Location: Crop Genetics and Breeding Research
2020 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
Objective 1A1, ARS researchers at Tifton, Georgia, examined genes in bermudagrass that are differentially expressed among Tifgreen and its mutants, RNA was isolated and RNA sequencing was performed.
Objective 1B1, ARS researchers at Tifton, Georgia, tested promising bermudagrass stem maggot (BSM) tolerant lines and compared them with split-plot controls and harvested 4 times. Some lines had lower BSM damage and higher yields than Tifton 85, the most popular variety. Future evaluations by ARS researchers at Tifton, Georgia, will determine the most appropriate lines to increase and use for further genetic improvement.
Objective 1B2, The first year of an 8 spray regime trial was conducted by ARS researchers at Tifton, Georgia, on Alicia and Tifton 85, with significant differences found among treatments. Multiple years of this research will refine the spray recommendations for hay producers in the Southeast.
Objective 2A, ARS researchers at Tifton, Georgia, determined 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, BC1F1 crosses were generated that contain the allele from ‘Honey Drip’ in the root-knot nematode (RKN) resistance gene region.
Objective 2B, ARS researchers at Tifton, Georgia, identified new genetic loci for root-knot nematode resistance in sorghum and developed markers associated with resistance. A new source of root-knot nematode resistance, different than the source from Honey Drip, was identified by genotyping resistant lines in the Chr. 3 quantitative trait loci (QTL) area that was found from Honey Drip. A line with resistance and a very different haplotype than Honey Drip was identified from a South African sweet sorghum line PI 144134. An F2 population (PI 144134 x Collier-susceptible) was created. This F2 population with 198 individuals was phenotyped for root-knot nematode egg number, root weight, and Brix. DNA was also extracted from the F2 plants, as well as from each parent, and 187 F2 progeny were selected for genotyping by sequencing. QTL were identified by ARS researchers at Tifton, Georgia, using single-marker analysis and a manuscript was generated.
Objective 2C2, ARS researchers at Tifton, Georgia, applied entomopathogenic fungi to sugarcane aphid-infested sorghum to identify strains that may reduce crop damage, field experiments were conducted in 2018 in Tifton, Georgia and Fort Valley, Georgia. Each location had five treatments: (a) Beauveria bassiania strain ABNB6 grown on sorghum grain, (b) Mycotrol ESO, Mycotrol contains Beauveria bassiana strain GHA, (c) Ancora, Ancora contains Isaria fumosorosea Apopka Strain 97, (d) water (negative control), and (e) Sivanto (positive control- flupyradifurone). Each treatment was applied to susceptible sorghum hybrid DKS53-53 in a randomized complete block design with four replicates. Despite a wet summer, none of the applied entomopathogens reduced sugarcane aphid number, reduced plant damage, nor did they increase grain yield in either location as compared to the treatment with water (the negative control). Thus, these three strains of entomopathogens were ineffective for controlling the sugarcane aphid under these field conditions. ARS researchers at Tifton, Georgia, decided not to repeat this test for another year because of the negative results and instead to focus our future efforts on strains that have been identified directly causing sugarcane aphid death under natural field conditions. Because ARS researchers at Tifton, Georgia, used entomopathogenic strains that are commercially available and commonly used, we published our results to help the larger sorghum community.
Objective 3A, during the winter of 2019-20, cover crops were established, maintained and harvested by ARS researchers at Tifton, Georgia, to obtain biomass weights or rolled to prepare for the summer planting of peanut and cotton. Peanut and cotton crops were successfully planted for the second year of assessment after cover crops.
Objective 3B, wheat (instead of rye) and carinata were planted and harvested by ARS researchers at Tifton, Georgia, for the first year of the winter rotation/tillage study. Forage sorghum was planted over all treatments after half of the plots were tilled.
Objective 4 is a new objective that was just added this fiscal year to the project plan. This objective’s goal is to 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. ARS researchers in Tifton, Georgia, will cooperate with University of Georgia in Tifton, Georgia, to conduct a genome wide association study using 300 diverse centipdedgrass lines. Morphological traits will be measured visually and by use of stationary cameras and drones to associate traits with genetic markers. Additionally, University of Georgia in Griffin, Georgia, will conduct a study with a ARS researcher at Tifton, Georgia, to examine the impact of ploidy level in centipedegrass on morphological traits such as drought tolerance and pollinator support.
Accomplishments
1. Identification of a new root-knot nematode resistance QTL in sorghum. The southern root-knot nematode (RKN) is the most common and destructive nematode species with a wide host range. Found in agricultural regions worldwide, farmers manage root-knot nematodes by applying nematicides, crop rotation, and the use of resistant cultivars. Sorghum is highly tolerant of RKN but some cultivars are able to support increased RKN population numbers. Higher numbers of RKN in the soil increases the risk of damage to subsequently planted susceptible crops. ARS researchers at Tifton, Georgia, previously identified a major quantitative trail locus (QTL) for RKN resistance on sorghum Chr. 3 but for a cultivar to maintain durable resistance, multiple resistance genes should be present in a plant. In this study these ARS researchers from Tifton, Georgia, and collaborators from the University of Georgia identified a new source of root-knot nematode resistance, created a genetic mapping population, and identified genetic markers associated with egg number and egg number per g of root. They found a single major QTL on Chr. 5 is associated with resistance to RKN. These regions on Chr. 5 and Chr. 3, from their respective parents, can be moved into elite, high-yielding sorghum by crossing for durable RKN resistance.
2. Survey of pollinating insects in centipedegrass lawns. In the U.S., turfgrasses are a major component of the landscape covering over 160,000 km2. Centipedegrass is a warm-season turfgrass that is often grown in the southeastern U.S. Recently honeybees were documented collecting pollen from the inflorescences of centipedegrass. With the decline of pollinators in abundance and diversity worldwide, ARS researchers in Tifton, Georgia, and scientists from the University of Georgia sought to survey the activity of bees in centipedegrass lawns in central and southern Georgia using nine lawns. 173 bees were collected from centipedegrass lawns of which 79% were Lasioglossum spp. (sweat bees), 7% were Halictus spp., and 4% were Melissodes spp. (long-horned bees). Other bees collected were Augochlorella spp. (sweat bees), Agapostemoa spp. (metallic green sweat bees), Bombus spp. (bumble bees), Megachile (leafcutter bees), Apis, Peponapis (squash bees), Ceratina (small carpenter bees), Ptilothrix, Svastra (long-horned bees), and Nomia spp. (sweat bees). Thus, our data shows that diverse genera of bees are residing in or in close proximity to lawns and foraging in and around the lawns seeking floral resources. With the knowledge that a large number of bees are present in centipedegrass lawns, homeowners and landscape managers should apply insecticides conservatively as certain insecticides are toxic to foraging bees in lawns.
3. Testing of entomopathogens to control sugarcane aphid in sorghum. The sugarcane aphid outbreak on U.S. sorghum began in 2013 near Beaumont, Texas, and by 2018 it spread to 21 states. Spreading by largely a single ‘super-clone’, this pest caused a yield decline on susceptible sorghum hybrids that ranged from 50-100% in infested fields. To control the sugarcane aphid, two insecticides are used in the U.S. with the same mode of action. As the number of insecticides available are limited to control sugarcane aphid on sorghum, ARS researchers in Tifton, Georgia, in collaboration with Fort Valley State University and Wingate University sought to determine if fungi that are pathogens to insects can be applied to reduce the damage caused by sugarcane aphids. Two strains of Beauveria bassiana and one strain of Isaria fumosorosea as well as water (negative control) and an insecticide Sivanto (positive control) were applied to a susceptible sorghum hybrid in field plots located in Tifton and Fort Valley, Georgia in 2018. As compared to the treatment with water, only the plots treated with Sivanto had less aphids and plant damage as well as more grain yield. Thus, these strains of fungi were ineffective for controlling the sugarcane aphid under our field conditions. This information is useful to growers and researchers as two of the strains used are commercially available and sold as Mycotrol and Ancora.
4. Population genetics of sugarcane aphids in North America. The sugarcane aphid has been a perennial pest to sorghum in the U.S. since 2013. Sugarcane aphids, although small in size, can build to tremendous numbers with 10,000 aphids being recorded on a single sorghum plant. Plant damage ranges from leaf pigmentation to plant death. ARS researchers in Tifton, Georgia, with the aid of colleagues who collected samples, discovered that the sugarcane aphids that were spreading in the U.S. on sorghum from 2013-2017 were predominantly one super-clone (one genotype). In this study sugarcane aphids were collected from seven states and one territory from Columbus grass (Sorghum almum Parodi), Johnsongrass, sorghum, sugarcane and giant miscanthus from 2013-2019 and were genotyped using genetic markers. They found that the super-clone was still pervasive in the U.S. in 2018 and that it is using giant miscanthus as an alternate host which can contribute to the pervasiveness of the pest through the cropping years.
5. Napier grass (Elephantgrass) as a bioenergy feedstock. Napier grass has the highest biomass productivity of any grass for cropping in the southeastern United States. This was a case study using Napier grass for production of bioethanol. ARS researchers in Tifton, Georgia, and Peoria, Illinois, determined the amount of bio-ethanol that would be produced under different yearly harvest schedules. Napier grass was grown for 5 years using low-input systems on fields in the Southeast. As long as the crop was fertilized (May) and harvested (December) production was consistent. In contrast, two cutting times per year (June and then again in December) led to dramatic declines in production beginning in Year 3. The 2nd and 4th year samples were analyzed for chemical composition and processed to ethanol using an ARS developed yeast suitable for this purpose. The ethanol yield per hectare was 9.0 and 12.8 cubic meters in the 2nd and 4th growing season, respectively. This will out-yield a corn production field at 180 bu/acre by a considerable margin. As such, this manuscript demonstrates that Napier grass cropped with a low-input system is suitable for production of advanced ethanol fuel but should only be harvested once per year for maximum ethanol production. This work will be of interest to the bioethanol producers and farmers located in the Southeast.
Review Publications
Bunphan, D., Knoll, J.E., Anderson, W.F. 2019. Yields of sesame vary dramatically under rain-fed conditions on marginal lands in Thailand. Australian Journal of Crop Science. 13(12):2075-2085.
Harris-Shultz, K.R., Armstrong, J.S., Jacobson, A. 2019. Invasive cereal aphids of North America: Biotypes, genetic variation, management, and lessons learned. Trends in Entomology. 15:99-122.
Paudyal, S., Armstrong, J.S., Harris-Shultz, K.R., Wang, H., Giles, K.L., Rott, P.C., Payton, M.E. 2019. Evidence of host plant specialization among the U.S. sugarcane aphid (Hemiptera: Aphididae) genotypes. Trends in Entomology. 15:47-58.
Dien, B.S., Anderson, W.F., Cheng, M., Knoll, J.E., Lamb, M., O Bryan, P.J., Singh, V., Sorensen, R.B., Strickland, T.C., Slininger, P.J. 2020. Field productivities of Napier grass for production of sugars and ethanol. ACS Sustainable Chemistry & Engineering. 8(4):2052-2060. https://dx.doi.org/10.1021/acssuschemeng.9b06637.
Armstrong, J.S., Harris-Shultz, K.R., Ni, X., Wang, H., Knoll, J.E., Anderson, W.F. 2019. Utilizing biodemographic indices to identify perennial bioenergy grasses as sugarcane aphid (Hemiptera: Aphididae) host plants. Trends in Entomology. 15:1-14.
Harris-Shultz, K.R., Davis, R.F., Wallace, J., Knoll, J.E., Wang, H. 2019. A novel QTL for root-knot nematode resistance is identified from a South African sweet sorghum line. Phytopathology. 109(6):1011-1017. https://doi.org/10.1094/PHYTO-11-18-0433-R.
