Location: Tropical Crops and Germplasm Research
2020 Annual Report
Objectives
1. Phenotype exotic sorghum germplasm for important agronomic traits to identify the most valuable accessions for sorghum breeding programs.
1a. Genetically-characterize sorghum accessions from the West-Central African diversity panel (WCADP).
1b. Phenotypically-characterize highly genetically diverse sorghum accessions from the WCADP.
1c. Phenotypically-characterize accessions from NPGS sweet sorghum germplasm.
2. Identify new sources of anthracnose and grain mold resistance through the evaluation of exotic sorghum germplasm from the National Plant Germplasm System (NPGS) sorghum germplasm collection for further introgression breeding.
2a. Identify new sources of host-plant resistance to anthracnose in the WCADP.
2b. Identify new sources of host-plant resistance to grain mold in the WCADP.
Approach
The focus of this research is to use genotypic and phenotypic characterization of National Plant Germplasm System (NPGS) sorghum germplasm to identify new sources of resistance to anthracnose and grain mold in exotic germplam. A total of 396 accessions from West-Central Africa countries will be characterized for host-plant resistance to both diseases followed by genetic characterization through genotype-by-sequence analysis. This information will be combined with phenotypic and genotypic characterization data from sorghum association panels and core subsets from the NPGS Ethiopian and Sudan collections to conduct a large genome wide association analysis. The results will discover new sources of disease resistance and identify novel molecular markers for breeding programs seeking disease resistance. Presently, sweet sorghum varieties utilized as a biofuel source have a narrow genetic base. Therefore, evaluation of sweet sorghum accessions present in the NPGS sorghum collection will be carried out to help to identify new germplasm to broaden genetic variability available for the development of new biofuel varieties of sorghum. For this purpose, a subset of NPGS sweet sorghum germplasm with high Brix values will be characterized for biofuel related traits in conjunction with a subset of the sorghum bioenergy association panel.
Progress Report
Multiple sorghum accessions were evaluated by the ARS scientist in Mayaguez, Puerto Rico, for anthracnose and grain mold resistance response. The second-year evaluation of 617 accessions from West-Central African countries identified multiple new sources of anthracnose resistance. Based on two years of data, 316 and 97 accessions were resistant and susceptible to anthracnose, respectively, and 204 accessions showed a variable response across years. The evaluation by ARS researchers at Mayaguez, Puerto Rico, of seed deterioration and germination found that 90 accessions are potentially resistant to grain mold. Of these, 49 accessions showed resistance to both, grain mold and anthracnose.
Near infrared spectroscopy (NIR) models are a fast, cost-effective and non-destructive method to evaluate sorghum grain quality and nutritional value. ARS researchers at Mayaguez, Puerto Rico in collaboration with ARS scientists at Manhattan, Kansas, calibrated a NIR system for protein concentration. The seed scanning of 617 accessions from West-Central African countries found that protein concentration varies from 4.1 to 15.5% with an average of 9.2%. The protein concentration of 22 accessions was above 13% suggesting these could be used to increase the nutritional value of sorghum. The NIR calibration process for tannin and starch content are being performed to include additional quality traits for the identification of valuable NPGS accessions which can be used by breeding programs in the U.S. and worldwide.
ARS researchers at Mayaguez, Puerto Rico, determined that genotypic and phenotypic characterization of sorghum accessions in the NPGS germplasm collection is necessary to provide sorghum breeders the knowledge and genomic tools necessary to utilize this germplasm more efficiently. In this regard, 617 sorghum accessions from West-African countries, previously characterized for anthracnose and grain mold resistance, and protein content, were genetically characterized through genotype-by-sequence (GBS). The GBS analysis resulted in the identification of 207,330 single nucleotide polymorphic (SNPs) with a frequency higher than 0.05. Population structure analysis based on 3,865 unlinked SNPs revealed nine ancestral populations. In total, 520 accessions (84%) were assigned to one of these populations with an ancestry membership coefficient greater than 0.60, while the remaining 97 accessions (16%) showed evidence of admixture. Further, genome-wide association analysis could be used to elucidate the anthracnose and grain mold resistant sources present in these accessions and will allow determination of the most adequate strategy for introgression of these disease-resistant sources into temperate-adapted germplasm through marker assisted selection.
ARS scientists in Mayaguez, Puerto Rico, in collaboration with ARS scientists from Lubbock, Texas, and Tifton, Georgia, and scientists from University of Florida identified novel anthracnose resistant loci present in sweet sorghum germplasm. Genome-wide association analysis based on 157,843 SNPs and 233 sweet sorghum accessions associated three genomic regions with anthracnose resistance response at four locations (Puerto Rico, Georgia, Florida and Texas). The distal genomic region of chromosome 8 was associated with resistance response observed in Florida, and associated SNP was located within a R-gene. Likewise, genomic regions in chromosome 1 and 8 were associated with resistance response observed in Georgia. Candidate gene analysis for both regions found a two genes cluster with salt stress/antifungal domains and an R-gene in chromosome 1 and 8, respectively. Both candidate genes were in linkage disequilibrium and less than 15 kb downstream of associated SNP. Resistance response in Texas and Puerto Rico were associated with a genomic region in chromosome 8 that enclose an R-gene. Candidate R-genes among accessions grown in Puerto Rico, Texas and Georgia were 18 kb apart suggesting that each gene might be specific for each location pathotype. The results revealed these resistant sources are different from those currently known in grain sorghum germplasm. It is imperative that these resistant sources be used effectively to increase the durability of anthracnose resistance in new biofuel sorghum varieties. When the goal is to develop cultivars for planting across a large geographical area, multiple sources of resistance that are effective against the local pathotypes need to be combined.
ARS researchers at Mayaguez, Puerto Rico, believe the identification of NPGS sweet sorghum germplasm with high sugar concentration (i.e. Brix) is necessary for the development of new biofuel sorghum varieties. ARS scientists in Mayaguez, Puerto Rico, and Tifton, Georgia, determined the sweetness (Brix) of 233 sweet sorghum accessions during two years. The analysis was used to select a subset of 62 accessions with high Brix (>10.0) for further evaluation in replicated trials in Puerto Rico. Results from the first-year evaluation identified 18 accessions with a Brix values ranging from 10.08 to 15.0, including 10 accessions that are resistant to anthracnose pathotypes from Puerto Rico, Georgia, Florida and Texas. Certainly, these sweet sorghum accessions might be used as parental lines for the development of new biofuel varieties with anthracnose resistance.
As part of a grant awarded by the U.S. Department of Energy, entitled “Uncovering novel sources of anthracnose resistance in population of genetically diverse sorghums”, two sets of recombinant inbred lines (RILs) from the nested association mapping (NAM), derived from the anthracnose-resistant sources SC265 (Burkina Faso) and SC1103 (Nigeria), are being evaluated by ARS researchers at Mayaguez, Puerto Rico, for anthracnose resistance response in Puerto Rico, Florida, Georgia and Texas for a second consecutive year. While another set of recombinant inbred lines (RILs) from NAM, derived from the anthracnose-resistant source SC1345 (Mali), is being evaluated for anthracnose resistance response in Puerto Rico. Genome scan based on GBS data of NAM and first year anthracnose resistance response of the three populations found multiple genomic regions associated with a resistant response. The analysis of SC265 population revealed that the distal region of chromosome 6 is controlling the resistance response in Puerto Rico, Georgia and Texas. The analysis of SC1103 found three genomic regions associated with resistance response. Indeed, both distal and top regions of chromosome 6 and 8, respectively, are controlling the resistance response in Puerto Rico, while the top of chromosome 8 control resistance response in Texas. These two genomic regions and the top of chromosome 9 control the resistance response in Florida. The analysis of SC1345 found a locus in chromosome 5 that is similar to the one previously found in resistant line SC112-14. The identification of multiple resistant sources is necessary to develop cultivars for planting across a large geographical area.
Accomplishments
1. Genomic dissection of anthracnose resistance in NPGS sweet sorghum collection. The establishment of sweet sorghum as an important biofuel crop requires the development of new varieties resistant to anthracnose, an endemic foliar disease in south and southeast United States. ARS scientists in Georgia, Texas and Puerto Rico, in collaboration with scientists from the University of Florida, determined that the anthracnose resistance response of 233 sweet sorghum accessions across four locations (Texas, Georgia, Florida and Puerto Rico) is mostly controlled by three loci in chromosomes 1 and 8. Candidate gene analysis found that these loci contain genes involved in salt stress/antifungal activity and pathogen recognition (i.e. R-gene). This research will lead to the development of new biofuel varieties with a broader spectrum of anthracnose resistance by the effective combination of multiple sources.
Review Publications
Kumi, F., Badji, A., Mwila, N., Odong, T., Ochwossemakula, M., Tusiime, G., Gibson, P., Biruma, M., Prom, L.K., Cuevas, H.E., Agbahoungba, S., Rubaihayo, P. 2019. New sources of sorghum resistant genotypes to downy mildew diseases in Uganda. Biodiversitas. 20(11):3391-3397. https://doi.org/10.13057/biodiv/d201136.
Prom, L.K., Cuevas, H.E., Isakeit, T., Magill, C. 2020. Screening sorghum accessions for resistance against anthracnose and grain mold through inoculating with pathogens. Journal of Experimental Agriculture International. 42(1):73-83. https://doi.org/10.9734/jeai/2020/v42i130453.
Cruet-Burgos, C.M., Cuevas, H.E., Prom, L.K., Knoll, J.E., Stutts, L., Vermerris, W. 2020. Genomic dissection of anthracnose (Colletotrichum sublineolum) resistance response in sorghum differential line SC112-14. G3, Genes/Genomes/Genetics. 10(4): 1403-1412. https://doi.org/10.1534/g3.120.401121.
Cuevas, H.E., Prom, L.K. 2020. Evaluation of genetic diversity, agronomic traits, and anthracnose resistance in the NPGS Sudan sorghum core collection. BMC Genomics. 21, 28. https://doi.org/10.1186/s12864-020-6489-0.
