Article

Genetic diversity of maize genotypes with variable resistance to Striga asiatica based on SSR markers

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Abstract

Genetic diversity among breeding populations is key in plant breeding programs. This study aimed to determine the extent of genetic diversity among 37 diverse maize genotypes using simple sequence repeat (SSR) markers. The maize genotypes were selected based on their variable resistance to Striga asiatica. Maize genotypes were fingerprinted using 18 polymorphic SSR markers. Marker and population diversity parameters were computed. A total of 191 alleles were detected and the number of effective alleles varied from 2 to 21 per locus with a mean of 11. The polymorphic information content (PIC) of the SSR markers varied from 0.59 to 0.96, with a mean of 0.80. Significant differences were observed among populations, individuals and within individuals. Within and among individual variances accounted for 85% and 13% of the total gene diversity. The genotypes were grouped into three main genetic clusters, which were not influenced by genotype origin. Mean genetic distance (0.43) and low geneflow (0.18) were observed among the populations. High mean genetic identity (0.65) was recorded, indicating potential genetic 'bottleneck' among the selected germplasm. The following open pollinated varieties; Border King, Colorado, CIMMYT's ZM OPVs, Mac Pearl, Shesha, Nel Choice, Natal 8Lines, Nel Choice QPM, Hickory King, Kep Select, Obatanpa and the Striga resistant synthetic variety DSTR-YSYN15 were selected from different clusters for breeding.

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... Haustoria undergo rapid cell differentiation to develop tracheal elements in the cortical cells. These elements develop into xylem vessels that achieve xylem-xylem or phloem connections with the host root system and enable the parasite to take water and nutrients (Makaza et al., 2021;Shayanowako et al., 2018;Wada et al., 2019). ...
... Pre-attachment resistance is, also, determined by Striga seeds' germination percentage, radicle length, furthest germination distance (FGD) and the number of attachments on the host root plant. These parameters depend on the germination-stimulant production level, germination inhibition, and low haustorial initiation (Gasura et al., 2019;Mallu et al., 2021;Mandumbu et al., 2019;Shayanowako et al., 2018). Other mechanisms of pre-attachment resistance have been stated by Mbuvi et al. (2017) who revealed that pre-attachment resistance could be due to the lgs1 mutation. ...
... the developed germplasm is then subjected to rigorous multi-environments' selection process in order to identify well adapted Striga resistant genotypes with different associated genes. Different approaches such as single seed descent, recurrent selection, half-sib, full-sib and S1 family selection methods all with hybrid breeding have proven successful in the development of Striga resistant germplasm (Afolayan et al., 2019;Ronald et al., 2016;Shayanowako et al., 2018;Yacoubou et al., 2021). ...
Article
Given their long-lasting seed viability, 15–20-year lifespan and their high seed production levels, a significant impact of parasitic plant Striga spp. on African food production is inevitable. Over the last decades, climate change has increasingly favoured the adaptability, spread and virulence of major Striga species, S. hermonthica and S. asiatica, across arable land in Sub-Saharan Africa (SSA). These parasitic weeds are causing important yield losses on several staple food crops and endangering food and nutritional security in many SSA countries. Losses caused by Striga spp. are amplified by low soil fertility and recurrent droughts. The impact of Striga parasitism has been characterized through different phenotypic and genotypic traits assessment of their host plants. Among all control strategies, host-plant resistance remains the most pro-poor, easy-to-adopt, sustainable and eco-friendly control strategy against Striga parasitism. This review highlights the impact of Striga parasitism on food security in SSA and reports recent results related to the genetic basis of different agronomic, pheno-physiological and biochemical traits associated with the resistance to Striga in major African cereal food crops.
... Haustoria undergo rapid cell differentiation to develop tracheal elements in the cortical cells. These elements develop into xylem vessels that achieve xylem-xylem or phloem connections with the host root system and enable the parasite to take water and nutrients (Makaza et al., 2021;Shayanowako et al., 2018;Wada et al., 2019). ...
... Pre-attachment resistance is, also, determined by Striga seeds' germination percentage, radicle length, furthest germination distance (FGD) and the number of attachments on the host root plant. These parameters depend on the germination-stimulant production level, germination inhibition, and low haustorial initiation (Gasura et al., 2019;Mallu et al., 2021;Mandumbu et al., 2019;Shayanowako et al., 2018). Other mechanisms of pre-attachment resistance have been stated by Mbuvi et al. (2017) who revealed that pre-attachment resistance could be due to the lgs1 mutation. ...
... the developed germplasm is then subjected to rigorous multi-environments' selection process in order to identify well adapted Striga resistant genotypes with different associated genes. Different approaches such as single seed descent, recurrent selection, half-sib, full-sib and S1 family selection methods all with hybrid breeding have proven successful in the development of Striga resistant germplasm (Afolayan et al., 2019;Ronald et al., 2016;Shayanowako et al., 2018;Yacoubou et al., 2021). ...
Article
Full-text available
Given their long-lasting seed viability, 15–20-year lifespan and their high seed production levels, a signifcant impact of parasitic plant Striga spp. on African food production is inevitable. Over the last decades, climate change has increasingly favoured the adaptability, spread and virulence of major Striga species, S. hermonthica and S. asiatica, across arable land in Sub-Saharan Africa (SSA). These parasitic weeds are causing important yield losses on several staple food crops and endangering food and nutritional security in many SSA countries. Losses caused by Striga spp. are amplifed by low soil fertility and recurrent droughts. The impact of Striga parasitism has been characterized through diferent phenotypic and genotypic traits assessment of their host plants. Among all control strategies, host-plant resistance remains the most propoor, easy-to-adopt, sustainable and eco-friendly control strategy against Striga parasitism. This review highlights the impact of Striga parasitism on food security in SSA and reports recent results related to the genetic basis of diferent agronomic, pheno-physiological and biochemical traits associated with the resistance to Striga in major African cereal food crops.
... The difference sought in this study was mainly attributed to the genetic variation among the assessed pearl millet genetic pool for grain yield, yield components, and resistance to S. hermonthica. High genetic variation among the tested genotypes is reported to increase the likelihood of developing recent and better Striga-resistant varieties (Shayanowako et al., 2018;Lobulu et al., 2021). Delayed DTF and reduced PH were recorded for some pearl millet genotypes when evaluated with Sh infestation and FOS inoculation compared to their uninoculated control, indicating the adverse effect of Striga on pearl millet growth and reproduction (Fig. 2). ...
... Poor stimulation of Sh seed germination and haustorium attachment (Fig. 5) suggested the low production of germination stimulants as a resistance mechanism of the selected genotypes. This agrees with the results of Shayanowako et al. (2018), who reported low induction of germination of Striga seed in resistant maize genotypes. Striga resistance genotypes are endowed with varied mechanisms, including low germination stimulants, mechanical root barriers, post-attachment hypersensitive reactions, and insensitivity to Striga toxins, all dependent on the genetic variation of the host (Ejeta, 2005;Haussmann et al., 2001). ...
... In the genetic diversity study of crops like maize, wheat, rice, and barley, SSR markers have been widely used [14,15]. In the assessment of genetic diversity, genetic structure, evolutionary origin, population structure, genome wide association mapping, fingerprinting, and plant breeding programs, application of SSR markers are also essential [3,[16][17][18][19][20]. SSR markers have the capacity of high variability from co-dominant and multi-allelic polymorphisms, and precise and fast detection [21]. ...
... Remarkably, genotypes viz. TK. 19 Table S2). These genotypes were also involved in one group in cluster IIIB by UPGMA method (Fig. 1) indicating that these inbred lines were unique and diverse from other maize inbred lines and thus these genotypes could be useful in maize breeding program. ...
Article
Full-text available
A total of 120 maize inbred lines were subjected to genetic diversity analysis by 40 SSR markers. The study revealed total alleles of 146 across 40 simple sequence repeat (SSR) markers, ranged from 2 to 8 with the average of 4 per locus. Gene diversity was observed with the mean value of 0.55, range from 0.11 to 0.71 among maize genotypes. Polymorphism Information Content (PIC) value was ranged from 0.10 to 0.76 with the mean value of 0.48. Umc1525 was the best marker in this study for identification of genotypes as revealed by its PIC values of 0.76. A wide range of genetic variability and PIC value were observed among maize genotypes designating that tested genotypes are invaluable genetic materials for breeding program. In UPGMA classification by molecular markers, the genotypes were identified three distinct clusters. The log-likelihood exposed by the population structure with the optimum K value of 4, pointed out that genotypes could be divided into four sub-populations. Genotypes involved in sub-population IV analyzed by population structure, which were one group in cluster IIIB constructed by UPGMA, indicating that genotypes in sub-population IV were unique and diverse from other maize genotypes. Principal coordinate analysis (PCoA) was performed to identify maize inbred lines into genetically diverged and similar genotypes. Based on this finding, genotypes viz. TK.19.17, TK.19.20, TK.19.21, TK.19.27, TK.19.28, TK19.31, TK.19.33, YZSI.20.006, YZSI.20.15, YZSI.20.16, YZSI.20.17, YZSI.20.26, YZSI.20.054, YZSI.20.036 and YZSI.20.027 were genetically diverged and useful in maize breeding program for exploitation of heterosis. Keywords: genetic diversity; maize inbred lines; SSR markers; PIC; clusters, population structure
... The marked reduction in grain yield observed in the resistant and susceptible benchmark indicates the occurrence of severe parasite infestation across the test environments, eliciting significant differences in resistance or susceptibility reactions among the inbred lines. The diversity panel used in our study displayed considerable phenotypic variation for the three Striga resistance-related traits recorded under Striga infestation, and this is consistent with the findings in other studies 25 . The significant line x environment interaction observed for traits measured under Striga infestation can be attributed to varying seasonal factors, soil pH, and nutrient levels 26 . ...
... Traits with high heritability increase the power of detecting SNPs in an association panel and thus allow the identification of a true association between a marker and a putative gene 15 . The high heritability estimates observed for Striga damage ratings and emerged Striga plants in this study is consistent is consistent with the results reported by Najar et al. 27 and Shayanowako et al. 25 . These findings, however, differ from those of Badu-Apraku et al. 28 , who recorded low heritability estimates (h 2 < 50) for emerged Striga plants and Striga damage ratings. . ...
Article
Full-text available
Striga hermonthica is a widespread, destructive parasitic plant that causes substantial yield loss to maize productivity in sub-Saharan Africa. Under severe Striga infestation, yield losses can range from 60 to 100% resulting in abandonment of farmers' lands. Diverse methods have been proposed for Striga management; however, host plant resistance is considered the most effective and affordable to small-scale famers. Thus, conducting a genome-wide association study to identify quantitative trait nucleotides controlling S. hermonthica resistance and mining of relevant candidate genes will expedite the improvement of Striga resistance breeding through marker-assisted breeding. For this study, 150 diverse maize inbred lines were evaluated under Striga infested and non-infested conditions for two years and genotyped using the genotyping-by-sequencing platform. Heritability estimates of Striga damage ratings, emerged Striga plants and grain yield, hereafter referred to as Striga resistance-related traits, were high under Striga infested condition. The mixed linear model (MLM) identified thirty SNPs associated with the three Striga resistance-related traits based on the multi-locus approaches (mrMLM, FASTmrMLM, FASTmrEMMA and pLARmEB). These SNPs explained up to 14% of the total phenotypic variation. Under non-infested condition, four SNPs were associated with grain yield, and these SNPs explained up to 17% of the total phenotypic variation. Gene annotation of significant SNPs identified candidate genes (Leucine-rich repeats, putative disease resistance protein and VQ proteins) with functions related to plant growth, development, and defense mechanisms. The marker-effect prediction was able to identify alleles responsible for predicting high yield and low Striga damage rating in the breeding panel. This study provides valuable insight for marker validation and deployment for Striga resistance breeding in maize. Maize (Zea mays L.) is an important cereal that plays a crucial role in alleviating food insecurity in sub-Saharan Africa (SSA) due to its high yield potential, ease in processing and low cost 1. However, its production is constantly hampered by a plethora of biotic stresses, including the parasitic weed Striga. Among the numerous Striga species endemic to Africa, Striga hermonthica (Del.) Benth is the most destructive and widespread, affecting cereals, including maize and sorghum (Sorghum bicolor L.) 2. Yield losses attributed to Striga infestation in maize range from 60 to 100% under severe field infestation, especially in marginal production areas where smallholder farmers cannot afford high inputs and other control measures 3. Striga hermonthica is an obligate root hemiparasite, which depends on its host for survival, notwithstanding its photosynthetic capacity after emergence from the soil 4. The parasite's lifecycle is intimately associated with its host to ensure its survival 5. The interaction between the parasitic plant and its host is initiated immediately a chemical compound known as strigolactone is released from the host plant. This chemical compound stimulates the germination of Striga seeds. Once the Striga seeds germinates, it establishes a connection with the roots of its host, extracting water, carbon and essential nutrients for its growth. The parasitic plant inflicts more damage on its host underground before its emergence from the soil, and this damage is accentuated in areas affected by sub-optimal soil fertility and recurrent drought 6. Striga hermonthica parasitism is characterized by chlorosis, firing of leaves around margins, wilting, stunting, poorly filled ears, and death under severe infestation 7. Striga resistance is a complex quantitative trait controlled by multiple genes/polygenes, and it is highly affected by environmental factors 8 .
... The marked reduction in grain yield observed in the resistant and susceptible benchmark indicates the occurrence of severe parasite infestation across the test environments, eliciting significant differences in resistance or susceptibility reactions among the inbred lines. The diversity panel used in our study displayed considerable phenotypic variation for the three Striga resistance-related traits recorded under Striga infestation, and this is consistent with the findings in other studies 25 . The significant line x environment interaction observed for traits measured under Striga infestation can be attributed to varying seasonal factors, soil pH, and nutrient levels 26 . ...
... Traits with high heritability increase the power of detecting SNPs in an association panel and thus allow the identification of a true association between a marker and a putative gene 15 . The high heritability estimates observed for Striga damage ratings and emerged Striga plants in this study is consistent is consistent with the results reported by Najar et al. 27 and Shayanowako et al. 25 . These findings, however, differ from those of Badu-Apraku et al. 28 , who recorded low heritability estimates (h 2 < 50) for emerged Striga plants and Striga damage ratings. . ...
Article
Full-text available
Striga hermonthica is a widespread, destructive parasitic plant that causes substantial yield loss to maize productivity in sub-Saharan Africa. Under severe Striga infestation, yield losses can range from 60 to 100% resulting in abandonment of farmers’ lands. Diverse methods have been proposed for Striga management; however, host plant resistance is considered the most effective and affordable to small-scale famers. Thus, conducting a genome-wide association study to identify quantitative trait nucleotides controlling S. hermonthica resistance and mining of relevant candidate genes will expedite the improvement of Striga resistance breeding through marker-assisted breeding. For this study, 150 diverse maize inbred lines were evaluated under Striga infested and non-infested conditions for two years and genotyped using the genotyping-by-sequencing platform. Heritability estimates of Striga damage ratings, emerged Striga plants and grain yield, hereafter referred to as Striga resistance-related traits, were high under Striga infested condition. The mixed linear model (MLM) identified thirty SNPs associated with the three Striga resistance-related traits based on the multi-locus approaches (mrMLM, FASTmrMLM, FASTmrEMMA and pLARmEB). These SNPs explained up to 14% of the total phenotypic variation. Under non-infested condition, four SNPs were associated with grain yield, and these SNPs explained up to 17% of the total phenotypic variation. Gene annotation of significant SNPs identified candidate genes (Leucine-rich repeats, putative disease resistance protein and VQ proteins) with functions related to plant growth, development, and defense mechanisms. The marker-effect prediction was able to identify alleles responsible for predicting high yield and low Striga damage rating in the breeding panel. This study provides valuable insight for marker validation and deployment for Striga resistance breeding in maize.
... La contribution élevée de la diversité génétique intra-population à la diversité génétique totale, observée dans notre matériel végétal, a été aussi mise en évidence par Lopes et al. (2015) dans une étude sur la diversité génétique des cultivars de maïs sweet corn utilisant des microsatellites (75 % de la variance due à la variance intra-population et 25 % due à la variance inter-population). Des résultats similaires ont été également obtenus sur l'étude de la diversité génétique de37 génotypes de maïs résistant au Striga avec 85 % de la variance due à la variance intrapopulation et 13 % due à la variance inter-population (Shayanowako et al., 2018). Compte tenu de cette contribution élevée de la diversité génétique intrapopulation à la diversité génétique totale, les cultivars de maïs violet cultivés au centre nord de la Côte d'Ivoire peuvent être considérés comme des sources potentielles de réservoir génétique pour la conservation in situ. ...
Article
Full-text available
Diversité morphologique et moléculaire des variétés locales de maïs (Zea mays L.) violet cultivées au centre-nord de la Côte d'Ivoire : implication à la conservation. Submission 21 st September 2023. Published online at https://www.m.elewa.org/Journals/ on 30 th November 2023. https://doi.org/10.35759/JABs.191.6 RÉSUMÉ Objectif : évaluer la diversité´ génétique au niveau morphologique et moléculaire du maïs (Zea mays violet collecté au centre-nord de la Côte d'Ivoire, principal zone productrice et définir une stratégie pour la conservation de ce maïs local. Méthodologie et résultats : 70 accessions de maïs violet évaluées sur la base de 18 caractères quantitatifs dans un dispositif alpha-lattice (10 X 7) en trois (03) répétitions. Les données agro-morphologiques recueillies ont été soumises à des analyses descriptives et multivariées. L'analyse en composantes principales (ACP) explique 78,67% de la variabilité. L'analyse hiérarchique des clusters répartit les accessions de la collection en sept groupes à partir de cinq caractères. La diversité au niveau moléculaire a été mesurée en utilisant 17 marqueurs microsatellites. La diversité génétique totale (He) a été de 0,30, tandis que la diversité à l'intérieur des accessions est de 19 % (FST). Conclusion et application des résultats: Ce travail constitue une première caractérisation des ressources génétiques locales des maïs violets, à l'aide de marqueurs morphologiques et microsatellites. La caractérisation agro morphologique et la caractérisation moléculaire à travers les marqueurs microsatellites a confirmé l'efficacité des deux méthodes pour caractériser les variétés de maïs violet mais la technique microsatellite permet une analyse beaucoup plus fine. Elle a permis d'acquérir une meilleure connaissance des relations génétiques existant entre les accessions de maïs violet. Bien que cette analyse mériterait sans doute d'être enrichie par l'apport d'autres marqueurs en plus grand nombre, elle a permis de révéler l'existence d'une diversité intra population. Les résultats combinés des données morphologiques et des données moléculaires permettront une première approche de génétique d'association. Etant donné que les maïs violet ont fait l'objet de très peu d'études en Côte d'Ivoire, les descripteurs identifiés pourraient constituer des critères de base de comparaison pour les investigations ultérieures. Mots clés : Zea mays, moléculaire, morphologique, violet N'da et al., J. Appl. Biosci. Vol: 191, 2023 Diversité morphologique et moléculaire des variétés locales de maïs (Zea mays L.) violet cultivées au centre-nord de la Côte d'Ivoire : implication à la conservation. ABSTRACT Objective: to assess the genetic 'diversity' at morphological and molecular level of purple maize (Zea mays) collected in north-central Côte d'Ivoire, the main production area, and to define a strategy for the conservation of this local maize. Methodology and results: 70 purple maize accessions evaluated on the basis of 18 quantitative traits in an alpha-lattice design (10 X 7) with three (03) replications. The agro-morphological data collected were subjected to descriptive and multivariate analyses. Principal component analysis (PCA) explained 78.67% of the variability. Hierarchical cluster analysis divided the collection's accessions into seven groups based on five characteristics. Diversity at the molecular level was measured using 17 microsatellite markers. Total genetic diversity (He) was 0.30, while diversity within accessions was 19% (FST). Conclusion and application of results: This work constitutes a first characterization of local genetic resources of purple maize, using morphological and microsatellite markers. Agro-morphological characterization and molecular characterization using microsatellite markers confirmed the effectiveness of both methods for characterizing purple maize varieties, but the microsatellite technique enables a much more detailed analysis. It has enabled us to gain a better understanding of the genetic relationships between purple maize accessions. Although this analysis would undoubtedly benefit from the addition of more markers, it has revealed the existence of intra-population diversity. The combined results of morphological and molecular data will enable a first approach to association genetics. Given that purple maize has been the subject of very few studies in Côte d'Ivoire, the descriptors identified could provide basic criteria for comparison in subsequent investigations.
... La contribution élevée de la diversité génétique intra-population à la diversité génétique totale, observée dans notre matériel végétal, a été aussi mise en évidence par Lopes et al. (2015) dans une étude sur la diversité génétique des cultivars de maïs sweet corn utilisant des microsatellites (75 % de la variance due à la variance intra-population et 25 % due à la variance inter-population). Des résultats similaires ont été également obtenus sur l'étude de la diversité génétique de37 génotypes de maïs résistant au Striga avec 85 % de la variance due à la variance intrapopulation et 13 % due à la variance inter-population (Shayanowako et al., 2018). Compte tenu de cette contribution élevée de la diversité génétique intrapopulation à la diversité génétique totale, les cultivars de maïs violet cultivés au centre nord de la Côte d'Ivoire peuvent être considérés comme des sources potentielles de réservoir génétique pour la conservation in situ. ...
Article
Full-text available
Diversité morphologique et moléculaire des variétés locales de maïs (Zea mays L.) violet cultivées au centre-nord de la Côte d'Ivoire : implication à la conservation. Submission 21 st September 2023. Published online at https://www.m.elewa.org/Journals/ on 30 th November 2023. https://doi.org/10.35759/JABs.191.6 RÉSUMÉ Objectif : évaluer la diversité´ génétique au niveau morphologique et moléculaire du maïs (Zea mays violet collecté au centre-nord de la Côte d'Ivoire, principal zone productrice et définir une stratégie pour la conservation de ce maïs local. Méthodologie et résultats : 70 accessions de maïs violet évaluées sur la base de 18 caractères quantitatifs dans un dispositif alpha-lattice (10 X 7) en trois (03) répétitions. Les données agro-morphologiques recueillies ont été soumises à des analyses descriptives et multivariées. L'analyse en composantes principales (ACP) explique 78,67% de la variabilité. L'analyse hiérarchique des clusters répartit les accessions de la collection en sept groupes à partir de cinq caractères. La diversité au niveau moléculaire a été mesurée en utilisant 17 marqueurs microsatellites. La diversité génétique totale (He) a été de 0,30, tandis que la diversité à l'intérieur des accessions est de 19 % (FST). Conclusion et application des résultats: Ce travail constitue une première caractérisation des ressources génétiques locales des maïs violets, à l'aide de marqueurs morphologiques et microsatellites. La caractérisation agro morphologique et la caractérisation moléculaire à travers les marqueurs microsatellites a confirmé l'efficacité des deux méthodes pour caractériser les variétés de maïs violet mais la technique microsatellite permet une analyse beaucoup plus fine. Elle a permis d'acquérir une meilleure connaissance des relations génétiques existant entre les accessions de maïs violet. Bien que cette analyse mériterait sans doute d'être enrichie par l'apport d'autres marqueurs en plus grand nombre, elle a permis de révéler l'existence d'une diversité intra population. Les résultats combinés des données morphologiques et des données moléculaires permettront une première approche de génétique d'association. Etant donné que les maïs violet ont fait l'objet de très peu d'études en Côte d'Ivoire, les descripteurs identifiés pourraient constituer des critères de base de comparaison pour les investigations ultérieures. Mots clés : Zea mays, moléculaire, morphologique, violet N'da et al., J. Appl. Biosci. Vol: 191, 2023 Diversité morphologique et moléculaire des variétés locales de maïs (Zea mays L.) violet cultivées au centre-nord de la Côte d'Ivoire : implication à la conservation. ABSTRACT Objective: to assess the genetic 'diversity' at morphological and molecular level of purple maize (Zea mays) collected in north-central Côte d'Ivoire, the main production area, and to define a strategy for the conservation of this local maize. Methodology and results: 70 purple maize accessions evaluated on the basis of 18 quantitative traits in an alpha-lattice design (10 X 7) with three (03) replications. The agro-morphological data collected were subjected to descriptive and multivariate analyses. Principal component analysis (PCA) explained 78.67% of the variability. Hierarchical cluster analysis divided the collection's accessions into seven groups based on five characteristics. Diversity at the molecular level was measured using 17 microsatellite markers. Total genetic diversity (He) was 0.30, while diversity within accessions was 19% (FST). Conclusion and application of results: This work constitutes a first characterization of local genetic resources of purple maize, using morphological and microsatellite markers. Agro-morphological characterization and molecular characterization using microsatellite markers confirmed the effectiveness of both methods for characterizing purple maize varieties, but the microsatellite technique enables a much more detailed analysis. It has enabled us to gain a better understanding of the genetic relationships between purple maize accessions. Although this analysis would undoubtedly benefit from the addition of more markers, it has revealed the existence of intra-population diversity. The combined results of morphological and molecular data will enable a first approach to association genetics. Given that purple maize has been the subject of very few studies in Côte d'Ivoire, the descriptors identified could provide basic criteria for comparison in subsequent investigations.
... MAS allow the selection of better-performing genotypes at early generations (Yacoubou et al. 2021). Using simple sequence repeats (SSRs) and single nucleotide polymorphisms (SNPs) markers, some elite genotypes for the breeding of Striga resistance were selected, and new markers have been identified, which significantly contributed to the differentiation of Striga tolerant and susceptible genotypes (Bawa et al. 2015;Shayanowako et al. 2018). Quantitative trait locus (QTL) for S. hermonthica resistance from local populations have been successfully transferred through backcross breeding into adaptable maize populations using MAS (Rich and Ejeta 2008). ...
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Pearl millet (Pennisetum glaucum [L.] R. Br.) is a drought-resilient and nutritious staple food crop widely cultivated in arid and semi-arid regions. Worldwide, pearl millet is ranked the 6th most widely produced cereal crop after wheat, rice, maize, barley, and sorghum, with a total production of 30.5 million tons on 32.1 million hectares. In Burkina Faso, it is the 3rd widely cultivated crop next to sorghum and maize, with a mean yield of 0.8 ton ha−1, far below the potential yield of 3.0 tons ha−1 attributable to various production challenges. Among the production constraints, the parasitic weed Striga species, particularly S. hermonthica is endemic and causes up to 80% yield losses under heavy infestation. Different control methods (e.g., cultural practices, chemicals and bio-herbicides) have been recommended, but they have been largely ineffective due to diverse and complex problems, including the life cycle, seed production, and prolonged seed dormancy of S. hermonthica; poor access and cost of implementation. Breeding for host plant resistance presents a cost-effective, environmentally friendly and affordable method for smallholder farmers to control and reduce Striga infestations and improve pearl millet yields. Therefore, the objectives of this study were to present the impact of S. hermonthica damage on pearl millet production and productivity and assess the effectiveness of different management methods of S. hermonthica with an emphasis on host plant resistance. The first section of the review assesses the impact of Striga infestation on pearl millet production, followed by the developmental stages of Striga, Striga infestation and damage management strategies, breeding for Striga resistance and other Striga control methods. The paper summarises genetic resources, new breeding technologies, and innovations for the precision and speed breeding of Striga-resistant cultivars. The review will guide the use of the best breeding strategies and accelerate the breeding of new pearl millet cultivars that are best-performing and resistant to S. hermonthica to reduce damage incurred by Striga infestations on farmers’ fields in Burkina Faso and related agro-ecologies.
... The advent of DNA or molecular markers has dramatically enhanced the efficiency of selecting accessions in conventional crop breeding. Molecular markers have been extensively exploited in assessing genetic diversity, identifying quantitative trait loci for genetic mapping and marker-assisted breeding (Shayanowako et al., 2018;Ghimire et al., 2019;Salgotra and Stewart, 2020). Unlike morphological markers, DNA markers are not prone to interactions with the environment (Jena and Chand, 2021). ...
Article
Fluted pumpkin ( Telfairia occidentalis Hook F.) is an underutilized indigenous leafy vegetable with enormous prospects for food security in sub-Saharan Africa. However, relatively little is known about genetic relationships and population structure in the species. In this study, 32 landraces of fluted pumpkin collected across three southern geographical regions in Nigeria were assessed for genetic diversity and population structure using 8 start codon-targeted (SCoT) makers. The polymorphic information content of the SCoT markers ranged from 0.48 in SCoT36 to 0.94 in SCoT28, with an average of 0.77. Hierarchical cluster dendrogram based on Ward's method and principal component analysis grouped the landraces into four clusters without affiliation to provenance. Overall, the mean values of the population genetic diversity parameters – Nei's gene diversity ( H ) and Shannon's information index ( I ) showed values of 0.28 ± 0.01 and 0.43 ± 0.02, respectively, implying a narrow genetic base for the landraces. The result was further corroborated by a very close Nei's genetic distance and identity among populations of the landraces. Furthermore, the south-west population exhibited the higher genetic diversity ( H = 0.31 ± 0.02 and I = 0.45 ± 0.03). Population structure analysis inferred three subpopulations for the accessions with varying degrees of allelic admixture. An analysis of molecular variance revealed that almost all the genetic variation occurred within (99%) than between (1%) populations. The findings shed light on the genetic diversity of southern Nigerian fluted pumpkin and have significant implications for the characterisation, conservation, exploitation and improvement of the species.
... Striga hermonthica is widely found in most SSA regions and is reported in Western, Central, and Eastern Africa. Striga asiatica is predominantly found in the Southern Africa sub-region (Ejeta & Gressel, 2007;Parker, 2012;Shayanowako et al., 2018). ...
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Parasitic Striga weeds severely damage cereal crops in sub‐Saharan Africa (SSA), leading to yield losses in susceptible varieties. A range of Striga control methods are commonly recommended, including cultural practices, chemical herbicides, biological control agents, and host resistance, either as solo treatments or in combinations of these approaches (i.e., integrated Striga management [ISM]). A limited number of studies compared the relative efficacy of the recommended Striga control methods, or their combinations for ISM, in cereal crop production in SSA. The objective of this paper was to undertake a meta‐analysis and provide a detailed comparison of the Striga control methods in the production of maize, sorghum, and the major millets, as a guide to effective Striga management. The study was conducted as a meta‐analysis of 66 research articles that reported on various control measures. The following agronomic data were collected: grain yield (GY) response of the assessed crops and Striga parameters such as damage rating score (SDR) and emergence count (SEC). Maize varieties possessing Striga‐resistant genes displayed high mean yield values at 2053.00 kg ha⁻¹, varying from 281.00 to 6260.00 kg ha⁻¹, and a mean SDR of 4.70, ranging from 2.00 to 7.00. Likewise, sorghum varieties with Striga resistance genes achieved greater GY with a mean yield response of 1738.00 kg ha⁻¹, ranging from 850.00 to 2162.00 kg ha⁻¹. A relatively low GY was achieved in maize and sorghum production when deploying ISM (e.g., cultural control + host resistance and host resistance + chemical herbicides) and chemical Striga control. Effective ISM and pre‐ and post‐emergent herbicides have not yet been identified for Striga control and yield gains. Striga damage negatively affected GY in maize, as revealed by the significant correlation (r = −0.36, P < 0.001) between GY and SDR. A relatively weak correlation was detected in maize between GY and SEC (r = 0.003, P = 0.96). Sorghum GY was negatively correlated with SEC, although nonsignificantly (r = −0.30, P = 0.36). Few studies have evaluated Striga control methods in pearl millet and finger millet, limiting the opportunity for an effective comparison. The study recommends SDR as the best selection criterion for improving GY performance in maize, while SEC and SDR are the parameters of choice in sorghum selection programs for better GY under Striga infestation. Overall, the meta‐analysis indicates that host resistance is the most effective method for controlling Striga infestation and boosting GY in maize and sorghum. There is an ongoing need for research into the best combinations of the reported control methods as a sound basis for the recommendation of an ISM package across target production environments of common cereals in Africa.
... Though there are numbers of marker technologies are available for diversity assessment namely phenological, morphological, biochemical as well as molecular (Govindaraj et al. 2015;Adu et al. 2019a, b) but the molecular marker-based analysis is the most preferred one due to independence on developmental stage and immunity towards environmental fluctuation (Smith and Smith 1992;Westman and Kresovich 1997;Govindaraj et al. 2015). In previous findings for diversity assessment in maize SSR markers were reported more informative (Yuan et al. 2000;Warburton et al. 2002;Pinto et al. 2003;Inghelandt et al. 2010;Shayanowako et al. 2018;Adu et al. 2019a, b;Adu et al. 2019b). Due to desirable features such as multi-allelic nature, high variability (Tautz 1989;Schug et al. 1998;Xu et al. 2013), enormous abundance, even distribution throughout the genome (Liu et al. 1996;Senior et al. 1996;Matsuoka et al. 2002;Wu et al. 2010;Xu et al. 2013), reproducibility (Vos et al. 1995;Senior and Heun 1993), co-dominant nature, SSR have become the marker of choice for genetic analysis in crops (Gupta and Varshney 2000). ...
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The present study comprised of 100 lines derived from teosinte × maize (DI-103) hybridization, which were evaluated for morphological as well as molecular diversity. The slight difference in GCV and PCV estimates for all the traits except grain yield per plant reflects genotypic variation without much influence of environmental factors. The high heritability coupled with high genetic advance for most of the traits elucidated the presence of additive gene effect in the governance of these traits. Genotyping with 76 SSR markers resulted in 377 alleles with an average 5 alleles per marker loci. Wider polymorphic information content (PIC) range from 0.29 to 0.86, reflects higher allelic variation and wide distribution in the population. The average gene diversity, heterozygosity, major allele frequency, and minor allele frequency were 0.48, 0.85, 0.58, and 0.48 respectively. Cluster analysis allocated 102 lines including, maize inbred (DI-103) and teosinte-parviglumis into 14 genetic groups which indicate uniqueness of lines in terms of molecular makeup. Linkage analysis using SSR data revealed ten linkage groups in maize. Maximum allelic contribution from maize (65.2%) and teosinte (59.4%) parent was recorded in MT-26 and MT-19 respectively. With 14 and 3 heterozygous segments MT-44 and MT-26 reflected maximum (37.5%) and minimum (2.4%) heterozygosity respectively. The Maximum recombination (52%) was recorded in the case of MT-40, whereas, the line MT-81 expressed the least recombination (30%). The results reflected a quite significant variability among derived lines and governed by introgression of teosinte alleles, which can be visualized by graphical genotype.
... Though there are numbers of marker technologies are available for diversity assessment namely phenological, morphological, biochemical as well as molecular (Govindaraj et al. 2015;Adu et al. 2019a, b) but the molecular marker-based analysis is the most preferred one due to independence on developmental stage and immunity towards environmental fluctuation (Smith and Smith 1992;Westman and Kresovich 1997;Govindaraj et al. 2015). In previous findings for diversity assessment in maize SSR markers were reported more informative (Yuan et al. 2000;Warburton et al. 2002;Pinto et al. 2003;Inghelandt et al. 2010;Shayanowako et al. 2018;Adu et al. 2019a, b;Adu et al. 2019b). Due to desirable features such as multi-allelic nature, high variability (Tautz 1989;Schug et al. 1998;Xu et al. 2013), enormous abundance, even distribution throughout the genome (Liu et al. 1996;Senior et al. 1996;Matsuoka et al. 2002;Wu et al. 2010;Xu et al. 2013), reproducibility (Vos et al. 1995;Senior and Heun 1993), co-dominant nature, SSR have become the marker of choice for genetic analysis in crops (Gupta and Varshney 2000). ...
Article
The present study comprised of 100 lines derived from teosinte × maize (DI-103) hybridization, which were evaluated for morphological as well as molecular diversity. The slight difference in GCV and PCV estimates for all the traits except grain yield per plant reflects genotypic variation without much influence of environmental factors. The high heritability coupled with high genetic advance for most of the traits elucidated the presence of additive gene effect in the governance of these traits. Genotyping with 76 SSR markers resulted in 377 alleles with an average 5 alleles per marker loci. Wider polymorphic information content (PIC) range from 0.29 to 0.86, reflects higher allelic variation and wide distribution in the population. The average gene diversity, heterozygosity, major allele frequency, and minor allele frequency were 0.48, 0.85, 0.58, and 0.48 respectively. Cluster analysis allocated 102 lines including, maize inbred (DI-103) and teosinte-parviglumis into 14 genetic groups which indicate uniqueness of lines in terms of molecular makeup. Linkage analysis using SSR data revealed ten linkage groups in maize. Maximum allelic contribution from maize (65.2%) and teosinte (59.4%) parent was recorded in MT-26 and MT-19 respectively. With 14 and 3 heterozygous segments MT-44 and MT-26 reflected maximum (37.5%) and minimum (2.4%) heterozygosity respectively. The Maximum recombination (52%) was recorded in the case of MT-40, whereas, the line MT-81 expressed the least recombination (30%). The results reflected a quite significant variability among derived lines and governed by introgression of teosinte alleles, which can be visualized by graphical genotype.
... Molecular markers are also used for screening crop genotypes for tolerance to biotic or abiotic stress. Using SSRs and SNPs markers, some elite genotypes for the breeding of Striga resistance are selected and new makers have been identified, which significantly contributed to the differentiation of Striga tolerant and susceptible genotypes (Bawa et al., 2015;Shayanowako et al., 2018). Molecular markers can better help in the assessment of relatedness in isogenic lines to determine families that can be bulked or discarded, which in turn can reduce maintenance costs (Dean et al., 1999). ...
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Striga hermonthica, causes up to 100% yield loss in maize production in Sub-Saharan Africa. Developing Striga-resistant maize cultivars could be a major component of integrated Striga management strategies. This paper presents a comprehensive over�view of maize breeding activities related to Striga resistance and its management. Scientific surveys have revealed that conventional breeding strategies have been used more than molecular breeding strategies in maize improvement for Striga re�sistance. Striga resistance genes are still under study in the International Institute for Tropical Agriculture (IITA) maize breeding programme. There is also a need to discover QTL and molecular markers associated with such genes to improve Striga resistance in maize. Marker Assistance Breeding is expected to increase maize breed�ing efficiency with complex traits such as resistance towards Striga because of the complex nature of the host-parasite relationship and its intersection with other environmental factors. Conventional alongside molecular tools and technical controls are promising methods to effectively assess Striga in Sub-Saharan Africa. KEYWORDS breeding strategies, maize, QTL, resistance, Striga
... The reason adduced for this result was that the markers used for the study were selected not based on Striga resistance because no SSR marker associated with Striga resistance existed in the maize database. Shayanowako et al. [33] also assessed genetic diversity among 37 maize genotypes with varying levels of resistance to Striga asiatica infestation using 18 SSR markers and reported wide genetic variability with three distinct genetic groups which did not follow the pedigree pattern or the levels of resistance in the genotypes. ...
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Striga hermonthica is a major stress of maize in sub-Saharan Africa (SSA). The International Institute of Tropical Agriculture (IITA), in collaboration with national scientists, have used team approach to investigate how best to solve the problem. Emphasis was on (i) establishing a reliable infestation technique for selecting resistant/tolerant genotypes, (ii) availability of appropriate germplasm and good sources of Striga resistance, (iii) use of appropriate breeding methods for incorporating resistance genes into adapted germplasm, and (iv) extensive multilocational evaluation to identify genotypes with stable performance. Host plant resistance, with additive-dominance model, has been the major control option for S. hermonthica infestation on maize. Recurrent selection, followed by hybridization of inbred lines developed from its products, have been used to identify high-yielding, stable hybrids for commercialization in SSA. In a study involving early-maturing tropical maize inbred lines, 24 single nucleotide polymorphism (SNP) markers significantly associated with grain yield, Striga damage, ears per plant, and ear aspect under Striga infestation were detected. In a quantitative trait loci (QTL) mapping study involving extra-early white BC 1 S 1 families obtained from TZEEI 29 ( Striga- resistant) and TZEEI 23 ( Striga susceptible) inbreds, 14 QTLs were identified for Striga resistance/tolerance traits. In a second QTL study involving the extra-early yellow F 2:3 families derived from the Striga- resistant parent (TZEEI 79) and the susceptible parent (TZdEEI 11), 12 QTL were identified for 4 Striga resistance/tolerance traits. QTL identified in the studies would be invaluable for rapid introgression of Striga resistance genes into maize genotypes using marker-assisted selection approaches after validation of QTL in inbreds.
... The establishment of a breeding population starts with classifying germplasm based on their genetic interrelationships using molecular markers. Simple sequence repeat (SSR) markers have been extensively used for the evaluation of genetic diversity in several crops including sorghum (Yusuf et al., 2018;Danquah et al., 2019), rice (Gasim et al., 2019;Suvi et al., 2020), wheat (Tekeu et al., 2017;Abbasov et al., 2018) and maize (Shayanowako et al., 2018;Adu et al., 2019). The wide use of SSR markers in genetic diversity studies is attributed to their abundance, co-dominance and multi-allelic nature (Powell et al., 1996). ...
Article
Genetic diversity is key for breeding population development, hybrid breeding, heterotic grouping and genetic analysis, among others. The objective of this study was to examine genetic interrelationships among elite sorghum genotypes bred for resistance to Striga hermonthica Del. Benth and S. asiatica (L.) Kuntze and compatible with a biological control agent Fusarium oxysporum f. sp. strigae (FOS) against Striga using 22 polymorphic simple sequence repeat (SSR) or microsatellite markers. The number of alleles per locus detected by the markers varied from 2 to 7 with a mean value of 4.23. The polymorphic information content (PIC) of the SSR markers ranged from 0.15 to 0.84 with a mean of 0.57 showing moderate discriminatory power of the primers. The neighbour-joining clustering algorithm classified the genotypes into three main groups, revealing narrow to moderate variations existing among the test genotypes. Overall, the genetic diversity revealed by the study will be useful for designed crosses and pyramiding of broad-based resistance genes to control Striga for sustainable sorghum production.
... Being codominant, SSRs markers are mainly employed in plant analysis due to their hyper variable nature, wide genome coverage, high reproducibility, reliability and discriminating ability, and ability to give high allelic variations (Ko et al., 2016), besides highly specific and polymorphic (Jones et al., 1997). Numerous studies have utilized SSR markers to assess genetic diversity and relationships among maize populations (Cömertpay et al., 2012;Aci et al., 2013;Nyaligwa et al., 2015;Shayanowako et al., 2018;Adeyemo and Omidiji, 2019). Li et al. (2006) studied 22 CIMMYT subtropical QPM and 24 Chinese inbred lines using 64 SSR markers and obtained two main clusters. ...
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Genetic diversity and phenotypic superiority are important attributes of parental inbred lines for use in hybrid breeding programs. In this study, genetic diversity among 30 maize (Zea mays L.) inbred lines comprising of 28 introductions from the International Maize and Wheat Improvement Center (CIMMYT), one from Indonesia and a locally developed, were evaluated using 100 simple sequence repeat (SSR) markers, as early screening for potential parents of hybrid varieties. All markers were polymorphic, with a total of 550 unique alleles detected on the 100 loci from the 30 inbred lines. Allelic richness ranged from 2 to 13 per locus, with an average of 5.50 alleles (na). Number of effective alleles (ne) was 3.75 per locus, indicating their high effectiveness in revealing diversity among inbred lines. Average polymorphic information content (PIC) was 0.624, with values ranging from 0.178 to 0.874, indicating high informativeness of the markers. High gene diversity was observed on Chromosomes 8 and 4, with high number of effective alleles, indicating their potential usefulness for QTL analysis. The UPGMA dendrogram constructed identified four heterotic groups within a similarity index of 0.350, indicating that these markers were able to group the inbred lines. The three-dimensional PCoA plot also supports the dendrogram grouping, indicating that these two methods complement each other. Inbred lines in different heterotic groups have originated from different backgrounds and population sources. Information on genetic diversity among the maize inbred lines are useful in developing strategies exploiting heterosis in breeding programs
... Molecular markers are also used for screening crop genotypes for tolerance to biotic or abiotic stress. Using SSRs and SNPs markers, some elite genotypes for the breeding of Striga resistance are selected and new makers have been identified, which significantly contributed to the differentiation of Striga tolerant and susceptible genotypes (Bawa et al., 2015;Shayanowako et al., 2018). Molecular markers can better help in the assessment of relatedness in isogenic lines to determine families that can be bulked or discarded, which in turn can reduce maintenance costs (Dean et al., 1999). ...
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Striga hermonthica, causes up to 100% yield loss in maize production in Sub-Saharan Africa. Developing Striga-resistant maize cultivars could be a major component of integrated Striga management strategies. This paper presents a comprehensive overview of maize breeding activities related to Striga resistance and its management. Scientific surveys have revealed that conventional breeding strategies have been used more than molecular breeding strategies in maize improvement for Striga resistance. Striga resistance genes are still under study in the International Institute for Tropical Agriculture (IITA) maize breeding programme. There is also a need to discover QTL and molecular markers associated with such genes to improve Striga resistance in maize. Marker Assistance Breeding is expected to increase maize breeding efficiency with complex traits such as resistance towards Striga because of the complex nature of the host-parasite relationship and its intersection with other environmental factors. Conventional alongside molecular tools and technical controls are promising methods to effectively assess Striga in Sub-Saharan Africa.
... The genotypes were sourced from the African Center for Crop Improvement (ACCI), Agriculture Research Council (ARC) of South Africa, National Plant Genetic Resources Center (NPGRC) of South Africa, the International Institute of Tropical Agriculture (IITA), Nigeria, and The International Maize and Wheat Improvement Center (CIMMYT) ( Table 1). Genotypes from ACCI, ARC, NPGRC and CIMMYT were open-pollinated varieties (OPV), which were selected for their moderate strigalactone biosynthesis (Shayanowako et al. 2018b ...
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Striga presents a major threat to cereal crop production in sub-Saharan Africa. A combined use of host resistance and biological control agents holds promise as a key strategy for sustainable, integrated Striga management in maize (Zea mays L.) production. The objective of this study was to determine resistance against Striga asiatica (L.) Kuntze and compatibility of selected maize genotypes to a biocontrol agent, Fusarium oxysporum f.sp. strigae (FOS), for integrated Striga management. Eighteen maize genotypes were evaluated under glasshouse and field conditions using three treatments: 1) maize genotypes sown without Striga infestation and FOS treatment (control), 2) maize genotypes grown under Striga infestation and; 3) FOS-treated maize genotypes grown under Striga infestation. The results showed that genotype-by-FOS interaction significantly (P < 0.05) affected all traits, except anthesis-to-silking interval, ear aspect score and Striga emergence count at 8 weeks after planting. All maize and Striga traits were significantly affected by FOS treatment (P < 0.001), although the efficacy of FOS seemed to be maize genotype dependent. Mean grain yield was 4.2 t ha⁻¹ for the control, 2.63 t ha⁻¹ for the FOS-treated and 2.17 t ha⁻¹ for the untreated genotypes. Overall, the combined effect of host resistance and inoculation of seed with FOS reduced parasitic infestations and Striga damage symptoms, resulting in improved agronomic performance. Five genotypes (ZM1523, ZM 1423, ZM 1421, NC QPM and Colorado) showed resistance to S. asiatica and compatibility to FOS. The study demonstrated the efficacy of host resistance and biological control in integrated management of S. asiatica in maize.
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The potential yield of maize (Zea mays L.) and other major crops is curtailed by several biotic, abiotic, and socio-economic constraints. Parasitic weeds, Striga spp., are major constraints to cereal and legume crop production in sub-Saharan Africa (SSA). Yield losses reaching 100% are reported in maize under severe Striga infestation. Breeding for Striga resistance has been shown to be the most economical, feasible, and sustainable approach for resource-poor farmers and for being environmentally friendly. Knowledge of the genetic and genomic resources and components of Striga resistance is vital to guide genetic analysis and precision breeding of maize varieties with desirable product profiles under Striga infestation. This review aims to present the genetic and genomic resources, research progress, and opportunities in the genetic analysis of Striga resistance and yield components in maize for breeding. The paper outlines the vital genetic resources of maize for Striga resistance, including landraces, wild relatives, mutants, and synthetic varieties, followed by breeding technologies and genomic resources. Integrating conventional breeding, mutation breeding, and genomic-assisted breeding [i.e., marker-assisted selection, quantitative trait loci (QTL) analysis, next-generation sequencing, and genome editing] will enhance genetic gains in Striga resistance breeding programs. This review may guide new variety designs for Striga-resistance and desirable product profiles in maize.
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CIMMYT is the source of improved maize (Zea mays L.) breeding material for a significant portion of the nontemperate maize growing world. Landraces which did not serve as sources for improved maize germplasm may contain untapped allelic variation useful for future breeding progress. Information regarding levels of diversity in different germplasm would help to identify sources for broadening Improved breeding pools and in seeking genes and alleles that have not been tapped in modern maize breeding. The objectives of this study were to examine the diversity in mate landraces, modern open pollinated varieties (OPVs), and inbred lines adapted to nontemperate growing areas to find unique sources of allelic diversity that may be used in maize improvement. Twenty-five simple sequence repeat markers were used to characterize 497 individuals from 24 landraces of maize from Mexico, 672 individuals from 23 CIMMYT improved breeding populations, and 261 CIMMYT inbred lines. Number of alleles, gene diversity per locus, unique alleles per locus, and population structure all differ between germplasm groups. The unique alleles found in each germplasm group represent a great reservoir of untapped genetic resources for maize improvement, and implications for hybrid breeding are discussed.
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A comparative characterization of 10 field populations of the maize (Zea mays var. indurata) landrace Nostrano di Storo was carried out using different types of PCR-based markers. The inbred line B73 and three synthetics (VA143, VA154 and VA157) selected from as many landraces were also used. Genetic diversity and relatedness were evaluated over 84 SSR and 53 I-SSR marker alleles using a total of 253 individual DNAs. Up to 23 alleles per SSR locus were scored while the average effective number of alleles per population was 6.99. Nei's total genetic diversity as assessed with SSR markers was HT = 0.851 while the average diversity within populations was HS = 0.795. The overall Wright's fixation index FST was as low as 0.066. Thus, more than 93% of the total variation was within population. Unique alleles over all SSR loci were found for six populations. An average of 17.7 marker alleles per I-SSR primer were scored with an effective number of marker alleles per locus of 1.34. The Shannon's diversity information index over all populations and I-SSR loci was 0.332, varying from 0.286 to 0.391. The extent of differentiation between populations was as low as GST = 0.091. Dice's genetic similarity matrices were estimated for both SSR and I-SSR markers. The mean genetic similarity coefficients within and between populations were respectively 0.269 and 0.217, for SSR markers, and 0.591 and 0.564, for I-SSR markers. UPGMA dendrograms displayed all field populations but one clustered into a distinct group, in which the synthetic VA154, selected from the Marano Vicentino landrace, was also included. One field population and the other two synthetics were clustered separately as well B73. The matrix correlation assayed by the Mantel's correspondence test was as high as 0.908. Findings suggest that, although a high variability can be found among plants, most plant genotypes belong to the same landrace called Nostrano di Storo. Although gene flow from commercial hybrids might have occurred, the large number of polymorphisms and the presence of both unique alleles and alleles unshared with B73 and synthetics are the main factors underlying the value of this flint maize landrace as a source of genetic variation and peculiar germplasm traits. Because of its exclusive utilization for human consumption, such a molecular marker characterization will be a key step for obtaining the IGP mark and so promote the in situ conservation and protection of the landrace Nostrano di Storo.
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A collection of Portuguese maize accessions representing a valuable source of genes for introduction into modern cultivars is stored at the Portuguese Plant Germplasm Bank (Banco Português de Germoplasma Vegetal—BPGV). To assess genetic diversity among inbreds, microsatellite analysis was carried out for 54 inbred lines representing the diversity of Portuguese dent and flint maize germplasm. Fifty American and other European elite inbreds were also analysed for comparison. Fifteen microsatellite loci distributed throughout the maize genome were chosen based on their repeat unit and base composition. A total of 80 alleles were detected with an average allele number of 5.33 per locus. Polymorphism information content (PIC) values and observed genetic distances showed the existence of large variability among inbreds. Cluster analysis indicated that almost all of the inbreds could be distinguished from each other and Portuguese inbreds were present in all clusters formed. These associations were consistent with the known pedigree records of the inbreds, confirming a mixed origin of Portuguese materials. Comparative analysis of microsatellite diversity among groups was established according to important traits for both breeding and line identification. This revealed that, although most of the genetic diversity (>95%) was attributable to differences among inbreds of different groups, the existence of phenotypic differentiation in endosperm colour, kernel type and cob colour could be suggested for grouping. These findings support the joint use of molecular and morphological traits in management of the germplasm collection. In this study, SSR markers proved to be effective to characterise and identify maize inbred lines, and demonstrate associations among them.
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 The utility of 131 simple sequence repeat (SSR) loci to characterize and identify maize inbred lines, validate pedigree, and show associations among inbred lines was evaluated using a set of 58 inbred lines and four hybrids. Thirteen sets of inbred parent-progeny triplet pedigrees together with four hybrids and their parental lines were used to quantify incidences of scoring that departed from expectations based upon simple Mendelian inheritance. Results were compared to those obtained using 80 restriction fragment length polymorphism (RFLP) probes. Over all inbred triplets, 2.2% of SSRs and 3.6% of RFLP loci resulted in profiles that were scored as having segregated in a non-Mendelian fashion. Polymorphic index content (PIC, a measure of discrimination ability) values ranged from 0.06 to 0.91 for SSRs and from 0.10 to 0.84 for RFLPs. Mean values for PIC for SSRs and RFLPs were similar, approximately 0.62. However, PIC values for nine SSRs exceeded the maximum PIC for RFLPs. Di-repeats gave the highest mean PIC scores for SSRs but this class of repeats can result in “stutter” bands that complicate accurate genotyping. Associations among inbreds were similar for SSR and RFLP data, closely approximating expectations from known pedigrees. SSR technology presents the potential advantages of reliability, reproducibility, discrimination, standardization and cost effectiveness over RFLPs. SSR profiles can be readily interpreted in terms of alleles at mapped loci across a broad range of maize germ plasm. Consequently, SSRs represent the optimum approach for the identification and pedigree validation of maize genotypes compared to other currently available methods.
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The magnitudes of the systematic biases involved in sample heterozygosity and sample genetic distances are evaluated, and formulae for obtaining unbiased estimates of average heterozygosity and genetic distance are developed. It is also shown that the number of individuals to be used for estimating average heterozygosity can be very small if a large number of loci are studied and the average heterozygosity is low. The number of individuals to be used for estimating genetic distance can also be very small if the genetic distance is large and the average heterozygosity of the two species compared is low.
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Through systematic and intensive efforts since 1975, CIMMYT has been successful in developing drought tolerant and nitrogen use effi cient tropical/subtropical maize germplasm through managed stress screening and extensive multi-location testing. Improved varieties formulated using such germplasm is being deployed in partnership with an array of public and private institutions in sub-Saharan Africa, Latin America and Asia. Recent work in sub-Saharan Africa and Asia led to the identifi cation of inbred lines with heat stress tolerance, as well as with combined drought and heat stress tolerance. In partnership with several public and private institutions worldwide, CIMMYT is at the forefront of identifying, validating and deploying production markers for important abiotic and biotic stresses affecting maize productivity in the tropics, besides selected quality traits. Molecular marker-assisted breeding is now an integral part of CIMMYT’s efforts to develop provitamin-enriched maize under the HarvestPlus Program, and is perhaps one of the fi nest examples of allele mining work leading to improved varieties. Accelerated development of improved maize cultivars and enhancing genetic gains in the stress-prone environments of the tropics/subtropics will require effective integration of doubled haploids, high throughput and reasonably precise field-based phenotyping (especially for key abiotic and biotic stresses), genomicsassisted breeding, breeding informatics and decision support tools/systems. Intensive public-private partnerships will also be needed to ensure deployment of climate resilient and nutritionally enriched tropical maize cultivars in the climate change vulnerable environments, especially in sub-Saharan Africa and South Asia.
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Recurrent selection under artificial S. hermonthica infestation has significantly reduced the number of emerged Striga plants and increased grain yield under Striga infestation in Broad-Based populations. These populations have been sources of varieties and inbred lines with consistently high levels of resistance to S. hermonthica across locations and seasons. The number of parasites attached to the roots of diverse lines was significantly correlated with the number of emerged parasites in the screenhouse and in the field as well as with a reduction in grain yield due to Striga. AFLP and SSR markers clearly separated 41 Striga resistant inbred lines from four populations into groups according to their source populations. The consistent ranking of the general combining ability effects of selected inbred lines across locations and seasons also indicates that the inbred lines had a stable genetic basis that controlled the Striga resistance traits. Unraveling the complex mechanisms of resistance to S. hermonthica using rapid and efficient screening tools can facilitate the improvement of maize for resistance to different populations of the parasite. © 2007 by World Scientific Publishing Co. Pte. Ltd. All rights reserved.
Article
A relatively quick, inexpensive and consistent protocol for extraction of DNA from expanded leaf material containing large quantities of polyphenols, tannins and polysaccharides is described. Mature strawberry leaves, which contain high levels of these secondary components, were used as a study group. The method involves a modified CTAB extraction, employing high salt concentrations to remove polysaccharides, the use of polyvinyl pyrrolidone (PVP) to remove polyphenols, an extended RNase treatment and a phenol-chloroform extraction. Average yields range from 20 to 84 μg/g mature leaf tissue for both wild and cultivated octoploid and diploidFragaria species. Results from 60 plants were examined, and were consistently amplifiable in the RAPD reaction with as little as 0.5 ng DNA per 25-μL reaction. Presently, this is the first procedure for the isolation of DNA from mature strawberry leaf tissue that produces consistent results for a variety of different species, both octoploid and diploid, and is both stable and PCR amplifiable before and after extended storage. This procedure may prove useful for other difficult species in the family Rosaceae.
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A set of 23 Quality Protein Maize (QPM) lines, including 13 lines developed in India and 10 lines at CIMMYT (International Maize and Wheat Improvement Center), Mexico, was analyzed using microsatellite or simple sequence repeat (SSR) markers. Polymorphic profiles for 36 SSR loci have aided in differentiating the QPM inbred lines. The study resulted in identification of SSR markers, such as bnlg439, phi037, bnlg125, dupssr34 andbnlg105, with high polymorphism information content in the selected QPM genotypes. Detection of 30 unique/rare SSR alleles could contribute to effective differentiation of 14 of the 23 QPM inbreds. An opaque2-specific microsatellite marker, phi057, also facilitated differentiation of opaque2-carrying QPM inbreds from the non-opaque genotypes. Analysis using SSR markers indicated high levels of heterozygosity in majority of the Indian QPM lines and in one CIMMYT QPM inbred, CML188. Cluster analysis using SSR data, followed by canonical discriminant analysis, clearly distinguished the Indian QPM inbreds from those developed at CIMMYT. The cluster patterns were largely in congruence with the available pedigree information of the QPM inbreds studied. The study demonstrates the effectiveness of SSR markers in QPM genotype discrimination and analysis of genetic relationships, and could potentially contribute towards effective utilization of the elite QPM germplasm in Indian maize breeding programmes.
Article
The parasitic weed Striga hermonthica (Del.) Benth. seriously limits sorghum [Sorghum bicolor (L.) Moench] production in Sub-Saharan Africa. As an outbreeder, S. hermonthica is highly variable with an extraordinary capacity to adapt to different hosts and environments, thereby complicating resistance breeding. To study genotype x environment (G x E) interaction for striga resistance and grain yield, nine sorghum lines, 36 F2 populations and five local checks were grown under striga infestation at two locations in both Mali and Kenya. Mean squares due to genotypes and G x E interaction were highly significant for both sorghum grain yield and area under striga severity progress curve(ASVPC, a measure of striga emergence and vigor throughout the season). For grain yield, the entry x location-within-country interaction explained most of the total G x E while for ASVPC, entry x country and entry x location-within-country interactions were equally important. Pattern analysis (classification and ordination techniques) was applied to the environment-standardized matrix of entry x environment means. The classification clearly distinguished Malian from Kenyan locations for ASVPC, but not for grain yield. Performance plots for different entry groups showed differing patterns of adaptation. The ordination biplot underlined the importance of entry x country interaction for ASVPC. The F2 derived from the cross of the striga-resistant line Framida with the striga-tolerant cultivar Seredo was the superior entry for both grain yield and ASVPC, underlining the importance of combining resistance with tolerance in striga resistance breeding. The observed entry x country interaction for ASVPC may be due to the entries' different reactions to climatic conditions and putative differences in striga virulence in Mali and Kenya.
Article
Information regarding diversity and relationships among breeding material is necessary for hybrid maize ( Zea mays L.) breeding. Simple-sequence repeat (SSR) analysis of the 60 loci distributed uniformly throughout the maize genome was carried out for 65 inbred lines adapted to cold regions of Japan in order to assess genetic diversity among the inbred lines and to assign them to heterotic groups. The mean value (0.69) of the polymorphic-index content (PIC) for the SSR loci provided sufficient discrimination-ability for the assessment of genetic diversity among the inbred lines. The correlation between the genetic-similarity (GS) estimates and the coancestry coefficient was significant ( r = 0.70). The average-linkage (UPGMA) cluster analysis and principal-coordinate analysis (PCOA) for a matrix of the GS estimates showed that the Northern flint inbred lines bred in Japan were similar to a Canadian Northern flint inbred line CO12 and a European flint inbred line F283, and that dent inbred lines bred in Japan were similar to BSSS inbred lines such as B73. These associations correspond to the known pedigree records of these inbred lines. The results indicate that SSR analysis is effective for the assessment of genetic diversity among maize inbred lines and for the assignment of inbred lines to heterotic groups.
Article
Breeding for resistance to Striga in maize (Zea mays), with paucity of donor source and known mechanisms of resistance, has been challenging. Here, post-attachment development of S. hermonthica was monitored on two maize inbreds selected for field resistance and susceptibility reactions to Striga at the International Institute of Tropical Agriculture. Haustorial invasion of the parasite into roots of these inbreds was examined histologically. Morphological differences were observed between roots of the susceptible and the resistant inbreds. The resistant maize had fewer Striga attachments, delayed parasitic development and higher mortality of attached parasites compared with the susceptible inbred. Striga on the susceptible inbred usually penetrated the xylem and showed substantial internal haustorial development. Haustorial ingress on the resistant inbred was often stopped at the endodermis. Parasites able to reach resistant host xylem vessels showed diminished haustorial development relative to those invading susceptible roots. These results suggest that the resistant inbred expresses a developmental barrier and incompatible response against Striga parasitism.
Integrating biotechnology, breeding, and agronomy in the control of the parasitic weed Striga spp in sorghum
  • G Ejeta
Ejeta, G. 2005. Integrating biotechnology, breeding, and agronomy in the control of the parasitic weed Striga spp in sorghum. In the Wake of the Double Helix: From the Green Revolution to the Gene Revolution Tuberosa, R., Phillips, R.L., Gale. M. (eds) Bologna, Italy. pp. 239-251.
Determination of levels of Striga germination Stimulants for maize gene bank accessions and elite inbred lines
  • H Karaya
  • K Njoroge
  • S Mugo
  • E Ariga
  • F Kanampiu
  • J Nderitu
Karaya, H., Njoroge, K., Mugo, S., Ariga, E., Kanampiu, F., Nderitu, J. 2012. Determination of levels of Striga germination Stimulants for maize gene bank accessions and elite inbred lines.
Análisis multivariante de la colección nuclear de la raza Avati Morotî de Paraguay
  • O J Noldin Almiron
Noldin Almiron, O.J. 2008. Análisis multivariante de la colección nuclear de la raza Avati Morotî de Paraguay. DEA en agronomía Universidad de Vigo, España.
GenAlEx 6.5: genetic analysis in Excel. Population genetic software for teaching and research-an update
  • P Peakall
  • R Smouse
Peakall, P., Smouse, R. 2012. GenAlEx 6.5: genetic analysis in Excel. Population genetic software for teaching and research-an update. Bioinformatics 28:2537-2539.
  • Nei M.