well in trial comparisons with commercial cultivars and seed released by the USDA program to the U.S. seed industry is used by them to develop the majority of the current U.S. crop. USDA carrot breeding selections with very good flavor and nematode resistance were among those with superior field performance, and unique, superior nematode resistance derived from USDA carrot germplasm contributes to reduced use of pesticides for production of the U.S. crop. Carrot populations selected for the expanding U.S. organic carrot industry were advanced in the breeding program. Genetic mapping populations and diverse germplasm were phenotyped for nematode and Alternaria leaf blight resistance, top size, flavor, and root pigment content. Molecular genetic markers were developed to incorporate these traits into new breeding stocks. The carrot genome sequence was completed in a collaborative project led by ARS scientists in Madison, Wisconsin and the University of California-Davis and has been used to provide molecular genetic markers to better understand angiosperm evolution, the basis of orange and purple carrot color, to identify genes associated with the domestication of carrot. Germplasm and tools developed facilitate carrot breeding and basic plant science research. Seed was produced from onions selected over the years for less damage under natural pressure from the insect Thrips tabaci. Selections were grown across environments and amounts and types of epicuticular waxes measured. Additionally, numbers of thrips were counted in field plots. Onions with relatively high levels of a specific wax (hentriacontanone-16 (H16)) on leaves had significantly more thrips damage than onions with lower amounts of H16. Selections were identified with relatively high amounts of total wax, but with lower amounts of the H16, that showed significantly less thrips damage. Selections with unique wax profiles have been crossed with low and high wax types to study genetics of these thrips resistant phenotypes. An experimental onion hybrid with low amounts of H16 was produced and provided to researchers in Ithaca, New York and in the private sector for assessment of field resistance to thrips. Genetic analyses were completed and molecular markers developed to aid in the development of onions with unique wax profiles for thrips resistance. Onion selections showing high levels of resistance to pink root and Fusarium basal rot were crossed with susceptible lines and segregating families developed. Families were evaluated in replicated trials for reactions to Fusarium and pink root. Deoxyribonucleic acid (DNA) has been isolated from families and single nucleotide polymorphisms (SNPs) genotyped for mapping of these disease resistances. Pink root resistance from three different sources was mapped to the same region on chromosome 4, and molecular markers tagging this region were identified. Fusarium resistance was mapped to regions on chromosomes 2 and 4 of onion, and markers were identified associated with these regions. Crosses were completed to develop red onion populations with resistance to both pink root and Fusarium basal rot. Cucumber hybrids occasionally produce off type plants with unacceptable fruits. These off-type plants were shown to be polyploids, likely originating from chromosome doubling during growth. After a doubling event, chromosomes can be lost and the plant slowly reverts back to the diploid or near-diploid state. Short stature and highly serrated leaves were good indicators of polyploid plants, and growers should use these characteristics to remove plants likely to be polyploids and avoid production of off-type fruits. Multiple new cucumber mapping populations were developed for framework or fine genetic mapping of genes controlling fruit size and shape, parthenocarpy fruit setting quantitative trait loci (QTL), and disease resistances (downy mildew, powdery mildew, angular leaf spot, and anthracnose). A panel of 300 cucumber lines were selected for genome-wide association study (GWAS). Phenotyping in both segregating and natural populations was conducted in a controlled growth chamber, greenhouses, or field locations for these traits. Genome wide or localized linkage maps are being developed for linkage analysis of these genes or QTL with molecular markers with emphasis on use of high throughput whole genome re- sequencing tools. The genome of the wild relative of cucumber, Cucumis hystrix was sequenced and assembled. Accomplishments 01 Genetic control of carrot tops. Field production of carrots is made difficult by the fact that they grow slower than most weeds early in the season. Weeds slow down the maturation of the carrot crop and small carrot tops make weed control expensive for carrot growers, requiring the application of herbicides for conventional production, or the use of hand weeding which can cost thousands of dollars per acre for organic production. ARS researchers from Madison, Wisconsin observed a wide range in the size of carrot tops in breeding populations, and in our earlier studies demonstrated that carrots with large tops suppress weed growth. These observations provided preliminary results leading to this study, where the genetic control of carrot top size was evaluated. Evaluating a diverse range of inbred strains of carrots and their hybrid combinations, a large amount of genetic control of carrot top size throughout the growing season was observed, especially near harvest time. This research suggests that there is a significant level of genetic control of carrot top size that carrot breeders can utilize in developing carrots with larger tops that will contribute to reduced inputs and economic savings for producers. These results are of interest to carrot growers and breeders, where seed companies are using this information in their breeding programs, as well as to plant scientists studying plant growth. 02 Thrips resistance in onion. Onion thrips are the most important insect pest of onion and control requires frequent insecticide applications. ARS researchers from Madison, Wisconsin selected onions with unique profiles of epicuticular waxes, which are associated with thrips resistance. Thrips prefer onions with higher amounts of a specific wax (hentriacontanone-16, H16), and selections were identified that have large amounts of total wax, but less of H16, and show thrips resistance. Deployment of onion cultivars with unique epicuticular waxes should reduce the build-up of thrips populations during onion production and cut in half the number of insecticide sprays for effective control, reducing costs for growers and overall environmental impact of pesticide use. 03 Molecular genetic markers for onions. Single nucleotide polymorphisms (SNPs) are robust genetic markers in the DNA, commonly occur among elite cultivars and populations, and are useful for genetic selection of superior types and fingerprinting of elite germplasm. Large numbers of SNPs were developed for onion and over 800 were genetically mapped. A high throughput genotyping array was constructed and used to estimate the relationships among important founder populations of onion from key world production regions. These SNPs are being used by public and private sector researchers for phylogenetic analyses, genetic mapping, gene tagging, and quality control of seed lots. 04 Accelerate cucumber breeding for disease resistances through marker- assisted selection. Downy mildew (DM) is at present the most important disease in U.S. cucumber production, and it has been especially devastating since 2004 when a new strain of the disease appeared, defeating the old resistance source. Powdery mildew (PM) is another important cucumber disease pathogen. High resistance to the new DM strain, and to PM, has been identified in some wild cucumber lines, such as PI (Plant Introduction) 197088 and PI 330628, but their direct use in cucumber breeding is difficult due to the complex genetics of resistance and unacceptable fruit quality. ARS scientists at Madison, Wisconsin with collaborators at North Carolina State University (Raleigh), Bayer Vegetable Seeds in the Netherlands, and Magnum Seeds, Inc. in Italy conducted multi-location, multi-year field trials to investigate responses to natural infection of both pathogens in plants derived from crosses with the two PI lines. Genetic analysis identified important genetic factors for the high resistance to the mildew pathogens. Molecular markers associated with the most important contributors of genes for resistance were developed, and they were successfully utilized as a selection tool (marker-assisted selection) during breeding for cucumbers with high DM and PM resistance. With this tool, we were able to bring multiple genes (each of which only contributes partial resistance) to elite pickling cucumber breeding lines. The resulting lines were shown to have high resistance in field trials; they also have good horticultural traits for field production, and they are of much interest to seed companies developing new cucumber varieties, and growers struggling with these diseases.
Impacts
(N/A)
Publications
- Xu, X., Ji, J., Xu, Q., Qi, X., Weng, Y., Chen, X. 2018. The major-effect quantitative trait locus CsARN6.1 encodes an AAA ATPase domain-containing protein that is associated with waterlogging stress tolerance by promoting adventitious root formation. Plant Journal. 93:917�930.
- Wang, Y., Vandenlangenberg, K., Wen, C., Wehner, T.C., Weng, Y. 2017. QTL mapping of downy and powdery mildew resistances in PI 197088 cucumber with genotyping-by-sequencing in RIL population. Theoretical and Applied Genetics. 131(3):597-611.
- Ma, C., Yang, J., Cheng, Q., Mao, A., Zhang, J., Wang, S., Weng, Y., Wen, C. 2018. Comparative analysis of miRNA and mRNA abundance in determinate cucumber by high-throughput sequencing. PLoS One. 13(1):e0190691.
- Havey, M.J., Ghavami, F. 2018. Informativeness of single nucleotide polymorphisms and relationships among onion populations from important world production regions. Journal of the American Society for Horticultural Science. 143(1):34-44.
- Mroz, T.L., Eves-Van Den Akker, S., Bernat, A., Skarzynska, A., Pryszcz, L. , Olberg, M., Havey, M.J., Bartoszewski, G. 2018. Transcriptome analyses of mosaic (MSC) mitochondrial mutants of cucumber in a highly inbred nuclear background. Genes, Genomes, Genetics. 8:953-965.
- Zhu, H., Sun, X., Zhang, Q., Song, P., Hu, Q., Zhang, X., Li, X., Hu, J., Pan, J., Sun, S., Weng, Y., Yang, L. 2018. GLABROUS (CmGL) encodes a HD- ZIP IV transcription factor playing roles in multicellular trichome initiation in melon. Theoretical and Applied Genetics. 131:569�579.
- Zhang, Q., Du, H., Lv, D., Xiao, T., Pan, J., He, H., Wang, G., Cai, R., Weng, Y., Pan, J. 2018. Efficient transposition of the retrotransposon Tnt1 in Cucumber (Cucumis sativus L.). Horticultural Plant Journal. 4(3) :111-116.
- Yang, S., Cai, Y., Liu, X., Dong, M., Zhang, Y., Chen, S., Zhang, W., Li, Y., Tang, M., Zhai, X., Weng, Y., Ren, H. 2018. A CsMYB6-CsTRY module regulates fruit trichome initiation in cucumber. Journal of Experimental Botany. 69(8):1887�1902.
- Liu, X., Ning, K., Che, G., Yan, S., Han, L., Gu, R., Li, Z., Weng, Y., Zhang, X. 2018. CsSPL functions as an adaptor between HD-ZIP III and CsWUS transcription factors regulating anther and ovule development in cucumber. Plant Journal. 94(3):535-547.
- Zhang, C., Chen, F., Zhao, Z., Hu, L., Liu, H., Cheng, Z., Weng, Y., Chen, P., Li, Y. 2018. Mutations in CsPID encoding a Ser/Thr protein kinase are responsible for round leaf shape in cucumber (Cucumis sativus L.). Theoretical and Applied Genetics. 131:1379-1389.
- Mezghani, N., Ruess, H.M., Tarchoun, N., Ben Amor, J., Simon, P.W., Spooner, D.M. 2018. Genotyping-by-sequencing reveals the origin of the Tunisian relatives of cultivated carrot. Genetic Resources and Crop Evolution. 65:1359-1368.
- Mezghani, N., Ruess, H.M., Tarchoun, N., Ben Amor, J., Simon, P.W., Spooner, D.M. 2018. Genotyping-by-sequencing reveals the origin of the Tunisian relatives of cultivated carrot. Genetic Resources and Crop Evolution. 65:1359-1368.
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Progress 10/01/16 to 09/30/17
Outputs
Progress Report Objectives (from AD-416): Objective 1: Evaluate Allium, Cucumis, and Daucus germplasm for genetic diversity in superior horticultural and product quality traits, including: resistance to diseases and pests; growth habit that reduces weed competition; processing quality for pickling cucumbers; postharvest storage capacity for long-storing onions; flavor and nutritional qualities; and provide all relevant information to GRIN. Objective 2: Identify genetic markers and construct detailed maps of genes and quantitative trait loci associated with disease and pest resistance, abiotic stress tolerance, end product quality, and yield components in onion, cucumber, and carrot. Objective 3: Determine the genetic basis and select for pigment, phytonutrient, and flavor content in onion, cucumber, and carrot, disease and pest resistances, and field components of yield, stress tolerance and market quality. Objective 4: Develop genetic stocks and genomic resources for onion, cucumber, and carrot using recurrent inbred lines, haploids, mutant stocks, and dense maps to capture new genetic variation for desired traits, and distribute them to researchers and commercial breeders. Approach (from AD-416): The long-term potential for improving a crop is only as great as the breadth of diversity that breeders utilize. Objective 1 targets evaluation of carrot, onion, and cucumber germplasm for traits important to growers and consumers. Discovery Goal 1: Identify unique phenotypic variation in germplasm collections and breeding stocks to improve nutritional and processing quality, disease resistance, stress tolerance, and yield of Allium, Cucumis, and Daucus vegetables, characterize observed variation and initiate genetic incorporation of these phenotypes into elite germplasm. Dense genetic maps are useful to improve the efficiency of crop improvement. For Objective 2 we will identify DNA polymorphisms in elite onion, cucumber, and carrot germplasm to construct genetic maps for marker-facilitated selection of major horticultural traits. Discovery Goal 2: Identify DNA polymorphisms in elite onion, cucumber, and carrot germplasm and construct detailed genetic maps for marker- facilitated selection of major horticultural traits. Efficient plant breeding depends on knowledge of the genetic basis of traits under selection. Objective 3 targets evaluation and genetic characterization of carrot, onion, and cucumber germplasm for traits important to growers and consumers. Discovery Goal 3: Develop populations to determine the patterns of inheritance of unique phenotypic variation in germplasm collections and breeding stocks to improve nutritional and processing quality, disease resistance, stress tolerance, and yield of Allium, Cucumis, and Daucus vegetables, phenotype observed variation among individuals in populations, and develop genetic models to explain observed genetic patterns. Information from germplasm evaluation and genetic analysis is useful and sets the stage for developing genetic and breeding stocks, and for establishing information resources for stakeholders. Objective 4 targets deployment of germplasm and resources. Discovery Goal 4: Incorporate valuable traits described in Discovery Goal 3 into elite germplasm and genetic stocks using marker-assisted selection and provide stakeholders with germplasm and databases including maps. Carrot populations with high nutritional value and novel colors were identified and advanced to increase seed production and expand testing. Experimental hybrid carrots from the USDA program performed very well in trial comparisons with commercial cultivars. USDA selections with very good flavor and nematode resistance were among those with superior field performance. Carrot populations selected for the expanding U.S. organic carrot industry were advanced in the breeding program. Biparental mapping populations and diverse germplasm were phenotyped for nematode and Alternaria leaf blight resistance, top size, flavor, and root pigment content, and molecular genetic markers were developed to expand to determine the genetic control of these traits and to better characterize the carrot genome and understand gene flow and the domestication of carrot. Germplasm and tools developed facilitate carrot breeding and basic plant science research. Seed was produced from onions selected over years under natural pressure from the insect Thrips tabaci. Selections were grown in the field and greenhouse and amounts and types of epicuticular waxes measured, as well as numbers of thrips were counted in field plots. Selections were identified with relatively high amounts of total wax, but with lower amounts of a specific ketone. These selections consistently supported fewer thrips and suffered less feeding damage compared with plants with greater amounts of this ketone. These selections with unique wax profiles have been used in crosses to study genetics of lower-wax phenotypes. An experimental onion hybrid with low amounts of the ketone was produced and provided to collaborators for assessment of field resistance to thrips. Onion selections showing high levels of resistance to pink root and Fusarium basal rot were crossed with susceptible lines and segregating families developed. Families were evaluated in replicated trials for reactions to Fusarium and pink root. Deoxyribonucleic acid (DNA) has been isolated from families and single nucleotide polymorphisms scored mapping of these disease resistances. Cucumber suffers severe damage when exposed to approximately 4 C for a few hours with light. These environmental conditions commonly occur early in the growing season and growers would benefit from tolerance to cold. Research was initiated on molecular analysis of a chloroplast-associated cold tolerance identified in the cucumber cultivar �Chipper.� Eventual identification of the molecular bases of this cold tolerance will allow breeders to screen populations for the trait. DNA was isolated from the chloroplasts of cold-tolerant and susceptible cucumbers, and is being sequenced. The DNA sequences will be evaluated for polymorphisms that may be associated with cold tolerance. Multiple new mapping populations were developed for framework or fine genetic mapping of genes controlling fruit size and shape, fruit weight, flowering time, plant architecture (vine length and hypocotyl length), parthenocarpy fruit setting quantitative trait loci (QTL). Phenotyping was conducted in a controlled growth chamber, greenhouses or field (multiple locations) for these traits. Genome wide or localized linkage maps are being developed for linkage analysis of these genes or QTL with molecular markers with emphasis on use of high throughout whole genome re- sequencing tools. The genome of the wild relative of cucumber, Cucumis hystrix was sequenced and assembled. A linkage map of C. hystrix was developed with genotyping by sequencing. Phenotypic characteristics associated with spontaneous polyploidization in cucumber were identified. Accomplishments 01 Identification of a carrot domestication gene. Very little is known about the molecular mechanisms involved in carrot domestication. ARS scientists in Madison, Wisconsin in conjunction with Polish scientists evaluated a cross between wild and cultivated carrot and mapped a region of the genome under selection during carrot domestication. We identified a candidate gen e in that region that is a member of a family of plant regulatory genes which are involved in organ development, including root tissue. Crop domestication provided the foundation for the establishment of early human civilizations and consequently an expanded knowledge of the genetic bases of domestication provides insights into early human knowledge and behavior. This research expands our knowledge of carrot tap root development and provides insights into traits that early plant breeders targeted during crop domestication. 02 Carrot gene flow. Studies of gene flow between crops and their wild relatives have implications for both farming and breeding management practices as well as understanding the risk of transgene escape. Wild carrot occurs widely across the U.S., but gene flow between wild and cultivated carrots has not been studied. ARS scientists in Madison, Wisconsin with collaborators in Tennessee utilized molecular genetic markers to evaluate carrot gene flow in two regions of the U.S. and discovered substantial gene flow indicating that both carrot pollen and seed transfer genetic information among wild and cultivated populations in the same geographic region. This research provides seed companies with knowledge of risks that wild carrots impose on carrot seed production, and insights into carrot pollination biology. 03 Thrips resistance in onion. Onion thrips is the most important insect pest of onion and control requires frequent insecticide applications. ARS researchers from Madison, Wisconsin selected onions with unique profiles of epicuticular waxes, which are associated with thrips resistance. Deployment of onion cultivars with unique epiculticular waxes should reduce the build-up of thrips populations during onion production and allow for fewer insecticide sprays, reducing costs for growers and overall environmental impact of pesticide use. 04 Spontaneous polyploidization in cucumber. Spontaneous polyploidization is a serious problem for growers because plants produce off-type fruits. Cucumber populations were evaluated for the type and frequency of polyploids. Multiple ploidies were found in single plants, and polyploidization was an on-going process likely associated with endoreduplication in seedlings. Seed and seedling characteristics were not good predictors of subsequent polyploids; however heavily serration of leaves was the best phenotypic trait for elimination of polyploidy cucumbers. These results allow growers to discard polyploidy plants at an early growth stage so they do not keep plants that will produce unmarketable fruit. 05 Quantitative trait loci (QTL) mapping of domestication-related traits in a semi-wild cucumber. Flowering time and fruit size are two important traits in domestication and crop evolution in cucumber, but little is known about their genetic basis. QTL mapping on flowering time and fruit size was conducted with populations derived from the cross between a landrace and the semi-wild cucumber. A linkage map with 267 molecular markers was developed. Flowering and fruit size/shape data were collected in Hancock, Wisconsin field trials in multiple years. Three flowering times were identified with one QTL playing the most important role in determining early flowering during domestication and another QTL being important in regulating flowering time within cultivated cucumbers. Eight fruit size QTLs were detected that regulate fruit elongation and increase of diameter in fruit development. Among them, one exhibited the largest effect on the determination of the round fruit shape characteristic of the semi-wild cucumber. This is the first report in cucumber to identify genes that control day-length sensitive flowering time as well as fruit size variations in the semi- wild cucumber. Results from this study are useful in efficient use of the semi-wild cucumber that has a number of traits for cucumber breeding. This work also provides new insights into the crop evolution of modern cucumber. 06 Genetic basis of round fruit shape in WI7239 cucumber. Fruit size and shape is an important quality trait in cucumber breeding, yet its genetic basis remains poorly understood. We conducted quantitative trait loci (QTL) mapping on round fruit shape using a population derived from a cross between a long fruited and a round fruited cucumber. Fruit length and diameter data were collected at three developmental stages in multiple years. We found two interacting QTLs that are responsible for fruit size variation in this population. Candidate gene search in the two QTL regions identified a candidate gene. This study revealed the unique genetic architecture of round fruit shape in WI7239 cucumber. It also highlights the power of QTL analysis for traits with a simple genetic basis but their expression is complicated by other factors. This is the first report in cucumber identifying two interacting QTL controlling round fruit shape. The work provides new insights into the genetic basis of fruit shape/size formation in cucumber. The results are also important in facilitating manipulation of fruit size in cucumber breeding. 07 Quantitative trait loci (QTL) mapping for parthenocarpic fruit set in cucumber. Parthenocarpy (production of fruit without fertilization) is a desirable trait with potential for increasing yield and quality in U. S. processing cucumber production. Many successful parthenocarpic fresh market cucumber varieties have been developed, but the genetic and molecular mechanisms for parthenocarpic expression in cucumber is largely unknown. We conducted QTL mapping with a novel phenotypic approach for parthenocarpic fruit set focusing on early fruit development. Seven QTLs associated with parthenocarpic fruit set were detected. Among them, one each on chromosomes 5 and 7 and two on chromosome 6 were consistently identified in all experiments. The chromosome 7 QTL played a more important role in early parthenocarpic fruit set. The results suggested that parthenocarpic fruit set can be accurately evaluated with as few as 20 nodes of growth. The QTLs identified in this study are a valuable resource for cucumber breeders interested in developing parthenocarpic cultivars and to researchers interested in the genetic and molecular mechanisms of parthenocarpic fruit set. 08 A novel protein involved in low-dosage ultraviolet B (UVB)-dependent hypocotyl elongation in cucumber. Understanding the mechanisms and control of hypocotyl elongation is important for greenhouse vegetable crop production. We identified a protein in cucumber, which regulates low-dosage ultraviolet B (LDUVB)-dependent hypocotyl elongation. We showed that hypocotyl elongation in cucumbers carrying a recessive allele of the gene for this protein was LDUVB-insensitive. We found the wild cucumber origin of this gene for local adaptation, which was under selection during domestication. While gene expression was inhibited by LDUVB, its transcript abundance was highly correlated with hypocotyl elongation rate and the expression level of cell elongation-related genes. In cucumber production, seedling plugs are often prepared in the greenhouse. Often there is excessive hypocotyl elongation due to environmental variations resulting in poor seedling quality. There may be potential use of this recessive gene in cucumber breeding for production in protected environments. 09 Cytological behaviors of synthetic tetraploid between cucumber and its wild relative C. hystrix. Wide hybridization is an important tool for crop improvement. Recently, we successfully developed a synthetic allotetraploid from interspecific cross between cucumber and its relative Cucumis hystrix-(2n = 2x =24) followed by chemical induction of chromosome doubling. The resulting allotetraploid was self- pollinated for three generations. We found that the fertility and seed setting of the amphidiploid plants was very low. In this study, we investigated the meiotic chromosome behavior in pollen mother cells with the aid of florescence in situ hybridization (FISH) aiming to understand the reasons of the low fertility and rate of seed setting in the amphidiploid plants. While homologous chromosome pairing seemed to be rather normal, chromosome laggards were common, which was caused primarily by asynchronous meiosis of chromosomes from the two donor genomes. We suggest that asynchronous meiotic rhythm between the two parental genomes is the main reason for the low fertility and low seed- set of the C. hystrix-cucumber amphidiploid plants. This work clarifies the reason for reduced male fertility of the synthetic tetraploid in successive self-pollinated generations, which helps efficient use of the amphidiploid in cucumber breeding through development of introgression lines.
Impacts
(N/A)
Publications
- Simon, P.W., Navazio, J.P., Colley, M., McCluskey, C., Zystro, J., Hoagland, L., Roberts, P.A., du Toit, L.J., Waters, T., Silva, E., Colquhoun, J., Nunez, J. 2017. The CIOA (Carrot Improvement for Organic Agriculture) project: location, cropping system and genetic background influence carrot performance including top height and flavour. Acta Horticulturae. 1153:1-8. doi: 10.17660/ActaHortic.2017.1153.1.
- Ellison, S., Iorrizo, M., Senalik, D., Simon, P.W. 2017. The next generation of carotenoid studies in carrot (Daucus carota L.). Acta Horticulturae. 1153:93-100. doi: 10.17660/ActaHortic.2017.1153.14.
- Iorizzo, M., Ellison, S., Van Deynze, A., Stoffel, K., Ashrafi, H., Iovene, M., Cavagnaro, P., Cheng, S., Zheng, P., Zheng, Z., Senalik, D., Spooner, D.M., Simon, P.W. 2017. Recent advance in carrot genomics. Acta Horticulturae. 1153:61-68. doi: 10.17660/ActaHortic.2017.1153.10.
- Bo, K., Wang, H., Pan, Y., Behera, T.K., Pandey, S., Wen, C., Wang, Y., Simon, P.W., Li, Y., Chen, J., Weng, Y. 2016. SHORT HYPOCOTYL 1 encodes a SMARCA3-like chromatin remodeling factor regulating elongation. Plant Physiology. 172(2):1273-1292. doi: 10.1104/pp.16.00501.
- Shiyab, S., Simon, P. 2017. Effects of direct and gradual salinity exposure on carrot (Daucus carota L.) seeds and recovery response. Academia Journal of Biotechnology (AJB). 5(3):038-043. doi: 10.15413/ajb. 2017.0127.
- Pan, Y., Liang, X., Gao, M., Liu, H., Meng, H., Weng, Y., Cheng, Z. 2016. Round fruit shape in WI7239 cucumber is controlled by two interacting quantitative trait loci with one putatively encoding a tomato SUN homolog. Theoretical and Applied Genetics. 130(3):573-586. doi: 10.1007/s00122-016- 2836-6.
- Wang, H., Li, W., Qin, Y., Pan, Y., Wang, X., Weng, Y., Chen, P., Li, Y. 2017. The cytochrome P450 gene CsCYP85A1 is a putative candidate for super compact-1 (scp-1) plant architecture mutation in cucumber (Cucumis sativus L.). Frontiers in Plant Science. 8:266. doi: 10.3389/fpls.2017.00266.
- Macko-Podgorni, A., Machaj, G., Stelmach, K., Senalik, D., Grzebelus, E., Iorizzo, M., Simon, P.W., Grzebelus, D. 2017. Characterization of a genomic region under selection in cultivated carrot (Daucus carota subsp. sativus) reveals a candidate domestication gene. Frontiers in Plant Science. 8. doi: 10.3389/fpls.2017.00012.
- Hou, F., Li, S., Wang, J., Kang, X., Weng, Y., Xing, G. 2017. Identification and validation of reference genes for quantitative real- time PCR studies in long yellow daylily, Hemerocallis citrina Borani. PLoS One. 12(3). doi: 10.1371/journal.pone.0174933.
- Del Valle-Echevarria, A.R., Sanseverino, W., Garcia-Mas, J., Havey, M.J. 2016. Pentatricopeptide repeat 336 as the candidate gene for paternal sorting of mitochondria (Psm) in cucumber. Theoretical and Applied Genetics. 129(10):1951-1959. doi: 10.1007/s00122-016-2751-x.
- Lietzow, C.D., Zhu, H., Pandey, S., Havey, M.J., Weng, Y. 2016. QTL mapping of parthenocarpic fruit set in North American processing cucumber. Theoretical and Applied Genetics. 129(12):2387-2401. doi: 10.1007/s00122- 016-2778-z.
- Ramirez-Madera, A.O., Miller, N.D., Spalding, E.P., Weng, Y., Havey, M.J. 2017. Spontaneous polyploidization in cucumber. Theoretical and Applied Genetics. 130(7):1481-1490. doi: 10.1007/s00122-017-2903-7.
- Mandel, J.R., Ramsey, A.J., Iorizzo, M., Simon, P.W. 2016. Patterns of gene flow between crop and wild carrot, Daucus carota (Apiaceae) in the United States. PLoS One. 11(9). doi.org/10.1371/journal.pone.0161971.
- Gao, M., Hu, L., Li, Y., Weng, Y. 2016. The chlorophyll-deficient golden leaf mutation in cucumber is due to a single nucleotide substitution in CsChlI for magnesium chelatase I subunit. Theoretical and Applied Genetics. 129(10):1961-1973. doi: 10.1007/s00122-016-2752-9.
- Han, Y., Pan, J., Thammapichai, P., Li, Z., Weng, Y. 2016. Asynchronous meiosis in Cucumis hystrix-cucumber synthetic tetraploids resulting in low male fertility. The Crop Journal. 4(4):275-279. doi: 10.1016/j.cj.2016.05. 003.
- Miao, H., Zhang, S., Wang, M., Wang, Y., Weng, Y., Gu, X. 2016. Fine mapping of virescent leaf gene v-1 in cucumber (Cucumis sativus L.). International Journal of Molecular Sciences. 17(10):1602. doi: 10.3390/ ijms17101602.
- Pan, Y., Qu, S., Bo, K., Gao, M., Haider, K.R., Weng, Y. 2017. QTL mapping of domestication and diversifying selection related traits in round- fruited semi-wild Xishuangbanna cucumber (Cucumis sativus L. var. xishuangbannanesis). Theoretical and Applied Genetics. 130(7):1531-1548. doi: 10.1007/s00122-017-2908-2.
- Zhu, H., Song, P., Koo, D., Guo, L., Li, Y., Sun, S., Weng, Y., Yang, L. 2016. Genome wide characterization of simple sequence repeats in watermelon genome and their application in comparative mapping and genetic diversity analysis. Biomed Central (BMC) Genomics. 17(1):557. doi: 10.1186/ s12864-016-2870-4.
- Mezghani, N., Ben Amor, J., Spooner, D.M., Simon, P.W., Mezghani, N., Boubaker, H., M'Rad Namji, A., Rouz, S., Hannachi, C., Neffati, M., Tarchoun, N. 2017. Multivariate analysis of morphological diversity among closely related Daucus species and subspecies in Tunisia. Genetic Resources and Crop Evolution. 64(8):2145-2159.
- Hou, S., Niu, H., Tao, Q., Wang, S., Gong, Z., Li, S., Weng, Y., Li, Z. 2017. A mutant in the CsDET2 gene leads to a systemic brassinosteriod deficiency and super compact phenotype in cucumber (Cucumis sativus L.). Theoretical and Applied Genetics. 130(8):1693-1703. doi: 10.1007/s00122- 017-2919-z.
- Chen, F., Fu, B., Pan, Y., Zhang, C., Wen, H., Weng, Y., Chen, P., Li, Y. 2017. Fine mapping identifies CsGCN5 encoding a histone acetyltransferase as putative candidate gene for tendril-less1 mutation (td-1) in cucumber. Theoretical and Applied Genetics. 130(8):1549-1558. doi: 10.1007/s00122- 017-2909-1.
- Ellison, S., Senalik, D., Bostan, H., Iorizzo, M., Simon, P. 2017. Fine mapping, transcriptome analysis, and marker development for Y2, the gene that conditions beta-carotene accumulation in carrot (Daucus carota L.). G3, Genes/Genomes/Genetics. 7(8)2665-2675. doi: 10.1534/g3.117.043067.
- Mezghani, N., Bouhila, A., Robbana, C., Rouz, S., Spooner, D.M., Simon, P. W., Ghrabi, Z., Neffati, M., Bouzbida, B., Hannachi, C. 2017. Morphological characterization of a Daucus L. germplasm collection in Tunisia. Acta Horticulturae. 1153:287-291. doi: 10.17660/ActaHortic.2017. 1153.42.
- Atbizu, C.I., Ruess, H., Senalik, D., Iorizzo, M., Simon, P.W., Spooner, D. M., Reitsma, K. 2017. Integrated molecular and morphological studies of Daucus. Acta Horticulturae. 1153:265-271. doi: 10.17660/ActaHortic.2017. 1153.39.
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Progress 10/01/15 to 09/30/16
Outputs
Progress Report Objectives (from AD-416): Objective 1: Evaluate Allium, Cucumis, and Daucus germplasm for genetic diversity in superior horticultural and product quality traits, including: resistance to diseases and pests; growth habit that reduces weed competition; processing quality for pickling cucumbers; postharvest storage capacity for long-storing onions; flavor and nutritional qualities; and provide all relevant information to GRIN. Objective 2: Identify genetic markers and construct detailed maps of genes and quantitative trait loci associated with disease and pest resistance, abiotic stress tolerance, end product quality, and yield components in onion, cucumber, and carrot. Objective 3: Determine the genetic basis and select for pigment, phytonutrient, and flavor content in onion, cucumber, and carrot, disease and pest resistances, and field components of yield, stress tolerance and market quality. Objective 4: Develop genetic stocks and genomic resources for onion, cucumber, and carrot using recurrent inbred lines, haploids, mutant stocks, and dense maps to capture new genetic variation for desired traits, and distribute them to researchers and commercial breeders. Approach (from AD-416): The long-term potential for improving a crop is only as great as the breadth of diversity that breeders utilize. Objective 1 targets evaluation of carrot, onion, and cucumber germplasm for traits important to growers and consumers. Discovery Goal 1: Identify unique phenotypic variation in germplasm collections and breeding stocks to improve nutritional and processing quality, disease resistance, stress tolerance, and yield of Allium, Cucumis, and Daucus vegetables, characterize observed variation and initiate genetic incorporation of these phenotypes into elite germplasm. Dense genetic maps are useful to improve the efficiency of crop improvement. For Objective 2 we will identify DNA polymorphisms in elite onion, cucumber, and carrot germplasm to construct genetic maps for marker-facilitated selection of major horticultural traits. Discovery Goal 2: Identify DNA polymorphisms in elite onion, cucumber, and carrot germplasm and construct detailed genetic maps for marker- facilitated selection of major horticultural traits. Efficient plant breeding depends on knowledge of the genetic basis of traits under selection. Objective 3 targets evaluation and genetic characterization of carrot, onion, and cucumber germplasm for traits important to growers and consumers. Discovery Goal 3: Develop populations to determine the patterns of inheritance of unique phenotypic variation in germplasm collections and breeding stocks to improve nutritional and processing quality, disease resistance, stress tolerance, and yield of Allium, Cucumis, and Daucus vegetables, phenotype observed variation among individuals in populations, and develop genetic models to explain observed genetic patterns. Information from germplasm evaluation and genetic analysis is useful and sets the stage for developing genetic and breeding stocks, and for establishing information resources for stakeholders. Objective 4 targets deployment of germplasm and resources. Discovery Goal 4: Incorporate valuable traits described in Discovery Goal 3 into elite germplasm and genetic stocks using marker-assisted selection and provide stakeholders with germplasm and databases including maps. Carrot populations with high nutritional value and novel colors were identified and advanced to increase seed production and expand testing. Experimental hybrid carrots from the USDA program performed very well in trial comparisons with commercial cultivars. USDA selections with very good flavor and nematode resistance were among those with superior field performance. The carrot genome sequence was completed and used to provide molecular genetic markers to better understand angiosperm evolution, the basis of orange and purple carrot color, and to identify genes associated with the domestication of carrot. Germplasm and tools developed facilitate carrot breeding and basic plant science research. Seed was produced from onions selected over years under natural pressure from the insect Thrips tabaci. Selections were grown in the field and greenhouse and amounts and types of epicuticular waxes measured, as well as numbers of thrips were counted in field plots. Lower wax phenotypes consistently support fewer thrips and suffer less feeding damage compared with plants with greater amounts of leaf waxes. Unique wax profiles have been identified among selections and are being assessed for thrips numbers and feeding damage. Selections with unique wax profiles have been used in crosses to study genetics of lower-wax phenotypes. An experimental low-wax hybrid of onion was produced and evaluated by researchers at Cornell University for field resistance to thrips, and this hybrid performed the best of all evaluated materials. Onions showing high levels of resistance to pink root and Fusarium basal rot were crossed with susceptibles, segregating families produced, and seed is being increased for disease evaluations. Deoxyribonucleic acid (DNA) is being isolated from families for genetic analyses, and replicated disease evaluations have been initiated. Nuclear-mitochondrial interactions are important for abiotic-stress tolerance and plant performance. A gene in cucumber that sorts mitochondrial DNAs transmitted to progenies has been precisely mapped and a candidate gene identified. This gene stabilizes mitochondrial ribosomes and allows plants with compromised ribosomes to survive. This result illustrates the advantage of cucumber for mutational analysis of mitochondrial genes and associated nuclear responses. Multiple new mapping populations were developed for framework or fine genetic mapping of genes controlling fruit size (length and width), fruit weight, flowering time, plant architecture (vine length and leaf size) parthenocarpy fruit setting, downy mildew, powdery mildew, and target leaf spot disease resistance quantitative trait loci (QTL). Phenotyping was conducted in both the greenhouse and field (multiple locations) for these traits. Genome wide or localized linkage maps are being developed for linkage analysis of these genes or QTL with molecular markers with emphasis on use of high throughout whole genome re-sequencing tools. The genome of the wild relative of cucumber, Cucumis hystrix was sequenced and assembled. A linkage map of C. hystrix is being developed with genotyping by sequencing. Machine trials were conducted in commercial fields. Accomplishments 01 Sequencing of the carrot genome. Development of genetic tools for carrot breeding derived from knowledge of the carrot genome has progressed in recent decades, but relatively little information on the carrot genome is available. ARS scientists in Madison, Wisconsin led an effort involving 20 scientists from seven countries to sequence the carrot genome and based on this information, we evaluated the evolution of carrots relative to related crops. We identified genes involved in basic cellular function, disease and stress resistance, pigment and flavor compound biosynthesis and accumulation, and we developed a molecular model for the major gene accounting for yellow and orange pigments in the carrot root. This research provides a foundation for plant genomics and evolution research, improvement of crop nutritional value, accelerated plant breeding, and improved crop production. 02 Carrot nematode resistance. Root-knot nematodes are a very important soil-borne pest attacking carrots, occurring in over 70% of the U. S. carrot production area and making carrots unmarketable with even a small amount of infection, unless expensive pesticides that threaten air quality are used for nematode control. ARS scientists in Madison, Wisconsin and collaborators discovered genetic resistance to the major nematodes threatening the U. S . crop, locating genes for resistance on five carrot chromosomes, with very high levels of resistance with some combinations of these genes. This research provides seed companies with germplasm and knowledge of molecular markers to facilitate breeding to develop nematode resistant cultivars for carrot growers to reduce the cost and environmental impact of carrot production. 03 Thrips resistance in onion. Onion thrips is the most important insect pest of onion and control requires frequent insecticide applications. ARS researchers from Madison, Wisconsin selected onions with lower amounts and types of epicuticular waxes, which are associated with thrips resistance. Deployment of onion cultivars with lower amounts of epiculticular waxes should reduce the build-up of thrips populations during onion production and allow for fewer insecticide sprays, reducing costs for growers and overall environmental impact of pesticide use. 04 Genetic markers in expressed sequences of garlic. Very few genetic polymorphisms (variation at the DNA level) are known in expressed sequences of garlic; the vast majority of polymorphisms developed for garlic have been anonymous genomic markers, making comparisons among independent studies difficult. ARS researchers from Madison, Wisconsin completed sequencing of expressed regions of the garlic deoxyribonucleic acid (DNA), and identified large numbers of genetic polymorphisms useful for genetic research on garlic. 05 Cucumber as a model system to study mitochondrial-nuclear interactions. Mitochondria are the powerhouses of the cell so mitochondrial function is important for plant growth and yield. ARS researchers from Madison, Wisconsin demonstrated that the mosaic mutants of cucumber are missing specific mitochondrial genes. Crossing of these mutants with diverse cucumber populations revealed a nuclear gene that stabilizes mitochondrial ribosomes involved in protein synthesis and allows mitochondrial mutants to survive. This research demonstrates the usefulness of cucumber to produce mitochondrial mutants and study nuclear responses and interactions important for plant performance and yield. 06 Trichome development in cucumber fruits. Trichomes (fruit spines) on cucumber fruits are an important fruit quality attribute, but little is known about the genetic and molecular basis of how these fruit spines are developed in cucumber. ARS scientists in Madison, Wisconsin identified a new spine-free mutant in cucumber that is under the control of a recessive gene CsGL3. The spine-free character in the mutant is because of insertion of long deoxyribonucleic acid (DNA) sequence called long terminal repeat retrotransposon which disrupted the function of normal wild type gene CsGL3. This research revealed important roles of this gene in cucumber epidermis spine initiation. Findings from the present study provide new insights into genetic control of trichome development in cucumber. This research provides fundamental knowledge about fruit development important for expanding basic insights into plant growth with application in plant breeding to increase crop productivity and quality. 07 Genetic basis of carpel number variation in cucumber. Carpel number (CN) is an important fruit quality trait of cucumber, but the genetic basis of CN variations is largely unknown. ARS scientists in Madison, Wisconsin found that CN is controlled by a simply inherited gene, Cn. With different but complementary research approaches, they found a single nucleotide mutation within the cucumber gene called CsCLV3, that is responsible for five-carpel fruits (a normal cucumber fruit has 3 carpels). This gene plays key roles in embryo development in plants. This study highlights the importance of integrated use of different research tools as well as next-gen high throughput sequencing in mapping and cloning genes that are difficult in accurate genotyping. The results provide new insights into the genetic control of carpel number variations in cucumber. This research provides fundamental knowledge about fruit development important for expanding basic insights into plant growth with application in plant breeding to increase crop quality. 08 Quantitative trait loci (QTL) mapping for downy mildew resistance in WI7120 cucumber. Downy mildew (DM) is the most devastating fungal disease of cucumber. Use of marker-assisted breeding for DM resistance in cucumber breeding is not widely available. ARS researchers in Madison, Wisconsin studied the genetic basis of DM resistance in the resistant line WI7120, and identified four QTL which together could explain 62-76% phenotypic variations. This study revealed two novel QTL for DM resistance and the unique genetic architecture of DM resistance in WI7120 conferring high level resistance to prevailing DM populations in multiple countries. The results provide molecular markers and important guidance on the use of DM resistance in WI7120 in cucumber breeding.
Impacts
(N/A)
Publications
- Tanumihardjo, S.A., Suri, D., Simon, P., Goldman, I.L. 2016. Vegetables of temperate climates: Carrot, parsnip and beetroot. In: Caballero, B., Finglas, P.M., Toldra, F., editors. Enclyclopedia of Food and Health. Volume 5. Waltham, MA:Academic Press. p. 387-392.
- Khrustaleva, L., Jiang, J., Havey, M.J. 2015. High-resolution tyramide- FISH mapping of markers tightly linked to the male-fertility restoration (Ms) locus of onion. Theoretical and Applied Genetics. 129(3):535-545. doi: 10.1007/s00122-015-2646-2.
- Pan, Y., Bo, K., Cheng, Z., Weng, Y. 2015. The loss-of-function GLABROUS 3 mutation in cucumber is due to LTR-retrotransposon insertion in a class IV HD-ZIP transcription factor gene CsGL3 that is epistatic over CsGL1. Biomed Central (BMC) Plant Biology. 15(1):302. doi: 10.1186/s12870-015- 0693-0.
- Li, S., Pan, Y., Wen, C., Li, Y., Liu, X., Zhang, X., Behera, T.K., Xing, G., Weng, Y. 2016. Integrated analysis in bi-parental and natural populations reveals CsCLAVATA3 (CsCLV3) underlying carpel number variations in cucumber. Theoretical and Applied Genetics. 129(5):1007-1022. doi: 10.1007/s00122-016-2679-1.
- Havey, M.J., Ahn, Y. 2016. Single nucleotide polymorphisms and indel markers from the transcriptome of garlic. Journal of the American Society for Horticultural Science. 141(1):62-65.
- Wen, C., Cheng, Q., Zhao, L., Mao, A., Yang, J., Yu, S., Weng, Y., Xu, Y. 2016. Identification and characterisation of Dof transcription factors in the cucumber genome. Scientific Reports. 6:23072. doi: 10.1038/srep23072.
- Shen, J., Zhao, J., Bartoszewski, G., Malepszy, S., Havey, M., Chen, J. 2015. Persistence and protection of mitochondrial DNA in the generative cell of cucumber is consistent with its paternal transmission. Plant And Cell Physiology. 56(11):2271-2282. doi: 10.1093/pcp/pcv140.
- Romanov, D., Divashuk, M., Havey, M.J., Khrustaleva, L. 2015. Tyramide- FISH mapping of single genes for development of an integrated recombination and cytogenetic map of chromosome 5 of Allium cepa. Genome. 58(3):111-119. doi: 10.1139/gen-2015-0019.
- Parsons, J., Matthews, W., Iorizzo, M., Roberts, P., Simon, P. 2015. Meloidogyne incognita nematode resistance QTL in carrot. Molecular Breeding. 35(5):114. doi: 10.1007/s11032-015-0309-2.
- Kole, C., Muthamilarasan, M., Henry, R., Edwards, D., Sharma, R., Abberton, M., Batley, J., Bentley, A., Blakeney, M., Bryant, J., Simon, P.W., et al. 2015. Application of genomics-assisted breeding for generation of climate resilient crops: progress and prospects. Frontiers in Plant Science. 6:563. doi: 10.3389/fpls.2015.00563.
- Yahyaa, M., Tholl, D., Cormier, G., Jensen, R., Simon, P.W., Ibdah, M. 2015. Identification and characterization of terpene synthases potentially involved in the formation of volatile terpenes in carrot (Daucus carota L.) roots. Journal of Agricultural and Food Chemistry. 63(19):4870-4878. doi: 10.1021/acs.jafc.5b00546.
- Staub, J.E., Gordon, V.S., Simon, P.W., Wehner, T.C. 2015. Chilling tolerant U.S. processing cucumber (Cucumis sativus L.): three advanced backcross and ten inbred backcross lines. HortScience. 50:1252-1254.
- Tan, J., Tao, Q., Niu, H., Zhang, Z., Li, D., Gong, Z., Weng, Y., Li, Z. 2015. A novel allele of monoecious (m) locus is responsible for elongated fruit shape and perfect flowers in cucumber (Cucumis sativus L.). Theoretical and Applied Genetics. 128(12):2483-2493. doi: 10.1007/s00122- 015-2603-0.
- Wen, C., Mao, A., Dong, C., Liu, H., Yu, S., Guo, Y., Weng, Y., Xu, Y. 2015. Fine genetic mapping of target leaf spot resistance gene cca-3 in cucumber, Cucumis sativus L. Theoretical and Applied Genetics. 128(12) :2495-2506. doi: 10.1007/s00122-015-2604-z.
- Zhang, H., Fan, J., Guo, S., Ren, Y., Gong, G., Zhang, J., Weng, Y., Davis, A., Xu, Y. 2016. Genetic diversity, population structure, and formulation of a core collection of 1,197 Citrullus accessions. HortScience. 51(1):23- 29.
- Xu, X., Yu, T., Xu, R., Shi, Y., Lin, X., Xu, Q., Qi, X., Weng, Y., Chen, X. 2015. Fine mapping of a dominantly inherited powdery mildew resistance major-effect QTL, Pm1.1, in cucumber identifies a 41.1 kb region containing two tandemly arrayed cysteine-rich receptor-like protein kinase genes. Theoretical and Applied Genetics. 129(3):507-516. doi: 10.1007/ s00122-015-2644-4.
- Lin, T., Wang, S., Zhong, Y., Gao, D., Cui, Q., Chen, H., Zhang, Z., Shen, H., Weng, Y., Huang, S. 2016. A truncated F-box protein confers the dwarfism in cucumber. Journal of Genetics and Genomics. 43(4):223-226. doi: 10.1016/j.jgg.2016.01.007.
- Iorizzo, M., Ellison, S., Senalik, D., Zeng, P., Satapoomin, P., Huang, J., Bowman, M., Iovene, M., Sanseverino, W., Cavagnaro, P., Yildiz, M., Spooner, D.M., Simon, P.W., et al. 2016. A high-quality carrot genome assembly provides new insights into carotenoid accumulation and asterid genome evolution. Nature Genetics. 48(6):657-666. doi: 10.1038/ng.3565.
- Wang, Y., VandenLangenberg, K., Wehner, T.C., Kraan, P.A.G., Suelmanm, J., Zheng, X., Owens, K., Weng, Y. 2016. QTL mapping for downy mildew resistance in cucumber inbred line WI7120 (PI 330628). Theoretical and Applied Genetics. doi: 10.1007/s00122-016-2719-x.
- Arbizu, C.I., Simon, P.W., Martinez-Flores, F., Ruess, H., Crespo, M.B., Spooner, D.M. 2016. Integrated molecular and morphological studies of the Daucus guttatus complex (Apiaceae). Systematic Botany. 41(2):479-492. doi: 10.1600/036364416X691948.
- Martinez-Flores, F., Arbizu, C.I., Reitsma, K., Juan, A., Simon, P.W., Spooner, D.M., Crespo, M.B. 2016. Lectotype designation for seven species names in the Daucus guttatus complex (Apiaceae) from the central and eastern Mediterranean basin. Systematic Botany. 41(2):464-478. doi: 10. 1600/036364416X691849.
- Nowicka, A., Sliwinska, E., Grzebelus, D., Baranski, R., Simon, P.W., Nothnagel, T., Grzebelus, E. 2016. Nuclear DNA content variation within the genus Daucus (Apiaceae) determined by flow cytometry. Scientific Horticulture. 209:132-138. doi: 10.1016/j.scienta.2016.06.023.
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Progress 10/01/14 to 09/30/15
Outputs
Progress Report Objectives (from AD-416): Objective 1: Evaluate Allium, Cucumis, and Daucus germplasm for genetic diversity in superior horticultural and product quality traits, including: resistance to diseases and pests; growth habit that reduces weed competition; processing quality for pickling cucumbers; postharvest storage capacity for long-storing onions; flavor and nutritional qualities; and provide all relevant information to GRIN. Objective 2: Identify genetic markers and construct detailed maps of genes and quantitative trait loci associated with disease and pest resistance, abiotic stress tolerance, end product quality, and yield components in onion, cucumber, and carrot. Objective 3: Determine the genetic basis and select for pigment, phytonutrient, and flavor content in onion, cucumber, and carrot, disease and pest resistances, and field components of yield, stress tolerance and market quality. Objective 4: Develop genetic stocks and genomic resources for onion, cucumber, and carrot using recurrent inbred lines, haploids, mutant stocks, and dense maps to capture new genetic variation for desired traits, and distribute them to researchers and commercial breeders. Approach (from AD-416): The long-term potential for improving a crop is only as great as the breadth of diversity that breeders utilize. Objective 1 targets evaluation of carrot, onion, and cucumber germplasm for traits important to growers and consumers. Discovery Goal 1: Identify unique phenotypic variation in germplasm collections and breeding stocks to improve nutritional and processing quality, disease resistance, stress tolerance, and yield of Allium, Cucumis, and Daucus vegetables, characterize observed variation and initiate genetic incorporation of these phenotypes into elite germplasm. Dense genetic maps are useful to improve the efficiency of crop improvement. For Objective 2 we will identify DNA polymorphisms in elite onion, cucumber, and carrot germplasm to construct genetic maps for marker-facilitated selection of major horticultural traits. Discovery Goal 2: Identify DNA polymorphisms in elite onion, cucumber, and carrot germplasm and construct detailed genetic maps for marker- facilitated selection of major horticultural traits. Efficient plant breeding depends on knowledge of the genetic basis of traits under selection. Objective 3 targets evaluation and genetic characterization of carrot, onion, and cucumber germplasm for traits important to growers and consumers. Discovery Goal 3: Develop populations to determine the patterns of inheritance of unique phenotypic variation in germplasm collections and breeding stocks to improve nutritional and processing quality, disease resistance, stress tolerance, and yield of Allium, Cucumis, and Daucus vegetables, phenotype observed variation among individuals in populations, and develop genetic models to explain observed genetic patterns. Information from germplasm evaluation and genetic analysis is useful and sets the stage for developing genetic and breeding stocks, and for establishing information resources for stakeholders. Objective 4 targets deployment of germplasm and resources. Discovery Goal 4: Incorporate valuable traits described in Discovery Goal 3 into elite germplasm and genetic stocks using marker-assisted selection and provide stakeholders with germplasm and databases including maps. Carrot populations with high nutritional value and novel colors were identified and advanced to increase seed production and expand testing. Experimental hybrid carrots from the USDA program performed very well in trial comparisons with commercial cultivars. USDA selections with very good flavor and nematode resistance were among those with superior field performance. Molecular genetic markers were developed to better understand the basis of purple carrot color and genes associated with the domestication of carrot. Germplasm and tools developed facilitate carrot breeding. Onion phenotypes with various amounts and types of epicuticular waxes were identified after field and greenhouse evaluations. Selections with specific amounts of waxes were selected and are being self-pollinated to produce true-breeding progenies for evaluations in choice and no-choice experiments with thrips, the most serious insect pest of onion. An experimental semi-glossy hybrid of onion was produced and provided to Cornell University for field evaluations of thrips resistance. New single nucleotide polymorphisms (SNP) were added to the genetic map of onion, resulting in over 800 SNP markers now mapped. Onion germplasm resistant to pink root and Fusarium basal rot was identified, crossed with a susceptible inbred, and segregating progenies produced. Phenotypic evaluations are underway and deoxyribonucleic acid (DNA) isolated for genetic analyses. Bulbs are being produced to produce F3 families for replicated disease evaluations. The mosaic mutants of cucumber were demonstrated to be a method to produce transcriptional knock-downs of mitochondrial genes. This opens the door for mutational analyses of mitochondrial genes and analyses of nuclear responses. New mapping populations were developed for framework or fine genetic mapping of genes controlling fruit size (length and width), fruit weight, flowering time, parthenocarpy fruit setting, anthracnose, angular leaf spot, and target leaf spot disease resistance quantitative trait loci (QTL). Phenotyping was conducted in multiple locations in both the greenhouse and field for these traits. Genome wide or localized linkage maps are being developed for linkage analysis of these genes or QTL with molecular markers with emphasis on use of high throughout whole genome re- sequencing tools. The genome of the wild relative of cucumber, Cucumis hystrix was sequenced and assembled. A linkage map of C. hystrix is being developed which will be used as a tool in marker-assisted identification of introgression lines. A DNA oligo-pool based fluoresce in situ hybridization (FISH) method was developed for efficient identification of chromosome pairing between homoeologous chromosomes. Machine trials were conducted in commercial fields. Accomplishments 01 Genetics of purple root color in carrots. One of the original colors of carrots ~1000 years ago was purple, due to anthocyanin pigments. There have been several studies reporting the likelihood that several genes control purple root color so ARS scientists, in collaboration with researchers from the Instituto Nacional de Tecnologia Agropecuaria (INTA) in Argentina, the University of Wisconsin - Madison, and the Yuzuncu Yil University in Turkey evaluated the genetic control of this trait. Two major genes controlling the presence or absence of purple color were identified, and in an unexpected discovery, a gene controlling acylation of anthocyanins was also found. These studies provide fundamental information about the genetics of purple color in carrots. The unexpected discovery of a gene controlling carrot acylation is important because acylation significantly influences the bioavailability and nutritional efficacy of anthocyanins. 02 Thrips resistance in onion. Onion thrips is the most important insect pest of onion for both bulb and seed production, requiring frequent insecticide applications. ARS researchers from Madison, WI completed genetic mapping that revealed two major chromosome regions that control amounts and types of epiculticular waxes in onion. Lower amounts of these waxes are associated with resistance to thrips. Deployment of onion cultivars with lower amounts of epiculticular waxes should reduce the build-up of thrips populations during onion production and allow for fewer insecticide sprays, reducing costs for growers and overall environmental impact of pesticide sprays. 03 Development of mitochondrial mutants in a higher plant. Mitochondrial function is important for plant growth, yield and seed production. There is presently no method to efficiently produce mutants in the mitochondrial deoxyribonucleic acid (DNA), important for genetic studies. ARS researchers from Madison, WI demonstrated that the mosaic mutants of cucumber are missing or have significantly fewer copies of specific genes in the mitochondrial DNA, and are therefore a useful tool to produce knock-downs of mitochondrial genes. These mitochondrial mutants will be important to study their effects on plant growth and development, as well as nuclear responses and interactions important for plant performance and yield. 04 Quantitative trait loci (QTL) mapping of fruit size. Fruit size is an important quality trait of cucumber, but the genetic mechanisms controlling these traits are largely unknown. Through multi-year and multi-location greenhouse and field trials, phenotypic data of fruit length and diameter, ARS researchers from Madison, WI collected at three development stages (anthesis, immature, and mature fruits) in six environments over four years. QTL analysis with three QTL models identified 29 consistent and distinct fruit size QTLs from which 12 consensus QTLs were inferred underlying fruit elongation and radial growth, which presented a dynamic view of genetic control of cucumber fruit development. Results from this study highlighted the benefits of QTL analysis with multiple QTL models and different mapping populations in improving the power of QTL detection. Results from this work provide insights into the genetic mechanisms of fruit size in cucumber. The molecular markers are useful in marker-assisted selection in cucumber breeding. 05 2014 public sector cucumber research priority global survey. For researchers in the public domain, it is important to know stakeholders� needs and prioritize their research to address critical issues in crop production. In 2014, researchers from ARS Madison, WI conducted a global survey for public sector cucumber research priorities among major stakeholder groups. Data from 38 respondents were analyzed and critical issues common to major market classes of cucumbers were identified, including priority issues for specific to market classes or geographic regions of cucumber production. For North American pickling and slicing cucumbers, additional research priorities included resistances to Phytophthora fruit rot and angular leaf spot, improvement of post-harvest fruit quality, and development of parthenocarpic varieties. This survey provides important research priority information for both public and private researchers. It is also an important reference for the industry stakeholders for decision- making. 06 Chromosome painting with oligo probes. Precise, efficient and accurate identification of chromosomal fragments or chromosomes is important in transferring useful genes from wild species into cultivated crops. Current methods are time consuming and lack precision for small alien chromatins. ARS researchers from Madison, WI developed an oligonucleotide (oligo) chromosome-painting technique in Cucumis species that will be applicable in any plant species with a sequenced genome. The bulked oligo probes can effectively paint and track a single chromosome in early meiotic stages and can be used to map the pairing of a single pair of homoeologous chromosomes in a hybrid between cucumber and its wild relative Cucumis hystrix. This is the first piece of work to prove that oligo painting works in plants, which provides a novel, efficient, and important tool to study homoeologous chromosome pairing to understand mechanisms of genetic recombination in distant hybrids in plants. 07 Quantitative trait loci (QTL) mapping of downy mildew (DM) resistance in cucumber. The DM is at present the most important fungal disease of cucumber. Good molecular markers for resistance to this pathogen are still lacking hindering progress of developing resistant lines through molecular breeding. ARS researchers from Madison, WI conducted a multi- location field screening test for responses to DM inoculation in a mapping population in cucumber and confirmed the major- and minor- effect QTL identified in for DM resistance in PI 330628. The results provide new insights into phenotypic and genetic mechanisms of DM resistance in cucumber.
Impacts
(N/A)
Publications
- Menda, N., Strickler, S.R., Edwards, J.D., Bombarely, A., Dunham, D.M., Martin, G.B., Mejia, L., Hutton, S.F., Havey, M.J., Maxwell, D.P., Mueller, L.A. 2014. Analysis of wild-species introgressions in tomato inbreds uncovers ancestral origins. Biomed Central (BMC) Genomics. 14(10):287-303.
- Ipek, M., Sahin, N., Ipek, A., Cansev, A., Simon, P.W. 2015. Development and validation of new SSR markers from expressed regions in the garlic genome. Scientia Horticulturae. 72(1):41-46.
- Bo, K., Ma, Z., Chen, J., Weng, Y. 2014. Molecular mapping reveals structural rearrangements and quantitative trait loci underlying traits with local adaptation in semi-wild Xishuangbanna cucumber (Cucumis sativus L. var. xishuangbannanesis Qi et Yuan). Theoretical and Applied Genetics. 128(1):25-39.
- Mroz, T.L., Havey, M.J., Bartoszewski, G. 2015. Cucumber possesses a single terminal alternative oxidase gene that is upregulated by cold stress and in the mosaic (MSC) mitochondrial mutants. Plant Molecular Biology Reporter. 33(6):1893-1906. doi:10.1007/s11105-015-0883-9.
- Cavagnaro, P.F., Iorizzo, M., Yildiz, M., Senalik, D.A., Parsons, J., Ellison, S., Simon, P.W. 2014. A gene-derived SNP-based high resolution linkage map of carrot including the location of QTL conditioning root and leaf anthocyanin pigmentation. Biomed Central (BMC) Genomics. 15:1118.
- Shen, J., Dirks, R., Havey, M.J. 2015. Diallel crossing among doubled haploids of cucumber reveals significant reciprocal-cross differences. Journal of the American Society for Horticultural Science. 140(2):178-182.
- Bag, S., Schwartz, H.F., Cramer, C.S., Havey, M.J., Pappu, H.R. 2014. Iris yellow spot virus (Tospovirus: Bunyaviridae): from obscurity to research priority. Molecular Plant Pathology. 16:27.
- Macko-Podgorni, A., Iorizzo, M., Smolka, K., Simon, P.W., Grzebelus, D. 2014. Conversion of a diversity arrays technology marker differentiating wild and cultivated carrots to a co-dominant cleaved amplified polymorphic site marker. Acta Biochimica Polonica. 61(1):19-22.
- Simon, P.W. 2014. Progress toward increasing intake of dietary nutrients from vegetables and fruits: The case for a greater role for the horticultural sciences. HortScience. 49(2):112-115.
- Rubinstein, M., Katzenellenbogen, M., Eshed, R., Rozen, A., Katzir, N., Colle, M., Yang, L., Grumet, R., Weng, Y., Sherman, A., Ophir, R. 2015. Ultrahigh-density linkage map for cultivated cucumber (Cucumis sativus L.) using a single-nucleotide polymorphism genotyping array. PLoS One. 10(4) :e0124101.
- Damon, S.J., Havey, M.J. 2014. Quantitative trait loci controlling amounts and types of epicuticular waxes in onion. Journal of the American Society for Horticultural Science. 139(5):597-602.
- Rudd, J., Devkota, R., Baker, J., Peterson, G., Lazar, M., Bean, B., Worrall, D., Baughman, T., Marshall, D.S., Sutton, R., Rooney, L., Nelson, L., Fritz, A., Weng, Y., Morgan, G., Seabourn, B.W. 2014. �TAM 112� Wheat, resistant to greenbug and wheat curl mite and adapted to the dryland production system in the Southern High Plains. Journal of Plant Registrations. 8(3):291-297.
- Arbizu, C., Ruess, H., Senalik, D., Simon, P.W., Spooner, D.M. 2014. Phylogenomics of the carrot genus (Daucus, Apiaceae). American Journal of Botany. 101(10):1666-1685.
- Arbizu, C., Reitsma, K.R., Simon, P.W., Spooner, D.M. 2014. Morphometrics of Daucus (Apiaceae): A counterpart to a phylogenomic study. American Journal of Botany. 101(11):2005-2016.
- Han, Y., Zhang, T., Thammapichai, P., Weng, Y., Jiang, J. 2015. Chromosome- specific painting in Cucumis species using bulked oligonucleotides. Genetics. 200(3):771-779.
- Zhou, Q., Miao, H., Li, S., Zhang, S., Wang, Y., Weng, Y., Zhang, Z., Huang, S., Gu, X. 2015. A sequencing-based linkage map of cucumber. Molecular Plant. 8(6):961-963.
- Del Valle-Echevarria, A.R., Kielkowska, A., Bartoszewski, G., Havey, M.J. 2015. The mosaic mutants of cucumber: a method to produce knock-downs of mitochondrial transcripts. G3, Genes/Genomes/Genetics. 5(6):1211-1221.
- Ali, A., Jansky, S. 2015. Fine screening for resistance to cold-induced sweetening in potato hybrids containing Solanum raphanifolium germplasm. Advances in Agriculture. Available:
- Weng, Y., Colle, M., Wang, Y., Yang, L., Rubinstein, M., Sherman, A., Ophir, R., Grumet, R. 2015. QTL mapping in multiple populations and development stages reveals dynamic quantitative trait loci for fruit size in cucumbers of different market classes. Theoretical and Applied Genetics. 128(9):1747-1763.
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Progress 10/01/13 to 09/30/14
Outputs
Progress Report Objectives (from AD-416): Objective 1: Evaluate Allium, Cucumis, and Daucus germplasm for genetic diversity in superior horticultural and product quality traits, including: resistance to diseases and pests; growth habit that reduces weed competition; processing quality for pickling cucumbers; postharvest storage capacity for long-storing onions; flavor and nutritional qualities; and provide all relevant information to GRIN. Objective 2: Identify genetic markers and construct detailed maps of genes and quantitative trait loci associated with disease and pest resistance, abiotic stress tolerance, end product quality, and yield components in onion, cucumber, and carrot. Objective 3: Determine the genetic basis and select for pigment, phytonutrient, and flavor content in onion, cucumber, and carrot, disease and pest resistances, and field components of yield, stress tolerance and market quality. Objective 4: Develop genetic stocks and genomic resources for onion, cucumber, and carrot using recurrent inbred lines, haploids, mutant stocks, and dense maps to capture new genetic variation for desired traits, and distribute them to researchers and commercial breeders. Approach (from AD-416): The long-term potential for improving a crop is only as great as the breadth of diversity that breeders utilize. Objective 1 targets evaluation of carrot, onion, and cucumber germplasm for traits important to growers and consumers. Discovery Goal 1: Identify unique phenotypic variation in germplasm collections and breeding stocks to improve nutritional and processing quality, disease resistance, stress tolerance, and yield of Allium, Cucumis, and Daucus vegetables, characterize observed variation and initiate genetic incorporation of these phenotypes into elite germplasm. Dense genetic maps are useful to improve the efficiency of crop improvement. For Objective 2 we will identify DNA polymorphisms in elite onion, cucumber, and carrot germplasm to construct genetic maps for marker-facilitated selection of major horticultural traits. Discovery Goal 2: Identify DNA polymorphisms in elite onion, cucumber, and carrot germplasm and construct detailed genetic maps for marker- facilitated selection of major horticultural traits. Efficient plant breeding depends on knowledge of the genetic basis of traits under selection. Objective 3 targets evaluation and genetic characterization of carrot, onion, and cucumber germplasm for traits important to growers and consumers. Discovery Goal 3: Develop populations to determine the patterns of inheritance of unique phenotypic variation in germplasm collections and breeding stocks to improve nutritional and processing quality, disease resistance, stress tolerance, and yield of Allium, Cucumis, and Daucus vegetables, phenotype observed variation among individuals in populations, and develop genetic models to explain observed genetic patterns. Information from germplasm evaluation and genetic analysis is useful and sets the stage for developing genetic and breeding stocks, and for establishing information resources for stakeholders. Objective 4 targets deployment of germplasm and resources. Discovery Goal 4: Incorporate valuable traits described in Discovery Goal 3 into elite germplasm and genetic stocks using marker-assisted selection and provide stakeholders with germplasm and databases including maps. New genetic sources of nematode resistance in carrots were reported and resistance was tested on a large-scale in California fields and found to improve carrot yield (pack-out) rates. USDA experimental carrot breeding entries were evaluated for field productivity and consumer quality traits and resistance to Alternaria leaf blight. New USDA hybrids performed very well in the trial, as did USDA germplasm. Flavor evaluation was also performed for all entries and new carrot flavor compounds were reported. New molecular markers were described and the expressions of genes involved in carotenoid biosynthesis were found to be differentially up- regulated in orange carrots, compared to yellow or white. Carrot breeding is more efficient with genetic information about important traits and molecular tools to facilitate the breeding progress. Onion germplasm were screened for resistance to pink root and Fusarium and amounts of epicuticular waxes. Traits genetically analyzed included anthocyanin contents, male-fertility restoration, leaf waxiness, and bulb colors. Lower amounts of epicuticular waxes were associated with fewer numbers and damage by onion thrips, the primary insect pest of onion. Major quantitative trait loci (QTL) controlling amounts and types of epicuticular waxes were mapped. QTL were identified controlling types and amounts of anthocyanins contributing to enhanced red color of onion bulbs. Families segregating for resistances to pink root and Fusarium basal rot were developed. New cucumber mapping populations were developed for framework or fine genetic mapping of genes controlling fruit size (length and width), fruit weight, flowering time, fruit set without pollination, and fungal pathogen resistance quantitative trait loci (QTLs). Phenotyping was conducted in multiple locations for these traits, both in the greenhouse and field. Genome wide or localized linkage maps are being developed for linkage analysis of these genes or QTL with molecular markers with emphasis on use of high throughout whole genome re-sequencing tools. Machine trials were conducted in commercial fields. Accomplishments 01 Gene expression in orange, yellow, and white carrots. Carrots today are usually orange due to the accumulation of carotenoid pigments that provide us with dietary vitamin A, but yellow and white carrots are also cultivated. The genes that account for these dramatic carrot color differences have not been characterized so ARS scientists at Madison, WI, in collaboration with University of Wisconsin researchers, evaluated the expression of several carrot genes in the carotenoid biosynthetic pathway in carrots of different colors. Two carotenoid biosynthetic genes were found to be expressed at much higher levels in orange carrots, than in yellow or white. These insights into the molecular basis of carotenoid accumulation in carrot help scientists understand the fundamental bases of biochemical pathways that provide essential vitamins, and suggest genetic and environmental variables that may increase, or limit, nutritional value of carrots and other vegetables. 02 Genetics and mapping of important traits of onion. Resistance to diseases, pollen fertility, and nutritional quality are under genetic control in onion. Using over 1000 indicators of genetic differences called single nucleotide polymorphisms (SNPs), these important characteristics of onion were placed onto onion genetic maps by ARS scientists in Madison, WI, and information about these SNPs was released without restrictions to stakeholders. This research is valuable to onion breeders since it provides them with valuable information for tracking these traits while they breed for improved onions for the U.S. market. 03 Genes involved in cucumber domestication. Genes for domestication- related traits in the semi-wild Xishuangbanna cucumber (XIS) (which is a landrace from the tropical southwest China with some unique traits that are useful for cucumber breeding) were located on the cucumber genetic linkage map by ARS scientists in Madison, WI. Twelve genes influencing flowering time, mature fruit length, diameter, and weight were located. Results from this study provide important information on the chromosomal and genetic basis of crop evolution in cucumber and the molecular markers associated with these genes will be useful in cucumber breeding. 04 Development of cucumber genetic and genomic resources for horticulturally important traits in cucumber. In collaboration with colleagues in Israel under a Binational Agricultural Research and Development (BARD) project, ARS scientists in Madison, WI developed an array of molecular markers for cucumber and evaluated these markers for their usefulness in locating genes affecting production and quality. Important genes were located and molecular markers associated with these genes will be useful in accelerating the process of cucumber breeding. 05 QTL mapping of downy mildew resistance in cucumber. In 2013, ARS scientists in Madison, WI conducted multi-location field screening tests for responses to the important cucumber disease, downy mildew, to place genes for disease resistance on the cucumber genetic map. We identified one major gene, and two minor genes for downy mildew resistance in a Plant Introduction line of cucumber (PI 330628). Results from this study provide new insights into phenotypic and genetic mechanisms of downy mildew resistance in cucumber that will help growers and plant breeders identify cucumber genes that impart disease resistance.
Impacts
(N/A)
Publications
- Grzebelus, D., Iorizzo, M., Senalik, D.A., Ellison, S., Cavagnaro, P., Macko-Podgorni, A., Heller-Uszynska, K., Kilian, A., Nothnagel, T., Allender, C., Simon, P.W., Baranski, R. 2014. Diversity, genetic mapping, and signatures of domestication in the carrot (Daucus carota L.) genome, as revealed by Diversity Arrays Technology (DArT) markers . Molecular Breeding. 33(3):625-637.
- Yang, L., Koo, D., Li, D., Zhang, T., Jiang, J., Luan, F., Renner, S.S., Henaff, E., Sanseverino, W., Garcia-Mas, J., Senalik, D.A., Simon, P.W., Weng, Y., et al. 2014. Next-generation sequencing, FISH mapping and synteny-based modeling reveal mechanisms of decreasing dysploidy in Cucumis. Plant Journal. 77(1):16-30.
- Duangjit, J., Welsh, K., Wise, M.L., Bohanec, B., Havey, M.J. 2014. Genetic analyses of anthocyanin concentrations and intensity of red bulb color among segregating haploid progenies of onion. Molecular Breeding. 34(1):75-85.
- Macko-Podgorni, A., Nowicka, A., Grzebelus, E., Simon, P.W., Grzebelus, D. 2013. DcSto: carrot Stowaway-like elements are abundant, diverse, and polymorphic. Genetica. 141(4-6):255-267.
- Schmaelzle, S., Gannon, B., Crawford, S., Arscott, S.A., Goltz, S., Palacios-Rojas, N., Pixley, K.V., Simon, P.W., Tanumihardjo, S.A. 2014. Maize genotype and food matrix affect the provitamin A carotenoid bioefficacy from staple and carrot-fortified feeds in Mongolian gerbils (Meriones unguiculatus). Journal of Agricultural and Food Chemistry. 62(1) :136-143.
- Du Toit, L.J., Derie, M.L., Christianson, C.E., Hoagland, L., Simon, P.W. 2014. First report of bacterial blight of carrot in Indiana caused by Xanthomonas hortorum pv. carotae . Plant Disease. 98(5):685.
- Reddy, S.K., Weng, Y., Rudd, J.C., Akhunova, A., Liu, R.S. 2013. Transcriptomics of induced defense responses to greenbug aphid feeding in near isogenic wheat lines. Plant Science. 212:26-36.
- 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.
- Havey, M.J. 2013. Single nucleotide polymorphisms in linkage disequilibrium with the male-fertility restoration (Ms) locus in open- pollinated and inbred populations of onion. Journal of the American Society for Horticultural Science. 138(4):306-309.
- Azhaguvel, P., Mornhinweg, D.W., Vidya-Saraswathi, D., Rudd, J.C., Chekhovskiy, K., Saha, M., Close, T.J., Dahleen, L.S., Weng, Y. 2014. Molecular mapping of greenbug (Schizaphis graminum) resistance gene Rsg1 in barley. Plant Breeding. 133(2):227-233.
- Saude, C., Simon, P.W., McDonald, M.R. 2014. Incidence and severity of cavity spot of carrot as affected by pigmentation, temperature, and rainfall. Plant Disease. 98(7):929-936.
- Lu, H., Lin, T., Klein, J., Wang, S., Qi, J., Zhou, Q., Sun, J., Zhang, Z., Weng, Y., Huang, S. 2014. QTL-seq identifies an early flowering QTL located near Flowering Locus T in cucumber. Theoretical and Applied Genetics. 127(7):1491-1499.
- Boateng, C.O., Schwartz, H.F., Havey, M.J., Otto, K. 2014. Evaluation of onion germplasm for resistance to Iris yellow spot (Iris yellow spot virus) and onion thrips, Thrips tabaci. Southwestern Entomologist. 39(2):237-260.
- Damon, S., Groves, R., Havey, M.J. 2014. Variation for epicuticular waxes on onion foliage and impacts on numbers of onion thrips. Journal of the American Society for Horticultural Science. 139(4):495-501.
- Yahyaa, M., Bar, E., Dubey, N.K., Meir, A., Davidovich-Rikanati, J., Hirschberg, J., Ali, R., Tholl, D., Simon, P.W., Tadmor, Y., Lewinsohn, E., Ibdah, M. 2013. Formation of norisoprenoid flavor compounds in carrot (Daucus carota L.) roots: characterization of a cyclic-specific carotenoid cleavage dioxygenase 1 gene. Journal of Agricultural and Food Chemistry. 61(50):12244-12252.
- Ipek, M., Ipek, A., Simon, P.W. 2014. Testing the utility of matK and ITS DNA regions for discrimination of Allium species. Turkish Journal of Botany. 38(2):203-212.
- von Kohn, C., Kielkowska, A., Havey, M.J. 2013. Sequencing and annotation of the chloroplast DNAs and identification of polymorphisms distinguishing normal male-fertile and male-sterile cytoplasms of onion. Genome. 56(12) :737-742.
- Ali, A., Mathews, W.C., Cavagnaro, P.F., Iorizzo, M., Roberts, P.A., Simon, P.W. 2014. Inheritance and mapping of Mj-2, a new source of root-knot nematode (Meloidogyne javanica) resistance in carrot. Journal of Heredity. 105(2):288-291.
- Bowman, M.J., Willis, D.K., Simon, P.W. 2014. Transcript abundance of phytoene synthase 1 and phytoene synthase 2 is associated with natural variation of storage root carotenoid pigmentation in carrot. Journal of the American Society for Horticultural Science. 139(1):63-68.
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Progress 10/01/12 to 09/30/13
Outputs
Progress Report Objectives (from AD-416): Objective 1: Evaluate Allium, Cucumis, and Daucus germplasm for genetic diversity in superior horticultural and product quality traits, including: resistance to diseases and pests; growth habit that reduces weed competition; processing quality for pickling cucumbers; postharvest storage capacity for long-storing onions; flavor and nutritional qualities; and provide all relevant information to GRIN. Objective 2: Identify genetic markers and construct detailed maps of genes and quantitative trait loci associated with disease and pest resistance, abiotic stress tolerance, end product quality, and yield components in onion, cucumber, and carrot. Objective 3: Determine the genetic basis and select for pigment, phytonutrient, and flavor content in onion, cucumber, and carrot, disease and pest resistances, and field components of yield, stress tolerance and market quality. Objective 4: Develop genetic stocks and genomic resources for onion, cucumber, and carrot using recurrent inbred lines, haploids, mutant stocks, and dense maps to capture new genetic variation for desired traits, and distribute them to researchers and commercial breeders. Approach (from AD-416): The long-term potential for improving a crop is only as great as the breadth of diversity that breeders utilize. Objective 1 targets evaluation of carrot, onion, and cucumber germplasm for traits important to growers and consumers. Discovery Goal 1: Identify unique phenotypic variation in germplasm collections and breeding stocks to improve nutritional and processing quality, disease resistance, stress tolerance, and yield of Allium, Cucumis, and Daucus vegetables, characterize observed variation and initiate genetic incorporation of these phenotypes into elite germplasm. Dense genetic maps are useful to improve the efficiency of crop improvement. For Objective 2 we will identify DNA polymorphisms in elite onion, cucumber, and carrot germplasm to construct genetic maps for marker-facilitated selection of major horticultural traits. Discovery Goal 2: Identify DNA polymorphisms in elite onion, cucumber, and carrot germplasm and construct detailed genetic maps for marker- facilitated selection of major horticultural traits. Efficient plant breeding depends on knowledge of the genetic basis of traits under selection. Objective 3 targets evaluation and genetic characterization of carrot, onion, and cucumber germplasm for traits important to growers and consumers. Discovery Goal 3: Develop populations to determine the patterns of inheritance of unique phenotypic variation in germplasm collections and breeding stocks to improve nutritional and processing quality, disease resistance, stress tolerance, and yield of Allium, Cucumis, and Daucus vegetables, phenotype observed variation among individuals in populations, and develop genetic models to explain observed genetic patterns. Information from germplasm evaluation and genetic analysis is useful and sets the stage for developing genetic and breeding stocks, and for establishing information resources for stakeholders. Objective 4 targets deployment of germplasm and resources. Discovery Goal 4: Incorporate valuable traits described in Discovery Goal 3 into elite germplasm and genetic stocks using marker-assisted selection and provide stakeholders with germplasm and databases including maps. New carrot germplasm was collected in Morocco and field trials were initiated for carrot, onion, and cucumber. Samples were collected for carrot and onion pigments and sugars, and disease evaluation was initiated for carrot nematode and alternaria, onion pink root & Fusarium, and cucumber anthracnose and powdery mildew resistances. Deoxyribonucleic acid (DNA) samples were collected for molecular marker evaluations in carrot, onion, and cucumbers. This research addressed Objectives 1-3 by evaluating germplasm for important traits, identifying markers and map locations, and determining the genetic basis of these traits. Objective 1: Evaluate Allium, Cucumis, and Daucus germplasm for genetic diversity in superior horticultural and product quality traits, including: resistance to diseases and pests; growth habit that reduces weed competition; processing quality for pickling cucumbers; postharvest storage capacity for long-storing onions; flavor and nutritional qualities; and provide all relevant information to the Germplasm Resources Advisory Council (GRIN). Objective 2: Identify genetic markers and construct detailed maps of genes and quantitative trait loci associated with disease and pest resistance, abiotic stress tolerance, end product quality, and yield components in onion, cucumber, and carrot. Objective 3: Determine the genetic basis and select for pigment, phytonutrient, and flavor content in onion, cucumber, and carrot, disease and pest resistances, and field components of yield, stress tolerance and market quality.
Impacts
(N/A)
Publications
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