scholarly journals Genetic diversity assessment of sorghum (Sorghum bicolor (L.) Moench) accessions using single nucleotide polymorphism markers

2019 ◽  
Vol 17 (5) ◽  
pp. 412-420
Author(s):  
G. Afolayan ◽  
S. P. Deshpande ◽  
S. E. Aladele ◽  
A. O. Kolawole ◽  
I. Angarawai ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Sorghum Bicolor ◽  
Agronomic Traits ◽  
Crop Improvement ◽  
Single Nucleotide ◽  
Breeding Programs ◽  
Diversity Assessment ◽  
Crop Research ◽  
International Crop Research Institute ◽  
Private Alleles

AbstractSorghum (Sorghum bicolor (L.) Moench) is an important resource to the national economy and it is essential to assess the genetic diversity in existing sorghum germplasm for better conservation, utilization and crop improvement. The aim of this study was to evaluate the level of genetic diversity within and among sorghum germplasms collected from diverse institutes in Nigeria and Mali using Single Nucleotide Polymorphic markers. Genetic diversity among the germplasm was low with an average polymorphism information content value of 0.24. Analysis of Molecular Variation revealed 6% variation among germplasm and 94% within germplasms. Dendrogram revealed three groups of clustering which indicate variations within the germplasms. Private alleles identified in the sorghum accessions from National Center for Genetic Resources and Biotechnology, Ibadan, Nigeria and International Crop Research Institute for the Semi-Arid Tropics, Kano, Nigeria shows their prospect for sorghum improvement and discovery of new agronomic traits. The presence of private alleles and genetic variation within the germplasms indicates that the accessions are valuable resources for future breeding programs.

scholarly journals Genetic diversity of released Malaysian rice varieties based on single nucleotide polymorphism markers

2020 ◽  
Vol 56 (No. 2) ◽  
pp. 62-70 ◽  
Author(s):  
Shahril Ab Razak ◽  
Nor Helwa Ezzah Nor Azman ◽  
Rahiniza Kamaruzaman ◽  
Shamsul Amri Saidon ◽  
Muhammad Fairuz Mohd Yusof ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Single Nucleotide Polymorphism ◽  
Crop Improvement ◽  
Snp Markers ◽  
Group Method ◽  
Chromosome 11 ◽  
Nucleotide Polymorphism ◽  
Rice Varieties ◽  
Single Nucleotide ◽  
K Value

Understanding genetic diversity is a main key for crop improvement and genetic resource management. In this study, we aim to evaluate the genetic diversity of the released Malaysian rice varieties using single nucleotide polymorphism (SNP) markers. A total of 46 released Malaysian rice varieties were genotyped using 1536 SNP markers to evaluate their diversity. Out of 1536 SNPs, only 932 SNPs (60.7%) represented high quality alleles, whereas the remainder either failed to amplify or had low call rates across the samples. Analysis of the 932 SNPs revealed that a total of 16 SNPs were monomorphic. The analysis of the SNPs per chromosome revealed that the average of the polymorphic information content (PIC) value ranged from 0.173 for chromosome 12 to 0.259 for chromosome 11, with an average of 0.213 per locus. The genetic analysis of the 46 released Malaysian rice varieties using an unweighted pair group method with arithmetic mean (UPGMA) dendrogram revealed the presence of two major groups. The analysis was supported by the findings from the STRUCTURE analysis which indicated the ∆K value to be at the highest peak at K = 2, followed by K = 4. The pairwise genetic distance of the shared alleles showed that the value ranged from 0.000 (MR159–MR167) to 0.723 (MRIA–Setanjung), which suggested that MR159 and MR167 were identical, and that the highest dissimilarity was detected between MRIA 1 and Setanjung. The results of the study will be very useful for the variety identification, the proper management and conservation of the genetic resources, and the exploitation and utilisation in future breeding programmes.

scholarly journals Importance of Genetic Diversity Assessment in Crop Plants and Its Recent Advances: An Overview of Its Analytical Perspectives

2015 ◽  
Vol 2015 ◽  
pp. 1-14 ◽  
Author(s):  
M. Govindaraj ◽  
M. Vetriventhan ◽  
M. Srinivasan
Keyword(s):  
Genetic Diversity ◽  
Food Production ◽  
Genetic Manipulation ◽  
Plant Genetic Resources ◽  
Crop Improvement ◽  
Genetic Material ◽  
Easy Access ◽  
Production Network ◽  
Gene Banks ◽  
Diversity Assessment

The importance of plant genetic diversity (PGD) is now being recognized as a specific area since exploding population with urbanization and decreasing cultivable lands are the critical factors contributing to food insecurity in developing world. Agricultural scientists realized that PGD can be captured and stored in the form of plant genetic resources (PGR) such as gene bank, DNA library, and so forth, in the biorepository which preserve genetic material for long period. However, conserved PGR must be utilized for crop improvement in order to meet future global challenges in relation to food and nutritional security. This paper comprehensively reviews four important areas; (i) the significance of plant genetic diversity (PGD) and PGR especially on agriculturally important crops (mostly field crops); (ii) risk associated with narrowing the genetic base of current commercial cultivars and climate change; (iii) analysis of existing PGD analytical methods in pregenomic and genomic era; and (iv) modern tools available for PGD analysis in postgenomic era. This discussion benefits the plant scientist community in order to use the new methods and technology for better and rapid assessment, for utilization of germplasm from gene banks to their applied breeding programs. With the advent of new biotechnological techniques, this process of genetic manipulation is now being accelerated and carried out with more precision (neglecting environmental effects) and fast-track manner than the classical breeding techniques. It is also to note that gene banks look into several issues in order to improve levels of germplasm distribution and its utilization, duplication of plant identity, and access to database, for prebreeding activities. Since plant breeding research and cultivar development are integral components of improving food production, therefore, availability of and access to diverse genetic sources will ensure that the global food production network becomes more sustainable. The pros and cons of the basic and advanced statistical tools available for measuring genetic diversity are briefly discussed and their source links (mostly) were provided to get easy access; thus, it improves the understanding of tools and its practical applicability to the researchers.

scholarly journals Genetic diversity assessment of Rice (Oryza sativa L.) germplasm using ssr markers

2015 ◽  
Vol 1 (1) ◽  
pp. 37-46 ◽  
Author(s):  
Ahasanul Hoque ◽  
Shamsun Nahar Begum ◽  
Lutful Hassan
Keyword(s):  
Genetic Diversity ◽  
Ssr Markers ◽  
Oryza Sativa L ◽  
Growth Duration ◽  
Breeding Programs ◽  
Diversity Assessment ◽  
Days To Heading ◽  
Early Maturing ◽  
Rice Genotypes ◽  
Selection Of

Diversity at molecular level among thirty rice genotypes, selected based on earliness and morphometric diversity was evaluated through five SSR markers associated with days to heading. Three primers viz., RM147, RM167 and RM215 showed polymorphism for growth duration related traits. A total of 17 alleles were detected among the 30 rice genotypes with an average of 5.66 alleles per locus. Polymorphism Information Content (PIC) ranged from 0.356 to 0.798 with an average of 0.543. A dendrogram based on total microsatellite polymorphism grouped 30 genotypes into four major clusters at 0.39 similarity coefficient differentiating early maturing genotypes from others. This information about the genetic diversity will be very useful for proper identification and selection of appropriate parents for future breeding programs, including gene mapping. The results also showed that microsatellite markers associated to genes or QTLs controlling growth duration properties are suitable tools for marker assisted selection (MAS) to select rice lines with short growth duration. DOI: http://dx.doi.org/10.3329/ralf.v1i1.22354 Res. Agric., Livest. Fish.1(1): 37-46, Dec 2014

scholarly journals Assessment of Genetic Diversity and Marker-Trait Associations Using Selected Early Maize Inbreds Derived From Local Landraces of Eastern Himalayan Regions

2021 ◽  
Author(s):  
E. Lamalakshmi Devi ◽  
Umakanta Ngangkham ◽  
Akoijam Ratankumar Singh ◽  
Bhuvaneswari S ◽  
Konsam Sarika ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Agronomic Traits ◽  
Crop Improvement ◽  
Mean Value ◽  
Cross Combination ◽  
High Genetic Diversity ◽  
Average Value ◽  
Maize Inbreds ◽  
High Level ◽  
Trait Associations

Abstract North- Eastern parts of India fall under Eastern Himalayan region and it is a diversity hotspot of many crops including maize. Evaluation of genetic diversity is required to tape the potentiality of genetic resources in any crop improvement programmes. In the present study, genetic diversity at fifty two microsatellite markers were conducted in 30 early maize inbreds developed from local landraces of NE India. Genetic diversity analysis revealed a total of 189 alleles with a mean of 3.63 alleles/ locus. The allele size ranged from 50 bp (phi 036) to 295 bp (p 101049) which revealed a high level of genetic diversity among the loci. The PIC among the 30 genotypes ranged from 0.17 (umc 1622) to 0.76 (umc 1153) with an average value of 0.49. The value of Expected Heterozygosity (HExp) ranged from 0.19 to 0.80 with an average of 0.57, whereas the Observed Heterozygosity (HObs) ranged from 0 to 0.89 with a mean of 0.14.The genetic dissimilarity between the genotype pairs ranged from 0.40 to 0.64 with a mean value of 0.57. Cluster analysis grouped the 30 inbreds into distinct three sub-clusters. Similarly, population structure and principal coordinate analysis) analysis also classified the 30 inbred lines into three-subpopulations. AMOVA revealed that 6% of total variance is due to differences among populations, while 94% of total molecular variance is accounted by within populations. Marker-trait associations showed a total of twelve SSR markers significantly associated with seven agronomic traits. From the present finding, these results show that the thirty maize inbreds have high genetic diversity which would be useful for choosing promising parents and for making cross combination based on genetic distance and clustering for genetic improvement programmes of maize.

scholarly journals Identification and Validation of a Core Single-Nucleotide Polymorphism Marker Set for Genetic Diversity Assessment, Fingerprinting Identification, and Core Collection Development in Bottle Gourd

2021 ◽  
Vol 12 ◽  
Author(s):  
Ying Wang ◽  
Xiaohua Wu ◽  
Yanwei Li ◽  
Zishan Feng ◽  
Zihan Mu ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Single Nucleotide Polymorphism ◽  
Snp Markers ◽  
Bottle Gourd ◽  
Snp Marker ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
The Core ◽  
Germplasm Collections ◽  
Diversity Assessment

Germplasm collections are indispensable resources for the mining of important genes and variety improvement. To preserve and utilize germplasm collections in bottle gourd, we identified and validated a highly informative core single-nucleotide polymorphism (SNP) marker set from 1,100 SNPs. This marker set consisted of 22 uniformly distributed core SNPs with abundant polymorphisms, which were established to have strong representativeness and discriminatory power based on analyses of 206 bottle gourd germplasm collections and a multiparent advanced generation inter-cross (MAGIC) population. The core SNP markers were used to assess genetic diversity and population structure, and to fingerprint important accessions, which could provide an optimized procedure for seed authentication. Furthermore, using the core SNP marker set, we developed an accessible core population of 150 accessions that represents 100% of the genetic variation in bottle gourds. This core population will make an important contribution to the preservation and utilization of bottle gourd germplasm collections, cultivar identification, and marker-assisted breeding.

scholarly journals Utilization of Molecular Marker Based Genetic Diversity Patterns in Hybrid Parents to Develop Better Forage Quality Multi-Cut Hybrids in Pearl Millet

Agriculture ◽  
2019 ◽  
Vol 9 (5) ◽  
pp. 97 ◽  
Author(s):  
Govintharaj Ponnaiah ◽  
Shashi Kumar Gupta ◽  
Michael Blümmel ◽  
Maheswaran Marappa ◽  
Sumathi Pichaikannu ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Distance ◽  
Pearl Millet ◽  
Morphological Traits ◽  
Forage Quality ◽  
Genotyping By Sequencing ◽  
Single Nucleotide ◽  
Breeding Programs ◽  
Clear Cut

Genetic diversity of 130 forage-type hybrid parents of pearl millet was investigated based on multiple season data of morphological traits and two type of markers: SSRs (Simple sequence repeats) and GBS identified SNPs (Genotyping by sequencing-Single nucleotide polymorphism). Most of the seed and pollinator parents clustered into two clear-cut separate groups based on marker based genetic distance. Significant variations were found for forage related morphological traits at different cutting intervals (first and second cut) in hybrid parents. Across two cuts, crude protein (CP) varied from 11% to 15%, while in vitro organic matter digestibility (IVOMD) varied from 51% to 56%. Eighty hybrids evaluated in multi-location trial along with their parents for forage traits showed that significant heterosis can be realized for forage traits. A low but positive significant correlation found between SSR based genetic distance (GD between parents of hybrid) and heterosis for most of the forage traits indicated that SSR-based GD can be used for predicting heterosis for GFY, DFY and CP in pearl millet. An attempt was made to associate marker-based clusters with forage quality traits, to enable breeders select parents for crossing purposes in forage breeding programs.

scholarly journals Magnitude of the genetic base of commercial popcorn and in recommendation in Brazil

2010 ◽  
Vol 10 (4) ◽  
pp. 289-297 ◽  
Author(s):  
Thiago Otávio Mendes de Paula ◽  
Leandro Simões Azeredo Gonçalves ◽  
Antonio Teixeira do Amaral Júnior ◽  
Érica Cristina de Oliveira ◽  
Vanessa Quitete Ribeiro da Silva ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Agronomic Traits ◽  
Group Formation ◽  
Distance Matrix ◽  
Molecular Data ◽  
Issr Markers ◽  
Private Institutions ◽  
Final Test ◽  
Breeding Programs ◽  
Public And Private

The purpose of this study was to quantify the genetic diversity among popcorn genotypes on the market and in the final test phase, suitable for three environments in Brazil, based on 11 agronomic traits and ISSR markers. In the environment Campos dos Goytacazes a more reliable group formation was observed than in the other environments. The molecular data indicated the presence of cultivars recommended in the same group, as in the case of UFVM2 Barão de Viçosa, IAC 125, Zélia and Jade. This result is an appeal to the few popcorn breeders in Brazil to pay particular attention to increase the genetic diversity among breeding programs conducted by public and private institutions in the country. There was virtually no correlation between the distance matrix obtained by the ISSR marker and the matrices obtained by the agronomic data.

scholarly journals Genetic dissimilarity among jabuticaba trees native to southwestern Paraná, Brazil

2011 ◽  
Vol 33 (2) ◽  
pp. 517-525 ◽  
Author(s):  
Moeses Andrigo Danner ◽  
Idemir Citadin ◽  
Simone Aparecida Zolet Sasso ◽  
Silvia Scariot ◽  
Giovani Benin
Keyword(s):  
Genetic Diversity ◽  
Mahalanobis Distance ◽  
Agronomic Traits ◽  
High Potential ◽  
Multivariate Techniques ◽  
Fruit Traits ◽  
Breeding Programs ◽  
Canonical Variables ◽  
Genetic Dissimilarity ◽  
Collection Sites

Knowledge on the genetic diversity within and between genotype groups is of great importance for breeding programs. The purpose of this study was to estimate the genetic dissimilarity among 36 native jabuticaba trees (Plinia cauliflora) from five sites in the southwestern region of Paraná, Brazil. Sixteen fruit traits were analyzed, based on multivariate techniques (canonical variables, Tocher and UPGMA), using Mahalanobis' distance as dissimilarity measure. By the techniques of clustering and graphic dispersion, together with the comparison of means, the genetic diversity among native jabuticaba trees was efficiently identified, indicating a high potential of these genotypes for breeding programs. The traits of greatest importance for dissimilarity were percentage of pulp and of skin, which are easily measured. The clustering structure is related to the collection sites and for breeding programs, genotypes from different sites should be crossed to generate progenies to be tested. Genotypes 'CV5' and 'VT3' should be conserved in genebanks, due to its important agronomic traits.

Genetic Diversity Assessment and its Importance on Crop improvement in Ethiopia: Potentials and challenges

2017 ◽  
Vol 23 (1) ◽  
Author(s):  
Obssi Dessalegn Hora ◽  
Abebaw Misganaw Amebaw
Keyword(s):  
Genetic Diversity ◽  
Food Production ◽  
Crop Production ◽  
Plant Genetic Resources ◽  
Crop Improvement ◽  
Genetic Material ◽  
Germplasm Conservation ◽  
Global Perspective ◽  
Easy Access ◽  
Diversity Assessment

Genetic diversity assessments of plant play a great role in a predictable area to improve agricultural production and productivity, to solve food uncertainty in developing world.  Many breeders has tried to  realized that crop with diverge genetic diversity  can be assessed , evaluated ,captured and stored in the form of superior  plant  genetic resources  such as gene bank, DNA library to  preserve genetic material for long period. However, the conserved genetically diversified plant must be utilized to improve crop production in order to solve future food and nutritional challenges. This paper reviews eight important areas; (i) Gaps in Developing Taxonomy of Ethiopian crops (ii) Monitoring diversity for crop improvement, (iii) Alterations in landscape features, (iv) Significance of Germplasm Conservation of crops, (v) Gap in morphological characterization, (vi) Global perspective of agro biodiversity and molecular evolution, (vii) Emergence of tissue culture technology in Ethiopia (viii) Germplasm improvement. It provides basic enlightenment for plant breeders for better understanding and rapid diversity assessment of crop, for better understanding and utilization of germplasm from gene banks to their applied breeding programs. With the advent of new biotechnological techniques, this process of conventional breeding is now being accelerated and carried out with more precision and speedy manner than the classical breeding techniques by using molecular markers to avoid taxonomic confusion. For sustainable food production, conventional plant breeding research should have integration with molecular marker assisted evaluation of crops genetic diversity and/or cultivar improvement will be achieved. As a result, availability and access to diverse genetic sources will ensure that the global food production network becomes more sustainable. The merit and demerit of the basic morphological characterizations are briefly discussed and their source links were provided to get easy access; thus, it improves the understanding of modern molecular tools and its practical applicability to the breeders. 

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