scholarly journals GENETIC DIVERSITY ASSOCIATED WITH AGRONOMIC TRAITS AND BIOTIC STRESSES USING SSR MARKERS IN SOME EGYPTIAN RICE GENOTYPES

2011 ◽  
Vol 2 (1) ◽  
pp. 109-126
Author(s):  
Y. El-Refaee ◽  
S. Sedeek ◽  
R. El-Shafey ◽  
B. Zayed
Keyword(s):  
Genetic Diversity ◽  
Ssr Markers ◽  
Agronomic Traits ◽  
Biotic Stresses ◽  
Rice Genotypes

scholarly journals Assessment of Genetic Diversity Among Intra- and Interspecific Lowland Rice using Morpho-agronomic Traits and SSR Markers

2021 ◽  
Author(s):  
Ayoni Ogunbayo ◽  
Moussa Sié ◽  
Glenn B. Gregorio ◽  
David Kolawole Ojo ◽  
Kayode Abiola Sanni ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Total Variation ◽  
Ssr Markers ◽  
Agronomic Traits ◽  
Structured Populations ◽  
Lowland Rice ◽  
Oryza Glaberrima ◽  
Environment Interaction ◽  
Rice Genotypes ◽  
Benin Republic

Abstract Rice is staple food in many countries of Africa and a major part of the diet in many others. However, Africa’s demand for rice exceeds production with the deficit of 40% being imported. One way to improve Africa’s rice production is through breeding high yielding varieties suitable for the different environment conditions. This study was conducted to assess the genetic variability and stability performance of 48 lowland rice genotypes including 37 interspecific (Oryza glaberrima × Oryza sativa ssp. indica) and 11 intraspecific (O. sativa ssp. indica × O. sativa ssp. indica) in 12 environments in Nigeria, Benin Republic and Togo using Additive Main Effect and Multiplicative Interaction (AMMI) and Genotype+ Genotype x Environment (GGE) biplot models. The combined analysis of variance revealed significant differences (P<0.01) among the genotypes, environments, and genotypes x environment interaction. Both the AMMI and GGE models identified NERICA-L8 and NERICA-LI2 as the best genotypes for cultivation across environments. Ouedeme environments in Benin Republic were the most stable and ideal for rice cultivation, while Ibadan sites were the most unstable. TOG 5681 had the least yield and was the most unstable across seasons. Genetic diversity was analyzed using 22 important morpho-agronomic traits and 50 simple sequence repeat (SSR) markers and the results were subjected to principal components analysis (PCA). The results revealed that the first eight PC axes (PC1–8) accounted for 75.13% of the total variation, while PC1–4 accounted for 50.39% of the total variation among rice genotypes. However, 10 of the 50 SSR markers were polymorphic and generated 49 alleles (average = 4.9 alleles per locus), suggesting moderate to substantial genetic diversity among the rice genotypes. The polymorphic information content (PIC) ranged from 0.24 to 0.65, with an average PIC value of 0.45. Two structured populations were observed which clustered into five heterotic groups and an outgroup, respectively. This suggests that heterosis could be exploited in the next hybridization program by crossing one of the genotypes in any SSR marker-defined cluster, with the rice accession TOG 5681 in cluster I. The results of this study suggest that morpho-agronomic traits should be used to compliment SSR data in rice diversity studies, especially if a few polymorphic SSR markers are to be used.

scholarly journals Genetic Diversity of Selected Rice Genotypes under Water Stress Conditions

Plants ◽  
2020 ◽  
Vol 10 (1) ◽  
pp. 27
Author(s):  
Mahmoud M. Gaballah ◽  
Azza M. Metwally ◽  
Milan Skalicky ◽  
Mohamed M. Hassan ◽  
Marian Brestic ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Water Stress ◽  
Drought Stress ◽  
Drought Tolerance ◽  
Ssr Markers ◽  
Similarity Index ◽  
Stress Conditions ◽  
Yield Potential ◽  
Drought Tolerant ◽  
Rice Genotypes

Drought is the most challenging abiotic stress for rice production in the world. Thus, developing new rice genotype tolerance to water scarcity is one of the best strategies to achieve and maximize high yield potential with water savings. The study aims to characterize 16 rice genotypes for grain and agronomic parameters under normal and drought stress conditions, and genetic differentiation, by determining specific DNA markers related to drought tolerance using Simple Sequence Repeats (SSR) markers and grouping cultivars, establishing their genetic relationship for different traits. The experiment was conducted under irrigated (normal) and water stress conditions. Mean squares due to genotype × environment interactions were highly significant for major traits. For the number of panicles/plants, the genotypes Giza179, IET1444, Hybrid1, and Hybrid2 showed the maximum mean values. The required sterility percentage values were produced by genotypes IET1444, Giza178, Hybrid2, and Giza179, while, Sakha101, Giza179, Hybrid1, and Hybrid2 achieved the highest values of grain yield/plant. The genotypes Giza178, Giza179, Hybrid1, and Hybrid2, produced maximum values for water use efficiency. The effective number of alleles per locus ranged from 1.20 alleles to 3.0 alleles with an average of 1.28 alleles, and the He values for all SSR markers used varied from 0.94 to 1.00 with an average of 0.98. The polymorphic information content (PIC) values for the SSR were varied from 0.83 to 0.99, with an average of 0.95 along with a highly significant correlation between PIC values and the number of amplified alleles detected per locus. The highest similarity coefficient between Giza181 and Giza182 (Indica type) was observed and are susceptible to drought stress. High similarity percentage between the genotypes (japonica type; Sakha104 with Sakha102 and Sakha106 (0.45), Sakha101 with Sakha102 and Sakha106 (0.40), Sakha105 with Hybrid1 (0.40), Hybrid1 with Giza178 (0.40) and GZ1368-S-5-4 with Giza181 (0.40)) was also observed, which are also susceptible to drought stress. All genotypes are grouped into two major clusters in the dendrogram at 66% similarity based on Jaccard’s similarity index. The first cluster (A) was divided into two minor groups A1 and A2, in which A1 had two groups A1-1 and A1-2, containing drought-tolerant genotypes like IET1444, GZ1386-S-5-4 and Hybrid1. On the other hand, the A1-2 cluster divided into A1-2-1 containing Hybrid2 genotype and A1-2-2 containing Giza179 and Giza178 at coefficient 0.91, showing moderate tolerance to drought stress. The genotypes GZ1368-S-5-4, IET1444, Giza 178, and Giza179, could be included as appropriate materials for developing a drought-tolerant variety breeding program. Genetic diversity to grow new rice cultivars that combine drought tolerance with high grain yields is essential to maintaining food security.

scholarly journals Genetic diversity of cucumber genotypes revealed by SSR markers and agronomic traits

Genetika ◽  
2019 ◽  
Vol 51 (2) ◽  
pp. 405-416
Author(s):  
Kalidas Pati ◽  
Das Munshi ◽  
Manjusha Verma ◽  
Kanti Behera ◽  
Lalit Arya
Keyword(s):  
Genetic Diversity ◽  
Ssr Markers ◽  
Agronomic Traits

Assessment of the genetic diversity and population structure of rice genotypes using SSR markers

2019 ◽  
Vol 70 (1) ◽  
pp. 76-86 ◽  
Author(s):  
William Titus Suvi ◽  
Hussein Shimelis ◽  
Mark Laing ◽  
Isack Mathew ◽  
Admire Isaac Tichafa Shayanowako
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Ssr Markers ◽  
Rice Genotypes

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 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 diversity by using morphological, biochemical and molecular approaches of selected basmati rice (Oryza sativa L.) varieties

2016 ◽  
Vol 8 (1) ◽  
pp. 69-76 ◽  
Author(s):  
A. Mishra ◽  
Pradeep Kumar ◽  
R. S. Sengar ◽  
P. Kumar ◽  
R. Singh ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Ssr Markers ◽  
Molecular Analysis ◽  
Oryza Sativa L ◽  
Quality Parameters ◽  
Basmati Rice ◽  
Molecular Approaches ◽  
Gel Consistency ◽  
Rice Genotypes ◽  
Selection Of

The study investigates the genetic diversity among the Basmati rice genotypes. Selected nine Basmati rice genotypes were studied for twelve morphological traits, biochemical parameters and for molecular analysis with 11 SSR markers. Pusa Sugandha 5 and Basmati 370, showed strong aroma while other varieties showed medium aroma. Alkali spreading value were intermediate in Basmati 386, Vallabh Basmati 22 and Vallabh Basmati 24 while other varieties showed high values. Pusa Basmati 1 and Basmati 386 showed soft category of gel consistency while in rest varieties it was under medium category. Amylose percentage in grains were ranged from 18.02% (Taraori basmati) to 22.0% (Basmati370). Molecular analysis with 11 SSR markers showed 125 allels with an average number of allels 11.36 per locus. All the markers showed specific type of banding pattern along with 82 polymorphic allels in different genotypes. This study focuses on application of statistical methods and techniques in analysis of genetic diversity of the agronomic data, biochemical aspects related to quality parameters and at the molecular level using SSR markers for clustering procedure making dendrogram that helps the more accurate selection of the superior basmati genotypes for the further studies of the breeders and researchers.

scholarly journals Similarity of 26 New Released Rice Varieties and Rice Parental Hybrids Based on 36 SSR Markers

2014 ◽  
Vol 33 (2) ◽  
pp. 71
Author(s):  
Untung Susanto ◽  
Satoto Satoto ◽  
Nofi A. Rohmah ◽  
Made Jana Mejaya
Keyword(s):  
Genetic Diversity ◽  
Phylogenetic Analysis ◽  
Ssr Markers ◽  
Rice Varieties ◽  
Average Value ◽  
Modified Method ◽  
Rice Chromosomes ◽  
Medium Level ◽  
Rice Genotypes ◽  
Parental Lines

More than 200 rice varieties had been released in Indonesia, but the genetic variability among those released varieties was suspected to be relatively low. Molecular markers, especially SSR could be used as a tool to disect the distinctness among rice genotypes, albeit phenotipically similar varieties. The technique could also be used to prove the authenticity of a variety. This research was aimed to obtain DNA fingerprinting data of new released rice varieties and hybrid parental lines using SSR markers. A total of 26 rice genotypes consisted of three upland, ten irrigated, five swampy rice varieties, along with eight hybrid parental lines were used in this experiments. The DNA was extracted from young leaf samples using CTAB modified method and was amplified with 36 SSR markers linked to important rice traits which spread accross the 12 rice chromosomes. The experiment was conducted in Plant Breeding Laboratory of Indonesian Center for Rice Research (ICRR) during 2012. The results showed that PIC value of the genotypes were mostly at medium level of the genetic diversity with the average value of 0.4451. The phylogenetic analysis showed that at the genetic distance of 10%, the genotypes were separated into 9 groups, i.e. Inpago 6, Inpara 5, and BH33d each stood alone while (Inpara 1, Inpara 2 , and Inpara 3); (Inpari 18 and Inpari 19, Inpago 4, Inpago 5, and Inpara 4); (Inpari 11, Inpari 12, Inpari 13, Inpari 14, Inpari 15, Inpari 16, Inpari 17, and Inpari 20); (GMJ6B, B6, and IR79156B); (PK21, BH95E, Bio9, and R14) each belong to one group. The grouping of the genotypes in this study seemed to follow the adaptation type to agro ecosystems. The hybrid parental lines tended to stay in different group from the inbred varieties. The application of these 36 SSR markers was able to distinguish among 26 genotypes rather distinctly.The use of more markers should give more powerful data to distinguish among genotypes.

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