Association of functional markers with flowering time in lentil

In the present study, a diverse panel of 96 accessions of lentil germplasm was used to study flowering time over environments and to identify simple sequence repeat markers associated with flowering time through association mapping. The study showed high broad sense heritability estimate (h ² bs=0.93) for flowering time in lentil. Screening of 534 SSR markers resulted in an identification of 75 SSR polymorphic markers (13.9%) across studied genotypes. These markers amplified 266 loci and generated 697 alleles ranging from two to 16 alleles per locus. Model-based cluster analysis used for the determination of population structure resulted in the identification of two distinct subpopulations. Distribution of flowering time was ranged from 40 to 70 days in subpopulation I and from 54 to 69 days in subpopulation II and did not skew either late or early flowering time within a subpopulation. No admixture was observed within the subpopulations. Use of the most accepted maximum likelihood model (P3D mixed linear model with optimum compression) of MTA analysis showed significant association of 26 SSR markers with flowering time at <0.05 probability. The percent of phenotypic explained by each associated marker with flowering time ranged from 2.1 to 21.8% and identified QTLs for flowering time explaining high phenotypic variation across the environments (10.7-21.8%) or in a particular environment (10.2-21.4%). In the present study, 13 EST-SSR showed significant association with flowering time and explained large phenotypic variation (2.3-21.8%) compared to genomic SSR markers (2.1-10.2%). Hence, these markers can be used as functional markers in the lentil breeding program to develop short duration cultivars.     

Inheritance studies of SSR and ISSR molecular markers and phylogenetic relationship of rice genotypes resistant to tungro virus

Multivariate analyses were performed using 13 morphological traits and 13 molecular markers (10 SSRs and three ISSRs) to assess the phylogenetic relationship among tungro resistant genotypes. For morphological traits, the genotypes were grouped into six clusters, according to D² statistic and Canonical vector analysis. Plant height, days to flowering, days to maturity, panicle length, number of spikelet per panicle, number of unfilled grain per panicle and yield were important contributors to genetic divergence in 14 rice genotypes. Based on Nei's genetic distance for molecular studies, seven clusters were formed among the tungro resistant and susceptible genotypes. Mantel's test revealed a significant correlation (r = 0.834*) between the morphological and molecular data. To develop high yielding tungro resistant varieties based on both morphological and molecular analyses, crosses could be made with susceptible (BR10 and BR11) genotypes with low yielding but highly resistant genotypes, Sonahidemota, Kumragoir, Nakuchimota, Khaiyamota, Khairymota and Kachamota. The chi-square analysis for seven alleles (RM11, RM17, RM20, RM23, RM80, RM108 and RM531) of SSR and five loci (RY1, MR1, MR2, MR4 and GF5) of three ISSR markers in F₂ population of cross, BR11 × Sonahidemota, showed a good fit to the expected segregation ratio (1:2:1) for a single gene model.     

Genetic diversity of cucumber estimated by morpho-physiological and EST-SSR markers

In the present study, genetic variation among 40 cucumber genotypes was analyzed by means of morpho-physiological traits and 21 EST-SSR markers. Diversity was observed for morpho-physiological characters like days to 50% female flowering (37–46.9, number of fruits/plant (1.33–5.80), average fruit weight (41–333), vine length (36–364), relative water content (58.5–92.7), electrolyte leakage (15.9–37.1), photosynthetic efficiency (0.40–0.75) and chlorophyll concentration index (11.1–28.6). The pair wise Jaccard similarity coefficient ranged from 0.00 to 0.27 for quantitative traits and 0.24 to 0.96 for EST-SSR markers indicating that the accessions represent genetically diverse populations. With twenty-one EST-SSR markers, polymorphism revealed among 40 cucumber genotypes, number of alleles varied 2–6 with an average 3.05. Polymorphism information content varied from 0.002 to 0.989 (mean = 0.308). The number of effective allele (Ne), expected heterozygosity (He) and unbiased expected heterozygosity (uHe) of these EST-SSRs were 1.079–1.753, 0.074–0.428 and 0.074–0.434, respectively. Same 21 EST-SSR markers transferability checked in four other Cucumis species: snapmelon (Cucumis melo var. momordica), muskmelon (Cucumis melo L.), pickling melon (Cucumis melo var. conomon) and wild muskmelon (Cucumis melo var. agrestis) with frequency of 61.9, 95.2, 76.2, and 76.2%, respectively. Present study provides useful information on variability, which can assist geneticists with desirable traits for cucumber germplasm utilization. Observed physiological parameters may assists in selection of genotype for abiotic stress tolerance also, EST-SSR markers may be useful for genetic studies in related species.     

Determination of genetic relationships among elite thermosensitive genic male sterile lines (TGMS) of rice (Oryza sativa L.) employing morphological and simple sequence repeat (SSR) markers

A set of morphological traits and SSR markers were used to determine the genetic relationship among 12 elite thermosensitive genic male sterile (TGMS) lines developed at three different research institutions of India. Agro-morphological data recorded on 20 morphological traits revealed a wide base of genetic variation and a set of four morphological traits could distinguish most of the TGMS lines. Analysis with 30 SSR markers (20 EST-SSRs and 10 genomic SSRs) revealed 27 markers to be polymorphic, amplifying a total of 83 alleles. Each SSR marker amplified 2-6 alleles with an average of 2.76 alleles per marker and a PIC value varying from 0.54 to 0.96. Cluster analysis based on SSR and morphological data clearly differentiated the lines according to their source of origin. Correlation analysis between morphological and molecular data revealed a very poor association (r = 0.06), which could be attributed to selection pressure, genetic drift, sampling error and unknown relationship among related lines. The SSR markers discriminated the genotypes distinctly and quantified the genetic diversity precisely among the TGMS lines. Data on the yield per plant indicated that the genotypes grouping under a similar cluster showed same heterotic behaviour as compared to the genotypes from different clusters when crossed to similar pollinators.     

Agro-Morphological Characterization and Genetic Dissection of Linseed (<i>Linum usitatissimum</i> L.) Genotypes

Linseed is a multipurpose crop and the crop needs further improvement to increase production and yield due to its high value and demand. This study aimed to assess the extent and pattern of genetic variability of forty linseed genotypes based on diverse agro–morphological and yield attributes. The field experiment was conducted following a Randomized Complete Block Design with three replications. Linseed germplasm showed a wide range of phenotypic expression, genetic variability and heritability for 30 studied traits. A low to high phenotypic coeffi- cient of variation (PCV) and genotypic coefficient of variation (GCV) were observed. The lowest genotypic (σ² g) and phenotypic variances (σ² p) were found in capsule diameter (CD), length of calyx (LC), capsule length (CL), seed length (SL), and seed breadth (SB). High broad-sense heritability (h²_b) with high genetic advance as a percentage of mean (GAM) were observed in days to germination started (DGS), days to 80% emergence (DE), plant height at 28 and 40 DAS, number of flowers (NFPP), filled capsules (NFCPP) and yield per plant (YPP) indicating additive gene action exists for these characters. Hierarchical cluster analysis separated 40 genotypes into five clusters, where Clusters I to V assembled with 13, 4, 4, 5 and 14 genotypes, respectively. Considering yield and yield attributes, Cluster-IV (G3, G4, G6, G10 and G31) genotypes showed promising while, Cluster-II (G2, G16, G35, G36) and Cluster-III (G1, G33, G39 and G40) genotypes were dominant on plant morphological traits. Based on principal component analysis (PCA), few characters such as YPP, NFPP, NFCPP, days to first flowering and capsule formation, early emergence, days to branch initiation and plant heights at different growth stages revealed important and effective traits for consideration in the selection of linseed breeding programs.     

Morphological and molecular genetic variations of oat genotypes grown in Kermanshah,Iran

Morphological traits and molecular markers are two common methods for genetic variation studies. Molecular markers, morphological traits methods and relationship between the two were used to study genetic variation among 43 oat genotypes and varieties. For this purpose, an augmented design was conducted in three replicates at 2008–2009 cropping season in the experimental field of Campus of Agriculture and Natural Resources of Razi University, Kermanshah, Iran. Four wild oat accessions (Avena sterilis) were added to evaluated genotypes in molecular experiment. Results showed a significant variation among genotypes for all morphological traits and they were classified based on this variation in four groups by WARD cluster analysis. In molecular experiment, 28 inter simple sequence repeat (ISSR) primers amplified 206 polymorph bands. Based on Jaccard similarity matrix, similarity among genotypes was varied from 0.23 to 0.66 and cluster analysis classified genotypes in seven groups by complete linkage method. The correlation between ISSR marker and morphological traits classifications was not significant. ISSR showed to be a helpful marker for genotype identity and separation as it put wild accessions in a group.     

Contrasting geographic patterns of genetic variation for molecular markers vs. phenotypic traits in the energy grass Miscanthus sinensis

Species and hybrids of Miscanthus are a promising energy crop, but their outcrossing mating systems and perennial life cycles are serious challenges for breeding programs. One approach to accelerating the domestication of Miscanthus is to harness the tremendous genetic variation that is present within this genus using phenotypic data from extensive field trials, high‐density genotyping and sequencing technologies, and rapidly developing statistical methods of relating phenotype to genotype. The success of this approach, however, hinges on detailed knowledge about the population genetic structure of the germplasm used in the breeding program. We therefore used data for 120 single‐nucleotide polymorphism and 52 simple sequence repeat markers to depict patterns of putatively neutral population structure among 244 Miscanthus genotypes grown in a field trial near Aberystwyth (UK) and delineate a population of 145 M . sinensis genotypes that will be used for association mapping and genomic selection. Comparative multivariate analyses of molecular marker and phenotypic data for 17 traits related to phenology, morphology/biomass, and cell wall composition revealed significant geographic patterns in this population. A longitudinal cline accounted for a substantial proportion of molecular marker variation (R² = 0.60, P = 3.4 × 10^?15). In contrast, genetic variation for phenotypic traits tended to follow latitudinal and altitudinal gradients, with several traits appearing to have been affected by divergent selection (i.e., Q_ST >> F_ST). These contrasting geographic trends are unusual relative to other plants and provide opportunities for powerful studies of phenotype–genotype associations and the evolutionary history of M. sinensis.     

Use of morphological traits and microsatellite markers to characterize the Tunisian cultivated and wild figs (Ficus carica L.)

We used 8 morphological traits and 17 simple sequence repeats loci to characterize 71 cultivated and wild Tunisian fig trees (Ficus carica L.). Significant morphological differences were inferred from leaf traits. The statistical analysis showed two major fig groups that indicated a common morphological basis. A total of 74 SSR alleles was revealed, defining 63 unique multilocus genotypes indicating a substantial genetic diversity. Based on multilocus SSR genotypes an identification key was established using MFC30, MFC3, MFC11 and MFC19 loci to identify figs. Analysis of variance components of linkage disequilibrium shown that among 136 pairs of loci, 32 present a significant gametic disequilibrium. The parameter D′²_IS (0.1284) was greater than D′²_ST (0.0079), a pointer of close to zero variance in total simple, and consequently the more pronounced independence of the 17 SSR loci. The majority of Ohta's variance components of linkage disequilibrium followed a pattern caused by genetic drift or a non-systematic disequilibrium profiles and natural selection occurs only for LMFC24-MFC8 pair loci in cultivated figs. Our results suggest that the morphological and SSR markers are suitable to characterize figs and should be recommended in conservation management strategy.     

Genetic analysis of morphological variation in Brassica oleracea using molecular markers

A cross between the open-pollinated Brassica oleracea cabbage cultivar Wisconsin Golden Acre and the hybrid broccoli cultivar Packman was used with molecular markers to investigate the genetic control of morphological variation. Twenty-two traits derived from leaf, stem, and flowering measurements were analyzed in 90 F₂ individuals that were also classified for genotype by restriction fragment length polymorphism (RFLP) markers. Seventy-two RFLP loci, which covered the mapped genome at an average of 10 map-unit intervals on all nine linkage groups, were tested individually for associations to phenotypic measurements by single factor ANOVA, and markers with significant associations (P<0.05) were used to develop multilocus models. These data were utilized to describe the location, parental contribution of alleles, magnitude of effect, and the gene action of trait loci. Single marker loci that were significantly associated (P<0.05) with trait measurements accounted for 6.7–42.7% of the phenotypic variation. Multilocus models described as much as 60.1% of the phenotypic variation for a given trait. In some cases, different related traits had common marker-locus associations with similar gene action and genotypic class ranking. The numbers, action, and linkages, of genes controlling traits estimated with marker loci in this population corresponded to estimates based on classical genetic methods from other studies using similar, or similarly-wide, crosses. There was no evidence that genome duplication accounted for a significant portion of multiple genes controlling trait loci over the entire genome, but possible duplications of trait loci were identified for two regions with linked, duplicated marker loci.     

Genetic diversity of switchgrass and its relative species in Panicum genus using molecular markers

Switchgrass (Panicum virgatum), a warm season C4 grass, is a promising crop for bioenergy-dedicated biomass production. Understanding of genetic diversity within Panicum genus will facilitate switchgrass breeding. Genetic relationships of 22 Panicum species from six continents including ninety-one USDA germplasm accessions were investigated by Sequence-Related Amplified Polymorphism (SRAP) and Expressed Sequence Tags-Simple Sequence Repeat (EST-SSR) markers. Eight hundred and twenty-six markers from 28 pairs of SRAP and 25 pairs of EST-SSR Primers were used to differentiate between accessions of a bulk of 25 genotypes. The results showed that there was high genetic diversity found in Panicum species. Most genetic variation was present among the different species and cluster analysis indicated that all the Panicum accessions could be distinguished by SRAP or EST-SSR. Dendrogram results reflected the phylogenetic relationships between Panicum species and Panicum amarum was found to be the closest species to switchgrass. Comparison between molecular markers revealed that SRAP methods were considered more efficient than EST-SSR for screening Panicum accessions.     

Genetic mapping and QTL analysis of agronomic traits in Indian <Emphasis Type="Italic">Mucuna pruriens</Emphasis> using an intraspecific F<Subscript>2</Subscript> population

Mucuna pruriens is a well-recognized agricultural and horticultural crop with important medicinal use. However, antinutritional factors in seed and adverse morphological characters have negatively affected its cultivation. To elucidate the genetic control of agronomic traits, an intraspecific genetic linkage map of Indian M. pruriens has been developed based on amplified fragment length polymorphism (AFLP) markers using 200 F ₂ progenies derived from a cross between wild and cultivated genotypes. The resulting linkage map comprised 129 AFLP markers dispersed over 13 linkage groups spanning a total distance of 618.88 cM with an average marker interval of 4.79 cM. For the first time, three QTLs explaining about 6.05–14.77% of the corresponding total phenotypic variation for three quantitative (seed) traits and, eight QTLs explaining about 25.96% of the corresponding total phenotypic variation for three qualitative traits have been detected on four linkage groups. The map presented here will pave a way for mapping of genes/QTLs for the important agronomic and horticultural traits contrasting between the parents used in this study.     

Salinity tolerance of Aegilops cylindrica genotypes collected from hyper-saline shores of Uremia Salt Lake using physiological traits and SSR markers

Uremia Salt Lake, in North West Iran, has a hyper-saline water. A rare highly salinity-tolerant grass species, Aegilops cylindrica grows along its shores. Salinity tolerance of 44 genotypes of Ae. cylindrica, mainly collected from the Lake, was evaluated under control and 400 mM NaCl conditions using the physiological traits of plant height, dry weight, proline content, Na⁺ and K⁺ concentrations as well as K⁺/Na⁺ ratio. To evaluate the association between microsatellite (EST-SSR and SSR) markers and salinity tolerance, 35 primer pairs were used. Results showed a significant variation in the 44 genotypes studied in terms of their traits except for proline content. Ten most salinity-tolerant genotypes were identified based on their ability to survive, to produce the highest dry weight, and to sustain the least leaf Na⁺ concentration under salinity stress. The very high negative correlation found between Na⁺ concentration and salinity tolerance revealed the importance of individual or a combination of Na⁺ exclusion and excretion mechanisms contributing to the hyper-salinity tolerance of these genotypes. Clustering analysis based on marker data divided the 44 studied genotypes into two groups that were consistent with their saline and non-saline geographical areas. Results of molecular markers showed that four microsatellite markers (Xgwm312, Xwmc170, Xgwm291 and Xgwm410) generated a distinguished banding pattern in ten most salinity-tolerant genotypes. These results supported previous reports on their linkage with Na⁺ exclusion genes (HKT1;5 and HKT1;4) in wheat, which provided further evidence of usefulness of both genes and the linked markers to the salinity tolerance of the halophytic grass family species.     

Identification of favorable SNP alleles and candidate genes responsible for inflorescence-related traits via GWAS in chrysanthemum

Key message

81 SNPs were identified for three inflorescence-related traits, in which 15 were highly favorable. Two dCAPS markers were developed for future MAS breeding, and six candidate genes were predicted.

Abstract

Chrysanthemum is a leading ornamental species worldwide and demonstrates a wealth of morphological variation. Knowledge about the genetic basis of its phenotypic variation for key horticultural traits can contribute to its effective management and genetic improvement. In this study, we conducted a genome-wide association study (GWAS) based on two years of phenotype data and a set of 92,617 single nucleotide polymorphisms (SNPs) using a panel of 107 diverse cut chrysanthemums to dissect the genetic control of three inflorescence-related traits. A total of 81 SNPs were significantly associated with the three inflorescence-related traits (capitulum diameter, number of ray florets and flowering time) in at least one environment, with an individual allele explaining 22.72–38.67% of the phenotypic variation. Fifteen highly favorable alleles were identified for the three target traits by computing the phenotypic effect values for the stable associations detected in 2 year-long trials at each locus. Dosage pyramiding effects of the highly favorable SNP alleles and significant linear correlations between highly favorable allele numbers and corresponding phenotypic performance were observed. Two highly favorable SNP alleles correlating to flowering time and capitulum diameter were converted to derived cleaved amplified polymorphic sequence (dCAPS) markers to facilitate future breeding. Finally, six putative candidate genes were identified that contribute to flowering time and capitulum diameter. These results serve as a foundation for analyzing the genetic mechanisms underlying important horticultural traits and provide valuable insights into molecular marker-assisted selection (MAS) in chrysanthemum breeding programs.

     

Evaluation of Genetic Diversity and Development of a Core Collection of Wild Rice (Oryza rufipogon Griff.) Populations in China

Common wild rice (Oryza rufipogon Griff.), the progenitor of Asian cultivated rice (O. sativa L.), is endangered due to habitat loss. The objectives of this research were to evaluate the genetic diversity of wild rice species in isolated populations and to develop a core collection of representative genotypes for ex situ conservation. We collected 885 wild rice accessions from eight geographically distinct regions and transplanted these accessions in a protected conservation garden over a period of almost two decades. We evaluated these accessions for 13 morphological or phenological traits and genotyped them for 36 DNA markers evenly distributed on the 12 chromosomes. The coefficient of variation of quantitative traits was 0.56 and ranged from 0.37 to 1.06. SSR markers detected 206 different alleles with an average of 6 alleles per locus. The mean polymorphism information content (PIC) was 0.64 in all populations, indicating that the marker loci have a high level of polymorphism and genetic diversity in all populations. Phylogenetic analyses based on morphological and molecular data revealed remarkable differences in the genetic diversity of common wild rice populations. The results showed that the Zengcheng, Gaozhou, and Suixi populations possess higher levels of genetic diversity, whereas the Huilai and Boluo populations have lower levels of genetic diversity than do the other populations. Based on their genetic distance, 130 accessions were selected as a core collection that retained over 90% of the alleles at the 36 marker loci. This genetically diverse core collection will be a useful resource for genomic studies of rice and for initiatives aimed at developing rice with improved agronomic traits.     

Validation of candidate gene markers for marker-assisted selection of potato cultivars with improved tuber quality

Tuber yield, starch content, starch yield and chip color are complex traits that are important for industrial uses and food processing of potato. Chip color depends on the quantity of reducing sugars glucose and fructose in the tubers, which are generated by starch degradation. Reducing sugars accumulate when tubers are stored at low temperatures. Early and efficient selection of cultivars with superior yield, starch yield and chip color is hampered by the fact that reliable phenotypic selection requires multiple year and location trials. Application of DNA-based markers early in the breeding cycle, which are diagnostic for superior alleles of genes that control natural variation of tuber quality, will reduce the number of clones to be evaluated in field trials. Association mapping using genes functional in carbohydrate metabolism as markers has discovered alleles of invertases and starch phosphorylases that are associated with tuber quality traits. Here, we report on new DNA variants at loci encoding ADP-glucose pyrophosphorylase and the invertase Pain-1, which are associated with positive or negative effect with chip color, tuber starch content and starch yield. Marker-assisted selection (MAS) and marker validation were performed in tetraploid breeding populations, using various combinations of 11 allele-specific markers associated with tuber quality traits. To facilitate MAS, user-friendly PCR assays were developed for specific candidate gene alleles. In a multi-parental population of advanced breeding clones, genotypes were selected for having different combinations of five positive and the corresponding negative marker alleles. Genotypes combining five positive marker alleles performed on average better than genotypes with four negative alleles and one positive allele. When tested individually, seven of eight markers showed an effect on at least one quality trait. The direction of effect was as expected. Combinations of two to three marker alleles were identified that significantly improved average chip quality after cold storage and tuber starch content. In F1 progeny of a single-cross combination, MAS with six markers did not give the expected result. Reasons and implications for MAS in potato are discussed.     

Development of EST-SSR markers through data mining and their use for genetic diversity study in Indian accessions of Jatropha curcas L.: a potential energy crop

Jatropha curcas L. is gaining importance as a potential energy crop. However, lack of sufficient numbers of molecular markers hinder current research on crop improvement in Jatropha. The expressed sequences tags (EST) sequences deposited in public databases, offers an excellent opportunity to identify simple sequence repeats (SSRs) through data mining, for further research on molecular breeding. In the present study 42,477 ESTs of J. curcas were screened, out of which 5,673 SSRs were identified with 48.8 % simple (excluding mononucleotide repeats) and 52.2 % compound repeat motifs. Amongst these repeat motifs, dinucleotide repeats were abundant (26.5 %), followed by trinucleotide (23.1 %) and tetranucleotide repeats (0.8 %). From these microsatellites, 32 EST-SSR (genic microsatellite) primer pairs were designed. These primers were used to analyze the genetic diversity among 42 accessions collected from different parts of India. Out of the 32 EST-SSR primers, 24 primer pairs exhibited polymorphism among the genotypes, with amplicons varying from one to eight, giving an average of 2.33 alleles per polymorphic marker. Polymorphic information content value ranged from 0.02 to 0.5 with an average of 0.402 indicating moderate level of informativeness within these EST-SSRs markers. The EST-SSR markers developed here will serve as a valuable resource for genetic studies, like linkage mapping, diversity analysis, quantitative trait locus/association mapping, and molecular breeding. The current study also revealed low diversity in the screened Indian Jatropha germplasm. Therefore, the future efforts must be made to broaden the gene pool of Jatropha for the creation of genetic diversity that can be further used for crop improvement through breeding.     

Identification of new TRAP markers linked to chlorophyll content, leaf senescence, and cell membrane stability in water-stressed wheat

In order to identify target region amplification polymorphism (TRAP) markers linked to three physiological traits in wheat (Triticum aestivum L.), the segregating F₄ population from the cross between drought-sensitive (Yecora Rojo) and drought-tolerant (Pavon 76) genotypes was made. The parents and 150 F₄ families were evaluated phenotypically for drought tolerance using two irrigation treatments [2.5 and 7.5 m³(H₂O) m^?2(soil)]. Using 40 different TRAP primer combinations tested for polymorphism in parental and F4 family genotypes, the results revealed that quantitative trait locus (QTL) for chlorophyll content was associated with TRAP 5, TRAP 14, and TRAP 20 and explained 18, 16, and 23 % phenotypic variation, respectively. The genetic distance between chlorophyll content QTL and TRAP 5, TRAP 14, and TRAP 20 were 12.3, 19.8, and 13.6 cM, respectively. QTL for flag leaf senescence was associated with TRAP 2, TRAP 3, TRAP 15, and TRAP 16 and explained 33, 27, 28, and 23 % phenotypic variations, respectively. The genetic distance between flag leaf senescence QTL and TRAP 2, TRAP 3, TRAP 15, and TRAP 16 were 9.4, 14.7, 18.1, and 17.3 cM, respectively. QTL for cell membrane stability was associated with TRAP 8, TRAP 9, and TRAP 37 and explained 27, 30, and 24 % phenotypic variation, respectively. The markers TRAP 8, TRAP 9, and TRAP 37 had genetic distances of 17.0, 10.0, and 9.0 cM, respectively. Therefore, these TRAP markers can be used in breeding for drought tolerance in wheat.     

Association mapping of agro-morphological characters among the global collection of finger millet genotypes using genomic SSR markers

Identification of alleles responsible for various agro-morphological characters is a major concern to further improve the finger millet germplasm. Forty-six genomic SSRs were used for genetic analysis and population structure analysis of a global collection of 190 finger millet genotypes and fifteen agro-morphological characters were evaluated. The overall results showed that Asian genotypes were smaller in height, smaller flag leaf length, less basal tiller number, early flowering and early maturity nature, small ear head length, and smaller in length of longest finger. The 46 SSRs yielded 90 scorable alleles and the polymorphism information content values varied from 0.292 to 0.703 at an average of 0.442. The gene diversity was in the range of 0.355 to 0.750 with an average value of 0.528. The 46 genomic SSR loci grouped the 190 finger millet genotypes into two major clusters based on their geographical origin by the both phylogenetic clustering and population structure analysis by STRUCTURE software. Association mapping of QTLs for 15 agro-morphological characters with 46 genomic SSRs resulted in identification of five markers were linked to QTLs of four traits at a significant threshold (P) level of ≤0.01 and ≤0.001. The QTL for basal tiller number was strongly associated with the locus UGEP81 at a P value of 0.001 by explaining the phenotypic variance (R ²) of 10.8 %. The QTL for days to 50 % flowering was linked by two SSR loci UGEP77 and UGEP90, explained 10 and 8.7 % of R ² respectively at a P value of 0.01. The SSR marker, FM9 found to have strong association to two agro-morphological traits, flag leaf width (P—0.001, R ²—14.1 %) and plant height (P—0.001, R ²—11.2 %). The markers linked to the QTLs for above agro-morphological characters found in the present study can be further used for cloning of the full length gene, fine mapping and their further use in the marker assisted breeding programmes for introgression of alleles into locally well adapted germplasm.