Location: Tropical Crops and Germplasm Research
2024 Annual Report
Objectives
Objective 1: Identify new sources of anthracnose and grain mold resistance through genome-wide association analysis of the NPGS tropical sorghum germplasm collection.
1.A: Establish an NPGS sorghum core collection from the Niger and Senegal collections based on genetic profile.
1.B: Identify new sources of host-plant resistance to anthracnose and rust in the subset of Niger and Senegal.
1.C: Identify new sources of host-plant resistance to grain mold in the subset of Niger and Senegal.
1.D: Identify new sources of host-plant resistance to anthracnose and rust in the sorghum Bioenergy Association Panel (BAP).
Objective 2: Determine which resistance sources from NPGS tropical sorghum germplasm collection are present in temperate-adapted germplasm.
2.A: Establish an NPGS sorghum mini-core set collection using publicly available genetic information.
2.B: High-throughput molecular marker development for anthracnose resistance loci.
2.C: Genome-wide association analysis for anthracnose resistance loci in NPGS mini-core set.
2.D: Inheritance of grain mold resistance in the Sudanese accession PI 267548.
Approach
The focus of this research is to use genotypic and phenotypic characterization of National Plant Germplasm System (NPGS) sorghum tropical germplasm to identify new sources of resistance to anthracnose, rust, and grain mold. Publicly available genomic characterization of NPGS sorghum germplasm collections from Niger (516 accessions) and Senegal (421 accessions) will be used to select a core subset that represent their genetic diversity. This core subset will be phenotyped for agronomically important traits and resistance to anthracnose, rust, and grain mold. Genome-wide association analysis will lead to the discovery of new disease-resistance loci and the identification of valuable germplasm for sorghum breeding programs. In parallel, the bioenergy sorghum association panel (BAP; 390 accessions) will be evaluated for anthracnose and rust resistance. Genome wide association analysis will lead to the discovery of new resistance loci in this germplasm. To improve our understanding of the distribution of the anthracnose resistance loci in the NPGS germplasm collection, a representative mini-core set will be established using publicly available genomic characterization of core sets from Ethiopia (374 accessions), Sudan (318 accessions), Yemen (394 accessions), West and Central Africa (617 accessions), Niger (516 accessions), Senegal (421 accessions), sweet sorghum (272 accessions) and the BAP (390 accessions). This NPGS mini-core set will be genotyped with seven molecular markers associated to anthracnose resistance and evaluated for anthracnose resistance response. Genome-wide association analysis as well as multiple regression analysis based on anthracnose resistance markers will be conducted to identify new resistance loci and to determine the interaction between resistant loci. A recombinant inbred lines (RILs) population derived from the grain mold resistant Sudanese accession PI 267548 and the elite susceptible line RTx430 will be developed and used to study the inheritance of resistance response. The RILs population will be evaluated for grain mold resistance and genetically characterized based on genotype-by-sequence analysis to construct a linkage map. Genomic regions associated with grain mold resistance observed in PI 267548 will be identified using inclusive composite interval mapping. The biparental mapping populations developed in this project will be available for the scientific community and will provide new temperate-adapted germplasm for sorghum breeding programs.
Progress Report
Progress was made on Sub-objective 1A: Establish a core collection of the NPGS sorghum collections from Niger and Senegal based on genetic profile. The NPGS sorghum collections from Niger, Nigeria and Senegal include 1,544 accessions that were genetically characterized with more than 82,000 SNPs using genotyping-by-sequencing (GBS) analysis. To improve its conservation and phenotyping analysis, the ARS scientist in Mayaguez, Puerto Rico, utilized this genetic characterization to establish a representative core set. The genetic relationship among these 1,544 accessions was determined using a subset of 10,489 unlinked SNPs. A total of four core sets of 154 (10% of total), 231 (15%), 308 (20%) and 386 (25%) accessions were established and compared to determine the most representative and genetically diverse set. The analysis found that both core sets of 308 and 386 accessions capture most of the genetic diversity of these collections. Consequently, the screening of either of these two core sets for agronomic traits and disease resistance are likely to identify valuable germplasm.
Progress was made on Sub-objective1D. Identify new sources of host-plant resistance to anthracnose and rust in the sorghum Bioenergy Association Panel (BAP). In 2024, the ARS scientist in Mayaguez, Puerto Rico completed the anthracnose resistance evaluation of 364 accessions from the sorghum bioenergy association panel (BAP). This first-year evaluation found 233 accessions with an anthracnose resistance response. The high frequency of resistant germplasm could be associated with a bias in the selection of germplasm to constitute the panel or that the disease pressure was low in the field. Thus, a second-year evaluation is necessary to determine the actual number of anthracnose resistant accessions.
Progress was made on Sub-objective 2A: Inheritance of anthracnose resistance in two tropical accessions from Ethiopia and Yemen; and Sub-objective 2B: Inheritance of grain mold resistance in the Sudanese accession PI 267548. The development of new sorghum germplasm is necessary to increase the genetic diversity of breeding programs. Three tropical sorghum germplasms from Ethiopia (PI 455606), Sudan (PI 267548) and Yemen (PI 486124) that showed anthracnose or grain mold resistance were crossed with the temperate adapted line RTx430. The F2 populations derived from these crosses are being evaluated in temperate regions to identify and select those segregants that flowered (i.e. non-photoperiod sensitive).
In addition to these objectives, other research projects were conducted by the ARS scientist in Mayaguez, Puerto Rico. As part of a proposal awarded by the National Plant Diseases Recovery System (NPDRS), the anthracnose and sugarcane aphid resistant line SC112-14 was crossed with the anthracnose resistant line SC1103 with the objective of pyramiding multiple sources of resistance into a common germplasm using marker assisted selection. Likewise, the introgression of anthracnose resistance loci into susceptible germplasm is necessary for its validation and to determine their effects in different genetic backgrounds. The previous genome-wide association analysis using a sorghum association panel and NPGS Ethiopian germplasm identified three anthracnose resistance loci on chromosome 5 and another on chromosome 9. In this regard, ARS scientists in Tifton, Georgia, College Station, Texas and Mayaguez, Puerto Rico, conducted a collaborative research project to introgress these four loci into the susceptible sweet sorghum line Early Honey using marker assisted selection. A total of 70 BC3F4 lines were developed which are composed of multiple profiles for these four anthracnose resistance loci. The evaluation of the anthracnose resistance response in these lines in Texas, Georgia and Puerto Rico validated two loci on chromosome 5 and the locus on chromosome 9. Two lines were resistant across the three locations and eleven lines were resistant in both Texas and Puerto Rico. The further inclusion of these lines in breeding programs could lead to the development of new anthracnose resistant sweet sorghum varieties for biofuel. Since the sorghum association panel (SAP) contains most of the genetic diversity and germplasm used in United States breeding programs, the ARS scientist in Mayaguez, Puerto Rico completed a three-year rust resistance evaluation of 270 accessions in the SAP in 2024. The evaluation found that 12 accessions were highly resistant, 39 moderately resistant and 219 susceptible to rust. Phylogenetic analysis between the 12 resistant lines showed that most of these lines have an admixture genetic background. Thus, the rust resistance response could not be associated with a specific sorghum race.
Accomplishments
1. A sorghum F-box protein control anthracnose resistance response.. The molecular defense system of sorghum against the anthracnose pathogen (Colletotrichum sublineola) is not well understood. Our previous genome-wide association analysis and family inheritance study delimited a genomic region on chromosome five with the candidate resistance gene Sobic.005G172300, encoding an F-box protein. To better understand the role of this gene in the defense against C. sublineola, gene expression following infection with C. sublineola was monitored by RNA sequencing in seedlings of sorghum. The analysis found that the upregulation of Sobic.005G172300 results in the transcriptional downregulation of key genes encoding ascorbic acid biosynthetic enzymes to generate an oxidative burst that suppresses C. sublineola infection. These findings contribute to our understanding of the complex interaction between sorghum and C. sublineola, as well as the sorghum defense response that promotes pathogen resistance. Moreover, this research provides insights into the development of new resistance germplasm for breeding programs through gene editing approaches.
Review Publications
Prom, L.K., Cuevas, H.E. 2023. Reaction of sorghum differentials to grain mold infection in Puerto Rico. American Journal of Plant Sciences. 14:1207-1213. https://doi.org/10.4236/ajps.2023.1411081.
Prom, L.K., Cuevas, H.E., Ahn, E.J., Isakeit, T.S., Magill, C.W. 2024. Correlations among agronomic traits obtained from sorghum accessions planted in a field infected with three important fungal diseases. Journal of Plant Studies. 13(1). Article 11. https://doi.org/10.5539/jps.v13n1p11.
Aviles-Noriega, A., Serrato Diaz, L.M., Giraldo-Zapata, M.C., Cuevas, H.E., Rivera-Vargas, L.I. 2024. The Sigatoka disease complex caused by Pseudocercospora spp. and other fungal pathogens associated with Musa spp. in Puerto Rico. Plant Disease. https://doi.org/10.1094/PDIS-03-23-0433-RE.
Wolf, E., Vela, S., Cuevas, H.E., Vermerris, W. 2024. A sorghum F-box protein induces an oxidative burst in the defense against Colletotrichum sublineola. Phytopathology. PHYTO-06-23-0184-R. https://doi.org/10.1094/PHYTO-06-23-0184-R.
Prom, L.K., Ahn, E.J., Perumal, R., Cuevas, H.E., Rooney, W.L., Isakeit, T.S., Magill, C.W. 2023. Genetic diversity and classification of Colletotrichum sublineola pathotypes using a standard set of sorghum differentials. The Journal of Fungi. 10(1). Article 3. https://doi.org/10.3390/jof10010003.
Cuevas, H.E., Knoll, J.E., Prom, L.K., Stutts, L.R., Vermerris, W. 2023. Genetic diversity, population structure and anthracnose resistance response in a novel sweet sorghum diversity panel. Frontiers in Plant Science. 14. Article 1249555. https://doi.org/10.3389/fpls.2023.1249555.
Cuevas, H.E., Prom, L.K. 2024. Association analysis of grain mould resistance in a core collection of NPGS Ethiopian sorghum germplasm. Plant Genetic Resources. https://doi.org/10.1017/S1479262124000157.
Thudi, M., Reddy, S., Dasharath Naik, Y., Reddy Cheruku, V., Reddy Sangireddi, M., Cuevas, H.E., Knoll, J.E., Louis, J., Kousik, C.S., Toews, M.D., Ni, X., Punnuri, S.M. 2024. Invasive sorghum aphid: a decade of research on deciphering plant resistance mechanisms and novel approaches in breeding for sorghum resistance to aphids. Crop Science. 64:2436-2458. https://doi.org/10.1002/csc2.21301.
Cuevas, H.E., Prom, L.K. 2024. The NPGS Sudanese sorghum core collection encloses novel grain mold resistant germplasm. Genetic Resources and Crop Evolution. https://doi.org/10.1007/s10722-024-02039-7.