Ali M. Missaoui

Molecular Markers for the Classification of Switchgrass ( Panicum virgatum L.) Germplasm and to Assess Genetic Diversity in Three Synthetic Switchgrass Populations

Information regarding the amount of genetic diversity is necessary to enhance the effectiveness of breeding programs and germplasm conservation efforts. Genetic variation between 21 switchgrass genotypes randomly selected from two lowland (‘Alamo’ and ‘Kanlow’) and one upland (‘Summer’) synthetic cultivars were estimated using restriction fragment length polymorphism (RFLP) markers. Comparison of 85 RFLP loci revealed 92% polymorphism between at least two genotypes from the upland and lowland ecotypes. Within ecotypes, the upland genotypes showed higher polymorphism than lowland genotypes (64% vs. 56%). ‘Kanlow’ had a lower percent of polymorphic loci than ‘Alamo’ (52% vs. 60%). Jaccard distances revealed higher genetic diversity between upland and lowland ecotypes than between genotypes within each ecotype. Hierarchical cluster analysis using Wards minimum variance grouped the genotypes into two major clusters, one representing the upland group and the other the lowland group. Phylogenetic analysis of chloroplast non-coding region trnL (UAA) intron sequences from 34 switchgrass accessions (6 upland cultivars, 2 lowland cultivars, and 26 accessions of unknown affiliation) produced a neighbor-joining dendrogram comprised of two major clusters with 99% bootstrap support. All accessions grouped in the same cluster with the lowland cultivars (‘Alamo’ and ‘Kanlow’) had a deletion of 49 nucleotides. Phenotypic identification of greenhouse-grown plants showed that all accessions with the deletion are of the lowland type. The deletion in trnL (UAA) sequences appears to be specific to lowland accessions and should be useful as a DNA marker for the classification of upland and lowland germplasm.

The effect of low plant density on response to selection for biomass production in switchgrass

Switchgrass (Panicum virgatum L.) is a model bioenergy species with a high biomass production from which renewable sources of fuel and electricity can be generated. The objective of this study was to perform divergent single-plant selection for biomass yield at low plant density, intermate the selected plants in polycrosses, and evaluate the performance of their half-sib (HS) progenies in sward and row plots. One thousand plants from ‘Alamo’ and ‘Kanlow’ populations were planted in unreplicated honeycomb trials with a plant spacing of 120 cm. Moving-ring selection was applied to select 15 high- and 15 low-yielding plants from each population. These were grown in separate polycrosses to create HS-families. Four HS-families from high- and 4 from low-yielding parents of Alamo and Kanlow, along with their bulks were evaluated for 3 years in sward plots with row spacing of 18 cm. Five HS-families from high- and five from low-yielding parents of Alamo and Kanlow were evaluated for 2 years in row plots spaced 76 cm along with their bulks. Overall, the row-plots had 20% higher biomass per unit area than the sward-plots. Across populations and plant densities, the highest-yielding HS-families produced between 2.0 and 9.3 t/ha more biomass than the lowest-yielding HS-families. The mean biomass of the HS-families from parents selected for high-yield was between 0.34 and 4 t/ha higher than the mean of the HS-families from the low-yielding parents. The annual response to selection for the mean and the bulk of the HS-families from the high yielding parents was 19 and 27% higher than the check. These results indicate that on average, high- and low-yielding parental genotypes were effectively selected from the two populations under low plant density.

Biomass production of herbaceous energy crops in the United States: field trial results and yield potential maps from the multiyear regional feedstock partnership

Current knowledge of yield potential and best agronomic management practices for perennial bioenergy grasses is primarily derived from small‐scale and short‐term studies, yet these studies inform policy at the national scale. In an effort to learn more about how bioenergy grasses perform across multiple locations and years, the U.S. Department of Energy (US DOE)/Sun Grant Initiative Regional Feedstock Partnership was initiated in 2008. The objectives of the Feedstock Partnership were to (1) provide a wide range of information for feedstock selection (species choice) and management practice options for a variety of regions and (2) develop national maps of potential feedstock yield for each of the herbaceous species evaluated. The Feedstock Partnership expands our previous understanding of the bioenergy potential of switchgrass, Miscanthus, sorghum, energycane, and prairie mixtures on Conservation Reserve Program land by conducting long‐term, replicated trials of each species at diverse environments in the U.S. Trials were initiated between 2008 and 2010 and completed between 2012 and 2015 depending on species. Field‐scale plots were utilized for switchgrass and Conservation Reserve Program trials to use traditional agricultural machinery. This is important as we know that the smaller scale studies often overestimated yield potential of some of these species. Insufficient vegetative propagules of energycane and Miscanthus prohibited farm‐scale trials of these species. The Feedstock Partnership studies also confirmed that environmental differences across years and across sites had a large impact on biomass production. Nitrogen application had variable effects across feedstocks, but some nitrogen fertilizer generally had a positive effect. National yield potential maps were developed using PRISM‐ELM for each species in the Feedstock Partnership. This manuscript, with the accompanying supplemental data, will be useful in making decisions about feedstock selection as well as agronomic practices across a wide region of the country.

Nodulation Response to Molybdenum Supplementation in Alfalfa and it's Correlation with Root and Shoot Growh in Low Ph Soil

ABSTRACT 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.

Insights into the Drought and Heat Avoidance Mechanism in Summer-Dormant Mediterranean Tall Fescue

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.

Phenotyping Winter Dormancy in Switchgrass to Extend the Growing Season and Improve Biomass Yield

Switchgrass is a prominent bioenergy crop. Like most perennial warm season species, switchgrass undergoes growth suspension in winter as a surviving strategy in temperate climates to protect their meristems from cold injuries and dehydration, while storage organs below ground drive spring regrowth when conditions become favourable. In this paper, we describe a reliable phenotyping method for winter dormancy in switchgrass using various traits including regrowth height after clipping in early fall (FRH), senescence percentage, date of spring regrowth (SRD), and flowering date (FD). FRH and senescence percentage appear to be reliable indicators of the onset of winter dormancy, whereby accessions that initiated dormancy early have a low FRH and a high senescence percentage. Even though it is difficult to have an exact assessment of the duration of dormancy because it is hard to determine with precision the date of growth suspension, SRD can be used as a surrogate indicator of the duration. Flowering date showed low correlations with all the traits and biomass yield suggesting that it may not be a reliable indicator for winter dormancy in switchgrass. Combining the variables FRH, senescence, and SRD in a selection index may provide a reliable tool to phenotype winter dormancy in switchgrass. The strong correlation of these variables with biomass yield makes them useful candidates for the manipulation of the duration of dormancy to increase the growing season and consequently improving biomass production. In southern regions with mild winters, it might be possible through intense selection to develop germplasm with much reduced dormancy or even non-dormant switchgrass germplasm.

Dissecting key adaptation traits in the polyploid perennial Medicago sativa using GBS-SNP mapping

Understanding key adaptation traits is crucial to developing new cultivars with broad adaptations. The main objective of this research is to understand the genetic basis of winter hardiness (WH) and fall dormancy (FD) in alfalfa and the association between the two traits. QTL analysis was conducted in a pseudo-testcross F1 population developed from two cultivars contrasting in FD (3010 with FD = 2 and CW 1010 with FD = 10). The mapping population was evaluated in three replications at two locations (Watkinsville and Blairsville, GA). FD levels showed low to moderate correlations with WH (0.22–0.57). Assessing dormancy in winter is more reliable than in the fall in southern regions with warm winters. The mapping population was genotyped using Genotyping-by-sequencing (GBS). Single dose allele SNPs (SDA) were used for constructing linkage maps. The parental map (CW 1010) consisted of 32 linkage groups spanning 2127.5 cM with 1377 markers and an average marker density of 1.5 cM/SNP. The maternal map (3010) had 32 linkage groups spanning 2788.4 cM with 1837 SDA SNPs with an average marker density of 1.5 cM/SNP. Forty-five significant (P < 0.05) QTLs for FD and 35 QTLs for WH were detected on both male and female linkage maps. More than 75% (22/28) of the dormancy QTL detected from the 3010 parent did not share genomic regions with WH QTLs and more than 70% (12/17) dormancy QTLs detected from CW 1010 parent were localized in different genomic regions than WH QTLs. These results suggest that the two traits have independent inheritance and therefore can be improved separately in breeding programs.