<p> Isostatic rebound and climatic changes throughout the Holocene have resulted in several periods of lowered water-levels in the Great Lakes watershed. The Early Holocene lowstand phase corresponds with the Paleoindian period in the Great Lakes Region (11,000-9000 YBP), and subsequent water-level rise has inundated Paleoindian archaeological sites. This research sought to reconstruct the water-level history of Rice Lake (located north of Lake Ontario) in order to identify areas of high potential for submerged prehistoric sites. </p> <p> Over 750 line km of detailed geophysical data (single-beam bathymetry) and 16 sediment cores were collected over a 30 km2 area of Rice Lake. Sediment cores were visually logged and analyzed for particle size, microfossils and microdebitage. Water-level reconstructions accounting for sediment infill and isostatic rebound of the lake record a post Lake Iroquois (after 12 ka BP) Early Holocene lowstand (~10-12 m below present level (bpl)) (EH-1). At 10 ka BP, gradually rising water-levels and establishment of wetlands as indicated by thecamoebian assemblages coincide with a newly discovered Paleoindian occupation of the Mcintyre basin, where quartz microdebitage was found. Waterlevel continued to rise to almost 2 m bpi until 6.5 ka BP, when warmer and drier temperatures caused a sudden drop in water-levels as recorded by a pollen hiatus. After 4 ka BP, water-levels quickly recovered and stabilized as shown by rapid recovery of pre-hiatus thecamoebian biofacies and the establishment of wild rice stands. </p> <p> The small number of known, well-preserved Great Lakes Paleoindian sites has limited analysis of Early Holocene population densities, migration patterns, cultural diffusion, or the chronology of settlement. The method of modelling water-level fluctuations and associated archaeological potential developed in this thesis represents a substantial advance in our understanding of Early Holocene archaeology in the Great Lakes. These methods will have broader application to exploration of submerged terrestrial landscapes elsewhere in the Great Lakes and will allow for future regional synthesis of archaeological site distribution and characteristics. </p> / Thesis / Doctor of Philosophy (PhD)

京都大学 / 新制・論文博士 / 博士(農学) / 乙第13499号 / 論農博第2903号 / 新制||農||1093(附属図書館) / 学位論文||R4||N5405(農学部図書室) / (主査)教授 舟川 晋也, 教授 樋口 浩和, 准教授 真常 仁志 / 学位規則第4条第2項該当 / Doctor of Agricultural Science / Kyoto University / DFAM

京都大学 / 新制・論文博士 / 博士(農学) / 乙第13520号 / 論農博第2908号 / 新制||農||1096(附属図書館) / 学位論文||R4||N5420(農学部図書室) / 京都府立医科大学 / (主査)教授 中﨑 鉄也, 教授 土井 元章, 教授 及川 彰, 准教授 田中 朋之 / 学位規則第4条第2項該当 / Doctor of Agricultural Science / Kyoto University / DGAM

京都大学 / 新制・課程博士 / 博士(農学) / 甲第24678号 / 農博第2561号 / 新制||農||1100(附属図書館) / 学位論文||R5||N5459(農学部図書室) / 京都大学大学院農学研究科応用生物科学専攻 / (主査)教授 佐藤 健司, 教授 菅原 達也, 教授 舟場 正幸 / 学位規則第4条第1項該当 / Doctor of Agricultural Science / Kyoto University / DGAM

京都大学 / 新制・課程博士 / 博士(農学) / 甲第24680号 / 農博第2563号 / 新制||農||1100(附属図書館) / 学位論文||R5||N5461(農学部図書室) / 京都大学大学院農学研究科応用生物科学専攻 / (主査)教授 寺内 良平, 教授 髙野 義孝, 教授 吉田 健太郎 / 学位規則第4条第1項該当 / Doctor of Agricultural Science / Kyoto University / DFAM

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Holistic and growth stage-specific screening is needed for identifying tolerant genotypes and for formulating strategies to mitigate the negative effects of abiotic stresses on crops. The objectives of this study were to characterize the genetic variability of 100 rice lines for early-season vigor, growth and physiological plasticity, and drought and temperature tolerance. Five studies were conducted to accomplish these objectives. In study 1 and 2, 100 rice genotypes consisting of several cultivars and experimental breeding lines were characterized for early-season vigor using several shoot and root morphological, physiological, and yield related traits. In study 3, low- and high-temperature tolerance assessed on select rice cultivars/hybrids during early-season. In study 4, genotypic variability in response to drought stress tolerance using morpo-physiological traits including roots was assessed under pot-culture conditions in a mini-greenhouse conditions. In study 5, the 100 rice genotypes were used to identify and validate SNP markers, and genome-wide association study (GWAS) to generate genotypic and phenotypic data with the objective of identifying new genetic loci controlling drought stress traits. Significant variability was recorded among rice genotypes and treatments for many traits measured. Early-season cumulative vigor response indices (CVRI) developed by summing individual responses indices for each trait varied among the rice genotypes, 21.36 (RU1404196) to 36.17 (N-22). Based on means and standard deviation of the CVRI, rice genotypes were classified as low- (43) and moderately low- (33), high- (16), and very high-vigor (5) groups. Total low-temperature response index values ranged from 18.48 to 23.15 whereas total high-temperature responses index values ranged from 42.01 to 48.82. Antonio, CLXL 745, and Mermentau were identified as sensitive to cold- and heat, and XL 753 was highly cold and heat tolerant genotypes tested. A cumulative drought stress response index (CDSRI) values varied between 14.7 (CHENIERE) and 27.9 (RU1402174) among the genotypes tested. This preliminary analysis of GWA indicated that substantial phenotypic and genotypic diversity exists in the 100 rice genotypes, despite their narrow genetic pool. The stress tolerant and high vigor rice genotypes will be valuable for rice breeders for developing new genotypes best suited under growing environments prone to early-season drought and temperature.

Rice is one of the most important cereal crops for the world population. Flowering time and seed development of rice are directly related to plant regional and ecological adaptions, and productive yield. In this dissertation, to gain knowledge of seed development in rice, the status of post-translational modifications (PTMs) in developing rice seeds was investigated. Numerous modified lysine sites in developing rice seeds were identified utilizing antibody-based affinity enrichment approaches and nano-HPLC/MS/MS analyses of acetylated, succinylated, crotonylated and 2-hydroxyisobutyrylated peptides. Functional annotation analyses indicated that a wide variety of vital biological processes were targeted by lysine PTMs. A number of modified histone and non-histone proteins were found to harbor multiple PTMs, and our findings showed that many modified histone sites were conserved across plant, human, and animal systems. Comprehensive analyses of lysine modification sites illustrated that the sites were highly sequence-specific for distinct motifs. Overall, this study provides a systematic analysis of lysine PTM proteome in plants, which will serve as the basis for future investigations of the regulatory mechanisms and functions of lysine PTMs. The mechanisms of flowering time variances in response to different photoperiods were further studied in the rice mutant, HSS. QTL-seq analysis identified a major effect on chromosome 6 responsible for the phenotypic divergence between Nipponbare (wild-type) and HSS rice. Sequence and mRNA expression analyses confirmed that allelic variants of Hd1 make HSS plants less sensitive to photoperiod by altering expression level of Hd3a. Diurnal expression pattern analyses revealed that DTH8 transcripts were largely affected by Hd1 expression level in both LD and SD. This result suggested that Hd1 may able to regulate DTH8 and DTH8-Hd1 complex abundance in response to day length in rice flowering time regulation. In addition, we discussed the functions of PTMs in flowering time regulation in rice.

Research was conducted at the Mississippi State University Delta Research and Extension Center from 2015 to 2018 to (1) determine the effects of sub-lethal concentrations of paraquat, metribuzin, fomesafen, and cloransulam-methyl applied at different rice growth stages, determine the effects on rice growth of simulated off-target paraquat applications at varying concentration based on a proportionally decreased carrier volume characterize rice response to a sub-lethal concentration of paraquat in combination with common POST and residual herbicides, assess whether starter N fertilizer or different N fertilizer management strategies can aide in rice recover after exposure to a sub-lethal concentration of paraquat, and define a maximum soil concentration of S-metolachlor that will allow rice to germinate and emerge. Rice yield was negatively affected following exposure to paraquat applied any time after rice emergence. Paraquat applications to rice in early reproductive growth reduced rough rice yield and seed germination the greatest. Paraquat plus metribuzin injured rice 68 to 69% 14 and 28 d after treatment (DAT), which was 10 to 13% greater than following paraquat alone or paraquat plus fomesafen. Pooled across metribuzin and fomesafen treatments, paraquat reduced rough rice yields 23%. Paraquat plus 10 different residual herbicides injured rice ≥51% 28 DAT and reduced rough rice yields ≥21%. In spite of starter N fertilizer applications, paraquat injured rice ≥41%, reduced height 57%, reduced dry weight prior to flooding 77%, delayed maturity 10 d, reduced dry weight at maturity 33%, and reduced rough rice yield 35%. Similar results were observed in the N Fertilizer Timing Study. Soil concentrations of s-metolachlor 28 DAT were 30, 31, 32, 36, 61, and 488 ppm following exposure to s-metolachlor applied at 0, 1/64, 1/32, 1/16, 1/4, and 1X concentration. A soil analysis would be the best option to determine levels of s-metolachlor prior to planting rice if an off-target herbicide movement containing s-metolachlor occurred. These data indicate that paraquat can have negative impact on rice growth and development. Therefore, it is crucial that if environmental conditions are conducive for off-target herbicide movement extreme caution should be exercised when applying paraquat adjacent to fields devoted to rice production.

Water level declines in the Mississippi River Valley Alluvial Aquifer (MRVAA) are attributed largely to withdrawals for rice (Oryza sativa L.) irrigation. This study was performed to determine if alternative irrigation strategies for rice could reduce withdrawal from the MRVAA without having an adverse effect on grain yield, grain quality, control of barnyardgrass, and profitability. Research was conducted in Stoneville, MS and 19 on-farm locations across the Delta region of Mississippi from 2014 through 2017 to determine the irrigation threshold for alternate wetting and drying (AWD) rice irrigation, the effect of AWD management on barnyardgrass control, and effects of irrigation water management practice, i.e., conventional flood via cascade (CONV), multiple side inlet (MSI), and MSI coupled with AWD, on aquifer withdrawal, rough rice grain yield, irrigation water use efficiency (IWUE), and net returns above irrigation costs. An AWD threshold of -20 cm below the soil surface had no adverse effect on grain yield or grain quality, reduced irrigation applied by 50%, and improved IWUE by 45% compared to a continuous flood (CF). Control of barnyardgrass in AWD was either maintained or improved compared to CF for both Clearfield and conventional rice production systems. At the production scale, up to 39% less water was applied to AWD compared to CONV and MSI. Rice grain yield for AWD was not different from either CONV or MSI, despite substantial reductions in water use. Relative to standard irrigation strategies, AWD maintained or increased net returns up to $238 ha-1 for pumping depths from 5.5 m to 122 m and diesel prices from $0.42 L-1 to $0.98 L-1. Irrigation water use efficiency was up to 59% greater for AWD relative to conventional systems due to the positive effects of the former on water use while maintaining yield. These data demonstrate that AWD can reduce withdrawal from the MRVAA while maintaining or improving yield and net returns relative to irrigation strategies currently employed across the midsouthern USA rice belt.