Assessment of the Genetic Structure and Diversity of Soybean (Glycine max L.) Germplasm Using Diversity Array Technology and Single Nucleotide Polymorphism Markers (original) (raw)
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Research Square (Research Square), 2022
Soybean (Glycine max (L.) is an important oil crop with production below the real need in Africa. To increase the production, substantial upgrading must be accomplished by enlarging the genetic potential of new cultivars that relays on the parents' genetic diversity. We aimed to assess the genetic diversity and the population structure of soybean accessions, therefore, evaluate soybean value in terms of use for breeding purposes. To accomplish this, a set of 282 soybean accessions were genotyped using the Diversity Array Technology Sequencing with a high throughput of the Single-nucleotide polymorphisms (SNPs). A total of 6,935 high-quality SNPs were identi ed across the whole soybean genome. The mean value of genetic diversity, major alleles frequency, minor alleles frequency, expected heterozygosity, and the polymorphism information content was respectively estimated at 0.35, 0.77, 0.22, 0.33, and 0.29. The analysis of molecular variance reveals that the variance among the populations is lower than the variance within the populations. The soybean accessions could be classi ed into two groups based on the model-based population structure and the principal coordinate analysis or into three groups based on the discriminant analysis of the principal component and the Neighbor-joining tree. The information provided in this study will be helpful for breeders.
Global Journal of Science Frontier Research, 2020
Soybean (Glycine max (L.) Merrill) is among the most important crops worldwide due to its numerous uses in feed, food, biofuel, and significant atmospheric nitrogen fixation capability. To understand the genetic diversity and population structure of tropical soybean germplasm, 89 genotypes from diverse sources were analyzed using 7,962 SNP markers. The AMOVA results showed low diversity among and high within the populations, while the polymorphism information content (PIC) was 0.27. Both phylogenetic and principal component analysis grouped the 89 soybean genotypes into three major clusters, while population structure grouped the soybean genotypes into two subpopulations. On the other, the average Roger genetic distances within the study population was 0.34.The low diversity reported in the studied soybean germplasm pool is particularly worrying, considering the new trends of climate change and the emergence of new pests and diseases of soybean. Therefore, in order to address these ...
PLOS ONE
Soybean (Glycine max) is an important legume that is used to fulfill the need of protein and oil of large number of population across the world. There are large numbers of soybean germplasm present in the USDA germplasm resources. Finding and understanding genetically diverse germplasm is a top priority for crop improvement programs. The current study used 20 functional EST-SSR and 80 SSR markers to characterize 96 soybean accessions from diverse geographic backgrounds. Ninety-six of the 100 markers were polymorphic, with 262 alleles (average 2.79 per locus). The molecular markers had an average polymorphic information content (PIC) value of 0.44, with 28 markers ≥ 0.50. The average major allele frequency was 0.57. The observed heterozygosity of the population ranged from 0–0.184 (average 0.02), while the expected heterozygosity ranged from 0.20–0.73 (average 0.51). The lower value for observed heterozygosity than expected heterozygosity suggests the likelihood of a population struc...
Agricultural Research, 2019
Genetic diversity among 45 genotypes of soybean (Glycine max (L.) Merr.) was assessed based on qualitative traits and 36 microsatellite markers. Forty-five genotypes were characterized for eleven morphological traits: leaf shape, leaf intensity of green colour, leaf size of lateral leaflet, plant growth habit, variation in hilum colour, cotyledon/flower colour, hairiness, hair colour, pod colour, testa colour and seed shape. Principal component analysis revealed that genotypes, namely JS-95-60, JS-20-103, JS20-69, JS-20-114, JS-20-49 and JS-335, were diverged from each other, and the range of polymorphic information content for microsatellite markers was 0.018-0.580. With 27 polymorphic SSR markers, a total of 71 alleles were amplified with an average of 1.97 alleles per locus. Eleven alleles were found to be unique to 45 genotypes. Soybean genotypes distributed in two clusters revealed diverse genetic background. Overall, the present study paves the way for better characterization of soybean genotypes and confirms India as one of the important centres of soybean domestication containing valuable genetically important assets for soybean improvement.
Genetics and molecular research : GMR, 2017
The genetic diversity study has paramount importance in breeding programs; hence, it allows selection and choice of the parental genetic divergence, which have the agronomic traits desired by the breeder. This study aimed to characterize the genetic divergence between 24 soybean genotypes through their agronomic traits, using multivariate clustering methods to select the potential genitors for the promising hybrid combinations. Six agronomic traits evaluated were number of days to flowering and maturity, plant height at flowering and maturity, insertion height of the first pod, and yield. The genetic divergence evaluated by multivariate analysis that esteemed first the Mahalanobis' generalized distance (D(2)), then the clustering using Tocher's optimization methods, and then the unweighted pair group method with arithmetic average (UPGMA). Tocher's optimization method and the UPGMA agreed with the groups' constitution between each other, the formation of eight distin...
IOP Conference Series: Earth and Environmental Science
Genetic diversity on soybean germplasm will determine the success of the soybean breeding program. The purpose of this research was to study the diversity of Indonesian soybean (Glycine max L. Merrill) germplasm based on agronomic traits and microsatellite markers in order to know the genetic relationship among the accessions. Genetic material used was 45 soybean accessions consisting of 14 genotypes introduced from nine countries, 26 landrace from 10 provinces in Indonesia, and five Indonesian high yield varieties. Morphological characterization performed on nine qualitative and four quantitative traits. The genetic relationships were estimated using three SSR markers. The results showed that cluster analysis based on agronomic traits clearly separate the soybean accessions of black seeds into one group with genetic distance range from 0.61 to 1. Other groups for accessions with yellow, green-yellowish and brown seed have genetic distance ranging from 0.46 to 1. Based on microsatellite markers, three primers showed polymorphism banding pattern. The number of alleles that are formed these three primers between four and five alleles with sizes ranged from 200 bp to 800 bp. Cluster analysis based on microsatellites markers showed that the genetic distance of 45 accessions ranged from 0.61 to 1.
Genetic Diversity Studies in Soybean [Glycine max (L.)Merrill] Genotypes
Genetic diversity among 20 soybean genotypes was worked out using Mahalanobis D 2 statistic. On the basis of genetic distance, the twenty genotypes were grouped into 5 clusters. Out of the 20 genotypes cluster II has the highest genotypes (9) followed by cluster III (4), cluster I and cluster IV (3 each) and cluster V had 1 genotype. The inter cluster divergence was observed to be highest between Cluster I and Cluster IV indicating that these two clusters were genetically diverse. Hence, the genotypes of Cluster I and Cluster IV could be utilized in hybridization program to achieve greater variability in the segregating generations. Among the different characters studied test weight followed by plant height, number of pods per plant and days to 50% flowering contributed maximum towards divergence.
International Journal of Chemical Studies, 2019
An experiment was conducted to assess the genetic diversity in soybean using Simple Sequence Repeat (SSR) diversity of 24 elite soybean genotypes were selected for high yield potential. The four primers showed reliable polymorphism produced a total of 92 bands of which 68 (75%) were polymorphic. Genetic similarity estimates based on simple matching coefficients revealed more genetic diversity among all the 24 elite lines, ranging from 0.143 to 1 indicating the distinctness of these genotypes under study. The dendrogram constructed using the UPGMA method separated these genotypes in two main groups each having two sub groups. The study also demonstrates high reliability, ease of applicability and importance of SSR markers in evaluating genetic variation among the genotypes of soybean.
Evaluation of Genetic Diversity in Different Genotypes of Soybean (Glycine max (L.) Merrill
Genotypic variations of twenty eight soybean genotypes were evaluated in a randomized complete block design during Rabi season, 2011 at Sher-e-Bangla Agricultural University, Bangladesh. The phenotypic variance was higher than the corresponding genotypic variance for most of the characters. High heritability coupled with high genetic advance was recorded for number of branches per plant, plant height, number of seeds per plant, number of pods per plant and 100-seed weight. This indicates the effectiveness of selection to improve these five characters. Plant height, pod length, number of seeds per pod, number of pods per plant, hundred seed weight, branches per plant, and number of seeds per pod showed significant positive correlation with seed yield. Based on inter genotypic distances F-85-11347, Australia, 86017-66-6, PK-327, MTD-452, Shohag, MTD-16, YESOY-4 are important for varietal improvement of soybean genotypes. Considering genetic variability, heritability and correlation analysis, emphasis should be given on traits during phenotypic selection and inter genotypic distances for genotypic selection for developing high yielding genotypes of soybean.
Genetic diversity analysis of soybean (Glycine max (L.) Merr.) genotypes making use of SSR markers
Australian Journal of Crop Science
In this study, we aimed to investigate the genetic diversity and polymorphism among 30 soybean genotypes maintained by the ARC using simple sequence repeat (SSR) markers. Soybean genotypes were characterized using 20 SSR primers. DNA was extracted using the standard cetyl trimethylammonium bromide method and amplified using PCR. Allele size was determined via comparison with a 100 base pair (bp) DNA ladder. Molecular data were analyzed, and a dendrogram and matrix were generated using GGT 2.0 software. A total of 216 alleles with an average of 10.8 alleles per locus were detected. The allele sizes ranged between 2 and 33 bp with an average of 18.7 bp. The polymorphic information content among genotypes varied from 0.85 (Satt001) to 0.75 (Satt43) with an average of 0.716, and heterozygosity ranged from 0.87 to 0.78 with an average of 0.7485. The most diverse genotypes were B 66 S 31, 69S 7, and R5-4-2 M, which indicated the efficiency of the SSR markers for the detection of genetic d...