Analysis of genetic diversity and population structure in Saharan maize (Zea mays L.) populations using phenotypic traits and SSR markers

Belalia, Nawel; Lupini, Antonio; Djemel, Abderahmane; Morsli, Abdelkader; Mauceri, Antonio; Lotti, Concetta; Khelifi-Slaoui, Majda; Khelifi, Lakhdar; Sunseri, Francesco

doi:10.1007/s10722-018-0709-3

Cited by 41 publications

(43 citation statements)

References 52 publications

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“…Further, the low variation in the genetic indices identified between the landraces as a group, and the reference populations showed that the two germplasm sets possessed similar genetic diversity ( Table 1 ). These results agreed with previous findings that tropical maize germplasm is highly diverse with H e > 0.3 [ 37 , 38 , 39 ]. The mean PIC obtained in the present study, 0.29 using 5974 DArTseq SNPs for the 208 maize accessions was higher than the 0.19 and 0.26 reported for tropical early-maturing maize inbred lines using 15,047 [ 30 ] and 7224 SNPs for a sample size of 94 and 134, respectively [ 20 , 27 ].…”

Section: Discussionsupporting

confidence: 93%

Genomic Analysis of Selected Maize Landraces from Sahel and Coastal West Africa Reveals Their Variability and Potential for Genetic Enhancement

Nelimor

Badu‐Apraku

Garcia‐Oliveira

et al. 2020

Genes

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Genetic adaptation of maize to the increasingly unpredictable climatic conditions is an essential prerequisite for achievement of food security and sustainable development goals in sub-Saharan Africa. The landraces of maize; which have not served as sources of improved germplasm; are invaluable sources of novel genetic variability crucial for achieving this objective. The overall goal of this study was to assess the genetic diversity and population structure of a maize panel of 208 accessions; comprising landrace gene pools from Burkina Faso (58), Ghana (43), and Togo (89), together with reference populations (18) from the maize improvement program of the International Institute of Tropical Agriculture (IITA). Genotyping the maize panel with 5974 DArTseq-SNP markers revealed immense genetic diversity indicated by average expected heterozygosity (0.36), observed heterozygosity (0.5), and polymorphic information content (0.29). Model-based population structure; neighbor-joining tree; discriminant analysis of principal component; and principal coordinate analyses all separated the maize panel into three major sub-populations; each capable of providing a wide range of allelic variation. Analysis of molecular variance (AMOVA) showed that 86% of the variation was within individuals; while 14% was attributable to differences among gene pools. The Burkinabe gene pool was strongly differentiated from all the others (genetic differentiation values >0.20), with no gene flow (Nm) to the reference populations (Nm = 0.98). Thus; this gene pool could be a target for novel genetic variation for maize improvement. The results of the present study confirmed the potential of this maize panel as an invaluable genetic resource for future design of association mapping studies to speed-up the introgression of this novel variation into the existing breeding pipelines.

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Section: Discussionsupporting

confidence: 93%

Genomic Analysis of Selected Maize Landraces from Sahel and Coastal West Africa Reveals Their Variability and Potential for Genetic Enhancement

Nelimor

Badu‐Apraku

Garcia‐Oliveira

et al. 2020

Genes

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“…On the contrary, kernels/row, kernels/plant, grain ash content and grain oil content were the least discriminator, as they had relatively short trait vectors, indicating that they may be less important in evaluating maize genotypes for drought/low N tolerance. The PCA-based grouping of Egyptian maize germplasm is in agreement with those obtained by several authors [36,53,54], who reported that plant height and ear height, ear length and yield were the most discriminating traits to identify maize populations in Eastern Serbia and Mexico, respectively.…”

Section: Dissimilarity Dendrogramsupporting

confidence: 90%

“…The present study investigated 19 maize genotypes (14 Egyptian hybrid cultivars and five populations) by 21 phenotypic traits. Although morphological analysis for genetic diversity assessment presents many limitations as low polymorphism and influence of environment on phenotypic expression [34], phenotypic traits were helpful as a preliminary evaluation of maize genetic diversity and provided practical and critical information required to characterize genetic resources [35,36].…”

Section: Discussionmentioning

confidence: 99%

Genetic Diversity Based on Morphological Traits of 19 Maize Genotypes Using Principal Component Analysis and GT Biplot

Al-Naggar

Shafik

Musa

2020

ARRB

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Among the phenotypic, biochemical, and molecular methods employed in assessment of genetic diversity, the phenotypic method has proven efficient for the assessment, description and classification of germplasm collections to enhance their use in maize breeding. The objectives of the present study were: (i) to assess the extent of genetic diversity in a collection of Egyptian commercial maize hybrids and populations, through field evaluation under water and N stressed and non-stressed conditions, using morphological data based on Principle Component Analysis (PCA), (ii) to measure the genetic distance among these genotypes using UPGMA cluster analysis and (iii) to assess the relationship between grain yield and yield-related traits of maize genotypes using GT-biplot analysis. A two-year field experiment was conducted in a split-split plot design with 3 replications, where 2 irrigation regimes, three N rates and 19 maize genotypes occupied the main plots, sub plots and sub-sub plots, respectively. The germplasm was assessed for 21 agronomic traits. Highly significant differences (P ≤ 0.01) were observed among the maize hybrids and populations for all measured traits. Results of the GT biplot in the present study indicated that high values of 100-Kernel weight, ears/plant, kernels/plant, kernels/row, plant height, nitrogen use efficiency, nitrogen utilization efficiency, and grain nitrogen content and short ASI could be considered reliable secondary traits for improving grain yield under stressed and non-stressed conditions. The highest genetic distance was found between G9 (SC-2055) and each of G15 (American Early Dent), G18 (Midland) or G19 (Ried Type). The Agglomerative Hierarchical Clustering based on phenotypic data assigned the maize genotypes into five groups. The different groups obtained can be useful for deriving the inbred lines with diverse features and diversifying the heterotic pools.

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“…The results revealed the potential of tropical maize landraces as a worthy source of genetic variation in maize improvement similar to findings by Nelimor et al (2019) when he investigated diversity among 196 maize landraces. Huge genetic diversity was observed among the J maize inbred lines derived from the "Redcore" landrace population and similar results were observed by Belalia et al (2018) when they genotyped landrace populations, therefore a worthy source of genetic variation. The implication for breeding is that lines from the landrace population can be used in breeding programs and variations between groups and within groups of the J lines can result in heterosis essential in hybrid development.…”

Section: Discussionsupporting

confidence: 71%

Molecular characterization of a farmer-preferred maize landrace population from a multiple-stress-prone subtropical lowland environment

Makore

Gasura

Souta³

et al. 2021

Biodiversitas

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Abstract. Makore F, Gasura E, Souta C, Mazamura U, Derera J, Zikhali M, Kamutando CN, Magorokosho C, Dari S. 2021. Molecular characterization of a farmer-preferred maize landrace population from a multiple-stress-prone subtropical lowland environment. Biodiversitas 22: 769-777. The study was conducted to assess genetic diversity of 372 maize lines using 116 single nucleotide polymorphism (SNP) markers. Three hundred and forty-seven lines were S1 lines (coded J lines) from a local maize landrace population and twenty-five were the widely used standard lines. The number of alleles per marker ranged from two to four and the average was three alleles. The average polymorphic information content (PIC) value of 0.405 indicates high genetic diversity for maize lines evaluated in this study. Population structure revealed three distinct sub-populations. Sub-population 1 contained two J lines; sub-population 2 contained five J lines and sub-population 3 contained the rest of the J lines and all the standard lines. Analysis of molecular variance (AMOVA) identified 22% variance among and 78% variance within the three subpopulations, indicating high gene exchange and low genetic differentiation. Hierarchical cluster analysis further divided the lines into nine subgroups placing some of the J lines into known heterotic groups', i.e., J30_3, J393_4, J393_3, and J393_1 in CIMMYT heterotic group B. Allelic variation observed can be a source of allele combination for breeding programs interested in widening their genetic base. The private alleles that were present in the J lines suggest availability of stress-tolerant genes that breeders can incorporate in new hybrids.

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Analysis of genetic diversity and population structure in Saharan maize (Zea mays L.) populations using phenotypic traits and SSR markers

Cited by 41 publications

References 52 publications

Genomic Analysis of Selected Maize Landraces from Sahel and Coastal West Africa Reveals Their Variability and Potential for Genetic Enhancement

Genomic Analysis of Selected Maize Landraces from Sahel and Coastal West Africa Reveals Their Variability and Potential for Genetic Enhancement

Genetic Diversity Based on Morphological Traits of 19 Maize Genotypes Using Principal Component Analysis and GT Biplot

Molecular characterization of a farmer-preferred maize landrace population from a multiple-stress-prone subtropical lowland environment

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