Sorghum Germplasm Collection Research Articles

Simple sequence repeats (SSR) marker-based analysis on the genetic variation and population structure of local and exotic sorghum germplasm collection conserved ex-situ in Sri Lanka

Simple sequence repeats (SSR) marker-based analysis on the genetic variation and population structure of local and exotic sorghum germplasm collection conserved ex-situ in Sri Lanka

Identification and Characterization of Mesotrione-Resistant Grain Sorghum [Sorghum bicolor (L.) Moench]: A Viable Option for Postemergence Grass Weed Control

Mesotrione is effective in controlling a wide spectrum of weeds in corn but not registered for postemergence use in sorghum because of crop injury. We screened a sorghum germplasm collection and identified two mesotrione-resistant sorghum genotypes (G-1 and G-10) and one susceptible genotype (S-1) in an in vitro plate assay. A mesotrione dose-response assay under greenhouse and field conditions confirmed that G-1 and G-10 are highly resistant compared to S-1. We found enhanced metabolism of mesotrione in G-1 and G-10 using HPLC assay, and a significant reduction in biomass accumulation was found in G-1 and G-10 plants pretreated with cytochrome P450 (CYP)-inhibitors malathion or piperonyl butoxide, indicating the involvement of CYPs in the metabolism of mesotrione. Genetic analyses using F1 and F2 progenies generated by crossing G-1 and G-10 separately with S-1 revealed that mesotrione resistance in sorghum is controlled by a single dominant gene along with several genes with minor effects.

Evaluation of a Subset of Ethiopia Sorghum Collection Germplasm from the National Genetic Resources Program of the United States Department of Agriculture for Anthracnose Resistance

Globally, one of the most devastating diseases of sorghum is anthracnose incited by Colletotrichum sublineola. During the 2019 and 2020 growing seasons, 94 and 64 accessions from the Ethiopian sorghum germplasm collection maintained by the National Genetic Resources Program of the United States Department of Agriculture were evaluated for anthracnose resistance. Seeds were planted in 1.8 m rows with 0.9 m row spacing in a randomized complete block design. The accessions and checks were replicated three times and 30 days after planting, inoculated by placing C. sublineola-colonized grains in the plant whorls. A total of 30 accessions, including PI533918, PI533923, PI534131 and PI534151 were resistant to the disease in both years. These identified resistant sources can be used in breeding programs to develop anthracnose-resistant lines and hybrids.

Genetic diversity of Ethiopian sorghum reveals signatures of climatic adaptation.

A large collection of Ethiopian sorghum landraces, characterized by agro-ecology and racial-group, was found to contain high levels of diversity and admixture, with significant SNP associations identified for environmental adaptation. Sorghum [Sorghum bicolor L. (Moench)] is a major staple food crop in Ethiopia, exhibiting extensive genetic diversity with adaptations to diverse agroecologies. The environmental and climatic drivers, as well as the genomic basis of adaptation, are poorly understood in Ethiopian sorghum and are critical elements for the development of climate-resilient crops. Exploration of the genome-environment association (GEA) is important for identifying adaptive loci and predicting phenotypic variation. The current study aimed to better understand the GEA of a large collection of Ethiopian sorghum landraces (n = 940), characterized with genome-wide SNP markers, to investigate key traits related to adaptation to temperature, precipitation and altitude. The Ethiopian sorghum landrace collection was found to consist of 12 subpopulations with high levels of admixture (47%), representing all the major racial groups of cultivated sorghum with the exception of kafir. Redundancy analysis indicated that agroecology explained up to 10% of the total SNP variation, and geographical location up to 6%. GEA identified 18 significant SNP markers for environmental variables. These SNPs were found to be significantly enriched (P < 0.05) for a priori QTL for drought and cold adaptation. The findings from this study improve our understanding of the genetic control of adaptive traits in Ethiopian sorghum. Further, the Ethiopian sorghum germplasm collection provides sources of adaptation to harsh environments (cold and/or drought) that could be deployed in breeding programs globally for abiotic stress adaptation.

The study of the sorghum genetic diversity using the mul¬tiplex microsatellite analysis

This study is focused on evaluation of the genetic structure and diversity of the national sorghum collection. Analyzing the genetic diversity of crop species is of great importance for genetic resources management and food security of any country. Huge genetic diversity of sorghum provides a great opportunity to improve the agronomic characteristics of this crop. The efficiency of microsatellite analysis has been demonstrated in many studies on the genetic diversity of different races and geographical groups of sorghum plants. Development of multiplex PCR analysis systems based on a set of polymorphic microsatellite loci will facilitate genetic tests on a large number of plant samples, thus making the research on sorghum diversity more efficient and comprehensive. A system of multiplex PCR analysis based on 12 polymorphic microsatellite loci was developed to perform single-stage high-throughput screening of cultivated and wild forms preserved in the sorghum germplasm collection. As a result of the microsatellite analysis of 200 sorghum plants, 229 alleles were detected. The studied loci showed high polymorphism. More than 17 alleles were identified in most loci, their polymorphic index content (PIC) ranging from 0.694 to 0.954. The value of the effective multiplex ratio (EMR) in the developed system was estimated at 0.833. The microsatellite analysis of sorghum accessions resulted in obtaining quantized gene expressions profiles, with a DNA profile for each accession, and revealed significant polymorphism among the plants of different sorghum varieties (races). The developed multiplex PCR system was shown to be efficient for evaluation of the genetic diversity and genetic relationships of sorghum plants from different races. The analysis of the obtained data using three bioinformatic techniques, NJ cluster analysis, PCoA, and the Bayesian model-based clustering, helped to classify the analyzed sorghum accessions into cluster groups according to their morphological and agronomic traits.

Genomic characterization of a core set of the USDA-NPGS Ethiopian sorghum germplasm collection: implications for germplasm conservation, evaluation, and utilization in crop improvement

BackgroundThe USDA Agriculture Research Service National Plant Germplasm System (NPGS) preserves the largest sorghum germplasm collection in the world, which includes 7,217 accessions from the center of diversity in Ethiopia. The characterization of this exotic germplasm at a genome-wide scale will improve conservation efforts and its utilization in research and breeding programs. Therefore, we phenotyped a representative core set of 374 Ethiopian accessions at two locations for agronomic traits and characterized the genomes.ResultsUsing genotyping-by-sequencing, we identified 148,476 single-nucleotide polymorphism (SNP) markers distributed across the entire genome. Over half of the alleles were rare (frequency < 0.05). The genetic profile of each accession was unique (i.e., no duplicates), and the average genetic distance among accessions was 0.70. Based on population structure and cluster analyses, we separated the collection into 11 populations with pairwise FST values ranging from 0.11 to 0.47. In total, 198 accessions (53%) were assigned to one of these populations with an ancestry membership coefficient of larger than 0.60; these covered 90% of the total genomic variation. We characterized these populations based on agronomic and seed compositional traits. We performed a cluster analysis with the sorghum association panel based on 26,026 SNPs and determined that nine of the Ethiopian populations expanded the genetic diversity in the panel. Genome-wide association analysis demonstrated that these low-coverage data and the observed population structure could be employed for the genomic dissection of important phenotypes in this core set of Ethiopian sorghum germplasm.ConclusionsThe NPGS Ethiopian sorghum germplasm is a genetically and phenotypically diverse collection comprising 11 populations with high levels of admixture. Genetic associations with agronomic traits can be used to improve the screening of exotic germplasm for selection of specific populations. We detected many rare alleles, suggesting that this germplasm contains potentially useful undiscovered alleles, but their discovery and characterization will require extensive effort. The genotypic data available for these accessions provide a valuable resource for sorghum breeders and geneticists to effectively improve crops.

Developing new markers and QTL mapping for greenbug resistance in sorghum [Sorghum bicolor (L.) Moench

Greenbug is a major damaging insect to sorghum production in the United States. Among various virulent greenbug biotypes, biotype I is the most predominant and severe for sorghum. To combat with the damaging pest, greenbug resistant sources were obtained from screening sorghum germplasm collection. This experiment was conducted to identify the genomic regions contributing resistance to greenbug biotype I in a sorghum accession, PI 607900. An F2 mapping population consisting of 371 individuals developed from a cross of the resistant line with an elite cultivar, BTx623 (susceptible) were tested and scored for their response to greenbug feeding in the greenhouse. Significant differences in resistance were observed between the two parental lines and among their F2 progeny in response to greenbug feeding at 7, 10, 14 and 21 days after infestation. A linkage map spanning a total length of 729.5 cM across the genome was constructed with 102 polymorphic SSR markers (69 genomic and 33 EST SSRs). Of those microsatellite markers, 48 were newly developed during this study, which are a useful addition for sorghum genotyping and genome mapping. Single marker analysis revealed 29 markers to be significantly associated with the plant response to greenbug feeding damage. The results from interval mapping, composite interval mapping and multiple interval mapping analyses identified four major QTLs for greenbug resistance on chromosome 9. These QTLs collectively accounted for 34–82 % of the phenotypic variance in greenbug resistance. Minor QTLs located on chromosome 3 explained 1 % of the phenotypic variance in greenbug resistance. The major allele for greenbug resistance was on chromosome 9 close to receptor-like kinase Xa21-binding protein 3. These markers are useful to screen more resistant genotypes. Furthermore, the markers tagged to QTL regions can be used to enhance the sorghum breeding program for greenbug resistance through marker-assisted selection and map-based cloning.

Improvement of crop protection against greenbug using the worldwide sorghum germplasm collection and genomics-based approaches

Successful development of new sorghum cultivars and hybrids to ensure sustainable production depends largely on the availability of genetic resources with desirable traits such as pest resistance. Our recent research has focused on improvement of crop protection against greenbugs using the worldwide germplasm collection and genomics-based approaches. First, we conducted the systematic evaluation of a worldwide germplasm collection in order to identify new sources of greenbug resistance. Twenty-one resistant lines were identified, which offered new sources of resistance to sorghum breeding. Molecular markers used to assess the genetic diversity among those resistant lines suggested relatively diverse resistant sources in the sorghum germplasm collection. More recently, a mapping project was executed to associate the resistance genes with sorghum chromosomes. The mapping data indicated one major and a minor quantitative trait loci reside on chromosome 9 and are responsible for resistance to greenbug. In addition, cDNA microarrays were used to monitor greenbug-induced gene expression in sorghum plants. This study has developed a transcriptional profile for sorghum in response to greenbug attack, which provides us with useful molecular information for discovery of greenbug resistance genes and a better understanding of the genetic mechanisms controlling host defences in sorghum.

Field Assessment of Anthracnose Disease Response for the Sorghum Germplasm Collection from the Mopti Region

Problem statement: Sorghum anthracnose (Colletotrichum sublineolum) is a highly variable pathogen and new sources of host plant resistance are required for the development of resistant sorghum varieties. Germplasm collections are an important source of host plant resistance and screening germplasm will be essential to identify new sources of resistance. Approach: The sorghum (Sorghum bicolor) collection from the Mopti region of Mali was inoculated with Colletotrichum sublineolum and evaluated for foliar anthracnose disease response in Isabela, Puerto Rico during the 2004 and 2005 growing seasons using a partially balanced lattice design with three replications. Results: A resistant response was observed for 45 of the 97 accessions in the collection and mean infection severity for the 52 susceptible accessions was 27.6%. An association was observed between resistance and the administrative district where the germplasm was collected. More than 50% of the accessions from the Bandiagara and Bankass districts showed a resistant response. The lowest frequency of resistant germplasm was observed for the Mopti district with 25% of the accessions showing a resistant response. The susceptible accessions from the Mopti district, however, showed the lowest mean infection severity. Approximately 44% of the accessions from the Douentza district showed a resistant response with the susceptible accessions showing the highest mean infection severity. These results suggest an association between annual rainfall and anthracnose resistance, with sorghum accessions from drier regions showing greater susceptibility. Anthracnose resistance also showed an association with sorghum race classification and race guinea accessions were more frequently resistant as compared to accessions classified as race durra or durra-bicolor. Conclusion: The results indicated that anthracnose resistant sorghum germplasm is frequent in the Mopti region of Mali and that ecogeographic origin and sorghum characterization information can be used to aid in germplasm selection or germplasm acquisition to identify anthracnose resistant sources.

Genetic diversity of transpiration efficiency in sorghum

Sorghum is the fifth most important grain crop and is becoming increasingly important as a biofuel feedstock due to its superior tolerance to water-deficit stress. Sorghum is commonly grown under rain-fed conditions in the Southern Plains in the U.S.A. and other semi-arid regions in the world. Thus, its production is strongly affected by the availability of soil water during the growing season. Enhancing transpiration efficiency (TE), defined as biomass accumulation per unit water transpired, may be an effective approach to increasing sorghum yield in arid and semi-arid regions under no or limited irrigation. In this report, we surveyed 341 sorghum accessions for variation in TE. A selection of 25 lines was used to confirm the initial survey and these accessions were studied in a greenhouse experiment over 2 years. TE in these selected lines varied from year to year; however, similar rank was observed in both studies. Several accessions with consistent high or low TE were identified. TE based on biomass production was strongly correlated with increased biomass accumulation rather than with reduced water use. Gas-exchange analysis indicated that low internal CO 2 concentration and enhanced photosynthetic capacity may be a factor accounting for the high TE in some lines; other physiological processes also contribute to the TE based on integrated biomass. The result suggests that considerable genetic variation in TE exists in the sorghum germplasm collection and that TE is strongly influenced by environment. The sorghum lines with contrasting TE may serve as an important genetic resource for identification of physiological mechanisms regulating TE and for improvement of this trait in sorghum breeding.

Variation for Anthracnose Resistance within the Sorghum Germplasm Collection from Mozambique, Africa

Variation for Anthracnose Resistance within the Sorghum Germplasm Collection from Mozambique, Africa

Allelic Frequency at the Rf3 and Rf4 Loci and the Genetics of A3 Cytoplasmic Fertility Restoration in Converted Sorghum Lines

Cytoplasmic‐nuclear male sterility (CMS) in sorghum [Sorghum bicolor (L.) Moench] is integral to hybrid seed production. One such CMS, A3, is controlled by a two gene gametophytic fertility restoration system involving two restoration alleles, Rf3 and Rf4, which are required for individual male gamete viability. A survey of the allelic frequencies of Rf3 and Rf4 in the sorghum germplasm collection was undertaken using 140 lines from the Sorghum Conversion Program. These lines were hybridized to two testers, A3FL3 (Rf3Rf3rf4rf4) and A3FL4 (rf3rf3Rf4Rf4). The resulting hybrids were evaluated for I2–KI pollen stainability and seed set to determine their fertility restoration reaction. Transcript analyses were performed on lines that contained restoration alleles to determine whether they fit the expected genetic model of fertility restoration. Three lines (SC306, SC512, and SC215) were found to restore fertility with both testers and thus contain both restoration alleles. The surveyed allelic frequency of Rf3 and Rf4 was 5.1 and 4.8%, respectively. Using transcript analyses, two exceptional lines were identified (SC306 and SC215) that carried Rf3 but did not confer enhanced transcript processing activity (TPA) of mitochondrial orf107 Enhanced TPA was thought to be tightly linked to or represent gene action of Rf3, but identification of these lines demonstrates that enhanced TPA is not required for fertility restoration and does not represent gene action of Rf3.

Comparative Assessment of Variation among Sorghum Germplasm Accessions Using Seed Morphology and RAPD Measurements.

The sorghum germplasm collection currently contains over 42 000 accessions, a number that is too large to manage efficiently. The specific objective of this research was to compare clusters developed from agronomic descriptors with phylogenetic groupings based on random amplified polymorphic DNA (RAPD) fingerprinting of selected sorghum [Sorghum bicolor (L.) Moench] races. Our intent was to identify one approach using agronomic descriptors that would most closely approximate the groupings produced by RAPD markers. Ninety-four accessions of sorghum were grouped into four of the five major races. Differences among accessions determined by various clustering procedures based on agronomic characteristics were compared with clusters developed by means of RAPD markers. Each race varied in the degree of similarity between the four clustering approaches taken and the information provided by RAPD fingerprinting. Test 2, standardization of data by Z-scores and cluster analysis using the complete set of data, provided the highest similarity score for the race bicolor, while Test 3, standardization of data by Z-scores and cluster analysis based on a reduced set of variables selected from principle component analysis, provided the highest similarity scores for the races guinea. Test 1, random selection, was highest for the races caudatum and durra. When averaged over all the races, Test 2 provided the highest similarity score. The results of this study indicate that no one approach to develop clusters by means of agronomic descriptors closely approximate the groupings produced by RAPD markers. These results underscore the need for further research in the evaluation of techniques used to develop core collections and their validity.

Breakdown of resistance to sorghum midge, Stenodiplosis sorghicola

Sorghum midge (Stenodiplosis sorghicola Coquillett) is an important pest of grain sorghum worldwide. Several sources of resistance to sorghum midge have been identified in the world sorghum germplasm collection, of which some lines show a susceptible reaction in Kenya. Therefore, we studied the insect density damage relationships for a diverse array of midge-resistant and midge-susceptible sorghum genotypes, and variation in association of glume and grain characteristics with expression of resistance to sorghum midge. AF 28 and IS 8891 showed resistance to sorghum midge both in India and Kenya; DJ 6514 and ICSV 197, which are highly resistant to sorghum midge in India, showed a susceptible reaction at Alupe, Kenya. Sorghum midge damage in general was greater in Kenya than that observed in India at the same level of midge density suggesting that the breakdown of resistance in Kenya is due to factors other than insect density. Glume length, glume breadth, and glume area were positively associated with susceptibility to sorghum midge at both locations. However, under natural infestation, the correlation coefficients were stronger in India than in Kenya. Grain mass at 3 and 6 days after anthesis was positively associated with susceptibility to midge in India, but did not show any association with midge damage in Kenya. Grain growth rate between 3 and 6 days after anthesis was more strongly correlated with susceptibility to midge in Kenya than in India. Variation in the reaction of sorghum genotypes across locations may be partly due to the influence of environment on association between glume and grain characteristics with susceptibility to sorghum midge, in addition to the possible differences in midge populations in different geographical regions.

Identification of stable sources of resistance in sorghum to midge and their reaction to leaf diseases

Sorghum midge ( Stenodiplosis (= Contarinia) sorghicola Coquillett) is an important pest of grain sorghum worldwide, and several sources of resistance have been identified in the world sorghum germplasm collection. DJ 6514 and the breading lines derived from it become susceptible to sorghum midge in Kenya. Therefore, we evaluated a diverse array of midge-resistant and -susceptible lines at Alupe, Kenya; and ICRISTAT Center, India, to identify lines with stable resistance across seasons and locations. The test material was also evaluated for resistance to leaf diseases at Alupe, Kenya; to identify lines with multiple resistance to sorghum midge and leaf diseases. Across seasons and locations; IS 3461, IS 8884, IS 8887, IS 8891, IS 19476, IS 22806, and AF 28 showed high to moderate levels of resistance to midge, and these lines will be useful for use in resistance breeding programs. Thirty-nine lines showed resistance to midge both under natural infestation and no-choice headcage screening at ICRISTAT Center, India, over four seasons, of which IS 18696, IS 22806, ICSV, 197, ICSV 745, ICSV 88032, PM 20710-2, DJ 6514, and AF 28 were highly resistant. Genotypes IS 3461, IS 8884, IS 8887, IS 8589, IS 19476, IS 22806, ICSV 736, ICSV 90003, and AF 28 showed moderate levels of resistance to both midge and leaf diseases at Alupe, Kenya; and these lines can be used as sources of multiple resistance to these pests. Lines IS 2766, IS 7148, IS 8733, and IS 8589, showed high levels of resistance to leaf diseases in Kenya. Resistance to midge breaks down in some lines at Alupe, Kenya; possibly because of the influence of environment on the expression of resistance or the possible differences in midge populations at different geographic locations.

The Use of Plant Genetic Resources.

Preface Acknowledgements Part I. Role of Genetic Resource Collections in Research and Breeding: 1. Germplasm collections and the public plant breeder K. S. Gill 2. Germplasm collections and the private plant breeder J. S. C. Smith and D. N. Duvick 3. Germplasm collections and the experimental biologist R. G. Palmer Part II. Use of Collections: 4. International use of a sorghum germplasm collection K. E. Prasada Rao, M. H. Mengesha and V. G. Reddy 5. Current use of potato collections J. G. Th. Hermsen 6. Use of collections in cereal improvement in semi-arid areas J. P. Srivastava and A. B. Damania 7. Limitations to the use of germplasm collections D. R. Marshall Part III. Size and Structure of Collections: 8. The case for large collections T. T. Chang 9. The Case for core collections A. H. D. Brown 10. The role of networks of dispersed collections P. M. Perret Part IV. Evaluation: 11. Characterisation and evaluation of okra S. Hamon and D. H. van Sloten 12. Evaluation of cereals in Europe G. Fischbeck 13. Evaluatling the germplasm of groundnut (Arachis hypogaea) and wild Arachis species at ICRISAT J. P. Moss, V. Ramanatha Rao and R. W. Gibbons 14. Practical considerations relevant to effective evaluation J. T. Williams 15. Principles and strategies of evaluation O. H. Frankel Part V. Wild Relatives of Crops: 16. Collection strategies for the wild relatives of field crops C. G. D. Cahpman 17. Wild relatives as sources of disease resistance J. J. Burdon and A. M. Jarosz 18. Ecological and genetic considerations in collecting and using wild relatives G. Ladizinsky Part VI. Technological or Scientific Innovations that Affect the use of Genetic Resources: 19. In vitro conservation and germplasm utilisation L. A. Withers 20. Screening for resistance to diseases P. H. Williams 21. Restriction fragments as molecular markers for germplasm evaluation and utilisation R. Bernatsky and S. D. Tanksley 22. Molecular biology and genetic resources W. J. Peacock Index.

The glossy trait in sorghum: Its characteristics and significance in crop improvement

Sorghum seedlings can be morphologically glossy or nonglossy: seedlings with dark green leaves (normal) are nonglossy, and seedlings with light yellow green and shining leaf surface are glossy. A systematic study of the world sorghum germplasm collection indicated a low frequency of accessions with the glossy trait (only 495 of 17 536 germplasm accessions screened). A large proportion (84%) of the glossy lines were of Indian origin but some were from elsewhere (Nigeria, Sudan, Cameroun, Ethiopia, Kenya, Uganda, South Africa, and Mexico). Most of the glossy lines are in the durra group but some are from the taxonomic groups guinea, caudatum, and bicolor. Glossy lines vary in morphological, anatomical, and agronomic attributes, many being extremely late or photoperiod-sensitive and very tall. Some lines are early maturing, intermediate to dwarf in height and agronomically good. Studies have indicated that glossy lines contribute to shootfly resistance and seedling drought resistance. Source material for the glossy trait is maintained by the Genetic Resources Unit at ICRISAT.