Many recent additions to the US Cotton Germplasm collection are uncharacterized for common germplasm descriptors. Our objective was to evaluate a subset of this germplasm for their potential to contribute to future plant improvement efforts. One hundred fifty four cotton germplasm lines from the former USDA cotton breeding program at Shafter, California were evaluated in the field (LSU AgCenter Northeast Research Station, Saint Joseph, LA) in 2003 along with three modern commercial varieties (Delta and Pine Land �Deltapearl�, �Fibermax 958�, and �Phytogen 355�). Due to limited seed availability, an unreplicated modified augmented statistical design-2 was used, with single row plots 6.14 m long sown at a rate of 7-10 plants m-1. The following descriptors were considered: leaf and calyx pubescence; flower maturity; leaf, pollen and petal color; petal spot; glanding; presence of extra floral nectarines; bract shape. High volume instrumentation (HVI) fiber properties: length, strength, micronaire uniformity, and elongation; and cotton fiber yield. Eleven germplasm lines had yields within 10% the check average, with the top three highest yielding germplasm lines being SA 1961, 1962 and 1960 yielding 1635, 1477, and 1439 lbs acre-1, respectively. SA 2085 could be used to reduce insect damage since it was nectariless. There were 26 germplasm lines graded as having smooth leaves which could be used to reduce the ovipositing of bollworm eggs and get cleaner lint at harvest. In this germplasm, 66 % evaluated had long fiber and the top three were SA 2093, 1983, and 2091, with fiber lengths of 1.27, 1.26, and 1.25 inches, respectively. Much of this germplasm evaluated (82%) had very strong fiber and the top three were SA 2036, 2085, and 2044, with 40.5, 40.0, and 39.7 G/tex, respectively. Six germplasm lines had very high elongation and the top three were SA 2092, 1968, and 2069, with 8.4, 8.1, and 8.1 %, respectively. Over half of the germplasm evaluated (55%) had fine micronaire of between 3.8 and 4.6. In summary, these recent additions to the US Cotton Germplasm Collection present a valuable resource for improving cotton varieties with resistance to insects, yield and fiber quality.

Genetic diversity is indispensable to sustain genetic gain in breeding programs. Cultivated sugarcane is a highly heterozygous hybrid derived from crossing two highly heterozygous parents. Sugarcane breeders traditionally rely on pedigree records to select parents. Molecular markers now make it possible to assess genetic diversity at the DNA level. Sixty three sugarcane clones were characterised using Target Region Amplification Polymorphism (TRAP) markers and pedigree relationship (Coefficient of parentage (COP)). The TRAP is a PCR-based marker with a fixed primer designed from Expressed Sequence Tag (EST) sequences paired with an arbitrary primer. It is supposed to unravel trait based polymorphism in the intronic- or exonic-regions of the genome. Ten genes evidently involved in sucrose accumulation (SUC), cold tolerance (CT) and trichome development (TRICH) were paired with four arbitrary primers. A total of 3,170 bands were scored of which 2,684 (85%) were polymorphic. Cluster and Multi Dimensional Scaling (MDS) analyses revealed a very narrow genetic diversity among the entries with genetic similarity (GS) ranging from 78 to 94%. Parentage did not seem to contribute to the grouping pattern in either the overall or individual gene family (SUC, CT and TRICH) clusters which was confirmed by the lack of correlation (r = -0.008) between the TRAP and COP-derived GS matrices. The complex genome of sugarcane and the strict assumptions inherent with estimating COP may account for this disparity. Analysis of Molecular Variance (AMOVA) revealed no structure in the population with regards to era of release (Pre- versus post-1980) with among clones accounting for up to 99% of the total variation and only 1% of variation attributable to era of release. Mixed Model Analysis on the MDS axes generally revealed no significant differences among era of release. Thus, pedigree records can enhance interpretation of marker-derived information especially in an interspecific crop like sugarcane where ancestral species possess and contribute different characteristics. Results from this study needs to be supplemented with sequence analysis of TRAP fragments to definitively relate the derived information to trait variation.

The loss of Louisiana's coastal wetlands has mandated the construction of diversion structures for reintroduction of a portion of the Mississippi River into Louisiana's coastal region for slowing or reversing marsh deterioration. The Davis Pond Freshwater Diversion Structure allows for a section of the Mississippi River water to be reintroduced into Louisiana's Barataria Basin. The reintroduced Mississippi River water contains elevated levels of nitrate and other nutrients from agricultural runoff primarily from the upper reaches of the Mississippi River drainage basin. These elevated nitrate levels have raised questions of possible eutrophication effects on Louisiana estuaries. The purpose of this study is to monitor changes in concentration of nutrients as the diverted Mississippi River input moves across a 9300 acre (3800ha) of ponded, freshwater marsh. Three sampling sites, inlet, outlet, and Lake Cataouatche, were established at the Davis Pond diversion and samples were collected during various discharge or pulsing events. Change in nutrient concentrations were measured between the inlet and the outlet of the ponded freshwater marsh. Results of the study show efficiency that NO₃-N removal was affected by discharge rate entering the ponded marsh. Discharge rates of 35m³/s showed that the system effectively removed NO₃-N concentrations in diverted river water that were greater than 1 ppm. In contrast, in the month of December, a high discharge rate, even thought nitrate was removed, a significant portion of the NO₃-N passed straight through the ponded system introducing a large amount of Nitrate-N into the lake Cataouatche. Results of the study indicate that the Davis Pond Freshwater Diversion acted conservatively in relation to phosphorus with only a small amount removed. The ponded wetland system acted as a source for ammonia and organic carbon. ICP and Standard Tests for Irrigation Water analyses proved all tested nutrient elements to fall within the low to medium or high to medium when compared to threshold range. Assessments of the capacity of the system to process and assimilate nutrients in diverted Mississippi River water is multifold and longer term evaluations must be performed in order to adequately assess the future capacity of freshwater marsh to process nutrients.

Cotton (Gossypium spp) is an important world crop. Although great improvements have been achieved through traditional breeding methods, cotton breeders are facing many problems, i.e., narrow genetic base, inability to use alien genes and difficulty in breaking gene linkages. Genetic transformations and quantitative trait loci (QTL) analyses are main tools used by breeders to overcome these problems. In this dissertation, an optimized cotton regeneration system from shoot apices was developed. The regeneration rate was increased to 85% by combining rooting induction, indole acetic acid (IAA) shock and graft techniques. The regeneration system is genotype-independent and the whole process takes 12 to 16 weeks. Transgenic cotton plants were obtained via Agrobacterium-mediated transformation using shoot apices as explants. Transformation rates were 0.67% and 1.01% for LBA 4404 with β-glucuronidase (GUS) gene and EHA 105 with Bar gene, respectively. Putative transgenic plants were confirmed by leaf GUS assay, kanamycin or herbicide (Liberty) leaf test, polymerase chain reaction (PCR) and southern blot analysis. Out of 151 polymorphic markers, 53 amplified fragment-length polymorphism (AFLP) markers were assigned to individual chromosomes or chromosome arms by using a set of aneuploid genetic stock. In the QTL analysis of cotton yield and yield components was conducted on an F_2:3 population derived from the intraspecific cross. A previously developed linkage map was used based on same population covering 1733.2 cM (37.7%) cotton genome (4700 cM). A total of 47 markers associated with yield and yield component traits were detected. Nine and seven QTL detected by interval mapping (IM) and composite interval mapping (CIM) methods, respectively, four of which were detected by both methods. For lint yield, two main QTL, explaining 27% of variation, were detected via CIM method. No QTL was detected for bolls per plant by IM method and one QTL explaining 8.56% variation was detected by CIM method. For number of fibers per seed, 23.7% of variation was explained by two main QTL detected by both IM and CIM methods. For mean weight per fiber, two QTL were detected via CIM. No QTL was detected for seed number per boll via either method.

Studies were conducted to evaluate rice competitiveness with red rice and how to utilize glufosinate- and imazethapyr-resistant rice in water-seeded rice to control red rice. In the interference study, CL 121, Cocodrie, Drew, and Jasmine were seeded to obtain 95, 190, and 290 plants/sq m. Red rice density was 0 or 20 red rice plants/sq m. Jasmine, a tall, vigorous tillering, mid-season cultivar was more competitive with red rice. With the exception of Cocodrie grown red rice free, no benefit existed from increasing the seeding rate above 190 plants/sq m. Another study examined the effect of permanent flood establishment in a glufosinate- and imazethapyr-resistant rice system. Glufosinate controlled hemp sesbania, red rice, barnyardgrass, and Amazon sprangletop at least 95%. Imazethapyr controlled hemp sesbania less than 35%. With one exception, barnyardgrass, red rice, and Amazon sprangletop control was at least 95%. Two postemergence imazethapyr applications controlled Amazon sprangletop 79%. All treatments reduced red rice panicle number to less than 1/sq m, but did not delay red rice panicle emergence with respect to rice panicle emergence. Delaying the permanent flood improved rice yield in an imazethapyr system, but not for glufosinate. Another study examined the effect of 500 g/ha glufosinate applied 14, 28, 42, 56, and 70 days after emergence fb 410 g/ha applied 7 d later on rice and red rice. All treatments controlled red rice 91 to 98%. Rice yield was optimized when applications occurred within 35 or 49 DAE for the red rice infested and red rice free treatments, respectively. The fourth study examined imazethapyr use in a water-seeded system receiving no tillage or tilled in the water prior to seeding. Herbicide treatments were 70 g/ha imazethapyr applied 1, 3, or 5 d fb 70 g/ha applied 12 or 19 d after draining the seeding flood (DADSF), 140 g/ha applied 12 or 19 DADSF, and a nontreated. All treatments controlled red rice 88 to 95% and barnyardgrass 73 to 94%. Rice yields did not reflect barnyardgrass control and were higher when the two imazethapyr applications were farther apart.

Best management practices are used by agricultural producers to control or reduce the transport and generation of contaminants to the water resources of the state, ultimately increasing the quality of surface and ground waters. One such practice is residue management used during sugarcane production. The impact of sugarcane residue may have on the retention and release of two herbicides namely; atrazine and metribuzin was the focus of this study is studied. Adsorption-desorption and transport behavior of herbicides are important processes that influence the amount of herbicide retained by the soil or crop residue and that which is susceptible to runoff or movement within the soil profile. Kinetic batch experiments were used to study the adsorption-desorption behavior of atrazine and metribuzin in sugarcane mulch residue and two surface soils. Atrazine retention was consistently stronger than metribuzin for both sugarcane residue and surface soils. To describe the retention of atrazine and metribuzin by the residue as it ages and across growing seasons, only one value (Kd) was needed for each herbicide, and this value is an order of magnitude greater then those determined for surface soils. Miscible displacement experiments under steady flow conditions were also carried out to examine the mobility of the metribuzin within soils. In addition field studies quantified the decay of sugarcane residue in the field following combine harvest. Amounts of residue cover varied with the growing season and variety. Half-lives of 126 to 171 days were determined for sugarcane residue as it remains in the field. With residue age mass decreases leaving greater percentages of more recalcitrant residue such as lignin. Fiber analysis identified these changes, there were no obvious relationships between herbicide retention distribution coefficients and percentage of lignin on a mass basis.

Sheath blight caused by the fungal pathogen fungus Rhizoctonia solani Kuhn, is an economically important disease of rice in the southern United States. The overall goal of this study was to identify proteins that were affected by sheath blight development by comparing protein expression patterns between the susceptible, wild-type cultivar Labelle and the resistant, mutant line LSBR-5. Protein samples were extracted from inoculated and non-inoculated rice leaf sheaths after 24 hrs and then loaded onto a Bio-Rad 2-DE gel system. Approximately 1,000 protein spots stained with Sypro-Ruby were reproducibly resolved in all gels used in the comparison analysis. The comparison analysis of relative abundances of protein spots between inoculated and non-inoculated samples was carried out with PDQUEST image analysis software. With MS/MS spectra produced by ESI-Q-TOF analysis, 27 out of a total of 36 protein spots were identified through NCBI nr and NCBI EST database searching with Mascot MS/MS Ion Search Engines (Matrix Sciences). Twenty two protein spots were detected in response to inoculation of both susceptible and resistant plants where 21 protein spots were up-regulated and 1 protein spot was down- regulated. Sixteen of the 22 proteins were identified. The presumed functions of the identified proteins were related to antifungal activity, energy metabolism, photosynthesis, protein degradation, and antioxidation. Eight of 16 identified proteins showed higher expression ratios in the inoculated LSBR-5 than in the inoculated Labelle. An additional 14 protein spots were detected in the response of the resistant LSBR-5. Eleven of 14 protein spots were identified with presumed functions relating to antifungal activity, signal transduction, energy metabolism, photosynthesis, molecular chaperone, protein degradation, and antioxidation. This study is the first to monitor protein expression patterns of the rice leaf-sheath responding to challenge by R. solani and to detect response differences between resistant mutant and susceptible parental material. The information and detected proteins in this study will serve as a solid foundation for future studies to elucidate induced defense mechanisms of rice when infected with R. solani.

Approximately 5 % of rice growing area in Louisiana experience poor seedling or stand development attributed to anaerobic decomposition of excess plant residue, which create strongly reducing or toxic soil conditions. This study investigated plant residue and flooding regime effects on soil properties as related to rice growth and seedling development. Field experiments were conducted at several commercial farms in Southwest Louisiana (which have experienced problem with rice stand development) to relate observed restricted rice growth to soil redox chemistry and other chemical and physical properties. Field experiments were also conducted at the Crowley Rice Research Station in which various rates of rice straw amendment were added to replicate field plots to determine effect on rice growth and methane emission. The study also include greenhouse experiments on plant residue effect on soil chemical properties as related to rice seedling development and growth including effect of plant residues sources (rice straw or alligator weed on rice seedling germination). These studies showed source and quantity of plant residue significantly affected rice seedling development and germination rates of various commercial rice varieties. Alternating flooded and drained cycles significantly increased growth and grain yield of rice as compared with continuous flooded treatments containing high level of soil plant residue. High rates of plant residue addition increased methane emission (7,350 kg/ha/season) as compared with treatment receiving no added plant residue (370 kg/ha/season). Alternating flooded and drained cycles as compared with continuously flooded resulted in a 50 % reduction in methane emission and increased grain yield by 30 % in treatment receiving 24 t/ha plant residue added. Alligator weed plant residue source had greater effect on rice seedling development as compared with rice straw. Adoption of alternately flooded and drained water management practice, which improves soil chemical properties, can substantially increase rice growth and yield as well as reduces atmosphere methane emission from Louisiana rice soils.

The effect of tillage and weed control programs on LCP 85-384 sugarcane (Saccharum spp. hybrids) growth and yield and on economics was evaluated over two growing seasons. When row shoulders and middles were not tilled in March soil temperature in the non-cultivated sugarcane drill early in the growing season was equal to that where March tillage was performed. Sugarcane and sugar yield were each equivalent for the full season tillage (off-bar tillage in March plus layby tillage in May) and the no-till program. Weeds were effectively controlled with a March application of hexazinone at 0.59 kg ai/ha plus diuron at 2.10 kg ai/ha. For the no-till program with herbicide banded in March compared with full season tillage, net return was increased $32.56/ha. In a subsequent study conducted at five locations sugar yield was increased 8.6% and net return was increased $152.68/ha when sugarcane was not tilled in March. Sugar yield was increased 8.0% and net return was increased $143.88/ha when layby tillage in May was eliminated. Mechanical removal of crop residue remaining on the soil surface three weeks after harvest of LCP 85-384 with a combine harvester was compared with burning. Tillage efficiency in March was not reduced when the residue was mechanically removed from the row top and placed in the row middle. Sugar yield was reduced an average of 7.9% when sugarcane residue was not removed compared with mechanical removal or burning in December. Research was expanded to also include mechanical removal of sugarcane residue in January, February, or March. For each residue removal treatment off-bar tillage in March (with or without) was included. Allowing crop residue to remain on the soil surface until March reduced both early season sugarcane height and shoot population when compared with December residue removal. Sugar yield was equivalent when crop residue was removed in December by burning or mechanically and averaged 8,670 kg/ha. Delaying mechanical removal of residue until February or March decreased sugar yields an average of around 13% compared with December burn or mechanical removal.

Potential outcrossing between Clearfield rice and red rice will have a direct impact on the management and long-term usefulness of imazethapyr technology for rice weed control. The principal objective of this research was to determine the rate and agronomic consequences for outcrossing between Clearfield rice and red rice in south Louisiana. Collection and analysis of red rice samples across two years and 24 commercial locations indicated that red rice infestation after imazethapyr application differed substantially at different Clearfield locations. Straw hull and awnless red rice was the principal biotype observed for both years. Red rice populations possessed extensive variation for agronomic traits such as plant height, panicle length, tillers/plant, seeds/plant, seed set and grain weight. Outcrossing occurred from all Clearfield rice varieties (¡®CL121¡¯, ¡®CL141¡¯ and ¡®CL161¡¯) to red rice. An average outcrossing frequency of 0.163% was observed in red rice samples collected in 2002 with a range of 0.017% to 0.583%. A four-fold increase in outcrossing frequency of 0.679% was found in red rice samples collected in 2003 with two locations exhibiting outcrossing > 1%. Outcrossing frequency did not correlate with any agronomic trait from the red rice samples across two years. Imazethapyr resistance was generally controlled by a single dominant gene, except in some F2 populations where significant deviations from expected resistant/susceptible ratios were detected. Similar results were observed in F2 populations for segregation of pubescent/glabrous leaves. F1 hybrids between Clearfield rice and red rice in general did not show increased fitness in flowering characteristics over Clearfield rice, as most hybrids did not flower or produce seeds in the field. However, increased fitness in F1 hybrids, derived from red rice samples collected in 2002, was detected over Clearfield rice for plant height, tillers/plant, and panicles/plant. Enhanced fitness in F1 hybrids from red rice samples collected in 2003 over Clearfield rice was exhibited for plant height, panicle length, spikelets/panicle, and panicles/plant. Results from this study indicate that outcrossing between Clearfield and red rice will occur rapidly at rates that warrant early-season field scouting and a rotation scheme for Clearfield rice to prolong usefulness of the imazethapyr technology.