- Evaluation of genetic diversity, agronomic traits, and anthracnose resistance in the NPGS Sudan Sorghum Core collection. - In total, 171 accessions (54%) were assigned to one of these populations, which covered 96% of the total genomic variation. - Integrated analysis of the Sudan core set and sorghum association panel indicated that a large portion of the genetic variation in the Sudan core set might be present in breeding programs but remains unexploited within some clusters of accessions.. - The new GBS data set generated in this study represents a novel genomic resource for plant breeders interested in mining the genetic diversity of the NPGS sorghum collection.. - 2020 Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0. - Full list of author information is available at the end of the article. - A core collection comprises a representative subset of approximately 10% of the entire germplasm collection and is used for in-depth phenotypic and genetic analyses [2]. - The present day sorghum breeding programs utilize only a limited portion of the genetic diversity available in the NPGS sorghum collection, whereas the diversity underlying economically important traits re- mains trapped within the tropical germplasm.. - Nevertheless, these panels comprise converted sorghum lines (i.e., lines adapted to temperate regions) that represent most of the genetic diversity in breeding programs. - Genomic characterization of the NPGS Ethiopia core set and Niger collection revealed that a limited portion of the sorghum genetic diversity is present in the association panels [22, 23]. - The genomic and phenotypic characterization of the NPGS germplasm is necessary to provide sorghum breeders and geneticists the knowledge and genomic tools necessary to utilize and conserve this germplasm. - Genomic diversity of NPGS Sudan core collection. - The GBS analysis of the NPGS Sudan core set resulted in the identification of 183,144 SNPs with a frequency higher than 0.05 and an average of one SNP per 3275 kb.. - The rate of heterozygosity was less than 0.11 at more than 90% of the SNPs, with an overall average of 0.05, indicating low genetic variation within accessions.. - Population structure of NPGS Sudan core collection Population structure analysis of the NPGS Sudan core collection revealed five ancestral populations (Fig. - To determine the potential use of the Sudan core collec- tion and to expand the genetic diversity in breeding pro- grams, we compared the allelic diversity of the core set with that of the SAP. - Most of the private alleles (99.6%) and 28,018 of the rare alleles (56%) in the Sudan core set were identified in the SAP. - The neighbor-joining cluster ana- lysis of the SAP and Sudan core set, based on 20,738. - Our results indicated that a large portion of the genetic variation in the Sudan core set might been used in breeding programs. - Phenotype diversity and anthracnose resistance response in the NPGS Sudan core collection. - The population structure of the Sudan core set was asso- ciated with phenotypic variation in six agronomic traits (Table 3. - 1 Population structure analysis of the NPGS Sudan core collection. - Each accession is represented by a vertical line partitioned into five colored segments that represent the estimated membership probabilities of the individual to each cluster c Distribution of pairwise identity by state (IBS) genetic distance amongst 318 accessions from NPGS Sudan core collection based on the analysis of 5366 unlinked SNPs. - Colored branches represent accessions belonging to the five population present in the NPGS Sudan core collection and admixture accessions are not colored. - The anthracnose resistance phenotype of the Sudan core accessions indicated that most accessions were suscep- tible to anthracnose (X = 3.44). - Previous studies showed most of the acces- sions classified as resistant in Puerto Rico were resistant at Georgia and Texas, USA [17, 29]. - inbreeding coefficient (F is ) in the NPGS Sudan core collection NPGS Sudan. - core collection. - Genetic characterization of the NPGS Sudan core collection provides a new genomic resource for the investigation of important agronomic traits. - The results of Q-Q plots indicated the in- clusion of the ancestry membership coefficient for five population is adequate to decrease the chance of spurious associations (Additional file 3: Fig. - Both genomic regions account for up to 28% of the observed Table 3 Phenotypic characterization of the five populations in the NPGS Sudan core collection evaluated at Isabela and Mayaguez, Puerto Rico in 2014 and 2016, respectively. - b Flowering time refers to the number of days until 50% of the plants in a plot reached anthesis. - c Plant height refers to the distance from the base of the main stalk to the top of the panicle. - d Panicle length refers to the distance from the base to the top of the panicle. - e Panicle diameter refers to the widest region of the panicle. - NPGS Sudan core set No. - The region in chromosome 4 explains 20% of the observed variation and is constituted by 30 kb block with four genes (Sobic.004G155600 – Sobic.004G155900).. - Each of these genome regions explains 1–4% of the observed variation,. - Amongst the multiple candidate genes within associated genomic regions, one locus in chromosome 6 constituted by the SNP S6_51222126 is lo- cated 2.4 kb upstream of the gene Sobic006G151500 that encode a cytokinin dehydrogenase. - One genomic re- gion in chromosome 4 explains 28% of the observed variation and is constituted by the SNP S4_49996017 lo- cated 3.5 kb upstream of the gene Sobic04G157700. - The genomic region in chromosome 6 explains 11% of the observed variation and is constituted by the SNP S6_46298267 located within the gene. - Each of these genome regions explains 1–7% of the observed variation, and together account for up to 25%. - The 14.31 kb genomic region in chromo- some 6 explains 7% of the variation and enclose three genes (Sobic06G095100 – Sobic06G095300). - Each genomic region in chromosome 2 explains 2% of the observed variation.. - The genomic region in chromosome 5 (SNP S explains 7% of the observed variation and is in a 6 kb intergenic region.. - Moreover, the photoperiod sensitivity of most of the germplasm limits the screening to tropical Table 5 Genomic regions associated with four agronomic traits. - and anthracnose resistance based on the genome-wide association study (GWAS) of the NPGS Sudan core collection.. - a Plant height refers to the distance from the base of the main stalk to the top of the panicle. - b Panicle length refers to the distance from the base to the top of the panicle. - c Panicle diameter refers to the widest region of the panicle. - e Flowering time refers to the number of days until 50% of the plants in a plot reached anthesis. - Today, most of the genetic diversity of NPGS collection remains untapped, while most of the improved varieties are genet- ically related because of inbreeding, and are therefore vul- nerable to abiotic and biotic stresses. - Nevertheless, most of the accession in the NPGS sorghum core collection lack phenotypic and. - To access the genetic diversity of the Sudan core set, we genetically characterized these accessions with the GBS platform previously used to genetically characterize the SAP [8] and the NPGS Ethi- opian collection [22]. - In fact, the collection site was un- known for 66% of the accessions, while the other 24% of the accessions were obtained from the Gezira Research Station, making it impossible to organize the core set based on geographic regions. - Therefore, the five popula- tions identified in the Sudan core set provide valuable. - 5 Manhattan plots for the genome-wide association study (GWAS) of plant height, panicle length and diameter, flowering time and anthracnose resistance in the NPGS Sudan core collection based on the analysis of 183,184 SNPs. - In this regard, phylogenetic analysis of the Sudan core set with the SAP, allows the selection of the most genetically diverse accessions for adaptation to temperate regions to expand the genetic diversity employed in breed- ing programs.. - Preservation of NPGS Sudan core collection. - Preserve most of the allelic diversity present in a germ- plasm collection is necessary for the security of agricul- ture [38]. - Redundancy of accessions is one of the biggest problems in germplasm collections because it re- quires the maintenance and screening of accessions that do not contribute to the diversity of the collection. - Previous studies showed that core collections based on either genotypic profiles or random selection could rep- resent the genetic diversity of the entire collection [3].. - 0.05) in the Sudan core set (22%) was lower than that observed in the NPGS Ethiopia core set (60% [22]. - Thus, the high frequency of the Durra genetic background and high frequency of rare al- leles in Sudanese populations 1 and 2 suggests that both of these populations originated from Ethiopia. - The frequency of rare alleles and heterozygosity rate are indi- cators of genetic diversity that could be used to measure the integrity of the collection during regeneration. - At this time, our analysis suggests that most of the genetic variation present in the NPGS Sudan collection should be available in its core set. - Genome-wide association study in NPGS Sudan core collection. - Genomic characterization of the Sudan core collection could be used to study economically important traits and develop marker–trait association via GWAS. - Deter- mination of the population structure is important for the identification of marker-trait association [46]. - Popu- lation structure of the Sudan core set explained up to 25% of the observed phenotypic variation in quantitative traits including FL, PH, PL, and PD. - Further integration of the Sudan core set with other sorghum diversity panels [8, 16] and NPGS core sets [22] may increase the phenotypic diversity and stat- istical power for the complete elucidation of these com- plex traits. - For instance, variation in the photoperiod sensitivity and panicle compactness of the NPGS Senegal collection was associated with several known sorghum genes [40]. - Allele frequency distribution of the SNP S located in the Tan1 gene (Sobic.004 g280800 [48]. - Although most of the iden- tify loci explain a small portion of the observed variation, they might can have significant effects in breeding popu- lations where population structure is absent. - The genetic variation of the SNP in chromosome 5 (S5_. - These gen- omic regions explain a limited portion of the observed variation indicating the presence of other loci. - Most previous inheritance studies of the an- thracnose resistance response showed single gene segre- gation [52–55]. - Phylogenetic analysis showed these resistance accessions represent the genetic variation in the Sudan core collection (Additional file 4:. - Most of the Sudan and SAP germplasm belong to the Caudatum race, therefore, their combined analysis could not increase the frequency of resistant alleles. - Evaluation of the NPGS germplasm belonging to Kaffir and Guinea races, and its further combination with the SAP and NPGS Sudan and Ethiopian core set, should enable the detection of add- itional resistance loci. - Recognition of the origin, evolu- tion, and dispersal of some anthracnose resistance genes will help us understand the variation observed in the re- sistant response within and among the NPGS core sets.. - Genomic characterization of the core collection revealed that it comprises five populations, whose effect- ive use could expand the genetic diversity of sorghum breeding programs. - This core set represents ~ 13.8% of the total NPGS Sudan collection and consists of acces- sions belonging to all five known sorghum races, Bicolor (14 accessions), Caudatum (169 accessions), Durra (26 accessions), Guinea (eight accessions), and Kafir (five ac- cessions), as well as intermediate races (96 accessions), according to the Germplasm Resource Information Net- work (GRIN. - The core set and five reference breeding lines (RTx430, RTx2911, BTx623, SC748–5, and SC112) were planted at the research farms of the USDA-Agricultural Research Service (ARS) Tropical N W) and Mayaguez N W), Puerto Rico, during the short day-length season (i.e., from Sep- tember to April) in 2014 and 2016, respectively. - FL was defined as the number of days until 50% of the plants within a plot reached anthesis. - PH referred to the average distance from the base of the main stalk at the soil level to the top of the panicle of three plants per plot at maturity. - PL and PD referred to the distance from the first rachis to the top of the panicle and the widest sec- tion of the panicle, respectively [59]. - Data of the three experiments were combined to perform ANOVA using the Proc mixed covtest procedure of SAS. - The Sudan core collection was subjected to GBS [6]. - The GBS library was prepared and se- quenced in four lanes of an Illumina HiSeq 2500 platform at the Biotechnology Center of the University of Wisconsin, Madison, WI. - Population structure analysis of the NPGS Sudan core set A pruned subset of 5366 unlinked SNPs (r 2 <. - Hierarchical organization of the genetic relatedness of 318 accessions from the USDA-NPGS Sudan germplasm collection based on the population structure analysis of 5000 unlinked SNPs. - Genome-wide association study (GWAS) of midrib color in the NPGS Sudan core collection. - Log quantile-quantile (Q-Q) p-value plots for the genome-wide association study (GWAS) of plant height, panicle length and diameter, flowering time and anthracnose resistance in the NPGS Sudan core collection. - HC wrote the first draft of the manuscript. - Comprehensive genotyping of the USA national maize inbred seed bank. - Genome-wide association mapping of anthracnose (Colletotrichum sublineolum) resistance in the U.S.. - Genomic characterization of a core set of the USDA-NPGS Ethiopian sorghum germplasm collection: implications for germplasm conservation, evaluation, and utilization in crop improvement. - Registration of partially converted germplasm from 44 accessions of the USDA-ARS Ethiopian and Sudanese sorghum collections. - Population structure of the NPGS Senegalese sorghum collection and its evaluation to identify new disease resistant genes
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