Location: Tropical Crops and Germplasm Research
2019 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 first-year evaluation of 540 accessions from West-Central African countries identified multiple possible new sources of anthracnose resistance. Indeed, a high number of accessions with resistance response (367) were observed suggesting that most should be possessing similar resistance genes. Initial evaluation based on germination and seed deterioration, a trait indicative of grain mold susceptibility, showed that some accessions possess genes for grain mold resistance. Genetic analyses are being conducted to determine a genetic relationship among these accessions and to identify genomic regions associated with the observed resistance response to both diseases.
The population structure of a germplasm collection describes the relationship of a group of individuals that evolved through the action of past selection pressure. In large germplasm collections, knowledge of this information is useful to establish adequate screening and conservation methods. The genetic analysis of the National Plant Germplasm System (NPGS) Sudan core collection, based on 5,366 unlinked single-nucleotide polymorphism (SNPs), showed that there are 5 ancestral populations and ~46% of the accessions are combinations among these populations. ARS researchers found that three populations had a high frequency of Caudatum genetic background, while the other two had high frequency of Durra genetic background. One of these populations showed a higher anthracnose resistance response indicating that further screening of accessions belonging to this cluster may result in the identification of additional resistant sources.
ARS scientists in Mayaguez, Puerto Rico studied the potential use of the NPGS Sudan core collection for the genomic dissection of agronomic traits through genome-wide association analysis of multiple phenotypic traits. For example, the association analysis of mid-rib color associated the same genomic regions in chromosome 6 that had been previously identified by scientists at the University of Illinois, confirming the accuracy of the genotypic data, the effectiveness of the populations’ structure analysis to decrease the chance of identifying spurious associations, and the statistical power of the analysis to dissect highly heritable traits. The association analysis for anthracnose resistance response in NPGS Sudan core collection suggested the presence of multiple sources of resistance at a low frequency. Thus, neither genomic region was associated with the observed resistant response. In contrast, association analysis for rust resistance identified a genomic region in chromosome 8 that explained 31% of the phenotypic variation. The Sudan core collection is an important germplasm resource that possesses new sources of anthracnose and rust disease resistance which can be introgressed into temperate-adapted germplasm by marker assisted selection.
The identification of novel anthracnose resistance sources present in sweet sorghum germplasm can avoid time-consuming introgression with non-sweet sorghums serving as donor to the resistant alleles. A diversity panel of 233 sweet sorghum accessions were evaluated by ARS scientists in Mayaguez, Puerto Rico for a second year in a replicated trial in Puerto Rico, Georgia, Florida and Texas. ARS researchers identified 29 resistant accessions across locations. To understand the genetic relationship among resistant accessions and to associate genomic regions with the observed resistance, the diversity panel was genetically characterized through a genotype-by-sequencing approach. The analysis identified 157,843 SNPs(single-nucleotide polymorphism) and the population structure analysis based on 2,345 unlinked SNPs separated most of the accessions (~70%) of the panel into 4 populations. Remarkably, most of the advanced germplasms are highly genetically related and are distributed among 3 populations, hence, a limited number of anthracnose resistant sources should be present in the panel. Additional genome-wide association analysis could provide further insight of the actual number of resistant sources present in the panel.
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) derived from the anthracnose-resistant sources SC265 (Burkina Faso) and SC1103 (Nigeria) are being evaluated for anthracnose resistance response in Puerto Rico, Florida, Georgia and Texas. In addition, four candidate genes for anthracnose resistance located in chromosome 5 and 9 are being sequenced in a subset of 96 accessions from Ethiopia and the sorghum association panel to identify valuable SNPs for molecular marker development.
Accomplishments
1. Genomic dissection of rust resistance in National Plant Germplasm System (NPGS) Sudan core collection. Breeding for rust resistance in sorghum is affected by the fact that screening is limited to natural field infection. Thus, the efficiency of field screening selection is low because disease pressure varies among selection cycles due to genotype x environmental interactions. Development of molecular markers associated with rust resistance increases the efficiency of selection regardless of disease pressure and environment. The rust resistance response in the NPGS Sudan core collection was determined based on two years of field evaluation. Genome-wide association analysis identified candidate genes within a genomic region in chromosome 8 associated with the observed resistance response. The molecular marker developed by ARS scientists in Mayaguez, Puerto Rico, within this genomic region now allows to effectively introgress this rust resistant loci into temperate adapted germplasm.
Review Publications
Cuevas, H.E., Fermin-Perez, R.A., Prom, L.K., Cooper, E., Bean, S.R., Rooney, W.L. 2019. Genome-wide association mapping of grain mold resistance in the U.S. sorghum association panel. The Plant Genome. 12:180070.
Prom, L.K., Cuevas, H.E., Isakeit, T., Perumal, R., Erathaimuthu, S. 2018. Mycoflora analysis and other measured parameters of sorghum seeds collected from Puerto Rico and Mexico. Plant Pathology Journal. 17(2):80-86. https://doi.org/10.3923/ppj.2018.80.86.
Prom, L.K., Cisse, N., Perumal, R., Cuevas, H.E. 2018. Response of sorghum lines and hybrids from the United States to long smut and grain mold. Journal of Agriculture and Crops. 4(11):152-156. https://doi.org/10.32861/jac.411.152.156.
Prom, L.K., Cuevas, H.E., Perumal, R., Isakeit, T., Magill, C. 2018. Inheritance of resistance of three sorghum lines to pathotypes of Colletotrichum sublineola, causal agent of anthracnose. Plant Pathology Journal. 17(2):75-79. https://doi.org/10.3923/ppj.2018.75.79.
