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Background Tall fescue (Lolium arundinaceum (Schreb.) S.J. Darbyshire) is a popular perennial grass species for livestock production and amenities in the United States. Tall fescue often forms a symbiotic relationship with fungal endophytes (Epichloë coenophiala) which provides increased plant tolerance to environmental stress compared to endophyte-free plants. However, whether this improved plant performance is the sole result of the unique relationship between the grass and the shoot-dwelling fungal endophyte of rhizosphere origin remains a question. This symbiosis possibly regulates the recruitment of beneficial soil microbial communities in endophyte-infected tall fescue rhizosphere and may offer enhanced nutrients and water acquisition, thereby, providing the plant with an increased tolerance level against environmental stresses. We compared the soil bacterial and fungal community composition and investigated possible community shifts in soil microbial populations based on endophyte infection in tall fescue by analyzing the 16s rRNA gene and ITS specific region. Results Our data revealed that bacterial community richness and the evenness indicated by Shannon Diversity Index (SDI) was greater than 4 in both endophyte-infected and endophyte-free tall fescue soil. In both types tall fescue soil, the prominent bacterial families were Planctomycetaceae, Balstocatellaceae_(subgroup_4), Chitinophagaceae, and Bacillaceae. In the case of soil fungal diversity, the SDI was overall low and ranged between 1.21 for endophyte-free and 1.27 for endophyte-infected tall fescue soil. The prominent fungal phyla were Basidiomycota and Ascomycota, and we observed a clear fungal community difference between endophyte-infected and endophyte-free soil at the phylum level. Moreover, endophyte-infected tall fescue soil showed a greater diversity at the genus level compared to endophyte-free tall fescue soil. In addition, plant-available soil phosphorus (P) is also influenced by the presence of endophytes in tall fescue. Conclusion Our results indicate that there is a tripartite relationship between tall fescue, the presence of fungal endophyte in the tall fescue, and the below-ground soil fungal communities. The dynamic of this three-way interaction perhaps contributes to the nutrient acquisition and stress tolerance by tall fescue possibly by recruiting a diverse array of potentially beneficial soil microbes.
Kishan Mahmud; Kendall Lee; Nicholas Hill; Ali Missaoui. Influence of Tall Fescue Epichloë endophytes on Rhizosphere Soil Microbiome. 2021, 1 .
AMA StyleKishan Mahmud, Kendall Lee, Nicholas Hill, Ali Missaoui. Influence of Tall Fescue Epichloë endophytes on Rhizosphere Soil Microbiome. . 2021; ():1.
Chicago/Turabian StyleKishan Mahmud; Kendall Lee; Nicholas Hill; Ali Missaoui. 2021. "Influence of Tall Fescue Epichloë endophytes on Rhizosphere Soil Microbiome." , no. : 1.
The major forces driving farm-level production for the ever-growing global population have relied upon mechanized farming techniques, synthetic inputs, and developing high-yielding crop varieties. Recently, however, there has been a gradual shift toward developing sustainable approaches addressing the potential use of beneficial traits of the soil-plant microbiome to establish a sustainable food supply as well as to maintain soil and plant health. The intricate relationship of the soil-plant microbiome complex often faces difficulty in the efficient translation for the broad spectrum of audiences across society. In recent years, there has been a growing need to formulate strategies and streamline the global sharing of the generated information on plant microbiome interactions. In this review, we discuss novel and emerging strategies to use indigenous microbial consortia and engineered exogenous microbial inoculants for rhizosphere engineering. In addition, this review also details the use of these microbial consortia to improve crop yields and environmental protection that are currently in practice.
Kishan Mahmud; Ali Missaoui; Kendall C. Lee; Bhawana Ghimire; Holly W. Presley; Shiva Makaju. Rhizosphere Microbiome Manipulation for Sustainable Crop Production. Current Plant Biology 2021, 27, 100210 .
AMA StyleKishan Mahmud, Ali Missaoui, Kendall C. Lee, Bhawana Ghimire, Holly W. Presley, Shiva Makaju. Rhizosphere Microbiome Manipulation for Sustainable Crop Production. Current Plant Biology. 2021; 27 ():100210.
Chicago/Turabian StyleKishan Mahmud; Ali Missaoui; Kendall C. Lee; Bhawana Ghimire; Holly W. Presley; Shiva Makaju. 2021. "Rhizosphere Microbiome Manipulation for Sustainable Crop Production." Current Plant Biology 27, no. : 100210.
Key message Mapping combined with expression and variant analyses in switchgrass, a crop with complex genetics, identified a cluster of candidate genes for leaf wax in a fast-evolving region of chromosome 7K. Abstract Switchgrass (Panicum virgatum L.) is a promising warm-season candidate energy crop. It occurs in two ecotypes, upland and lowland, which vary in a number of phenotypic traits, including leaf glaucousness. To initiate trait mapping, two F2 mapping populations were developed by crossing two different F1 sibs derived from a cross between the tetraploid lowland genotype AP13 and the tetraploid upland genotype VS16, and high-density linkage maps were generated. Quantitative trait locus (QTL) analyses of visually scored leaf glaucousness and of hydrophobicity of the abaxial leaf surface measured using a drop shape analyzer identified highly significant colocalizing QTL on chromosome 7K (Chr07K). Using a multipronged approach, we identified a cluster of genes including Pavir.7KG077009, which encodes a Type III polyketide synthase-like protein, and Pavir.7KG013754 and Pavir.7KG030500, two highly similar genes that encode putative acyl-acyl carrier protein (ACP) thioesterases, as strong candidates underlying the QTL. The lack of homoeologs for any of the three genes on Chr07N, the relatively low level of identity with other switchgrass KCS proteins and thioesterases, as well as the organization of the surrounding region suggest that Pavir.7KG077009 and Pavir.7KG013754/Pavir.7KG030500 were duplicated into a fast-evolving chromosome region, which led to their neofunctionalization. Furthermore, sequence analyses showed all three genes to be absent in the two upland compared to the two lowland accessions analyzed. This study provides an example of and practical guide for trait mapping and candidate gene identification in a complex genetic system by combining QTL mapping, transcriptomics and variant analysis.
Peng Qi; Thomas H. Pendergast; Alex Johnson; Bochra A. Bahri; Soyeon Choi; Ali Missaoui; Katrien M. Devos. Quantitative trait locus mapping combined with variant and transcriptome analyses identifies a cluster of gene candidates underlying the variation in leaf wax between upland and lowland switchgrass ecotypes. Theoretical and Applied Genetics 2021, 134, 1 -19.
AMA StylePeng Qi, Thomas H. Pendergast, Alex Johnson, Bochra A. Bahri, Soyeon Choi, Ali Missaoui, Katrien M. Devos. Quantitative trait locus mapping combined with variant and transcriptome analyses identifies a cluster of gene candidates underlying the variation in leaf wax between upland and lowland switchgrass ecotypes. Theoretical and Applied Genetics. 2021; 134 (7):1-19.
Chicago/Turabian StylePeng Qi; Thomas H. Pendergast; Alex Johnson; Bochra A. Bahri; Soyeon Choi; Ali Missaoui; Katrien M. Devos. 2021. "Quantitative trait locus mapping combined with variant and transcriptome analyses identifies a cluster of gene candidates underlying the variation in leaf wax between upland and lowland switchgrass ecotypes." Theoretical and Applied Genetics 134, no. 7: 1-19.
Switchgrass (Panicum virgatum L.) is a perennial warm-season grass that can serve dual purposes, forage and biofuel feedstock. Because the cell wall accounts for more than half the dry matter weight, breeding for both objectives will largely depend on cell wall components which include cellulose, hemicellulose, and lignin. We used NIRS to measure crude protein, neutral detergent fiber, acid detergent fiber, hemicellulose, cellulose, and Klason lignin to conduct QTL mapping in an F1 population derived from a cross between tetraploid lowlands AP13 and B6 with 285 progenies. Of the three major cell wall components of the dry matter, cellulose was the highest (34.51–41.40%), followed by hemicellulose (25.48–33.55%), and Klason lignin (9.70–13.23%). Mapping of biomass and forage quality traits was done using two linkage maps with 2772 SNP markers. We identified 37 significant QTL for all six traits with the highest percentage variance explained by individual QTL in all traits ranging from 4.89 to 8.57%. There are 9 chromosome regions with colocalized QTL of different traits, indicating either pleiotropic gene action or tight linkage between the genes. Improvement of switchgrass for forage and biofuel feedstock quality would benefit from the selection of QTL that contribute directly to the target phenotypes. The frequency of favorable QTL alleles can be enhanced through Genomic Selection.
Rasyidah M. Razar; Shiva Makaju; Ali M. Missaoui. QTL mapping of biomass and forage quality traits measured using near-infrared reflectance spectroscopy (NIRS) in switchgrass. Euphytica 2021, 217, 1 -12.
AMA StyleRasyidah M. Razar, Shiva Makaju, Ali M. Missaoui. QTL mapping of biomass and forage quality traits measured using near-infrared reflectance spectroscopy (NIRS) in switchgrass. Euphytica. 2021; 217 (3):1-12.
Chicago/Turabian StyleRasyidah M. Razar; Shiva Makaju; Ali M. Missaoui. 2021. "QTL mapping of biomass and forage quality traits measured using near-infrared reflectance spectroscopy (NIRS) in switchgrass." Euphytica 217, no. 3: 1-12.
Nitrogen (N) in the agricultural production system influences many aspects of agroecosystems and several critical ecosystem services widely depend on the N availability in the soil. Cumulative changes in regional ecosystem services may lead to global environmental changes. Thus, the soil N status in agriculture is of critical importance to strategize its most efficient use. Nitrogen is also one of the most susceptible macronutrients to environmental loss, such as ammonia volatilization (NH3), nitrous oxide (N2O) emissions, nitrate leaching (NO3), etc. Any form of N losses from agricultural systems can be major limitations for crop production, soil sustainability, and environmental safeguard. There is a need to focus on mitigation strategies to minimize global N pollution and implement agricultural management practices that encourage regenerative and sustainable agriculture. In this review, we identified the avenues of N loss into the environment caused by current agronomic practices and discussed the potential practices that can be adapted to prevent this N loss in production agriculture. This review also explored the N status in agriculture during the COVID-19 pandemic and the existing knowledge gaps and questions that need to be addressed.
Kishan Mahmud; Dinesh Panday; Anaas Mergoum; Ali Missaoui. Nitrogen Losses and Potential Mitigation Strategies for a Sustainable Agroecosystem. Sustainability 2021, 13, 2400 .
AMA StyleKishan Mahmud, Dinesh Panday, Anaas Mergoum, Ali Missaoui. Nitrogen Losses and Potential Mitigation Strategies for a Sustainable Agroecosystem. Sustainability. 2021; 13 (4):2400.
Chicago/Turabian StyleKishan Mahmud; Dinesh Panday; Anaas Mergoum; Ali Missaoui. 2021. "Nitrogen Losses and Potential Mitigation Strategies for a Sustainable Agroecosystem." Sustainability 13, no. 4: 2400.
Predicting alfalfa biomass and crop yield for livestock feed is important to the daily lives of virtually everyone, and many features of data from this domain combined with corresponding weather data can be used to train machine learning models for yield prediction. In this work, we used yield data of different alfalfa varieties from multiple years in Kentucky and Georgia, and we compared the impact of different feature selection methods on machine learning (ML) models trained to predict alfalfa yield. Linear regression, regression trees, support vector machines, neural networks, Bayesian regression, and nearest neighbors were all developed with cross validation. The features used included weather data, historical yield data, and the sown date. The feature selection methods that were compared included a correlation-based method, the ReliefF method, and a wrapper method. We found that the best method was the correlation-based method, and the feature set it found consisted of the Julian day of the harvest, the number of days between the sown and harvest dates, cumulative solar radiation since the previous harvest, and cumulative rainfall since the previous harvest. Using these features, the k-nearest neighbor and random forest methods achieved an average R value over 0.95, and average mean absolute error less than 200 lbs./acre. Our top R2 of 0.90 beats a previous work’s best R2 of 0.87. Our primary contribution is the demonstration that ML, with feature selection, shows promise in predicting crop yields even on simple datasets with a handful of features, and that reporting accuracies in R and R2 offers an intuitive way to compare results among various crops.
Christopher Whitmire; Jonathan Vance; Hend Rasheed; Ali Missaoui; Khaled Rasheed; Frederick Maier. Using Machine Learning and Feature Selection for Alfalfa Yield Prediction. AI 2021, 2, 71 -88.
AMA StyleChristopher Whitmire, Jonathan Vance, Hend Rasheed, Ali Missaoui, Khaled Rasheed, Frederick Maier. Using Machine Learning and Feature Selection for Alfalfa Yield Prediction. AI. 2021; 2 (1):71-88.
Chicago/Turabian StyleChristopher Whitmire; Jonathan Vance; Hend Rasheed; Ali Missaoui; Khaled Rasheed; Frederick Maier. 2021. "Using Machine Learning and Feature Selection for Alfalfa Yield Prediction." AI 2, no. 1: 71-88.
Background Switchgrass (Panicum virgatum) undergoes winter dormancy by sensing photoperiod and temperature changes. It transitions to winter dormancy in early fall following at the end of reproduction and exits dormancy in the spring. The duration of the growing season affects the accumulation of biomass and yield. In this study, we conducted QTL mapping of winter dormancy measured by fall regrowth height (FRH) and normalized difference vegetation index (NDVI), spring emergence (SE), and flowering date (FD) in two bi-parental pseudo-F1 populations derived from crosses between the lowland AP13 with the lowland B6 (AB) with 285 progenies, and the lowland B6 with the upland VS16 (BV) with 227 progenies. Results We identified 18 QTLs for FRH, 18 QTLs for NDVI, 21 QTLs for SE, and 30 QTLs for FD. The percent variance explained by these QTLs ranged between 4.21–23.27% for FRH, 4.47–24.06% for NDVI, 4.35–32.77% for SE, and 4.61–29.74% for FD. A higher number of QTL was discovered in the BV population, suggesting more variants in the lowland x upland population contributing to the expression of seasonal dormancy underlying traits. We identified 9 regions of colocalized QTL with possible pleiotropic gene action. The positive correlation between FRH or NDVI with dry biomass weight suggests that winter dormancy duration could affect switchgrass biomass yield. The medium to high heritability levels of FRH (0.55–0.64 H2) and NDVI (0.30–0.61 H2) implies the possibility of using the traits for indirect selection for biomass yield. Conclusion Markers found within the significant QTL interval can serve as genomic resources for breeding non-dormant and semi-dormant switchgrass cultivars for the southern regions, where growers can benefit from the longer production season.
Rasyidah M. Razar; Ali Missaoui. QTL mapping of winter dormancy and associated traits in two switchgrass pseudo-F1 populations: lowland x lowland and lowland x upland. BMC Plant Biology 2020, 20, 1 -15.
AMA StyleRasyidah M. Razar, Ali Missaoui. QTL mapping of winter dormancy and associated traits in two switchgrass pseudo-F1 populations: lowland x lowland and lowland x upland. BMC Plant Biology. 2020; 20 (1):1-15.
Chicago/Turabian StyleRasyidah M. Razar; Ali Missaoui. 2020. "QTL mapping of winter dormancy and associated traits in two switchgrass pseudo-F1 populations: lowland x lowland and lowland x upland." BMC Plant Biology 20, no. 1: 1-15.
BackgroundSwitchgrass (Panicum virgatum) undergoes winter dormancy by sensing photoperiod and temperature changes. It transitions to winter dormancy in early fall following at the end of reproduction and exits dormancy in the spring. The duration of the growing season affects the accumulation of biomass and yield. In this study, we conducted QTL mapping of winter dormancy measured by fall regrowth height (FRH) and normalized difference vegetation index (NDVI), spring emergence (SE), and flowering date (FD) in two bi-parental pseudo-F1 populations derived from crosses between the lowland AP13 with the lowland B6 (AB) with 285 progenies, and the lowland B6 with the upland VS16 (BV) with 227 progenies. ResultsWe identified 18 QTLs for FRH, 18 QTLs for NDVI, 21 QTLs for SE, and 30 QTLs for FD. The percent variance explained by these QTLs ranged between 4.21 – 23.27% for FRH, 4.47 – 24.06% for NDVI, 4.35 – 32.77% for SE, and 4.61 – 29.74% for FD. A higher number of QTL was discovered in the BV population, suggesting more variants in the lowland x upland population contributing to the expression of seasonal dormancy underlying traits. We identified 9 regions of colocalized QTL with possible pleiotropic gene action. The positive correlation between FRH or NDVI with dry biomass weight suggests that winter dormancy duration could affect switchgrass biomass yield. The medium to high heritability levels of FRH (0.55 – 0.64 H2) and NDVI (0.30 – 0.61 H2) implies the possibility of using the traits for indirect selection for biomass yield. ConclusionMarkers found within the significant QTL interval can serve as genomic resources for breeding non-dormant and semi-dormant switchgrass cultivars for the southern regions, where growers can benefit from the longer production season.
Rasyidah Mohamad Razar; Ali Missaoui. QTL mapping of winter dormancy and associated traits in two switchgrass pseudo-F1 populations: lowland x lowland and lowland x upland. 2020, 1 .
AMA StyleRasyidah Mohamad Razar, Ali Missaoui. QTL mapping of winter dormancy and associated traits in two switchgrass pseudo-F1 populations: lowland x lowland and lowland x upland. . 2020; ():1.
Chicago/Turabian StyleRasyidah Mohamad Razar; Ali Missaoui. 2020. "QTL mapping of winter dormancy and associated traits in two switchgrass pseudo-F1 populations: lowland x lowland and lowland x upland." , no. : 1.
Background Switchgrass (Panicum virgatum) undergoes winter dormancy by sensing photoperiod and temperature changes. It transitions to winter dormancy in early fall following at the end of reproduction and exits dormancy in the spring. The duration of the growing season affects the accumulation of biomass and yield. In this study, we conducted QTL mapping of winter dormancy measured by fall regrowth height (FRH) and normalized difference vegetation index (NDVI), spring emergence (SE), and flowering date (FD) in two bi-parental pseudo-F1 populations derived from crosses between the lowland AP13 with the lowland B6 (AB) with 285 progenies, and the lowland B6 with the upland VS16 (BV) with 227 progenies. Results We identified 18 QTLs for FRH, 18 QTLs for NDVI, 21 QTLs for SE, and 30 QTLs for FD. The percent variance explained by these QTLs ranged between 4.21 – 23.27% for FRH, 4.47 – 24.06% for NDVI, 4.35 – 32.77% for SE, and 4.61 – 29.74% for FD. A higher number of QTL was discovered in the BV population, suggesting more variants in the lowland x upland population contributing to the expression of seasonal dormancy underlying traits. We identified 9 regions of colocalized QTL with possible pleiotropic gene action. The positive correlation between FRH or NDVI with dry biomass weight suggests that winter dormancy duration could affect switchgrass biomass yield. The medium to high heritability levels of FRH (0.55 – 0.64 H2) and NDVI (0.30 – 0.61 H2) implies the possibility of using the traits for indirect selection for biomass yield. Conclusion Markers found within the significant QTL interval can serve as genomic resources for breeding non-dormant and semi-dormant switchgrass cultivars for the southern regions, where growers can benefit from the longer production season.
Rasyidah Mohamad Razar; Ali Missaoui. QTL mapping of winter dormancy and associated traits in two switchgrass pseudo-F1 populations: lowland x lowland and lowland x upland. 2020, 1 .
AMA StyleRasyidah Mohamad Razar, Ali Missaoui. QTL mapping of winter dormancy and associated traits in two switchgrass pseudo-F1 populations: lowland x lowland and lowland x upland. . 2020; ():1.
Chicago/Turabian StyleRasyidah Mohamad Razar; Ali Missaoui. 2020. "QTL mapping of winter dormancy and associated traits in two switchgrass pseudo-F1 populations: lowland x lowland and lowland x upland." , no. : 1.
Background Winter freezing temperature impacts alfalfa (Medicago sativa L.) persistence and seasonal yield and can lead to the death of the plant. Understanding the genetic mechanisms of alfalfa freezing tolerance (FT) using high-throughput phenotyping and genotyping is crucial to select suitable germplasm and develop winter-hardy cultivars. Several clones of an alfalfa F1 mapping population (3010 x CW 1010) were phenotyped for FT using a cold chamber. The population was genotyped with SNP markers identified using genotyping by sequencing (GBS) and the QTL associated with FT were mapped on the parent-specific linkage maps. The ultimate goal is to develop non-dormant and winter-hardy alfalfa cultivars that can produce extended growth in the areas where winters are often mild. Results Alfalfa FT screening method optimized in this experiment comprises three major steps; clone preparation, acclimation, and freezing test. Twenty clones of each genotype were tested, where 10 samples were treated with freezing temperature, and 10 were used as controls. A moderate positive correlation (r ~ 0.36, P < 0.01) was observed between indoor FT and field-based winter hardiness (WH), suggesting that the indoor FT test is useful as an indirect selection method for winter hardiness of alfalfa germplasm. We detected a total of 20 QTL for four traits; visual rating-based FT, percentage survival (PS), treated to control regrowth ratio (RR), and treated to control biomass ratio (BR). Some QTL overlapped with WH QTL reported previously, suggesting a genetic relationship between FT and WH. Some favorable QTL from the winter-hardy parent (3010) potentially represented the genic region of a cold tolerance gene, the c-repeat binding factor (CBF). These QTL were located on the terminal end of chromosome 6 which is considered a location of the CBF homologs in alfalfa.Conclusions The indoor freezing tolerance selection method reported here is valuable for alfalfa breeders to accelerate breeding cycles through indirect selection. The QTL and associated markers add to the genomic resources needed by the alfalfa research community and can be used in marker-assisted selection (MAS) for alfalfa cold tolerance improvement.
Laxman Adhikari; Shiva O. Makaju; Orville M. Lindstrom; Ali Mekki Missaoui. Mapping Freezing Tolerance QTL in Alfalfa Based on Indoor Phenotyping. 2020, 1 .
AMA StyleLaxman Adhikari, Shiva O. Makaju, Orville M. Lindstrom, Ali Mekki Missaoui. Mapping Freezing Tolerance QTL in Alfalfa Based on Indoor Phenotyping. . 2020; ():1.
Chicago/Turabian StyleLaxman Adhikari; Shiva O. Makaju; Orville M. Lindstrom; Ali Mekki Missaoui. 2020. "Mapping Freezing Tolerance QTL in Alfalfa Based on Indoor Phenotyping." , no. : 1.
Background Switchgrass (Panicum virgatum) undergoes seasonal growth changes based on the perception of photoperiod and temperature. It transitions to winter dormancy in early fall, breaks dormancy in the spring, and resumes the cycle starting from flowering which is the cue for senescence. The length of the growing season can impact biomass accumulation and yield. In this study, we conducted QTL mapping of winter dormancy measured by fall regrowth height (FRH) and normalized difference vegetation index (NDVI), spring emergence (SE), and flowering date (FD) in two bi-parental pseudo-F1 populations derived from crosses between the lowland AP13 with the lowland B6 (AB) with 285 progenies, and the lowland B6 with the upland VS16 (BV) with 227 progenies. Results We identified 18 QTLs for FRH, 18 QTLs for NDVI, 21 QTLs for SE, and 30 QTLs for FD. The percent variance explained by these QTLs ranged between 4.21 – 23.27% for FRH, 4.47 – 24.06% for NDVI, 4.35 – 32.77% for SE, and 4.61 – 29.74% for FD. A higher number of QTL was discovered in the BV population, suggesting more variants in the lowland x upland population contributing to the expression of seasonal dormancy underlying traits. We identified 9 regions of colocalized QTL with possible pleiotropic gene action. The positive correlation between FRH or NDVI with dry biomass weight suggests that winter dormancy duration could affect switchgrass biomass yield. The medium to high heritability levels of FRH (0.55 – 0.64 H2) and NDVI (0.30 – 0.61 H2) implies the possibility of using the traits for indirect selection for biomass yield. Conclusion Markers found within the significant QTL interval can serve as genomic resources for breeding non-dormant and semi-dormant switchgrass cultivars for the southern regions, where growers can benefit from the longer production season.
Rasyidah Mohamad Razar; Ali Missaoui. QTL mapping of winter dormancy and associated traits in two switchgrass pseudo-F1 populations: lowland x lowland and lowland x upland. 2020, 1 .
AMA StyleRasyidah Mohamad Razar, Ali Missaoui. QTL mapping of winter dormancy and associated traits in two switchgrass pseudo-F1 populations: lowland x lowland and lowland x upland. . 2020; ():1.
Chicago/Turabian StyleRasyidah Mohamad Razar; Ali Missaoui. 2020. "QTL mapping of winter dormancy and associated traits in two switchgrass pseudo-F1 populations: lowland x lowland and lowland x upland." , no. : 1.
Background Switchgrass (Panicum virgatum) undergoes seasonal growth changes based on the perception of photoperiod and temperature. It transitions to winter dormancy in early fall, breaks dormancy in the spring, and resume the cycle starting from flowering which is the cue for senescence. The length of growing season can impact the biomass accumulation and yield. In this study, we conducted QTL mapping of winter dormancy measured by fall regrowth height (FRH) and normalized difference vegetation index (NDVI), spring emergence (SE), and flowering date (FD) in two bi-parental pseudo-F1 populations derived from crosses between the lowland AP13 with the lowland B6 (AB) with 285 progenies, and the lowland B6 with the upland VS16 (BV) with 227 progenies. Methods Pearson correlation coefficient between phenotypic traits was calculated to determine if some traits can be as surrogates for other traits. Broad-sense heritabilities were calculated to determine the inheritance, and QTL mapping was conducted for two-years phenotypic data to identify QTLs associated with the trais. Results We identified 18 QTLs for FRH, 18 QTLs for NDVI, 21 QTLs for SE, and 30 QTLs for FD. The ranges of percent variance explained by these QTLs varied between 4.21–23.27% for FRH, 4.47–24.06% for NDVI, 4.35–32.77% for SE, and 4.61–29.74% for FD. A higher number of QTL was discovered in the BV population, suggesting more variants in the lowland x upland population contributing to the expression of seasonal dormancy underlying traits. We identified 9 regions of colocalized QTL with possible pleiotropic gene action. The positive correlation between FRH or NDVI with dry biomass weight suggests that winter dormancy level could affect switchgrass biomass yield. The medium to high heritability levels of FRH (0.55–0.64 H2) and NDVI (0.30–0.61 H2) support the possibility of using the traits for indirect selection for biomass yield. Conclusion Markers found within the significant QTL interval can serve as genomic resource for breeding non-dormant and semi-dormant switchgrass cultivars for the southern regions, where growers can benefit from the longer production season.
Rasyidah Mohamad Razar; Ali Missaoui. QTL mapping of winter dormancy and associated traits in two switchgrass pseudo-F1 populations: lowland x lowland and lowland x upland. 2020, 1 .
AMA StyleRasyidah Mohamad Razar, Ali Missaoui. QTL mapping of winter dormancy and associated traits in two switchgrass pseudo-F1 populations: lowland x lowland and lowland x upland. . 2020; ():1.
Chicago/Turabian StyleRasyidah Mohamad Razar; Ali Missaoui. 2020. "QTL mapping of winter dormancy and associated traits in two switchgrass pseudo-F1 populations: lowland x lowland and lowland x upland." , no. : 1.
In agroecosystems, nitrogen is one of the major nutrients limiting plant growth. To meet the increased nitrogen demand in agriculture, synthetic fertilizers have been used extensively in the latter part of the twentieth century, which have led to environmental challenges such as nitrate pollution. Biological nitrogen fixation (BNF) in plants is an essential mechanism for sustainable agricultural production and healthy ecosystem functioning. BNF by legumes and associative, endosymbiotic, and endophytic nitrogen fixation in non-legumes play major roles in reducing the use of synthetic nitrogen fertilizer in agriculture, increased plant nutrient content, and soil health reclamation. This review discusses the process of nitrogen-fixation in plants, nodule formation, the genes involved in plant-rhizobia interaction, and nitrogen-fixing legume and non-legume plants. This review also elaborates on current research efforts involved in transferring nitrogen-fixing mechanisms from legumes to non-legumes, especially to economically important crops such as rice, maize, and wheat at the molecular level and relevant other techniques involving the manipulation of soil microbiome for plant benefits in the non-legume root environment.
Kishan Mahmud; Shiva Makaju; Razi Ibrahim; Ali Missaoui. Current Progress in Nitrogen Fixing Plants and Microbiome Research. Plants 2020, 9, 97 .
AMA StyleKishan Mahmud, Shiva Makaju, Razi Ibrahim, Ali Missaoui. Current Progress in Nitrogen Fixing Plants and Microbiome Research. Plants. 2020; 9 (1):97.
Chicago/Turabian StyleKishan Mahmud; Shiva Makaju; Razi Ibrahim; Ali Missaoui. 2020. "Current Progress in Nitrogen Fixing Plants and Microbiome Research." Plants 9, no. 1: 97.
In the article [1], in ‘Methods’ section and ‘G x E and heritability’ subsection, there is an error in the formula of heritability (H2).
Laxman Adhikari; Shiva Om Makaju; Ali M. Missaoui. Correction to: QTL mapping of flowering time and biomass yield in tetraploid alfalfa (Medicago sativa L.). BMC Plant Biology 2019, 19, 452 -1.
AMA StyleLaxman Adhikari, Shiva Om Makaju, Ali M. Missaoui. Correction to: QTL mapping of flowering time and biomass yield in tetraploid alfalfa (Medicago sativa L.). BMC Plant Biology. 2019; 19 (1):452-1.
Chicago/Turabian StyleLaxman Adhikari; Shiva Om Makaju; Ali M. Missaoui. 2019. "Correction to: QTL mapping of flowering time and biomass yield in tetraploid alfalfa (Medicago sativa L.)." BMC Plant Biology 19, no. 1: 452-1.
The genetic and genomic basis of flowering time and biomass yield in alfalfa (Medicago sativa L.) remains poorly understood mainly due to the autopolyploid nature of the species and the lack of adequate genomic resources. We constructed linkage maps using genotyping-by-sequencing (GBS) based single dose allele (SDA) SNP and mapped alfalfa timing of flowering (TOF), spring yield (SY), and cumulative summer biomass (CSB) in a pseudo-testcross F1 population derived from a fall dormant (3010) and a non-dormant (CW 1010) cultivars. We analyzed the quantitative trait loci (QTL) to identify conserved genomic regions and detected molecular markers and potential candidate genes associated with the traits to improve alfalfa and provide genomic resources for the future studies. This study showed that both fall dormant and non-dormant alfalfa cultivars harbored QTL for early and late flowering, suggesting that flowering time in alfalfa is not an indicator of its fall dormancy (FD) levels. A weak phenotypic correlation between the flowering time and fall dormancy (FD) in F1 and checks also corroborated that alfalfa FD and TOF are not the predictors of one another. The relationship between flowering time and alfalfa biomass yield was not strong, but the non-dormant had relatively more SY than dormant. Therefore, selecting superior alfalfa cultivars that are non-dormant, winter-hardy, and early flowering would allow for an early spring harvest with enhanced biomass. In this study, we found 25 QTL for TOF, 17 for SY and six QTL for CSB. Three TOF related QTL were stable and four TOF QTL were detected in the corresponding genomic locations of the flowering QTL of M. truncatula, an indication of possible evolutionarily conserved regions. The potential candidate genes for the SNP sequences of QTL regions were identified for all three traits and these genes would be potential targets for further molecular studies. This research showed that variation in alfalfa flowering time after spring green up has no association with dormancy levels. Here we reported QTL, markers, and potential candidate genes associated with spring flowering time and biomass yield of alfalfa, which constitute valuable genomic resources for improving these traits via marker-assisted selection (MAS).
Laxman Adhikari; Shiva Om Makaju; Ali M. Missaoui. QTL mapping of flowering time and biomass yield in tetraploid alfalfa (Medicago sativa L.). BMC Plant Biology 2019, 19, 1 -15.
AMA StyleLaxman Adhikari, Shiva Om Makaju, Ali M. Missaoui. QTL mapping of flowering time and biomass yield in tetraploid alfalfa (Medicago sativa L.). BMC Plant Biology. 2019; 19 (1):1-15.
Chicago/Turabian StyleLaxman Adhikari; Shiva Om Makaju; Ali M. Missaoui. 2019. "QTL mapping of flowering time and biomass yield in tetraploid alfalfa (Medicago sativa L.)." BMC Plant Biology 19, no. 1: 1-15.
Alfalfa leaf rust caused by the fungal pathogen Uromyces striatus compromises forage yield and quality. We investigated the genetic basis of leaf rust resistance in alfalfa using a F1 mapping population segregating for resistance to the disease in addition to segregation for fall dormancy (FD) and winter hardiness (WH). The objective of this work was to map quantitative trait loci (QTL) associated with alfalfa leaf rust resistance using genotyping-by-sequencing (GBS) SNP markers in the biparental F1 mapping population. The female parent 3010 displayed susceptibility to rust while the male parent CW 1010 was moderately resistant. The mapping population consisted of 184 F1 progenies that were planted with the parents in a randomized complete block (RCBD) design with three replications at Watkinsville and Blairsville, GA. Four clones generated from stem cuttings of each genotype were planted in each replication. Phenotyping rust severity (RS) was based on the NAAIC visual rating scores of 1–5. RS and FD exhibited a negative phenotypic correlation (r = −0.26). RS and WH also exhibited a negative correlation (r = −0.27) suggesting that the dormant and winter hardy genotypes were more susceptible to leaf rust than the non-dormant and cold sensitive. Four QTL for alfalfa leaf rust resistance and one QTL for rust susceptibility were identified in the CW 1010 genetic map while three QTL for rust susceptibility were identified in the 3010 parent. The most important QTL Us-RustR1 explained 13% (R2 = 0.13) of the phenotypic variance. This study suggests that leaf rust resistance in alfalfa is most likely incomplete and has polygenic inheritance. Comparative genome analysis of QTL regions using sequences of significant SNPs revealed homology to M. truncatula sequences that were previously reported for their role in plant defense mechanisms. Validation of the QTLs in different genetic backgrounds as well as fine mapping of the QTL regions would be the next step of this research. The markers presented in this study would be valuable resources for alfalfa genetic improvement via marker-assisted selection (MAS).
Laxman Adhikari; Ali M. Missaoui. Quantitative trait loci mapping of leaf rust resistance in tetraploid alfalfa. Physiological and Molecular Plant Pathology 2019, 106, 238 -245.
AMA StyleLaxman Adhikari, Ali M. Missaoui. Quantitative trait loci mapping of leaf rust resistance in tetraploid alfalfa. Physiological and Molecular Plant Pathology. 2019; 106 ():238-245.
Chicago/Turabian StyleLaxman Adhikari; Ali M. Missaoui. 2019. "Quantitative trait loci mapping of leaf rust resistance in tetraploid alfalfa." Physiological and Molecular Plant Pathology 106, no. : 238-245.
Summer dormancy is an evolutionary response that some perennial cool-season grasses adopted as an avoidance strategy to escape summer drought and heat. It is correlated with superior survival after severe summer droughts in many perennial grass species originating from Mediterranean environments. Understanding the genetic mechanism and environmental determinants of summer dormancy is important for interpreting the evolutionary history of seasonal dormancy and for the development of genomic tools to improve the efficiency of genetic selection for this important trait. The objectives of this research are to assess morphological and biochemical attributes that seem to be specific for the characterization of summer dormancy in tall fescue, and to validate the hypothesis that genes underlying stem determinacy might be involved in the mechanism of summer dormancy. Our results suggest that vernalization is an important requirement in the onset of summer dormancy in tall fescue. Non-vernalized tall fescue plants do not exhibit summer dormancy as vernalized plants do and behave more like summer-active types. This is manifested by continuation of shoot growth and high root activity in water uptake during summer months. Therefore, summer dormancy in tall fescue should be tested only in plants that underwent vernalization and are not subjected to water deficit during summer months. Total phenolic concentration in tiller bases (antioxidants) does not seem to be related to vernalization. It is most likely an environmental response to protect meristems from oxidative stress. Sequence analysis of the TFL1 homolog CEN gene from tall fescue genotypes belonging to summer-dormant and summer-active tall fescue types showed a unique deletion of three nucleotides specific to the dormant genotypes. Higher tiller bud numbers in dormant plants that were not allowed to flower and complete the reproductive cycle, confirmed that stem determinacy is a major component in the mechanism of summer dormancy. The number of variables identified in these studies as potential players in summer dormancy in tall fescue including vernalization, TFL1/CEN, water status, and protection from oxidative stress are a further confirmation that summer dormancy is a quantitative trait controlled by several genes with varying effects and prone to genotype by environment interactions.
Ali M. Missaoui; Dariusz P. Malinowski; William E. Pinchak; Jaime Kigel. Insights into the Drought and Heat Avoidance Mechanism in Summer-Dormant Mediterranean Tall Fescue. Frontiers in Plant Science 2017, 8, 1 .
AMA StyleAli M. Missaoui, Dariusz P. Malinowski, William E. Pinchak, Jaime Kigel. Insights into the Drought and Heat Avoidance Mechanism in Summer-Dormant Mediterranean Tall Fescue. Frontiers in Plant Science. 2017; 8 ():1.
Chicago/Turabian StyleAli M. Missaoui; Dariusz P. Malinowski; William E. Pinchak; Jaime Kigel. 2017. "Insights into the Drought and Heat Avoidance Mechanism in Summer-Dormant Mediterranean Tall Fescue." Frontiers in Plant Science 8, no. : 1.
Molybdenum (Mo) is a critical micronutrient for nitrogen (N) fixation in legumes. Low pH limits the availability of Mo, thereby reducing nodulation and N fixation. This study investigates the effect of Mo supplementation on alfalfa nodulation and its correlation with root and shoot biomass in low-pH soil. Three experiments were conducted in the greenhouse, involving 14 genotypes of alfalfa subjected to four different treatments, unlimed low-pH soil (5.2) with Mo applied (lithium (Li)−Mo+), low-pH soil (5.2) without Mo (Li−Mo−), limed soil (pH 7.3) with Mo applied (Li+Mo+), and limed soil (pH 7.3) without Mo (Li+Mo−). Foliar application of Mo resulted in a significant increase in nodule counts in the 14 alfalfa cultivars grown in low-pH soil (5.2) even though to a lesser extent than in limed soil with neutral pH (7.3). The increase in number of nodules correlated positively with plant root weight and upper plant biomass.
Laxman Adhikari; Ali M. Missaoui. Nodulation response to molybdenum supplementation in alfalfa and its correlation with root and shoot growth in low pH soil. Journal of Plant Nutrition 2017, 40, 2290 -2302.
AMA StyleLaxman Adhikari, Ali M. Missaoui. Nodulation response to molybdenum supplementation in alfalfa and its correlation with root and shoot growth in low pH soil. Journal of Plant Nutrition. 2017; 40 (16):2290-2302.
Chicago/Turabian StyleLaxman Adhikari; Ali M. Missaoui. 2017. "Nodulation response to molybdenum supplementation in alfalfa and its correlation with root and shoot growth in low pH soil." Journal of Plant Nutrition 40, no. 16: 2290-2302.
Two main types of summer dormancy in tall fescue [Schedonorus arundinaceus (Schreb.) Dumort] are recognized, eco-dormancy and endo-dormancy. Endo-dormancy is a physiological response to environmental signals leading to slowing of metabolic activity in meristematic tissues and most likely controlled by circadian clock genes. Therefore, it is genetically inherited and allelic variation among and between summer-dormant and non-dormant varieties is expected. The main objective of this study was to explore the association between dormancy and various candidate genes. Twenty-three genes were amplified and sequenced in two dormant and two non-dormant checks. Nucleotide variants unique to each group were converted to kompetitive allele specific PCR markers and were tested on 52 dormant and non-dormant accessions. Five markers, from the genes CONSTANS and TERMINAL FLOWER showed significant associations (R2 = 0.10 to 0.13, p < 0.05) with field phenotypic scores. These two genes are known to modulate meristem determinacy and growth, suggesting that meristem determinacy is probably one of the mechanisms involved in summer dormancy in tall fescue. Another five markers showed significant associations with the surrogate germination phenotype (R2 = 0.13 to 0.20, p < 0.05). One marker originated from dormancy-associated MADS-box gene sequence, three markers originated from auxin response factors sequences, and one marker was derived from heat shock proteins sequences. These results confirm the implication of photoperiod and temperature in the regulation of summer dormancy. A selection index combining these markers may be valuable for the differentiation between dormant and non-dormant tall fescue genotypes.
Ruyue Ding; Ali M. Missaoui. Candidate gene association with summer dormancy in tall fescue. Euphytica 2017, 213, 58 .
AMA StyleRuyue Ding, Ali M. Missaoui. Candidate gene association with summer dormancy in tall fescue. Euphytica. 2017; 213 (3):58.
Chicago/Turabian StyleRuyue Ding; Ali M. Missaoui. 2017. "Candidate gene association with summer dormancy in tall fescue." Euphytica 213, no. 3: 58.
Tall fescue [Lolium arundinaceum (Schreb.) Darbysh] is a cool-season perennial grass with two major types of germplasm, Continental and Mediterranean. Most Mediterranean germplasm exhibit summer dormancy even when conditions are favorable for growth. Phenotyping summer dormancy in the field is difficult and costly. The objectives of this study are to develop a low-cost surrogate phenotyping approach for summer dormancy. The environmental cues that trigger dormancy in the mother plant would act similarly on seed dormancy and germination and thus may be used as a surrogate phenotype. Germination tests were conducted under various combinations of photoperiod and temperature using two summer-dormant and two non-dormant checks in growth chamber conditions. Combinations of six temperatures (18, 20, 22, 28, 30, 32, and 34°C) and five photoperiods (0:24, 12:12, 14:8, 16:8, and 24:0 h light/dark) were tested for their effect on germination. The data showed that temperature had a larger effect on germination than photoperiod, with higher temperatures reducing the germination of dormant but non-dormant checks. A total of 168 accessions were evaluated for dormancy in field conditions using a combined score of plant regrowth height and senescence based on digital image analysis. Twenty six putative non-dormant and 30 dormant accessions were selected for seed germination testing to establish a correlation between seed germination and field dormancy. The data showed that the ratio of seed germination at 30°C relative to 20°C under the 24 h light photoperiod correlates well (r = 0.7) with field dormancy phenotypes and has potential to be used as proxy for phenotyping summer dormancy in tall fescue. Copyright © 2016. . Copyright © by the Crop Science Society of America, Inc.
R. Ding; A.M. Missaoui. Phenotyping Summer Dormancy in Tall Fescue: Establishment of a Surrogate Phenotype and a Dormancy Rating System in Humid Environments. Crop Science 2016, 56, 2579 -2593.
AMA StyleR. Ding, A.M. Missaoui. Phenotyping Summer Dormancy in Tall Fescue: Establishment of a Surrogate Phenotype and a Dormancy Rating System in Humid Environments. Crop Science. 2016; 56 (5):2579-2593.
Chicago/Turabian StyleR. Ding; A.M. Missaoui. 2016. "Phenotyping Summer Dormancy in Tall Fescue: Establishment of a Surrogate Phenotype and a Dormancy Rating System in Humid Environments." Crop Science 56, no. 5: 2579-2593.