An Analysis of Genetic Variability and Population Structure in Wheat Germplasm Using Microsatellite and Gene-Based Markers

Pour-Aboughadareh, Alireza; Poczai, Péter; Etminan, Alireza; Jadidi, Omid; Kianersi, Farzad; Shooshtari, Lia

doi:10.3390/plants11091205

Cited by 21 publications

(10 citation statements)

References 36 publications

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“…Aegilops and Triticum species are the most important relatives of bread wheat. Knowledge of genetic diversity in these natural resources can provide an opportunity for future wheat-breeding programs [ 47 ]. Despite various studies that have exhibited the excellent breeding potential of these species, their genetic potential is still mainly underutilized [ 48 ].…”

Section: Discussionmentioning

confidence: 99%

Association Analysis for Some Biochemical Traits in Wild Relatives of Wheat under Drought Stress Conditions

Pour-Aboughadareh

Jadidi

Shooshtari

et al. 2022

Genes

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In the present study, we estimated genetic diversity and population structure in 186 accessions of Triticum and Aegilops species using 24 simple sequence repeat markers (SSR). Furthermore, an association analysis was performed for antioxidant activities, including guaiacol peroxidase (GPX), ascorbate peroxidase (APX), peroxidase (POX), catalase (CAT), and dry matter (DM) under two control and drought stress conditions. Our findings showed that drought treatment significantly decreased DM, whereas activities of all antioxidant enzymes were increased compared to the control conditions. The results of correlation analysis indicated that, under drought stress conditions, all biochemical traits had a positive and significant association with each other and with dry matter. In the molecular section, the results of the analysis of molecular variance (AMOVA) indicated that the molecular variation within species is more than within them. The dendrogram obtained by cluster analysis showed that grouping the investigated accessions was in accordance with their genomic constitutions. The results of association analysis revealed 8 and 9 significant marker–trait associations (MTA) under control and drought stress conditions, respectively. Among identified MTAs, two associations were simultaneously found in both growing conditions. Moreover, several SSR markers were associated with multiple traits across both conditions. In conclusion, our results could provide worthwhile information regarding marker-assisted selection for the activity of antioxidant enzymes in future breeding programs.

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Section: Discussionmentioning

confidence: 99%

Association Analysis for Some Biochemical Traits in Wild Relatives of Wheat under Drought Stress Conditions

Pour-Aboughadareh

Jadidi

Shooshtari

et al. 2022

Genes

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“…Areas with high species diversity need urgent conservation measures to secure this germplasm and ensure food security for future generations [6]. Wild species normally contain a diverse gene source for new alleles and are ideal for plant breeding programs [18]. Genetic diversity is an important criterion to consider in prioritizing populations for conservation purposes [19].…”

Section: Discussionmentioning

confidence: 99%

“…The polymorphic information content (PIC) values of the markers can provide an estimate of discrimination power in a set of accessions by taking into consideration both the number of alleles and the relative frequencies of each allele [16]. This indicates that the SSR markers will become a useful tool for genetic variation studies and for genotype identification and similarity analysis in Strychnos spinosa, which are properties required for plant breeding programs [18].…”

Section: Genetic Diversity Observed and Expected Heterozygosity And P...mentioning

confidence: 99%

Assessing Genetic Variation among Strychnos spinosa Lam. Morphotypes Using Simple Sequence Repeat Markers

Mbhele,

Zharare,

Zimudzi

et al. 2023

Plants

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Strychnos spinosa Lam., commonly known as green monkey orange, is a highly valued indigenous fruit tree in South Africa with potential for domestication and commercialization. However, no study has reported on the molecular diversity of Strychnos spinosa morphotypes. Therefore, this study aimed to determine genetic variation among 32 Strychnos spinosa morphotypes using simple sequence repeat (SSR) markers. Fourteen amplified SSR markers produced 159 alleles, with a mean of 5.68 per locus. The polymorphic information content (PIC) values ranged from 0.22 (Ssp_1) to 0.84 (Ssp_6). Morphotypes were clustered in a biplot based on their genetic distances. The dendrogram chiefly discriminated morphotypes according to variation of pericarp texture. The population structure had the highest delta value K = 3, thus the 32 morphotypes were divided into three subpopulations based on the Bayesian approach. The affinities produced by the population structure agreed with the genetic distance of closely related morphotypes. This study is the first to report on SSR marker development and their successful use for genetic diversity and population structure studies of Strychnos spinosa. It provides insights into the molecular characterisation of Strychnos spinosa. This can lead to breeding programs and crop improvement programs, particularly in varietal developmental programs, which can contribute to alleviating food security challenges.

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“…The difference between the number of alleles and the number of effective alleles shows the presence of rare alleles that exist in one or a few genotypes and can be used to identify them. If the markers are selected from different parts of the genome, there will be little solidarity between them, and as a result, more components are needed to justify the total changes and proper distribution of markers throughout the genome means more accurate and better measurement of molecular diversity due to proper sampling of the entire genome [31,32,33,34]. Therefore, the results of different studies show that the markers investigated in this study are scattered in different regions of the genome like SCoT and ISSR [35,36,37] and showed the diversity between parents.…”

Section: E Ciency Of Markersmentioning

confidence: 99%

Investigation Of Genetic Diversity Of Different Rapeseed (brassica napus l.) Genotypes And Yield Prediction Using Machine Learning Models

Norouzi

Ahangar

Payghamzadeh

et al. 2023

Preprint

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Background Seed yield is controlled by additive and non-additive effects of genes, so predicting seed yield is one of the most important goals of rapeseed breeding in agricultural research. However, there is less information about the yield estimation of canola using neural network. In this research, three models of Multi-Layer Perceptron (MLP) neural network, Radial Basis Function (RBF) neural network and Support Vector Machine (SVM) were used to predict rapeseed yield. Network training was performed using phenological, morphological, yield and yield components, as well as data obtained from molecular markers of 8 genotypes and 56 hybrids. Results The obtained from the comparison of the efficiency of the models showed that the MLP model was able to predict the hybrid yield with the RMSE, MAE and R2 equal to 226, 183 and 92% and the use of phenotypic data as model inputs in direct crosses with the highest accuracy. In the genetic evaluation section, according to the indicators obtained, it was found that molecular study is a powerful tool that can provide valuable information to the breeder. The results showed that among the 40 primers investigated, the ISJ10 primer had more resolving power than the other primers. Conclusions The use of molecular and phenotypic data as input data in the model showed that the MLP model had a lower error value in terms of RMSE and MAE and a higher R2 than direct crosses in predicting the performance of reciprocal crosses. The proposed neural network model makes it possible to estimate the performance of each of the hybrids of the parents studied before crossing, which helps the breeder to focus on the best possible hybrids.

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An Analysis of Genetic Variability and Population Structure in Wheat Germplasm Using Microsatellite and Gene-Based Markers

Cited by 21 publications

References 36 publications

Association Analysis for Some Biochemical Traits in Wild Relatives of Wheat under Drought Stress Conditions

Association Analysis for Some Biochemical Traits in Wild Relatives of Wheat under Drought Stress Conditions

Assessing Genetic Variation among Strychnos spinosa Lam. Morphotypes Using Simple Sequence Repeat Markers

Investigation Of Genetic Diversity Of Different Rapeseed (brassica napus l.) Genotypes And Yield Prediction Using Machine Learning Models

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