Progress 06/04/13 to 03/11/18
Outputs
Progress Report Objectives (from AD-416): 1. Genetically-characterize sorghum accessions from Ethiopia and other nations and apply the genetic marker data to select core subsets of accessions for evaluation for host-plant resistance to anthracnose and grain mold. 2. With ARS cooperators, conduct multi-locational evaluations of selected sorghum accessions to identify potential new sources of host- plant resistance to anthracnose and grain mold pathotypes predominant in Puerto Rico and in Texas. 3. With ARS cooperators, develop experimental populations for identifying, characterizing, and mapping the genes that confer host-plant resistance to anthracnose and grain mold pathotypes and for identifying genetic markers closely linked to those resistance traits. 3a. Employ genome-wide association studies (GWAS) to identify genes that confer host-plant resistance to anthracnose. 3b. Employ GWAS to identify genes that confer host-plant resistance to grain mold pathotypes. 4. Evaluate selected sweet sorghum germplasm accessions to identify lines with robust culms, superior sugar content, dry matter production, and host-plant resistance to anthracnose. Approach (from AD-416): The focus of this research is to determine the genetic control of anthracnose and grain mold, to identify molecular markers for breeding programs seeking disease resistance, and to discover new sources of resistance present in exotic germplasm. Genome-wide association studies will be employed to understand the genetic control and locate the genome regions of the anthracnose and grain mold resistance genes. The genetic and morphological characterization of sorghum collection from Ethiopia and Sudan will be applied to develop core subsets for further association studies, and to identify new sources of host resistance. Presently, sweet sorghum varieties utilized as a biofuel source have a narrow genetic base. Therefore, evaluation of sweet sorghum accessions present in the US 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. This is the final report for the project 6090-21000-053-00D which terminated in March 2018. Most of planned field experiments were completed prior to the start of new project. Knowledge on the inheritance of anthracnose resistance was substantially improved over the last five years of the project. ARS researchers in Mayaguez, Puerto Rico, completed the evaluation of 335 accessions from the sorghum association panel (SAP) and found 75 resistant accessions to anthracnose across multiple locations. These lines enclose the majority of the genetic diversity present in SAP as a whole, suggesting the presence of multiple sources of resistance. Phylogenetic analysis revealed high genetic divergence among these different sources suggesting that a representative subset of 10 to 15 anthracnose-resistant accessions could be used by breeders as multiple sources of resistance. Molecular markers and candidate resistant genes for anthracnose resistance were identified by genome-wide association studies (GWAS). Three resistance loci at the distal region of chromosome five were identified, nevertheless, these loci only explained 56% of the observed phenotypic variation, implying that the presence of other resistance sources are not detected. Candidate genes within these loci were related to R-gene families, signaling cascade and transcriptional reprograming and suggesting that the resistance response is controlled by multiple defense mechanisms. To identify new genes for anthracnose resistance, ARS researchers at Mayaguez, Puerto Rico, phenotypically and genetically characterized multiple exotic sorghum accessions belonging to the USDA-ARS National Plant Germplasm System (NPGS) sorghum collection. The genomic characterization of two core-set of 376 and 351 accessions from Ethiopia and Sudan, respectively, was completed and a total of 148,476 and 208,081 single nucleotide polymorphisms (SNP) were identified, respectively. These genomic resources are available for sorghum breeders and geneticists to effectively improve the crop with its own natural genetic variability. Evaluation of the Ethiopian core-set revealed a high frequency (37%) of anthracnose-resistant accessions. To uncover resistance alleles present in SAP at low frequency, the genomic and anthracnose resistance response data of the Ethiopian accessions and SAP accessions were merged and subjected to GWAS analysis. ARS researchers at Mayaguez, Puerto Rico, identified one novel locus on chromosome 9 that explains 26% of the observed phenotypic variation. Candidate gene analysis related this locus with R-gene families. Since this locus is present in SAP at low frequency (0.02), it was demonstrated that the integration of NPGS exotic germplasm into SAP is the most adequate strategy to uncover additional resistance genes while allowing to identify exotic germplasm with alleles not present in breeding programs. Evaluation of anthracnose resistance of the Sudan core-set and Senegal germplasm collections showed that the frequency of resistant accessions in the Sudan core-set (12%) was significantly lower than the observed in Senegal germplasm (50%) and Ethiopia core-set (37%). Since Caudatum, Durra and Guinea are the most frequent sorghum races in Sudan, Ethiopia and Senegal collections, respectively, the work suggests that the establishment of a diversity panel with high frequency of Guinea germplasm is the most appropriate approach to increase the frequency and detection of rare alleles in SAP. To understand the inheritance of anthracnose resistance, ARS researchers at Mayaguez, Puerto Rico, evaluated three sets of recombinant inbred lines derived from accessions QL3 (India), IS18760 (Sudan) and SC112-14 (Ethiopia). The work showed that the anthracnose resistant response in QL3 and IS18760 is controlled by multiple loci that provide resistance against particular location pathotypes. In contrast, resistant response present in SC112-14 is controlled by one major locus in chromosome five that provides resistance against pathotypes from Puerto Rico, Georgia, Florida and Texas. ARS researchers at Mayaguez, Puerto Rico, delimited this locus to a 23 kb genomic region enclosing three candidate genes, including Sobic.005G17230 identified by previous GWAS. Based on this family approach and GWAS study it was concluded that the gene Sobic. 005G17230 controls the resistance response observed in SC112-14. This gene belongs to a family of genes encoding F-box proteins suggesting its involvement in signaling cascades and transcriptional reprograming, rather than recognition of pathotype-associated molecular patterns. To understand the inheritance of grain mold resistance, ARS researchers at Mayaguez, Puerto Rico, identified multiple sources of resistance through the evaluation of temperate adapted germplasm from SAP and from NPGS exotic sorghum germplasms from Ethiopia, Sudan and Senegal. Evaluation of grain mold of SAP accessions identified nine resistant accessions (Red Amber, SC15, 6550-Summac, SC13, Keller, Kansas Orange, Rox Orange, SC309 and SC609). In cooperation with scientists from USDA- ARS at Manhattan, Kansas, ARS researchers at Mayaguez, Puerto Rico, determined the grain quality of these accessions. It was found that tannin content among resistant accessions ranged from 0.0 to 49.2 CE/gram indicating other seeds components and traits are also controlling the resistance response. Molecular markers and candidate resistant genes for grain mold resistance were identified by GWAS analysis. Two resistance loci in chromosome 4 and 10 were associated with seed germination, while two resistance loci in chromosome 1 and 8 were associated with seed rating. Candidate gene and expression analysis identified genes related to biosynthesis of anthocyanin, transcription factors and R-genes that have high gene expressions at floral initiation stages. The limited number of grain mold resistant sources in temperate adapted germplasm encouraged the researchers to identify new sources in exotic sorghum germplasm. In this regard, ARS researchers at Mayaguez, Puerto Rico, evaluated Sudanese, Ethiopian and Senegalese core-sets for grain mold resistance. The study showed low frequency of resistant accessions (3%) among Ethiopian and Sudanese germplasm, and a higher frequency (8%) among Senegalese germplasm. These results are useful to select the most valuable exotic germplasm for conversion and/or introgression programs. The USDA-ARS NPGS sweet sorghum collection is the primary source of genetic diversity for the development of new sweet sorghum varieties for biofuel production. In the last five years, ARS researchers at Mayaguez, Puerto Rico, evaluated 1,801 sweet sorghum accessions of which 566 had a Brix value over 10.0%. These results were used to select a subset of 233 sweet sorghum accessions for anthracnose resistance evaluation, and further genomic and biofuel characterization. Results from a replicated trial at Puerto Rico, Georgia, Florida and Texas identified 83 anthracnose resistant accessions across locations. Accomplishments 01 The NPGS preserve the largest sorghum germplasm collection in the world with more than 42,000 accessions. The characterization of this exotic germplasm at a genome-wide scale improves conservation efforts and its utilization in research and breeding programs. ARS researchers at Mayaguez, Puerto Rico, evaluated three representative subsets of accessions from the Ethiopian, Sudanese and Senegalese NPGS germplasm collection to identify new sources of anthracnose and grain mold resistant. Genomic characterization and cluster analysis of these subsets found Ethiopian and Sudanese germplasm are highly genetic diverse while Senegalese germplasm is moderate genetically diverse. The anthracnose response evaluation found that even the frequency of resistance is high within Ethiopian and Senegalese germplasm both enclose only few sources of resistance genes. The genomic characterization and diversity analysis of the Ethiopian subset help to select genetically diverse accessions to be included in the conversion program at Texas A&M University in College Station, Texas. 02 The identification and mapping of anthracnose resistant genes is imperative to increase resistance durability and pyramid multiple resistance genes to develop varieties with broader disease resistance. Therefore, the anthracnose resistance response present in the sorghum line SC112-14 (Cs-SC112) was delimited to a single candidate gene, improving our understanding of the molecular resistant response. Among 335 accessions available to breeders from a previously genotyped sorghum association panel (SAP), ARS researchers at Mayaguez, Puerto Rico, found that 75 accessions were resistant to anthracnose. These accessions showed high genetic diversity and multiple resistance sources suggesting a representative subset of 10�15 resistant accessions could be used by breeders as multiple sources of resistance. We identified three loci within a region on chromosome 5 by GWAS analysis and one of the locus was similar to the previously identified locus in the resistant line SC112-14. The anthracnose resistant evaluation and GWAS of 376 accessions from NPGS Ethiopian germplasm collection identified one novel locus on chromosome 9 related to R-gene families. These four loci and associated molecular markers will allow the effective use of these resistance sources in breeding programs. 03 Genomic dissection of grain mold resistance response. Grain mold is a complex disease involving multiple pathogens. The identification and mapping of grain mold resistance loci is necessary to increase the efficiency of breeding programs through marker assisted selection (MAS) and to make adequate use of resistance sources. Among 335 accessions available to breeders from a previously genotyped sorghum association panel (SAP), ARS researchers in Mayaguez, Puerto Rico, found that 9 accessions were grain mold resistance. Using genome-wide association study (GWAS) scans we identified four loci associated with seed germination and rating. These four loci and associated molecular markers will allow the implementation of MAS in breeding programs, and suggests that the observed resistance response is determined by few loci that provide resistance against multiple pathotypes.
Impacts
(N/A)
Publications
- Cuevas, H.E., Prom, L.K., Rosa, G.M. 2018. Population structure of the NPGS Senegalese sorghum collection and its evaluation to identify new disease resistant genes. PLoS One. 13(2). e0191877. Available:
- Prom, L.K., Cisse, N., Perumal, R., Cuevas, H.E. 2017. Screening of sorghum lines against long smut and grain mold pathogens. International Journal of Plant Pathology. 8:23-27.
- Harris-Shultz, K.R., Ni, X., Wadl, P.A., Wang, X., Wang, H., Huang, F., Flanders, K., Seiter, N., Kerns, D., Meagher Jr, R.L., Xue, Q., Reisig, D., Buntin, D., Cuevas, H.E., Brewer, M., Yang, X. 2017. Microsatellite markers reveal a predominant sugarcane aphid (Homoptera: Aphididae) clone is found on sorghum in seven states and one territory of the USA. Crop Science. 57:2064-2072.
- Wang, M.L., Xin, Z., Burow, G.B., Chen, J., Vankus, P.J., Pinnow, D.L., Tonnis, B.D., Cuevas, H.E., Yu, J. 2017. Evaluation of sweet sorghum accessions for seedling cold tolerance using both lab and field cold germination test. Journal of Agricultural Science and Botany. 1(1):1-8.
- Cuevas, H.E., Prom, L.K., Copper, E.A., Knoll, J.E., Ni, X. 2018. Genome- wide association mapping of anthracnose (Collectotrichum sublineolun) resistance in the U.S. sorghum association panel. The Plant Genome. II:170099.
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Progress 10/01/16 to 09/30/17
Outputs
Progress Report Objectives (from AD-416): 1. Genetically-characterize sorghum accessions from Ethiopia and other nations and apply the genetic marker data to select core subsets of accessions for evaluation for host-plant resistance to anthracnose and grain mold. 2. With ARS cooperators, conduct multi-locational evaluations of selected sorghum accessions to identify potential new sources of host- plant resistance to anthracnose and grain mold pathotypes predominant in Puerto Rico and in Texas. 3. With ARS cooperators, develop experimental populations for identifying, characterizing, and mapping the genes that confer host-plant resistance to anthracnose and grain mold pathotypes and for identifying genetic markers closely linked to those resistance traits. 3a. Employ genome-wide association studies (GWAS) to identify genes that confer host-plant resistance to anthracnose. 3b. Employ GWAS to identify genes that confer host-plant resistance to grain mold pathotypes. 4. Evaluate selected sweet sorghum germplasm accessions to identify lines with robust culms, superior sugar content, dry matter production, and host-plant resistance to anthracnose. Approach (from AD-416): The focus of this research is to determine the genetic control of anthracnose and grain mold, to identify molecular markers for breeding programs seeking disease resistance, and to discover new sources of resistance present in exotic germplasm. Genome-wide association studies will be employed to understand the genetic control and locate the genome regions of the anthracnose and grain mold resistance genes. The genetic and morphological characterization of sorghum collection from Ethiopia and Sudan will be applied to develop core subsets for further association studies, and to identify new sources of host resistance. Presently, sweet sorghum varieties utilized as a biofuel source have a narrow genetic base. Therefore, evaluation of sweet sorghum accessions present in the US 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. Multiple sorghum accessions were evaluated by ARS scientists in Mayaguez, Puerto Rico, for anthracnose and grain mold resistance response. Sixty accessions from the National Plant Germplasm System (NPGS) Sudan core collection that were identified as possible sources of anthracnose resistance in initial un-replicated trials were evaluated in a replicated trial to determine their actual resistance response. The results showed 41 accessions as new anthracnose resistant sources. Likewise, a two location grain mold evaluation of the NPGS Sudan core collection identified accessions having grain mold resistance genes. Nineteen accessions showed superior seed rating signifying the presence of grain weathering resistant genes. Likewise, 42 accessions had more than 80% germination rate indicating presence of a grain mold resistant mechanism. Twelve accessions showed superior seed rating and high germination rate, and are the most suited to be integrated into sorghum breeding programs. Presently, genetic analyses are being conducted to determine the genetic relationship among these anthracnose and grain mold resistant accessions to identify the most genetically diverse germplasm. The genomic characterization of germplasm is necessary to preserve and select the most genetically diverse accessions to be integrated into breeding programs. Genotype-by-sequence analysis of the NPGS Sudan core collection resulted in the identification of 260,691 single nucleotide polymorphism (SNPs). Approximately 80% of the SNPs (208,081) have minor allele frequency larger than 0.05, and thus, are well suited for genome wide association analysis (GWAS). Population structure and cluster analysis are being conducted using a subset of unlinked SNPs to identify high genetic relatedness among accessions (i.e. duplicates) and to establish a subset of accessions for extensive phenotyping analysis. The grain mold resistance response of 27 accessions from the U.S sorghum association panel were evaluated in a replicated field trial under high humidity conditions (>85% relative humidity) by ARS scientists in Mayaguez, Puerto Rico. Seventeen accessions showed grain weathering resistance, however, only eight had seed germination rates higher than 75%. Seven accessions showed superior grain weathering resistance germination rates, and could be considered as important sources of grain mold resistance. In order to determine the tannin content of these seven grain mold resistant accessions, compositional analysis of whole seeds was performed using near-infrared (NIR) spectroscopy. Tannin content ranged from 0 to 49 mg catechin equivalents (CE)/g, and were distributed into 3 categories: 1) low tannin content (3 accessions with 0, 10 and 11 mg CE/g), moderate content (2 accessions with 25 and 27 mg CE/g) and high content (2 accessions with 43 and 49 mg CE/g). Accessions with low tannin content possess valuable grain mold resistance genes for use in sorghum breeding programs. The identification of genomic regions associated with disease resistance genes is essential for the identification of novel loci and the development of molecular tools for breeding programs. ARS scientists in Mayaguez, Puerto Rico, used genome wide association analysis with the U.S. sorghum association panel to identify two anthracnose resistant locus in chromosome 1 and 5. These loci were associated with 58% of the resistant accessions, indicating that other resistant loci are present in the association panel at low frequencies. These loci are associated with the sorghum Caudatum race. The locus at chromosome 5 is similar to that identified in mapping populations derived from sorghum lines SC112-14 and SC414-12E, while the locus at chromosome 1 is novel. The pyramiding of multiple resistance loci is necessary to develop new sorghum varieties with broad anthracnose resistance. As part of a grant awarded by the U.S. Department of Energy, entitled �Genomic dissection of anthracnose resistance response in sorghum [Sorghum bicolor (L.) Moench]�, three sets of recombinant inbred lines (RILs) derived from the resistant sources SC112-14, IS18760 and QL3 were evaluated by ARS scientists in Mayaguez, Puerto Rico, for anthracnose resistance response in Gainesville, Florida, College Station, Texas, Tifton, Georiga and Isabela, Puerto Rico. The QL3 and IS18760 RILs populations were susceptible to anthracnose pathotypes present in Florida and Georgia. In Texas and Puerto Rico, these two populations showed a resistance response segregation with a high frequency of susceptible genotypes. Remarkably, the RILs population derived from SC112-14 showed the expected anthracnose resistant response segregation (1:1) in the four locations. High density linkage maps were constructed for the three RIL populations using genotype x sequence analysis that resulted in the identification of 952, 1008, and 1355 SNPs in the RILs population SC112- 14, QL3 and IS18760, respectively. Genome mapping analysis for SC112-14 RILs population resulted in the identification of one locus in chromosome 5 that control resistance in Florida, Georgia, Texas and Puerto Rico. Greenhouse evaluation of 33 recombinant inbred lines against 10 pathotypes from Texas, Georgia, and Puerto Rico confirmed these results. Likewise, the preliminary genome mapping analysis for anthracnose resistant response in IS18760 and QL3 RILs populations resulted in the identification of one locus in chromosome 4 for Texas and Puerto Rico pathotypes. These preliminary results will be confirmed during a second year field experiment and by greenhouse evaluation of a selected representative subset of RIL populations. Understanding the genetic mechanism involved in the synthesis and regulation of carotenoids in sorghum seeds is a necessary step to develop new high-carotenoid sorghum varieties. In cooperation with scientists at The Grain Quality Structure Research Unit (GQSRU), Manhattan, Kansas, a diversity panel composed of 300 sorghum accessions were evaluated by ARS scientist in Mayaguez, Puerto Rico, for carotenoid content in Isabela, Puerto Rico. Seeds of the panels are being analyzed for carotenoid content and locus associated with carotenoid content will be identified by genome wide association analysis.
Impacts
(N/A)
Publications
- Cosme-Reyes, S.M., Cuevas, H.E., Zhang, D., Oleksyk, T.K., Irish, B.M. 2016. Genetic diversity of naturalized cacao (Theobroma cacao L.) in Puerto Rico. Tree Genetics and Genomes. doi: 10.1007/s11295-016-1045-4.
- Prom, L.K., Perumal, R., Cuevas, H.E., Radwan, G., Katile, S., Isakeit, T., Magill, C. 2016. Assessing the vulnerability of sorghum converted lines to anthracnose and downy mildew infection. Journal of Agriculture and Crops. 2(10):101-106.
- Prom, L.K., Radwan, G., Perumal, R., Cuevas, H.E., Katile, S., Isakeit, T., Magill, C. 2017. Grain biodeterioration of sorghum converted lines inoculated with a mixture of Fusarium thapsinum and Curvularia lunata. Plant Pathology Journal. 16:19-24.
- Cuevas, H.E., Rosa-Valentin, G., Hayes, C.M., Rooney, W.L., Hoffmann, L. 2017. Genomic characterization of a core set of the USDA-NPGS Ethiopian sorghum germplasm collection: implications for germplasm conservation, evaluation, and utilization in crop improvement. BMC Genomics. doi: 10. 1186/s12864-016-3475-7.
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Progress 10/01/15 to 09/30/16
Outputs
Progress Report Objectives (from AD-416): 1. Genetically-characterize sorghum accessions from Ethiopia and other nations and apply the genetic marker data to select core subsets of accessions for evaluation for host-plant resistance to anthracnose and grain mold. 2. With ARS cooperators, conduct multi-locational evaluations of selected sorghum accessions to identify potential new sources of host- plant resistance to anthracnose and grain mold pathotypes predominant in Puerto Rico and in Texas. 3. With ARS cooperators, develop experimental populations for identifying, characterizing, and mapping the genes that confer host-plant resistance to anthracnose and grain mold pathotypes and for identifying genetic markers closely linked to those resistance traits. 3a. Employ genome-wide association studies (GWAS) to identify genes that confer host-plant resistance to anthracnose. 3b. Employ GWAS to identify genes that confer host-plant resistance to grain mold pathotypes. 4. Evaluate selected sweet sorghum germplasm accessions to identify lines with robust culms, superior sugar content, dry matter production, and host-plant resistance to anthracnose. Approach (from AD-416): The focus of this research is to determine the genetic control of anthracnose and grain mold, to identify molecular markers for breeding programs seeking disease resistance, and to discover new sources of resistance present in exotic germplasm. Genome-wide association studies will be employed to understand the genetic control and locate the genome regions of the anthracnose and grain mold resistance genes. The genetic and morphological characterization of sorghum collection from Ethiopia and Sudan will be applied to develop core subsets for further association studies, and to identify new sources of host resistance. Presently, sweet sorghum varieties utilized as a biofuel source have a narrow genetic base. Therefore, evaluation of sweet sorghum accessions present in the US 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. In 2016, multiple sorghum accessions were evaluated by ARS scientists in Mayaguez, Puerto Rico, for anthracnose and grain mold resistance response. The second year evaluation of the core subset from Sudan (292 accessions) for anthracnose and grain mold resistance was completed and compared to evaluation from year one. A total of 60 accessions showed an anthracnose resistance response across years. In addition, a subset of 161 accessions from Senegal was evaluated for both anthracnose and grain mold at two locations (Isabela and Mayaguez). The screening identified 78 anthracnose- resistant accessions, while 15 accessions presented grain mold resistance. These results are being confirmed in an additional replicated trial. The anthracnose and grain mold resistance response previously identified in a U.S. sorghum association panel was confirmed in an additional replicated trial. A subset of 53 anthracnose-resistant accessions were re- evaluated and results confirmed the resistant response for 45 accessions. Likewise, a subset of 43 grain mold-resistant accessions were re- evaluated and results confirmed the resistant response for 27 accessions from the U.S. sorghum association panel. Presently, genetic analyses are being conducted to determine the genetic relationship among these resistant accessions. The preservation and adequate use of the National Plant Germplasm System (NPGS) sorghum collection require knowledge of genetic diversity present in the collection in order to understand phenotype diversity and to identify highly genetically related accessions. In this regard, the genetic diversity present in the Senegal NPGS sorghum collection was studied using the 161 accessions evaluated for anthracnose resistance and 20 Simple Sequence Repeat (SSR) markers evenly distributed across the sorghum genome. Population structure and cluster analysis separated the collection into 4 populations. A total of 150 (93%) accessions were assigned to one of these populations with an ancestry membership coefficient larger than 0.70. The 60 anthracnose resistant accessions were distributed among these population suggesting the existence of four resistant sources. The U.S. NPGS sweet sorghum collection includes ~2,180 accessions however, not all are actually sweet sorghum accessions. ARS scientists in Mayaguez, Puerto Rico, characterized the sugar content (Brix) for 881 sweet sorghum accessions using total stem juice from three plants pressed with a three-roller sugarcane mill. The Brix values of these accessions ranged from 0 to 16.4�, and 43 accessions had Brix values greater than 10�. The results were combined with those obtained in year 1 to select a subset of 233 accessions for further evaluation in a replicated trial. This subset will allow the identification of high brix sweet sorghums that will be screened for biofuel related traits and anthracnose resistance. As part of a grant awarded by the U.S. Department of Energy, entitled �Genomic dissection of anthracnose resistance response in sorghum [Sorghum bicolor (L.) Moench]�, during the first year of this proposal, seed of three sets of recombinant inbred lines (RILs) were increased for evaluation at multiple locations. These 300 RILs are being evaluated in Gainesville, Florida; College Station, Texas; and Tifton, Georgia, for anthracnose resistance response. In parallel, a high density linkage map with 500 single nucleotide polymorphism (SNP) sites was constructed for the RIL population derived from the cross of SC112-14 x PI609251. This linkage map was used to select a representative subset of 20 RILs that were evaluated in the greenhouse against ten particular anthracnose pathotypes from Puerto Rico; Texas; Arkansas and Georgia. The results indicate that a cluster of genes at chromosome 5 control the anthracnose resistant response. In cooperation with scientists at the Grain Quality Structure Research Unit (GQSRU), Manhattan, Kansas, ARS scientists in Mayaguez, Puerto Rico, are evaluating tropical sorghum accessions with superior grain quality and grain composition and genotyping the tropical accessions for use as breeding material for temperate-zone adaptability. Accomplishments 01 High throughput method to evaluate disease resistance in sorghum. Foliar phase of anthracnose, caused by Colletotrichum (C.) sublineolum is the most important leaf disease of sorghum. Due to the hyper- variable nature of the fungus, continuous evaluation of sorghum germplasm to identify new sources of resistance is imperative. Field and greenhouse evaluations for anthracnose resistance, especially with large numbers of sorghum lines/accessions can be expensive, time consuming and require large spaces and labor. In this study, 16 sorghum lines were evaluated by putting a drop of the mixture of C. sublineolum isolates suspension on each side of the midrib of adaxial excised leaves plated on half-strength potato dextrose agar medium and concurrently as whole plants inoculated with a mixture of C. sublineolum isolates-colonized grain and conidial suspension in the greenhouse. Each line exhibited the same reaction when challenged with C. sublineolum either using the excised leaf assay or screened in the greenhouse, indicating that the excised leaf assay is as effective in identifying susceptibility or resistance to the anthracnose pathogen. In both screening methods, SC748 was the only resistant line. The excised leaf assay was completed in 4 days while the greenhouse evaluation was finalized 44 days post-inoculation. Thus, the excised leaf method offers several advantages in screening sorghum for anthracnose resistance such as reducing the time for conducting the experiment, labor, space and increasing the number of isolates that can be tested within a short period.
Impacts
(N/A)
Publications
- Cuevas, H.E., Prom, L.K., Erpelding, J.E. 2015. Tapping the US sweet sorghum collection to identify biofuel germplasm. Sugar Tech. 17(4)428-438.
- Cuevas, H.E., Prom, L.K., Isakeit, T., Radwan, G. 2015. Assessment of sorghum germplasm from Burkina Faso and South Africa to identify new sources of resistance to grain mold and anthracnose. Crop Protection. 79:43-50.
- Prom, L.K., Cuevas, H.E., Isakeit, T., Droleskey, R.E. 2015. Excised leaf method for high volume evaluation of sorghum germplasm for resistance against Colletotrichum sublineolum. Plant Pathology. 15(1):11-16.
- Prom, L.K., Isakeit, T., Cuevas, H.E., Rooney, W., Perumal, R., Magill, C. 2015. Reaction of sorghum lines to zonate leaf spot and rough leaf spot. Plant Health Progress. 16(4):230-234.
- Cuevas, H.E., Chengbo, Z., Haibao, T., Prashant, K., Sayan, D., Yann-Rong, L., Ge, Z., Clement, T., Upadhyaya, H., Hash, C., Patterson, A.H. 2016. The evolution of photoperiod-sensitive flowering in sorghum, a genomic model for panicoid grasses. Genome Biology. doi: 10.1093/molbev/msw120.
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Progress 10/01/14 to 09/30/15
Outputs
Progress Report Objectives (from AD-416): 1. Genetically-characterize sorghum accessions from Ethiopia and other nations and apply the genetic marker data to select core subsets of accessions for evaluation for host-plant resistance to anthracnose and grain mold. 2. With ARS cooperators, conduct multi-locational evaluations of selected sorghum accessions to identify potential new sources of host- plant resistance to anthracnose and grain mold pathotypes predominant in Puerto Rico and in Texas. 3. With ARS cooperators, develop experimental populations for identifying, characterizing, and mapping the genes that confer host-plant resistance to anthracnose and grain mold pathotypes and for identifying genetic markers closely linked to those resistance traits. 3a. Employ genome-wide association studies (GWAS) to identify genes that confer host-plant resistance to anthracnose. 3b. Employ GWAS to identify genes that confer host-plant resistance to grain mold pathotypes. 4. Evaluate selected sweet sorghum germplasm accessions to identify lines with robust culms, superior sugar content, dry matter production, and host-plant resistance to anthracnose. Approach (from AD-416): The focus of this research is to determine the genetic control of anthracnose and grain mold, to identify molecular markers for breeding programs seeking disease resistance, and to discover new sources of resistance present in exotic germplasm. Genome-wide association studies will be employed to understand the genetic control and locate the genome regions of the anthracnose and grain mold resistance genes. The genetic and morphological characterization of sorghum collection from Ethiopia and Sudan will be applied to develop core subsets for further association studies, and to identify new sources of host resistance. Presently, sweet sorghum varieties utilized as a biofuel source have a narrow genetic base. Therefore, evaluation of sweet sorghum accessions present in the US 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. In 2015, multiple sorghum accessions were evaluated by ARS scientists in Mayaguez, Puerto Rico for anthracnose and grain mold resistance response. The first year evaluation of the core subset from Sudan (350 accessions) and the second year/location evaluation of 727 accessions from the U.S. sorghum association panel (377 lines) and a subset of the National Plant Germplasm System (NPGS) Ethiopian collection (350 lines) were completed. From the two year/location evaluation of the U.S. sorghum association panel, ARS scientists in Mayaguez, Puerto Rico identified 54, 20, and 54 lines with anthracnose, rust, and grain mold resistance. The U.S. sorghum association panel is extensively used in private and public breeding programs since these lines are photoperiod insensitive, therefore, these sources of resistant are available for the development of new varieties. Determining the fertility reaction of sorghum accessions (i.e. restorer or maintainer) is essential to establish initial breeding program in the adequate genetic background. In this regard, ARS scientists in Mayaguez, Puerto Rico crossed 30 exotic sorghum accessions from Ethiopia, Burkina Faso, and South Africa, and through cooperators in Lubbock, Texas, 75 additional lines with the androsterile line ATx623 to determine their fertility reaction. The progenies of these crosses were evaluated in Isabela, P.R. resulting in the identification of six accessions as maintainer lines. These results will be used to establish appropriate breeding schemes for these sorghum accessions. The U.S. NPGS sweet sorghum collection includes ~2,180 accessions however, not all are actually sweet sorghum. ARS scientists in Mayaguez, Puerto Rico characterized the sugar content (Brix) for half of the accessions in this collection using total stem juice from three plants pressed with a three-roller sugarcane mill. The analyses identified 103 accessions with a Brix value of 15.0, of which 6 accessions had a Brix value of 20.0. These sweet sorghum accessions with high sugar concentration will be re-evaluated in different environments/years to identify the most valuable accessions for the development of new sweet sorghum biofuel varieties. The genetic diversity present in the Ethiopian NPGS sorghum collection was studied by ARS scientists in Mayaguez, Puerto Rico using 148,475 single nucleotide polymorphism (SNPs) identified through the genotype by sequence analysis of 374 accessions. Population structure analysis employing a subset of 935 SNPs across the genome identified 3 subpopulations with an average pair-wise genetic distance among accessions of 0.30 to 0.35. Remarkably, none of the accessions had a similar genetic profile and less than 5% of the accessions showed a close genetic relationship (e.g. genetic distance = 0.10). Moreover, when compared with accessions in the U.S. sorghum association panel, it was found that two of the three subpopulations are not well represented in this panel. Therefore, this core subset of accessions from the Ethiopian NPGS collection should be employed to identify valuable genes for breeding programs, and to develop further molecular screening techniques based on genotypic analysis. Sorghum ergot is caused by three species of the fungus Claviceps spp. (C. africana, C. sorghicola, and C. sorghi). In America and the Caribbean, C. africana is the only ergot specie documented since mid-1996. ARS scientists in Mayaguez, Puerto Rico, began a morphological characterization of ergot isolates from different regions in Puerto Rico. The high morphological diversity observed among isolates prompted initiation of a genetic characterization of the isolates in order to clarify if other species may be present in the island. Accomplishments 01 Identification of new sources of grain mold, anthracnose and rust resistance. A two-location field evaluation study of the U.S. sorghum association panel conducted by ARS scientists in Mayaguez, Puerto Rico identified new sources of anthracnose and grain mold resistance. Six accessions showed high seed rate score (>2.0) and germination (>90%), while nine accessions showed resistance to both anthracnose and rust. These 15 accessions are adapted to temperate regions and could be immediately integrated into private and public sorghum improvement programs for the development of new resistant varieties. 02 Identification of sweet sorghum germplasm with high sugar content. The U.S. National Plant Germplasm System (NPGS) sweet sorghum collection is the primary source of genetic diversity for the development of new sweet sorghum varieties for biofuel production. The phenotypic characterization of this germplasm for biofuel traits is essential to make adequate use of the germplasm for improvement of current lines. The evaluation of half of this collection using sugar content (Brix) identified 103 accessions with high sugar content (Brix value = 15.0). Five accessions from the U.S. and one from Sudan had a Brix value = 20. 0 and could be used as parental lines for the development of new sweet sorghum biofuel varieties.
Impacts
(N/A)
Publications
- Rodriguez-Bonilla, L., Cuevas, H.E., Montero-Rojas, M., Bird-Pico, F., Luciano-Rosario, D., Siritunga, D. 2015. Assessment of genetic diversity of sweet potato in Puerto Rico. PLoS One. 9(12):e116184. doi:10.1371/ journal.pone.0116184.
- Irish, B.M., Cuevas, H.E., Simpson, S.A., Scheffler, B.E., Sardos, J., Ploetz, R., Goenaga, R.J. 2014. Musa spp. germplasm management: microsatellite fingerprinting of USDA-ARS National Plant Germplasm System (NPGS) collection. Crop Science. 54:2140-2151.
- Cuevas, H.E., Prom, L.K., Erpelding, J.E. 2015. Inheritance and molecular mapping of anthracnose resistance genes present in sorghum line SC112-14. Molecular Breeding. 34(4):1943-1953.
- Yildiz, M., Cuevas, H.E., Sensoy, S., Erdinc, C., Baloch, F.S. 2015. Transferability of cucurbita SSR markers for genetic diversity assessment of Turkish bottle gourd (Lagenaria siceraria) genetic resources. Biochemical Systematics and Ecology. 59:45-53.
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Progress 10/01/13 to 09/30/14
Outputs
Progress Report Objectives (from AD-416): 1. Genetically-characterize sorghum accessions from Ethiopia and other nations and apply the genetic marker data to select core subsets of accessions for evaluation for host-plant resistance to anthracnose and grain mold. 2. With ARS cooperators, conduct multi-locational evaluations of selected sorghum accessions to identify potential new sources of host- plant resistance to anthracnose and grain mold pathotypes predominant in Puerto Rico and in Texas. 3. With ARS cooperators, develop experimental populations for identifying, characterizing, and mapping the genes that confer host-plant resistance to anthracnose and grain mold pathotypes and for identifying genetic markers closely linked to those resistance traits. 3a. Employ genome-wide association studies (GWAS) to identify genes that confer host-plant resistance to anthracnose. 3b. Employ GWAS to identify genes that confer host-plant resistance to grain mold pathotypes. 4. Evaluate selected sweet sorghum germplasm accessions to identify lines with robust culms, superior sugar content, dry matter production, and host-plant resistance to anthracnose. Approach (from AD-416): The focus of this research is to determine the genetic control of anthracnose and grain mold, to identify molecular markers for breeding programs seeking disease resistance, and to discover new sources of resistance present in exotic germplasm. Genome-wide association studies will be employed to understand the genetic control and locate the genome regions of the anthracnose and grain mold resistance genes. The genetic and morphological characterization of sorghum collection from Ethiopia and Sudan will be applied to develop core subsets for further association studies, and to identify new sources of host resistance. Presently, sweet sorghum varieties utilized as a biofuel source have a narrow genetic base. Therefore, evaluation of sweet sorghum accessions present in the US 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. Progress was made on all four objectives of the project plan. In 2014, we completed the first year evaluation of the U.S. sorghum association panel (377 lines) for anthracnose and grain mold resistance. Concurrently, 380 Ethiopian exotic accessions were phenotypically characterized and evaluated for anthracnose and grain mold resistance. Through cooperators in Lubbock, Texas, these Ethiopian lines were also sampled at post- flowering stage to determine dhurrin content, which is associated with drought tolerance. A set of 60 sorghum converted lines, not present in the National Plant Germplasm System (NPGS) sorghum germplasm collection, were phenotypically characterized and evaluated for anthracnose and grain mold resistance. In addition, fresh seed from these lines were sent to collaborators in Texas and Georgia for phenotypic evaluation and to determine their photoperiod response. The narrow genetic diversity present among improved sweet sorghum varieties and the need to identify additional germplasm for the development of new sorghum cultivars for biofuel led us to evaluate the sweet sorghum accessions present in the NPGS collection. A sweet sorghum diversity panel of 270 accessions was evaluated for a second year for biofuel traits [e.g. sugar content (Brix), dry matter, juicy volume, etc. ]. At the same time, 1,000 sweet sorghum accessions from the NPGS collection were characterized for its sugar (Brix) content. About 44 exotic accessions showed Brix values ranging from 15.0 to 20.8, while multiple accessions with resistance to anthracnose and rust were also identified. The Ethiopian sorghum accessions constitute the largest geographical group in the NPGS collection. A stratified sample of 380 accessions based on sorghum races present in the NPGS Ethiopian sorghum collection were genetically characterized by Genotype by Sequence, and the analysis identified more than 100,000 single nucleotide polymorphism (SNPs) across the genome. Currently, analysis is directed to identify the most valuable SNPs for association mapping and to determine the population structure of the subset. Significant Activities that Support Special Target Populations: The scientist mentored six undergraduate students from the University of Puerto Rico at Mayaguez during their summer internship at our research station. The students had the opportunity to work with the scientist to learn techniques such as DNA isolation, genetic and phenotype characterization of sorghum germplasm. In addition, the scientist is mentoring one graduate student from the University of Puerto Rico at Mayaguez who is characterizing isolates of Claviceps spp. and evaluating ergot resistance in sorghum. Accomplishments 01 Genome mapping of anthracnose resistant genes against pathotypes from Texas and Arkansas present in SC112-14. The identification of new genes for anthracnose resistance and associated molecular markers is needed for the development of new, highly resistant varieties. One hundred twenty nine recombinant inbred lines (RIL) derived from the anthracnose resistant line SC112-14 and the susceptible line PI 609251 were developed during this year. The anthracnose resistance response against pathotypes from Texas, Arkansas, and Georgia were characterized for a subset of 50 RILs. The results showed that a series of nearest single loci at the distal region of chromosome 5 control the resistance response against pathotypes from Texas and Arkansas. These two loci are also in proximity with the anthracnose resistance locus for pathotypes from Puerto Rico. Simple sequence repeat markers associated with these resistances were developed, and can be used to select resistant genotypes in Texas, Arkansas and Puerto Rico. 02 Identification of new sources of grain mold resistance. Grain mold, caused by a complex of pathogenic and opportunistic fungi, is one of the most important diseases affecting sorghum production worldwide. Resistant cultivars provide the most effective method to control this disease. A 2-year evaluation of 80 exotic sorghum accessions from South Africa and Burkina Faso resulted in the identification of 9 accessions with grain mold resistance. Remarkably, the panicle of two accessions, one from South Africa (PI 61666) and another from Burkina Faso (PI 586182), have commercial potential, making them suitable for their immediate integration into sorghum breeding programs. 03 Identification of new sweet sorghum germplasm for biofuel. Recent demand for biofuel has caused a re-evaluation of sweet sorghum as a source of energy. However, improvement in sugar content and disease resistance are needed to make sweet sorghum a viable energy source. The screening of 950 sweet sorghum accessions from the NPGS collection resulted in the identification of new germplasm for biofuel sorghum breeding programs. Nine accessions from South Africa (PI 144335), Ethiopia (PI 455286), Zimbabwe (PI 155518, PI 155555), Sudan (PI 562267) and USA (PI 648098, PI 648091, PI 648080, and PI 643003) showed superior biofuel performance across years. The integration of these germplasms into sorghum breeding programs will aid in the development of new biofuel cultivars.
Impacts
(N/A)
Publications
- Cuevas, H.E., Prom, L.K., Erpelding, J.E., Brotons, V. 2014. Assessment of genetic diversity and anthracnose disease response among Zimbabwe sorghum germplasm. Plant Breeding. DOI:10.1111/pbr.12133.
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Progress 10/01/12 to 09/30/13
Outputs
Progress Report Objectives (from AD-416): 1. Genetically-characterize sorghum accessions from Ethiopia and other nations and apply the genetic marker data to select core subsets of accessions for evaluation for host-plant resistance to anthracnose and grain mold. 2. With ARS cooperators, conduct multi-locational evaluations of selected sorghum accessions to identify potential new sources of host- plant resistance to anthracnose and grain mold pathotypes predominant in Puerto Rico and in Texas. 3. With ARS cooperators, develop experimental populations for identifying, characterizing, and mapping the genes that confer host-plant resistance to anthracnose and grain mold pathotypes and for identifying genetic markers closely linked to those resistance traits. 3a. Employ genome-wide association studies (GWAS) to identify genes that confer host-plant resistance to anthracnose. 3b. Employ GWAS to identify genes that confer host-plant resistance to grain mold pathotypes. 4. Evaluate selected sweet sorghum germplasm accessions to identify lines with robust culms, superior sugar content, dry matter production, and host-plant resistance to anthracnose. Approach (from AD-416): The focus of this research is to determine the genetic control of anthracnose and grain mold, to identify molecular markers for breeding programs seeking disease resistance, and to discover new sources of resistance present in exotic germplasm. Genome-wide association studies will be employed to understand the genetic control and locate the genome regions of the anthracnose and grain mold resistance genes. The genetic and morphological characterization of sorghum collection from Ethiopia and Sudan will be applied to develop core subsets for further association studies, and to identify new sources of host resistance. Presently, sweet sorghum varieties utilized as a biofuel source have a narrow genetic base. Therefore, evaluation of sweet sorghum accessions present in the US 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. This research project initiated in June 2013 and replaces project 6635- 21000-049-00D. During the fiscal year, germplasm from Ethiopia was requested from the National Plant Germplasm System (NPGS) and planted in the field for evaluation for host plant disease resistance. The U.S. sorghum association panel (377 lines) are being evaluated for anthracnose and grain mold resistance. A total of 1,000 sweet sorghum accessions are being evaluated for sugar content (Brix) and lodging. A sweet sorghum diversity panel of 270 accessions is being evaluated for sugar content. Germplasm from the former USDA-ARS sorghum conversion program (terminated 20 years ago) have not been introduced into the sorghum germplasm collection maintained by NPGS. In this regard, 65 lines were indentified in our seed storage facilities, and regenerated to increase seed numbers and viability. These lines are being evaluated for disease resistance, agronomical traits, and photoperiod sensitivity. A stratified sample of 380 accessions based on sorghum races present in the Ethiopian sorghum collection was planted in the greenhouse for DNA isolation. The DNA from each accession was effectively isolated and its quality tested for use in Genotype by Sequence analysis. The genetic control of an anthracnose resistance gene present in PI533918 was determined by the analysis of observed segregation in a F2 population. This gene has been mapped to the distal region of chromosome five, flanked by two simple sequence repeat markers, and not associated with the anthracnose resistance gene present in SC748. This information will be valuable in order to introgress and pyramid these genes with other resistance genes. Significant Activities that Support Special Target Populations: The scientist mentored three undergraduate students from the University of Puerto Rico-Mayaguez, Campus during their summer internship at our research station facilities. The students had the opportunity to work with the scientist to learn techniques such as DNA isolation, hydrolysis capacity and phenotype characterization of sorghum germplasm. Accomplishments 01 Genome mapping of anthracnose resistance gene present in PI533918. The anthracnose resistance gene present in PI533918 was delimited to a 9.2 cM region at the distal region of sorghum chromosome five. Simple sequence repeats markers within this region were developed and evaluated by ARS scientists in Mayaguez, Puerto Rico, in order to provide a molecular tool to be used in sorghum breeding programs directed to introgress and pyramid multiple resistance genes. The incorporation of this gene, with previously identified resistance gene, will prolong and broaden the control of anthracnose disease. 02 Rescue of converted sorghum germplasm. ARS scientists in Mayaguez, Puerto Rico identified and seed regenerated sixty five converted lines of sorghum that were not present in the NPGS sorghum collection and sent these to Griffin, Georgia for long-term storage. This germplasm is novel and could serve as a valuable genetic resource for public and industry breeders.
Impacts
(N/A)
Publications
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