scholarly journals Construction of Soybean Mutant Diversity Pool (MDP) Lines and an Analysis of Their Genetic Relationships and Associations Using TRAP Markers

Agronomy ◽  
2020 ◽  
Vol 10 (2) ◽  
pp. 253 ◽  
Author(s):  
Dong-Gun Kim ◽  
Jae Il Lyu ◽  
Min-Kyu Lee ◽  
Jung Min Kim ◽  
Nguyen Ngoc Hung ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Linear Model ◽  
Agronomic Traits ◽  
Genetic Relationships ◽  
Mixed Linear Model ◽  
Mutation Breeding ◽  
Population Variation ◽  
Phenotypic Traits ◽  
Single Factor Analysis ◽  
Mutant Lines

Mutation breeding is useful for improving agronomic characteristics of various crops. In this study, we conducted a genetic diversity and association analysis of soybean mutants to assess elite mutant lines. On the basis of phenotypic traits, we chose 208 soybean mutants as a mutant diversity pool (MDP). We then investigated the genetic diversity and inter-relationships of these MDP lines using target region amplification polymorphism (TRAP) markers. Among the different TRAP primer combinations, polymorphism levels and polymorphism information content (PIC) values averaged 59.71% and 0.15, respectively. Dendrogram and population structure analyses divided the MDP lines into four major groups. According to an analysis of molecular variance (AMOVA), the percentage of inter-population variation among mutants was 11.320 (20.6%), whereas mutant intra-population variation ranged from 0.231 (0.4%) to 14.324 (26.1%). Overall, intra-population genetic similarity was higher than that of inter-populations. In an analysis of the association between TRAP markers and agronomic traits using three different statistical approaches based on the single factor analysis (SFA), the Q general linear model (GLM), and the mixed linear model (Q+K MLM), we detected six significant marker–trait associations involving five phenotypic traits. Our results suggest that the MDP has great potential for soybean genetic resources and that TRAP markers are useful for the selection of soybean mutants for soybean mutation breeding.

Genetic diversity among Italian melon inodorus (Cucumis melo L.) germplasm revealed by ISSR analysis and agronomic traits

2011 ◽  
Vol 9 (2) ◽  
pp. 214-217 ◽  
Author(s):  
S. Sestili ◽  
A. Giardini ◽  
N. Ficcadenti
Keyword(s):  
Agronomic Traits ◽  
Genetic Relationships ◽  
Molecular Data ◽  
Inter Simple Sequence Repeat ◽  
Phenotypic Traits ◽  
Phenotypic Data ◽  
Morphological And Molecular Data ◽  
And Cluster Analysis ◽  
Almost All ◽  
Issr Primers

The genetic relationships among 13 melon inodorus populations that were collected in southern Italy were assessed using 100 inter-simple-sequence repeat (ISSR) primers and 15 morphological traits. The dihaploid line Nad-1 and the cultivar Charentais-T, both of which belong to the botanical variety cantalupensis, were used as reference accessions in the molecular analysis. A total of 358 polymorphic bands were obtained from 39 of the 100 ISSR primers used, and 15 phenotypic traits were scored and used for genetic-similarity calculations and cluster analysis. The resulting dendrograms based on the ISSR and phenotypic data allowed almost all of the melon genotypes to be distinguished on the basis of the skin colour of the fruits. Mantel's test revealed a good correlation between the morphological and molecular data in their ability to detect genetic relationships among melon ecotypes (r = 0.50, P = 0.99). The data obtained confirm the effectiveness of this approach, and open new perspectives to reveal possible molecular associations with the phenotypic traits analysed.

scholarly journals Characterization of Genetic Diversity in Accessions of Prunus salicina Lindl: Keeping Fruit Flesh Color Ideotype While Adapting to WaterStressed Environments

Agronomy ◽  
2019 ◽  
Vol 9 (9) ◽  
pp. 487 ◽  
Author(s):  
Acuña ◽  
Rivas ◽  
Brambilla ◽  
Cerrillo ◽  
Frusso ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Candidate Genes ◽  
Stress Resistance ◽  
Prunus Persica ◽  
Agronomic Traits ◽  
Phenotypic Traits ◽  
Flesh Color ◽  
Japanese Plum ◽  
Prunus Salicina

The genetic diversity of 14 Japanese plum (Prunus salicina Lindl) landraces adapted to an ecosystem of alternating flooding and dry conditions was characterized using neutral simple sequence repeat (SSR) markers. Twelve SSRs located in six chromosomes of the Prunus persica reference genome resulted to be polymorphic, thus allowing identification of all the evaluated landraces. Differentiation between individuals was moderate to high (average shared allele distance (DAS) = 0.64), whereas the genetic diversity was high (average indices polymorphism information content (PIC) = 0.62, observed heterozygosity (Ho) = 0.51, unbiased expected heterozygosity (uHe) = 0.70). Clustering and genetic structure approaches grouped all individuals into two major groups that correlated with flesh color. This finding suggests that the intuitive breeding practices of growers tended to select plum trees according to specific phenotypic traits. These neutral markers were adequate for population genetic studies and cultivar identification. Furthermore, we assessed the SSR flanking genome regions (25 kb) in silico to search for candidate genes related to stress resistance or associated with other agronomic traits of interest. Interestingly, at least 26 of the 118 detected genes seem to be related to fruit quality, plant development, and stress resistance. This study suggests that the molecular characterization of specific landraces of Japanese plum that have been adapted to extreme agroecosystems is a useful approach to localize candidate genes which are potentially interesting for breeding.

Assessing heat stress tolerance and genetic diversity among exotic and Indian wheat genotypes using simple sequence repeats and agro-physiological traits

2015 ◽  
Vol 15 (3) ◽  
pp. 208-220 ◽  
Author(s):  
K. T. Ramya ◽  
Neelu Jain ◽  
Nikita Gandhi ◽  
Ajay Arora ◽  
P. K. Singh ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Heat Stress ◽  
Stress Tolerance ◽  
Ssr Markers ◽  
Agronomic Traits ◽  
Polymorphic Information Content ◽  
Group Method ◽  
Phenotypic Traits ◽  
Heat Stress Tolerance ◽  
Simple Sequence

Genetic diversity and relationship of 92 bread wheat (Triticum aestivum L.) genotypes from India and exotic collections were examined using simple sequence repeat (SSR) markers and phenotypic traits to identify new sources of diversity that could accelerate the development of improved wheat varieties better suited to meet the challenges posed by heat stress in India. Genetic diversity assessed by using 82 SSR markers was compared with diversity evaluated using five physiological and six agronomic traits under the heat stress condition. A total of 248 alleles were detected, with a range of two to eight alleles per locus. The average polymorphic information content value was 0.37, with a range of 0.04 (cfd9) to 0.68 (wmc339). The heat susceptibility index was determined for grain yield per spike, and the genotypes were grouped into four categories. Two dendrograms that were constructed based on phenotypic and molecular analysis using UPGMA (unweighted pair group method with arithmetic mean) were found to be topologically different. Genotypes characterized as highly heat tolerant were distributed among all the SSR-based cluster groups. This implies that the genetic basis of heat stress tolerance in these genotypes is different, thereby enabling wheat breeders to combine these diverse sources of genetic variability to improve heat tolerance in their breeding programmes.

scholarly journals Genetic associations in the detection of QTLs for wheat spike-related traits

2015 ◽  
Vol 50 (2) ◽  
pp. 149-159 ◽  
Author(s):  
Ljiljana Brbaklić ◽  
Dragana Trkulja ◽  
Ankica Kondić-Špika ◽  
Nikola Hristov ◽  
Srbislav Denčić ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Linear Model ◽  
Gene Diversity ◽  
Polymorphic Information Content ◽  
Association Studies ◽  
Mixed Linear Model ◽  
General Linear ◽  
Genetic Associations ◽  
Trait Associations

The objective of this work was to assess the genetic diversity and population structure of wheat genotypes, to detect significant and stable genetic associations, as well as to evaluate the efficiency of statistical models to identify chromosome regions responsible for the expression of spike-related traits. Eight important spike characteristics were measured during five growing seasons in Serbia. A set of 30 microsatellite markers positioned near important agronomic loci was used to evaluate genetic diversity, resulting in a total of 349 alleles. The marker-trait associations were analyzed using the general linear and mixed linear models. The results obtained for number of allelic variants per locus (11.5), average polymorphic information content value (0.68), and average gene diversity (0.722) showed that the exceptional level of polymorphism in the genotypes is the main requirement for association studies. The population structure estimated by model-based clustering distributed the genotypes into six subpopulations according to log probability of data. Significant and stable associations were detected on chromosomes 1B, 2A, 2B, 2D, and 6D, which explained from 4.7 to 40.7% of total phenotypic variations. The general linear model identified a significantly larger number of marker-trait associations (192) than the mixed linear model (76). The mixed linear model identified nine markers associated to six traits.

scholarly journals The Formation of Test Arrays and a Core Collection in Cucumber Using Phenotypic and Molecular Marker Data

2002 ◽  
Vol 127 (4) ◽  
pp. 558-567 ◽  
Author(s):  
Jack E. Staub ◽  
Fenny Dane ◽  
Kathleen Reitsma ◽  
Gennaro Fazio ◽  
Anabel López-Sesé
Keyword(s):  
Genetic Diversity ◽  
Heat Stress ◽  
Disease Resistance ◽  
Downy Mildew ◽  
Core Collection ◽  
Genetic Relationships ◽  
Population Variation ◽  
Fruit Rot ◽  
Plant Introductions ◽  
The Core

Genetic relationships among 970 cucumber (Cucumis sativus L.) plant introductions (PIs) in the U.S. National Plant Germplasm System (NPGS) were assessed by observing variation at 15 isozyme loci. Allozyme frequency data for these PIs were compared to allozyme variation in heirloom and modern (H&M) cultivars released from 1846-1985 (H&M cultivars; 178 accessions), and experimental commercial (EC) germplasm (EC germplasm; 82 accessions) in use after 1985. Multivariate analysis defined four distinct groups of accessions (Groups A-D), where Group A consisted of PIs received by the NPGS before 1992, Group B contained PIs from India and China obtained by NPGS after 1992, Group C consisted of EC germplasm, and Group D contained H&M cultivars. Morphological, abiotic stress (water and heat stress tolerance) and disease resistance evaluation data from the Germplasm Resources Information Network (GRIN) for the PIs examined were used in conjunction with estimates of population variation and genetic distance estimates to construct test arrays and a core collection for cucumber. Disease resistance data included the evaluation of angular leafspot [Pseudomonas lachrymans (E.F. Smith) Holland], anthracnose [Colletotrichum lagenarium (Ross.) Ellis & Halst], downy mildew [Pseudoperonospora cubensis (Berk. & Curt) Rostow], rhizoctonia fruit rot (Rhizoctonia solani Kuhn), and target leafspot [Corynespora cassiicola (Berk. & Curt) Wei] pathogenicity. The test arrays for resistance-tolerance to angular leafspot, anthracnose, downy mildew, rhizoctonia fruit rot, target leafspot, and water and heat stress consisted of 17, 16, 17, 16, 17, 16, and 16 accessions, respectively. The core collection consisted of accessions in these test arrays (115) and additional 32 accessions that helped circumscribe the genetic diversity of the NPGS collection. The core collection of 147 accessions (115 + 32) represents ≈11% of the total collection's size (1352). Given estimates of genetic diversity and theoretical retention of diversity after sampling, this core collection could increase curatorial effectiveness and the efficiency of end-users as they attempt to identify potentially useful germplasm.

scholarly journals Assessment of the genetic diversity and population structure of groundnut germplasm collections using phenotypic traits and SNP markers: Implications for drought tolerance breeding

PLoS ONE ◽  
2021 ◽  
Vol 16 (11) ◽  
pp. e0259883
Author(s):  
Seltene Abady ◽  
Hussein Shimelis ◽  
Pasupuleti Janila ◽  
Shasidhar Yaduru ◽  
Admire I. T. Shayanowako ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Drought Tolerance ◽  
Agronomic Traits ◽  
Snp Markers ◽  
Phenotypic Traits ◽  
Environment Interaction ◽  
Optimum Conditions ◽  
Pod Yield ◽  
Germplasm Collections

Profiling the genetic composition and relationships among groundnut germplasm collections is essential for the breeding of new cultivars. The objectives of this study were to assess the genetic diversity and population structure among 100 improved groundnut genotypes using agronomic traits and high-density single nucleotide polymorphism (SNP) markers. The genotypes were evaluated for agronomic traits and drought tolerance at the International Crop Research Institute for the Semi-Arid Tropics (ICRISAT)/India across two seasons. Ninety-nine of the test genotypes were profiled with 16363 SNP markers. Pod yield per plant (PY), seed yield per plant (SY), and harvest index (HI) were significantly (p < 0.05) affected by genotype × environment interaction effects. Genotypes ICGV 07222, ICGV 06040, ICGV 01260, ICGV 15083, ICGV 10143, ICGV 03042, ICGV 06039, ICGV 14001, ICGV 11380, and ICGV 13200 ranked top in terms of pod yield under both drought-stressed and optimum conditions. PY exhibited a significant (p ≤ 0.05) correlation with SY, HI, and total biomass (TBM) under both test conditions. Based on the principal component (PC) analysis, PY, SY, HSW, shelling percentage (SHP), and HI were allocated in PC 1 and contributed to the maximum variability for yield under the two water regimes. Hence, selecting these traits could be successful for screening groundnut genotypes under drought-stressed and optimum conditions. The model-based population structure analysis grouped the studied genotypes into three sub-populations. Dendrogram for phenotypic and genotypic also grouped the studied 99 genotypes into three heterogeneous clusters. Analysis of molecular variance revealed that 98% of the total genetic variation was attributed to individuals, while only 2% of the total variance was due to variation among the subspecies. The genetic distance between the Spanish bunch and Virginia bunch types ranged from 0.11 to 0.52. The genotypes ICGV 13189, ICGV 95111, ICGV 14421, and ICGV 171007 were selected for further breeding based on their wide genetic divergence. Data presented in this study will guide groundnut cultivar development emphasizing economic traits and adaptation to water-limited agro-ecologies, including in Ethiopia.

scholarly journals Genetic Diversity among Lathyrus ssp. Based on Agronomic Traits and Molecular Markers

Agronomy ◽  
2020 ◽  
Vol 10 (8) ◽  
pp. 1182 ◽  
Author(s):  
Meriem Miyassa Aci ◽  
Antonio Lupini ◽  
Giuseppe Badagliacca ◽  
Antonio Mauceri ◽  
Emilio Lo Presti ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Molecular Markers ◽  
Protein Content ◽  
Structure Analysis ◽  
Agronomic Traits ◽  
Gene Diversity ◽  
Polymorphic Information Content ◽  
Phenotypic Traits ◽  
Principal Coordinates Analysis ◽  
Principal Coordinates

Grasspea (Lathyrus sativus L.) and its relatives are considered resilient legumes due to their high ability to cope with different stresses. In this study, the genetic diversity of three Lathyrus species (L. sativus, L cicera and L. ochrus) was assessed by agronomic traits and molecular markers (Simple Sequence Repeat-SSR) in order to detect accessions useful for future breeding strategies. Phenotypic traits showed a high significant variation in which 1000 seed weight (1000 SW) and protein content appeared the most discriminant, as observed by principal component analysis (PCA). SSR analysis was able to detect forty-eight different alleles with an average of 9.6 allele per locus, and a Polymorphic Information Content (PIC) and a gene diversity of 0.745 and 0.784, respectively. Cluster analysis based on agronomic traits as well as molecular data grouped accessions by species but not by geographical origin. This result was confirmed by Principal Coordinates Analysis (PCoA) and Structure Analysis as well. Moreover, genetic structure analysis revealed a high genetic differentiation between L. ochrus and the other species. Analysis of MOlecular Variance (AMOVA) displayed a greater genetic diversity within species (77%) than among them (23%). Finally, a significant positive correlation was observed between agronomic and genetic distances (Mantel’s test). In conclusion, the variability detected within accessions in each species and the differences among species may be useful to plan next breeding programs, focusing on biomass production as well as protein content.

scholarly journals Identification of Novel Marker–Trait Associations for Lint Yield Contributing Traits in Upland Cotton (Gossypium hirsutum L.) Using SSRs

2021 ◽  
Vol 12 ◽  
Author(s):  
Pawan Kumar ◽  
Somveer Nimbal ◽  
Rajvir Singh Sangwan ◽  
Neeraj Budhlakoti ◽  
Varsha Singh ◽  
...  
Keyword(s):  
Gossypium Hirsutum ◽  
Linear Model ◽  
Agronomic Traits ◽  
Crop Improvement ◽  
Mixed Linear Model ◽  
Lint Yield ◽  
Cotton Crop ◽  
Significant Marker ◽  
Improvement Programs ◽  
Trait Associations

Improving the yield of lint is the main objective for most of the cotton crop improvement programs throughout the world as it meets the demand of fiber for textile industries. In the current study, 96 genotypes of Gossypium hirsutum were used to find novel simple sequence repeat marker-based associations for lint yield contributing traits by linkage disequilibrium. Extensive phenotyping of 96 genotypes for various agronomic traits was done for two consecutive years (2018 and 2019) in early, normal, and late sown environments. Out of 168 SSR markers screened over the 96 genotypes, a total of 97 polymorphic markers containing 293 alleles were used for analysis. Three different models, i.e., mixed linear model (MLM), compressed mixed linear model (CMLM), and multiple locus mixed linear model (MLMM), were used to detect the significant marker–trait associations for six different environments separately. A total of 38 significant marker–trait associations that were common to at least two environments were considered as promising associations and detailed annotation of the significant markers has been carried out. Twenty-two marker–trait associations were found to be novel in the current study. These results will be very useful for crop improvement programs using marker-assisted cotton breeding.

scholarly journals Genetic Diversity among Isolates of Phytophthora sojae in Anhui Province of China based on ISSR-PCR Markers

2018 ◽  
Vol 143 (4) ◽  
pp. 304-309 ◽  
Author(s):  
Dong Liu ◽  
Ping Li ◽  
Jiulong Hu ◽  
Kunyuan Li ◽  
Zhenyu Zhao ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
Genetic Differentiation ◽  
Genetic Relationships ◽  
Inter Simple Sequence Repeat ◽  
Phytophthora Sojae ◽  
Anhui Province ◽  
Population Variation ◽  
Spatial Distance ◽  
Similarity Coefficients

To explore genetic differentiation and the genetic relationships of Phytophthora sojae in Anhui Province, the inter-simple sequence repeat (ISSR) technique was used to analyze the genetic diversity of P. sojae. One hundred and sixty ISSR fragments were observed, including 129 (80.6%) polymorphic bands. This suggested that abundant genetic diversity existed among P. sojae in Anhui Province. The pairwise genetic similarity coefficients among the 62 strains ranged from 0.72 to 0.96, with a mean value of 0.85, indicating that there was a high level of genetic variation. Phytophthora sojae strains were divided into five clusters based on neighbor-joining (NJ) analysis, and the clustering was not related to geographic source, according to Mantel’s test (r = 0.3938). In addition, the clustering of strains from the same geographical source had little relationship to the year of collection. Analysis of molecular variance (AMOVA) showed that 16.65% of the genetic variation was derived from the collection area and 83.35% of the genetic variation was within-population variation. The genetic flow between different geographical sources ranged from 0.623 to 2.773, with a mean of 1.325, suggesting that gene exchange was frequent. Genetic distance and the genetic differentiation coefficient were not related to spatial distance.

scholarly journals ​Binasoybean-6: A High Yielding Mutant Soybean Variety Developed through Sustainable Mutation Breeding

2022 ◽  
Author(s):  
M.A. Malek ◽  
R.M. Emon ◽  
M.K. Khatun ◽  
M.S.H. Bhuiyan ◽  
Adedze Yawo Mawunyo Nevame ◽  
...  
Keyword(s):  
Gamma Rays ◽  
Agronomic Traits ◽  
Insect Pests ◽  
Mutation Breeding ◽  
Superior Performance ◽  
Food Protein ◽  
Soybean Variety ◽  
Ecological Zones ◽  
Commercial Cultivation ◽  
Mutant Lines

Background: Soybean is an important source of food, protein and oil and hence more research is essential to increase its yield under different agro-ecological conditions, including stress. In this regard, four popular soybean varieties viz. Shohag, BDS-4, BAU-S/64 and BARI Soybean-5 were irradiated using Co60 gamma rays to create genetic variation for earliness, higher seed yield and other desirable agronomic traits. Methods: The experiments were conducted at Bangladesh Institute of Nuclear Agriculture (BINA) Headquarters farm, Mymensingh during 2006-2009 and 28 elite mutant lines were selected for evaluation. The mutant line, SBM-22 derived from mother variety BARI Soybean-5 irradiated with 300Gy of gamma rays was found to be superior compared to other mutants. Considering the superior performance of mutant SBM-22 including 28 mutants and mother check variety BARI Soybean-5, were evaluated through different trials. The evaluation trials were conducted at different agro-ecological zones of the country during Rabi season (January to April) of 2010-2018. Result: Significant variations were observed both in individual location and over locations for all traits. Reactions to major diseases and insect-pests infestation were also studied. Due to better performance of the mutant SBM-22, Bangladesh Institute of Nuclear Agriculture (BINA) applied to the National Seed Board (NSB) of Bangladesh for registration as an important soybean variety “Binasoybean-6”. Consequently, the NSB of Bangladesh registered SBM-22 as an improved soybean variety in 2019 as Binasoybean-6 for commercial cultivation.

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