Location: Tropical Crops and Germplasm Research
2023 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
This is the final report for the project 6090-21000-058-000D which terminated in March 2023 and was replaced by 6090-21000-062-000D. Substantial results were realized over the 5 years of the project.
Significant progress was made on Objective 1: Phenotype exotic sorghum germplasm for important agronomic traits to identify the most valuable accessions for sorghum breeding programs. A total of 564 accessions from the National Plant Germpasm System (NPGS) West-Central Africa collection were phenotypically and genetically characterized. The genetic characterization of these accessions identified 216,655 single nucleotide polymorphisms (SNPs) suitable for genome-wide association analysis and population structure analysis. The genetic diversity of the NPGS West-Central Africa germplasm consists of nine ancestral populations that could be used to improve their conservation and phenotypic characterizations by limiting conservation to the most genetically diverse accessions. Phenotypic analyses showed that some of these populations exhibit variations for agronomic traits as a result of human and environmental selection. This genetic and phenotypic information together with other genetic characterizations will be used to establish a mini core set for NPGS sorghum germplasm collection. The evaluation of a sweet sorghum diversity panel of 233 accessions across two years in Puerto Rico and Georgia showed 62 accessions with high Brix values across locations and years. Subsequent evaluation of these accessions showed 10 accessions with Brix values ranging from 10 to 15 and with resistance to anthracnose which could be used as parental lines for the development of new biofuel varieties.
The development of sorghum varieties with high nutritional value requires the identification of germplasm with high protein concentration. The analysis of protein among 228 tropical accessions from NPGS West-Central Africa germplasm collection showed 16 accessions with high protein concentration (= 12.84%). The protein concentration of accessions from countries located in the western regions of Africa (Mali, Togo, Benin, Senegal, Ghana, Nigeria, and Burkina Faso) was higher than in accessions from the southeastern regions (Burundi, Kenya, Uganda and Rwanda) of Africa. The accessions from Mali showed the highest protein concentrations. The results suggest that environmental factors could be selecting for seed protein concentration. Likewise, analyses based on seed color showed that those with white and lighter color (white, light brown and light red) have higher protein concentration than brown and red seeds. Sorghum racial classification among the 228 accessions showed that those belonging to the Guinea race or intermediate with this race have higher protein concentration. Therefore, the identification of other accessions with high protein concentration could be directed to the Guinea race from the West region of Africa.
The development of new sorghum varieties with higher drought tolerance and sugarcane aphid resistance is necessary for sorghum breeding programs. As part of a one-year grant awarded by USAID-ARS Participating Agency Service Agreement (PASA) collaborative research funds, entitled “Novel sorghum lines tolerant to drought and resistant to sugarcane aphids for food security in Honduras”, ARS scientists in Mayaguez, Puerto Rico in collaboration with University of Zamorano in Honduras made 10 crosses among five sorghum varieties that showed drought tolerance and/or sugarcane aphid resistance. The progenies of these crosses were advanced to the F2 generation and most superior plants selected and advanced to F3 families. These F3 are being evaluated for drought tolerance and sugarcane aphid resistance in Honduras. Also, a sorghum breeding population of 300 lines developed by Quisqueya University in Haiti were evaluated for sugarcane aphid resistance, drought tolerance and agronomic traits at University of Zamorano. The evaluation identified 12 promising lines with good agronomic traits for further evaluation in replicated trials.
Significant progress was made on Objective 2 Identify new sources of anthracnose and grain mold resistance through the evaluation of exotic sorghum germplasm from the NPGS sorghum germplasm collection for further introgression breeding. The evaluation of NPGS West-Central African germplasm collection identified multiple new sources of anthracnose, rust and grain mold resistance. A total of 312 accessions were resistant to anthracnose of which 32 were also resistant to rust. The germination and seed rating evaluation NPGS West-Central Africa germplasm found that 35 accessions were resistant to grain mold. Remarkably, six accessions (PI 585585, PI 155780, PI 156445, PI 527590, PI 496285 and PI 527546) were resistant to grain mold, anthracnose and rust.
The identification of genomic regions associated with resistance to anthracnose, rust and grain mold disease is imperative for the development of new resistant varieties and to select the most valuable tropical sorghum germplasm for conversion programs. Genome-wide association analysis using 564 accessions from NPGS West-Central Africa germplasm collection and the 216,655 SNPs showed that genomic regions in chromosomes 2, 3, 5, 9 and 10 were associated with anthracnose resistance. These five loci have not been previously identified in tropical or temperate germplasm. The number of resistance loci identified in NPGS West-Central Africa germplasm was higher than those in the Ethiopian, Sudanese and Yemen collections suggesting this germplasm is an important reservoir of disease resistance genes and suggested the existence of multiple sources which can be used by breeding programs. Grain mold resistance response is mainly determined by seed germination and quality. The GWAS for seed germination associated six genomic regions in chromosomes 1, 3, 4, 6, and 7 with the observed resistance response variation. The loci explained 32% of the phenotypic variation being the locus in chromosome 1 the most significant (p-value = 1.0E-22). The GWAS analysis for seed quality rate identified one locus in chromosome 7 that explained a limited portion of the observed variation. Likewise, GWAS analysis for rust disease found two loci at chromosome 8 that explained a limited portion of the observed variation. These loci provide an insight of the genetics controlling fungal diseases and lead to the selection of resistant germplasm based on its genetic profile.
Accomplishments
1. Identification of accessions with high protein concentration. The development of new sorghum varieties with higher nutritional value might lead to increase its human consumption. In collaboration with ARS scientists in Manhattan, Kansas, and ARS researchers in Mayaguez, Puerto Rico, identified 16 tropical accessions from West Africa countries and belonging to Guinea sorghum race with white or light brown color with high protein concentration. This discovery paves the way for crop improvement programs to mining the NPGS sorghum collection from West Africa for high protein.
