Location: Crop Genetics and Breeding Research
2024 Annual Report
Objectives
1. Characterize and improve internode length and stem maggot resistance in bermudagrass.
1A. Using RNA Sequencing, identify candidate genes that regulate internode length in bermudagrass.
1B. Develop integrated pest management strategies for mitigation of the Bermudagrass Stem Maggot (BSM).
2. Develop genetic markers and biocontrol agents to reduce root-knot nematode and aphid damage in sweet sorghum.
2A. Determine if the root-knot nematode resistance gene can be moved from Honey Drip to susceptible or moderately resistant sorghum cultivars by marker-assisted selection and thus confer or improve resistance.
2B. Identify new genetic loci for root-knot nematode resistance and develop markers associated with resistance.
2C. Investigate the use of entomopathogenic fungi to control sugarcane aphid in sorghum.
3. Assess lupin and carinata as renewable bio-based products and soil enhancement cover crops.
3A. Assess the economic and environmental impact of lupin as a winter crop cover within a summer row crop rotation.
3B. Determine the effects of Brassica carinata grown as a winter crop on soil quality and subsequent summer row crop production.
4. Develop genomic technologies for centipede grass and use those technologies to understand and improve desirable ecological and aesthetic traits for this species. Work may include, but is not limited to, water and nutrient efficiency, resilience to foot traffic, color, and pollinator support.
Approach
Objective 1: For characterization of internode length in turf bermudagrass, total ribonucleic acid (RNA) will be extracted from the leaf and stem tissue of bermudagrasses. RNA samples will be sent for library preparation and sequencing. The transcriptome will be reconstructed and differentially expressed genes will be identified and then confirmed for internode length via real-time Polymerase chain reaction (PCR). For stem maggot resistance, forage bermudagrass germplasm will be selected from the bermudagrass core collection for further evaluation for yield, quality and tolerance to Bermudagrass Stem Maggot (BSM) and tested in the field in two side by side plots (one sprayed and one not sprayed) and replicated four times in a randomized complete block design. Most tolerant lines for further analysis for yield and quality traits will be determined and used for release and use for crosses.
Objective 2: The root-knot nematode resistance gene will be moved from ‘Honey Drip’ to susceptible or moderately resistant sorghum cultivars by marker-assisted selection. Furthermore, new genetic loci for root-knot nematode resistance will be identified by creating a mapping population using a source of resistance different than ‘Honey Drip’. In collaboration with ARS fungal curator, naturally occurring entomopathogenic fungal isolates will be obtained from sugarcane aphids. Entomopathogenic fungi will be applied to susceptible sorghum to determine if these strains can control sugarcane aphids.
Objective 3: The economic and environmental impact of lupin with and without rye as a winter crop cover within a summer row crop rotation will be determined using rotating main crops of peanut and cotton over years with different cover crops during the winter (narrow leaf lupin, white lupin, white lupin + cereal rye, narrow leaf lupin + cereal rye, cereal rye, and fallow. Half the covers will be harvested and the other half rolled. Changes in soil fertility and yields will be determined. The effects of Brassica carinata grown as a winter crop on soil quality and subsequent summer row crop production an experiment will be determined by rotating carinata and rye planted as a winter cover with sorghum and soybean as rotating summer crops.
Objective 4: For the genetic mapping of desirable turf traits in centipedegrass, a genome-wide association study will be conducted using a population of approximately 300 vegetatively propagated lines replicated in the field. Morphological traits will be measured for two years after establishment. Single nucleotide polymorphisms (SNPs) will be created from each line using genotyping by sequencing and the genome of a centipedegrass line will be sequenced. SNPs will be aligned to the reference sequence and SNPs will be identified that are associated with the traits. For the identification of pollinators of centipedegrass inflorescences, a collection of centipedegrass lines will be grown in large field plots. In collaboration with an entomologist, pollinators will be documented that transit into each plot and those directly pollinating the inflorescences.
Progress Report
This is the final report for the project 6048-21000-030-000D which terminated in January 2024. For the characterization of internode length in turf bermudagrass in Objective 1, gene expression differences among Tifgreen and its somatic mutants MiniVerde and TifEagle and an unrelated line Tifway were examined for genes involved in dwarfism. One of the most repressed transcripts in RNA sequencing was a homolog to a gibberellin (GA) receptor. This transcriptional difference was confirmed in MiniVerde and TifEagle using quantitative Polymerase chain reacton (PCR). Yet, application of GA to all the plants showed increased shoot elongation in all treated lines and thus other gibberellin receptors must be functional in these lines. Endogenous GA levels were measured in these lines and the most common gibberellins in plants, GA1, GA3, GA4, and GA24 were not detected in these lines. GA9 was significantly higher in MiniVerde and TifEagle than Tifgreen and Tifway with more than double the concentrations of GA9. GA53 levels were significantly higher in Tifgreen as compared to TifEagle, MiniVerde, and Tifway. Tifgreen had almost 7 times as much GA53 than TifEagle and MiniVerde and 37 times as much GA53 as Tifway. For GA29, Tifway had higher endogenous GA29 concentrations than Tifgreen, MiniVerde, and TifEagle. Thus, bermudagrass is unusual in that it lacks the common GAs seen in plants, MiniVerde and TifEagle do respond to the application of gibberellin, and endogenous levels of GA have been altered in these dwarf lines.
For stem maggot resistance in Objective 1, a small number of forage bermudagrass accessions have been identified as having significantly more tolerance to bermudagrass stem maggot (BSM) than the most productive current forage bermudagrass cultivar (Tifton 85). Testing began by evaluating the full forage bermudagrass core collection at multiple locations. The 18 most tolerant and productive accessions were tested for four years to determine the yield reduction due to BSM compared to the current forage cultivars. Five accessions had significantly less yield reduction from BSM during the July and August harvest as well as significantly more biomass (forage) production. Two of these accessions are being increased. One of these is a hybrid cross that is currently being processed for cultivar release which will enable it to be licensed by commercial spriggers to distribute to growers. Crosses of tolerant lines with other cultivars are being performed. Current hay producers need to know the most economical insecticide control of their current BSM susceptible bermudagrass fields. Trials were conducted over 5 years to determine that one to two pyrethroid sprays within two weeks of the previous clippings would control up to 90% of the BSM damage and yield reduction. These findings have been communicated to bermudagrass hay growers by the University of Georgia Forage Extension specialist.
For Objective 2, markers were developed for the root knot nematode (RKN) resistance gene from the sweet cultivar ‘Honey Drip’ located on sorghum chromosome 3. These markers were used to backcross the quantitative trait locus (QTL) region into several nematode-susceptible lines. BC1F6 selections were inoculated with RKN in the greenhouse along with their susceptible parents, and nematode reproduction was quantified. The total number of eggs and number of eggs per gram of root were significantly lower for Honey Drip and BC1F6 selections than for the susceptible parents, demonstrating that this genetic region confers resistance to RKN in susceptible genetic backgrounds. A new quantitative trait locus (QTL) for RKN resistance was identified in an F2 population from the cross between PI 144134 (resistant) x Collier (susceptible). This QTL is located on sorghum chromosome 5.
Also under Objective 2, fungal entomopathogens were tested as biocontrol agents for sugarcane aphid (now also known as sorghum aphid) on field-grown grain sorghum at Tifton and Fort Valley, Georgia. Two strains of Beauvaria bassiana (one liquid commercial formulation and one grown on sterilized grain) and one strain of Isaria fumosorosea (liquid commercial formulation) were sprayed on aphid infested sorghum plants, as well as water (negative control) and flupyradifurone insecticide (positive control). Positive control plants had significantly fewer aphids, less visible damage, and greater biomass and grain yield per plant than all other treatments. The fungal pathogen treatments were not different from the negative control, demonstrating that these particular fungal pathogens do not control sugarcane aphid under field conditions.
Three naturally-occurring fungal entomopathogens of sugarcane aphid were isolated from Georgia and identified by ARS scientists in Tifton, Georgia and Ithaca, New York. The fungi were identified as Akanthomyces dipterigenus (formerly Lecanicillium longisporum), and two Neoconidiobolus species. Samples of each isolate have been deposited in the ARS Collection of Entomopathogenic Fungi (ARSEF).
For Objective 3, both narrow-leaf lupin and white lupin either with or without cereal rye were evaluated as winter cover crops between rotations of summer cotton and peanut. ARS researchers at Tifton, Georgia also were able to determine whether these winter crops would be economical for producers. White lupin has the advantage of being useful as animal feed in the form of baleage (wet encased hay). The five-year trial indicated that the winter cover crops did not significantly affect the yield of peanut or cotton, either positively or negatively. Thus, using lupins only as a cover crop (and incorporated into the soil) was not economical to growers except when the white lupin could be harvested and fed to animals or sold as baleage. Evaluation of feed quality of the baleage from white lupin with and without cereal rye confirmed that it would be excellent as an animal feed. Brassica carinata (oil seed that can be used for alternative aviation fuel or biodiesel) was grown either consecutively or alternated with wheat during the winter growing season to evaluate the economics of growing these two crops between summer crop rotations of soybeans and sorghum. After initial analysis there were no significant differences in yield or economic benefits between the winter crop treatments, but further analyses are underway.
For Objective 4, which was added later when new congressionally mandated funds came for turf in 2020, a centipedegrass genome-wide association study (GWAS) population was established. This population consists of 295 diploid centipedegrass lines with 4 replicates and was planted in Tifton, Georgia on Sept 8, 2021. Genotyping by sequencing was performed and 72,523 single nucleotide polymorphisms (SNPs) were aligned to a centipedegrass reference sequence. To date, we currently have two-year data for chlorophyll content, fall cover retention, stigma color, leaf length, leaf width, reflectance, and spring green up. We have collected one year data for days to flower (assessed weekly), inflorescence height, internode length, pollinator visits for stigma color, seed head density, and time of day for pollinator abundance.
Accomplishments
1. Insecticide control of bermudagrass stem maggot (BSM). Knowledge of the susceptibility of currently grown bermudagrass [Cynodon dactylon (L.) Pers.] cultivars to the bermudagrass stem maggot (BSM; Atherigona reversura) is needed to initiate an integrated pest management (IPM) strategy to manage this exotic pest. USDA /ARS scientists along with scientists from the University of Georgia, in Tifton compared the severity of damage and yield among different pesticide application protocols. Either one or two zeta-cypermethrin or spinosad applications separately or together were applied on ‘Alicia’ and ‘Tifton 85’ bermudagrasses. Generally, zeta-cypermethrin treatments alone resulted in significantly greater herbage accumulation compared to the negative control (no insecticides) for both cultivars (p < 0.01). Regardless of cultivar, spinosad only treatments were no better than the negative control (p > 0.31). Two pyrethroid applications resulted in greater net profit compared to all other insecticide treatments. This information was immediately dispersed to forage growers by University of Georgia extension. It is estimated that a single application of zeta-cypermethrin increased net returns by $25.79 acre-1 above the negative control. Two applications of zeta-cypermethrin increased net returns above the negative control by $34.60 acre-1 due to approximately 2000 lb acre-1 increase in herbage yield.
2. First quantitative trait locus (QTL) in maize (Zea mays) identified for resistance to the southern root-knot nematode (SRKN) (Meloidogyne incognita). The SRKN can feed on the roots of maize grown in sandy soils and can cause yield losses of 30% or greater in heavily infested fields. Furthermore, increases in SRKN density in the soil may reduce the yield for subsequently planted susceptible crops. The use of maize hybrids with resistance to SRKN could prevent an increase in SRKN density, yet no genetic regions have been identified that confer host resistance. In this study, a B73 (susceptible) x Ky21 (resistant) S5 recombinant inbred line (RIL) population was phenotyped for total number of eggs (TE) and root weight. This population has been previously genotyped using single nucleotide polymorphisms (SNPs). By utilizing the SNP data with the phenotype data, ARS researchers at Tifton, Georgia identified a single QTL on chromosome 5 that explained 15% of the phenotypic variation (PV) for the number of eggs and 11% of the PV for the number of eggs per g of root (EGR). Resistance from Ky21 was recessive. Thus, the first QTL for SRKN resistance in maize has been identified and could be incorporated into maize hybrids.
3. Hedgehog grain aphid is a super-clone in the Southwest. Hedgehog grain aphid (HGA), Sipha maydis, has an extremely large host range including economically important cereal, pasture, and wild grasses. HGA was first detected in California in 2007 and has since spread from the southwestern to the southeastern states. HGA can cause extensive damage to grasses because of its phytotoxic saliva as well as it being a vector of viruses. Little is known of its genetics and its current distribution and thus ARS researchers at Tifton, Georgia and Stillwater, Oklahoma and Oklahoma State University collaborated to answer these questions. To assess genetic diversity of this aphid, two gene fragments were sequenced from samples collected from 2016-2022 on 11 grass hosts in Colorado, New Mexico, and Utah and all were identical in sequence. Additionally, 6 simple sequence repeat markers were created and all HGA samples generated identical alleles. Furthermore, field surveys conducted in 2021-2022 did not detect HGA in New Mexico, Oklahoma, Texas, and Wyoming and only found HGA on wild grasses in Colorado and Utah. These data suggest a dominant clonal lineage exists in the southwestern U.S. which is useful for chemical and host resistance control. Also, the range of HGA has become reduced as compared to its distribution from 2015-2017. Continual monitoring is necessary as HGA has the potential to pose a significant threat to cereal agriculture production in the U.S.
4. Sugarcane aphid entomopathogens identified. The invasive sugarcane aphid has been an economically important pest to sorghum since it was first found in the U.S. in 2013. Two insecticides, Sivanto and Transform, have been used for its control, but both have similar modes of action. A need exists for an alternative form of sugarcane aphid control in case the aphid develops pesticide resistance (which commonly occurs for insects) and for organic sorghum production. In this study ARS researchers at Tifton, Georgia and Ithaca, New York identified naturally occurring fungi that kill sugarcane aphids on sorghum grown in Georgia over three years at five farms. From morphological and molecular data, the fungi Akanthomyces dipterigenus, Neoconidiobolus thromboides, and Neoconidiobolus sp. were identified infecting sugarcane aphids from the farms sampled. The identification of these fungi and their preservation allows the potential of a biologically based insecticide to be developed.
5. New aphid identified in Georgia. Aphids are a major pest to agriculture as they damage plants by removing plant sap and serve as a vector for plant viruses. Although aphids are small in size, aphid populations can be extremely large due to their short generation times and high reproductive rates. Introduced aphids can have devastating impacts on U.S. agriculture. ARS researchers in Tifton, Georgia and the Florida Department of Agriculture and Consumer Services identified Melanaphis donacis on giant reed in Tifton, Georgia. This identification was performed by morphological and molecular analysis. Previously this aphid had only been identified in the U.S. in California. We suspect that further examination of giant reed throughout the southeastern U.S. may identify additional aphid colonies. The known hosts, giant reed, clumping bamboos, and common reed may be impacted. This finding was also reported in the Florida Department of Agriculture and Consumer Service’s magazine TRI-OLOGY.
Review Publications
Taylor, M., Harris-Shultz, K.R., Armstrong, J.S., Hayashida, R., Mornhinweg, D.W., Hoback, W. 2023. Distribution, host range expansion, and genetic diversity of hedgehog grain aphid in central United States. Southwestern Entomologist. 48(4):757-770. https://doi.org/10.3958/059.048.0401.
Harris-Shultz, K.R., Halbert, S.E., Moore, M., Ni, X. 2024. First record of Melanaphis donacis (Hemiptera: Aphididae) in Georgia. Journal of Entomological Science. 59(4):524-527. https://doi.org/10.18474/JES23-105.
Rios, E.F., Lopez, Y., Munoz, P., Dubeux, J., Vendramini, J., Wallau, M., Grossman, A., Anderson, W.F., Baxter, L., Harris-Shultz, K.R., Castillo, M.S., Saha, M.C., Quesenberry, K., Blount, A., Reith, P., Kenworthy, K. 2023. Newell bermudagrass: a public release from the USDA cynodon collection. Journal of Plant Registrations. 17:605-615. https://doi.org/10.1002/plr2.20318.
Sapkota, S., Harris-Shultz, K.R., Strickland, T.C., Anderson, W.F. 2022. Identification of cultured and diazotrophic bacterial endophytes in warm-season grasses. PhytoFrontiers. 3(2):411-419. https://doi.org/10.1094/PHYTOFR-10-22-0110-R.
Sapkota, S., Kaur, R., Harris-Shultz, K.R., Wang, H., Koo, D., Nabukalu, P., Jespersen, D. 2023. Creation and characteristics of tetraploid and mixoploid centipedegrass. Crop Science. 63:2569-2582. https://doi.org/10.1002/csc2.21011.
Castrillo, L., Harris-Shultz, K.R. 2024. Entomophthoralean and hypocrealean fungal pathogens of the sugarcane aphid, Melanaphis sacchari (Hemiptera: Aphididae), on sorghum in Georgia . Journal of Invertebrate Pathology. 204:108107. https://doi.org/10.1016/j.jip.2024.108107.
Anderson, W.F., Powell, J., Hanna, W.W., Burton, G., Davis, M. 2024. Registration Coastcross II forage bermudagrass. Journal of Plant Registrations. 18:250-253. https://doi.org/10.1002/plr2.20357.
Muktar, M.S., Bizuneh, T., Anderson, W.F., Assefa, Y., Negawo, A.T., Abel Teshome, G., Haile, E., Muchugi, A., Feyissa, T., Jones, C.S. 2023. Analysis of global napier grass (Cenchrus purpureus) collections reveals high genetic diversity among genotypes with some redundancy between collections. Scientific Reports. 13, 14509. https://doi.org/10.1038/s41598-023-41583-7.
