栽培大豆和野生大豆在很多表型上存在比較大的差異，這些差異包括種子大小，豆莢的個數，含油量和蛋白含量以及光合作用能力等。在本研究中，我們利用之前發表的31 株大豆重測序鑒定出的在栽培或者野生群體中固定的單核苷酸多態性位元點（SNP）資料進行分析，目的在於找出潛在的受選擇區域以及鑒定出受到固定SNP 位點影響的與我們關心的性狀相關的基因。我們的研究結果表明，人工選擇的強度要比自然選擇的強度大很多，同時我們利用這些SNP資料鑒定出了幾個可能受選擇的區域。我們結合已經發表的一些數量性狀（豆莢數目，種子酪氨酸含量）的QTL 的資訊，找到了一些在這些QTL 裡面可能起到主要作用的主效基因。結合KEGG 通路，我們發現了一些在植物激素信號轉导通路，植物體與病原相互作用通路，週期節律性通路，澱粉和蔗糖合成相關的通路，碳固定通路上面栽培和野生大豆差異比較大的基因，這些基因可能是人工選擇和自然選擇的產物。我們從中可以看到人工選擇和自然選擇的印記。根據在野生大豆裡面固定而在家養大豆裡面是中頻的那些SNP 的分佈情況，我們推測第四號染色體在自然選中可能具有比較大的作用。另外我們還發現第八號染色體在家養和野生之間的分化程度比較大。在所有的受SNP 位點影響的基因中，有三分之一的基因都在這條染色體上。我們進一步分析這些基因發現，很多重要農藝性狀比如矮化，根的生長，抗除草劑，抗病，抗旱等相關的基因都在這裡面。我們的這些發現對於將來高產大豆的遺傳和分子育種會有比較大的幫助。 / Cultivated and wild soybeans exhibit morphological differences in many traits, such as seed size, pod number, protein and oil content, photosynthesis capacity, etc. Here, we analyzed the fixed SNPs in both cultivated and wild soybeans reported previously by our lab for two aims: one is to search the candidate regions under selection; the other is to identify traits-related genes possessing fixed SNPs leading to non-synonymous changes. Our results indicated that artificial selection is much stronger than natural selection. We identified candidate genomic regions and genes under artificial selection, which play a vital role in several traits of interests including pod number and seed tyrosine content. By searching the Kyoto Encyclopedia of Genes and Genomes (KEGG) database, we further discovered those important genes impacted by domestication and natural selection were enriched in several pathways including plant hormone transduction, plant-pathogen interaction, circadian rhythm, starch and sucrose metabolism, and carbon fixation pathway. Our analysis also suggested that Chromosome04 (Chr04) is important for fitness of wild accessions because that most of the residual SNPs fixed in wild soybeans showed intermediate frequency in cultivated accessions. Significantly, we observed considerable divergence between wild and cultivated accessions on Chr08. Detailed analysis indicated that nearly 30% of the genes located on Chr08 with SNPs fixed either in cultivated or wild soybeans. These genes were associated with many important agronomic traits including dwarfing, root growth, herbicide resistance, pathogen resistance, drought/salt tolerance. Our modeling results would be beneficial for genetic modification and molecule breeding in soybean in the near future. / Detailed summary in vernacular field only. / Pan, Shengkai. / Thesis (M.Phil.)--Chinese University of Hong Kong, 2013. / Includes bibliographical references (leaves 85-101). / Abstracts also in Chinese. / ABSTRACT --- p.i / 摘要 --- p.Iii / Acknowledgements --- p.iv / Table of Contents --- p.v / List of Tables --- p.viii / List of Fignres --- p.ix / Chapter CHAPTER 1 --- LITERATURE REVIEW --- p.1 / Chapter 1.1 --- Morphology differences --- p.2 / Chapter 1.2 --- Herbicide --- p.4 / Chapter 1.2.1 --- Sulfonylureas herbicides --- p.4 / Chapter 1.2.2 --- Herbicide resistance --- p.5 / Chapter CHSPTER 2 --- METHODS --- p.8 / Chapter 2.1 --- SNP detection --- p.9 / Chapter Fignre 2.1. --- SOAPsnp flow chart --- p.10 / Chapter 2.2 --- Fixed SNPs detection --- p.10 / Chapter 2.2.1 --- Fixed SNPs in the wild population at low frequency (FWLC) or at intermediate frequency (FWIC) in the cultivated population --- p.11 / Chapter 2.2.2 --- Fixed SNPs in the cultivated population at low frequency (FCLW) or at intermediate frequency (FCIW) in the wild population --- p.11 / Chapter 2.3 --- InDel detection --- p.12 / Chapter 2.3.1 --- Statistics of conserved InDels in the wild population at low frequency (CWLC), intermediate (CWIC), or high frequency (CWHC) in the cultivated population --- p.13 / Chapter 2.3.2 --- Identification of conserved InDels in the cultivated population at low frequency (CCLW), intermediate (CCIW), or high frequency (CCHW) in the wild population --- p.13 / Chapter 2.4 --- Result visualization --- p.14 / Chapter CHAPTER 3 --- RESULTS --- p.15 / Chapter 3.1 --- Number of fixed SNPs and conserved InDels in cultivated accessions is much more than in wild accessions --- p.16 / Chapter 3.2 --- Candidate regions under selection --- p.24 / Chapter 3.2.1 --- Analysis of wild-unique distribution on Chromosome 04 --- p.24 / Chapter 3.2.2 --- Analysis of distribution on Chromosome 08 --- p.25 / Chapter 3.3 --- Other analysis on fixed SNPs --- p.35 / Chapter 3.3.1 --- Genes with amino acid code changes caused by SNPs fixed in the cultivated population at low frequency in wild population --- p.35 / Chapter 3.3.2 --- Genes with amino acid code changes caused by SNPs fixed in the wild population at low frequency in the cultivated population --- p.44 / Chapter 3.3.3 --- Genes with non-synonymous caused by SNPs fixed in both cultivated and wild populations --- p.56 / Chapter 3.3.4 --- Analysis combining KEGG pathway with genes containing amino acid code change sites resulted from fixed SNPs --- p.60 / Chapter CHAPTER 4 --- DISCUSSION --- p.75 / Chapter 4.1 --- Differences between cultivated and wild soybeans --- p.76 / Chapter 4.2 --- Roles of fixed SNPs in the wild and cultivated populations study --- p.76 / Chapter 4.3 --- The possible reason for number of fixed SNPs and conserved InDels in cultivated soybeans is much more than that in wild soybeans --- p.77 / Chapter 4.3.1 --- Artificial selection is much stronger than natural selection --- p.77 / Chapter 4.3.2 --- Bottleneck in domestication process of cultivated soy bean --- p.78 / Chapter 4.4 --- Notes about fixed SNPs in the gene regions --- p.79 / Chapter 4.5 --- Possible reason for divergence in Chromosome 08 --- p.79 / Chapter 4.6 --- Possible reason for unique pattern of SNPs fixed in wild accessions on Chromosome 04 --- p.80 / Chapter CHAPTER 5 --- PROSPECTIVE --- p.81 / REFERENCES --- p.84

M. Tech. Agriculture / This study evaluated plant growth and symbiotic performance of two soybean genotypes inoculated with five inoculant formulations (i.e. EMDPeat, EMDLiquid, SoyLiquid, SoyPeat and Granular) and a Control of the Bradyrhizobium japonicum strain WB74 at three field sites in Mozambique and a pot experiment in South Africa. The sole aim was to assess whether the inoculant formulations can increase nitrogen fixation and plant growth on the two soybean genotypes.

Bibliography: leaves 134-145. The improvement of drought tolerance of commercial soybean varieties via indirect selection for transpiration efficiency (TE) in breeding programs was investigated. The extent and nature of variation for TE among soybean genotypes were established through glasshouse experiments under well watered conditions, and confirmed in the field under contrasting water stress conditions. The results suggest that increasing TE will be a beneficial strategy to improve soybean grain yield at the crop level, and a protocol developed suited to indirect selection for high TE soybean genotypes under a range of environments. This will have immediate application in the development of soybean varieties specifically adapted to the dryland production areas of the Australian sub-tropics.

Master of Science / Department of Agronomy / William T. Schapaugh Jr / Sudden Death Syndrome (SDS) in soybean, (Glycine max ( L.) Merr.) caused by Fusarium virguliforme, is an increasing problem in commercial soybean production due to the yield loss associated with the disease. Screening for genetic resistance requires extensive visual evaluations. Canopy spectral reflectance may be an indirect tool for selection of SDS resistance as well as grain yield in large segregating populations. The objective of this study was to estimate SDS resistance and seed yield in large diverse soybean populations using canopy spectral reflectance. Spectral reflectance, disease index, maturity and yield were measured on two populations consisting of 160 nested association mapping recombinant inbred lines and checks; and 140 commercial cultivars with checks. Populations were grown in three environments in 2015 and 2016 with historic SDS disease pressure. Entry, environment, and entry by environment sources of variation were significant for disease index, yield, maturity and spectral reflectance. Changes in season average reflectance were correlated to disease index, yield and maturity. Estimation models of disease index, yield and maturity were created with season averages as well as individual day readings for both populations. Season average and individual day models accounted for 11% to 77% of the phenotypic variation in disease and 41% to 93% of yield variation when measurements were taken at the height of disease pressure. Models for disease index and yield models were able to predict significant portions of the phenotypic variation between entries at most environments. These results suggest that it may be possible to estimate resistance to SDS and grain yield in soybeans using spectral reflectance in breeding populations.

Thesis (MSc. (Botany)) -- University of Limpopo, 2015 / Soybean is an important source of high quality protein and oil for both humans and animals, especially in protein formulations for pharmaceutical and nutriceutical use. This crop is adversely affected by both biotic and abiotic stresses impacting on its productivity. Soybean productivity can be improved via techniques such Agrobacterium-mediated genetic transformation. Soybean is recalcitrant and depends on suitable explants from which new shoots can be regenerated and be amenable for transformation. The goal of this study was to produce transgenic soybean plants that are tolerant to drought stress through Agrobacterium tumefaciens-mediated transformation. Multiple shoot induction on double and single coty-node explants, obtained from soybean seedlings derived from seeds germinated in vitro on Murashige and Skoog culture medium supplemented with cytokinins was studied. The effect of different concentrations of benzyladenine (1.57, 2.00 and 4.00 mg/l), and benzyladenine (2.00 mg/l) in combination with kinetin (1.00 mg/l) was tested. The results show that the double coty-node explants produce the highest number of shoots per explant, an average of 7.93 shoots on Murashige and Skoog medium supplemented with 2.00 mg/l benzyladenine. The lowest number being 1.87 shoots obtained from single coty-node explants cultured on Murashige and Skoog medium containing 4.00 mg/l benzyladenine. The single coty-node explants showed lower frequency (10–57%) of shoot induction when compared to the double coty-node explants (50–83%). The suitability of aminoglycoside antibiotics (hygromycin, tetracycline and rifampicin) for efficient elimination of Agrobacterium tumefaciens after co-cultivation was tested using a well agar diffusion assay. Co-culturing double coty-node explants with Agrobacterium containing pTF 101 vector carrying the Oryza cystatin 1 gene resulted in 76.6, 63.3 and 60.0% shoot regeneration on Murashige and Skoog shoot induction media (shoot induction medium 1, shoot induction medium 2 and shoot induction medium 3) containing hygromycin, tetracycline and rifampicin at 500 mg/l respectively. These antibiotics showed the highest zones of inhibition against pTF 101 using the well agar diffusion assay. On the other hand, 85% plant regeneration was obtained during in vivo transformation following Agrobacterium injection into seedlings. These results imply that vi both in vitro and in vivo protocols were suitable for transgenic shoot regeneration and plant establishment since all the plants continued surviving in the presence of 6.00 mg/l glufosinate-ammonium. Future work will focus on screening of transgenic plants using beta-glucuronidase and isolating the protein encoded by the Oryza cystatin 1 gene to further confirm the generation of transformed plants carrying the gene of interest.

The objective of this thesis was to investigate the genomic changes that have occurred due to the effects of long-term artificial selection applied by soybean breeders. A total of 42 cultivars from six different breeding programs, comprising the multi-generational pedigree of OAC Bayfield were genotyped with molecular markers and chromosomal inheritance was tracked throughout the pedigree. The graphical genotype profile of the 20 chromosomes revealed substantial allelic structure that has been built up in certain chromosomes, in the form of specific linkage blocks, which have been conservatively inherited. A selective sweep analysis using microsatellite markers was performed using the members of OAC Bayfield’s pedigree to identify genomic regions that have retained a molecular selective signature through OAC Bayfield in the varieties derived from it. Overall, there was a high level of agreement between the identified quantitative trait loci (QTL) and the phenotypic traits that would have been expected to be under breeders’ selection.

Thesis(Ph.D.(Botany)) --University of Limpopo,2019 / Genetic transformation offers great opportunities for rapidly introducing, selecting or inducing desired characteristics in various leguminous plants for breeding purposes. But, this technique remains aloof for soybean improvement due to challenges such as genotype specificity, inefficient regeneration protocols and the rapid loss of viability in seeds required to develop explants. However, the rate of seed deterioration and its influence on in-vitro plant genetic transformation differs according to the age, storage duration and moisture content of the seeds used. The moisture status of the seeds is usually high during harvesting and deterioration (loss of viability) starts to occur when seeds are stored under ambient conditions for long periods. This seed deterioration also results in a phenomenon called “recalcitrance”, which is predominantly realised in soybean. In the present study, selected soybean genotypes were analysed for: (i) the efficiency of germination using seeds stored for 0, 3, 6 and 9-months under ambient conditions (ii) the effect of seed storage on in-vitro multiple shoot induction, (iii) the competency of the selected soybean genotypes on callus induction and Agrobacterium-mediated genetic transformation and (iv) the evaluation of protein profiles of the genotypes following co-cultivation of cotyledonary node explants with A. tumefaciens. The results obtained in this study showed that, seed stored for more than 3-months had reduced rates of germination, seedling development and in-vitro shoot multiplication. In particular, seed stored for 9-months showed a significant drop in seed germination, and less than 50% overall seed germination (Dundee-42%, LS678- 49%, TGx140-2F-44% and TGx1835-10E-48%) except for LS677 and Peking with 52 and 55%, respectively. The efficiency of multiple shoot induction also decreased with the prolonged seed storage, with all genotypes recording overall decline from about 96% to 40% regeneration efficiency over this period. The mean number of induced shoots decreased from more than 10.5 to 4.2 shoots per explant, for each genotype. The results obtained clearly indicated that efficient in-vitro shoot induction depended largely on seed storage duration, viability and significantly differed according to genotype. Following the evaluation for callus induction and Agrobacterium-mediated genetic transformation frequencies, the results indicated that the responses were genotype specific. This trend was consecutively observed in all soybean cultivars used (LS677, LS678, Dundee, Peking, TGx1740-2F and TGx1835-10E). Furthermore, the responses of the genotypes were also dependent on the culture media composition,especially, plant growth regulators and antibiotics. Amongst the cultivars used, Peking demonstrated the highest callus induction capacity (more than 70%) on MS-A and the mean number of shoots induced (1.65) using cotyledonary explants co-cultivated with Agrobacterium. This was followed by LS677 (1.42 shoots), LS678 (1.40 shoots), Dundee (1.30 shoots), TGx1835-10E (0.80 shoots) and TGx1740-2F (0.75 shoots), respectively. These genotypes also demonstrated low yields of proteins, extracted using a TCA buffer, and separated by means of two-dimensional polyacrylamide gel electrophoresis. The one-dimensional and two-dimensional profiles of proteins extracted from explants infected with Agrobacterium differed significantly to those expressed without co-cultivation of cotyledonary nodes with bacteria. These observations suggested that, the infection and co-cultivation of explants with Agrobacterium may have caused the expression of new proteins. Newly expressed proteins could also be found to either promote or inhibit transgene integration and expression on the cotyledonary node explants transformed with Agrobacterium tumefaciens for trait improvement. This study has clearly demonstrated that soybean production is confronted with a myriad of stress factors, including seed storage and quality problems due to unfavourable storage duration and weather conditions, amongst others. Thus, soybean seeds used for germination, callus induction, multiple shoot induction and genetic improvement should be harvested at R8 stage after reaching physiological maturity (with 20-35% seed moisture content) to avoid any mechanical damage, shattering or loss of seed viability. / National Research Foundation

Thesis (M.Sc. Agriculture (Crop Science)) -- University of Limpopo, 2011 / The nature and magnitude of the genotype by environment interactions is important to identify superior and stable genotypes under the target environments. This will assist to maximize specific adaptation and to speed up the transfer of new cultivars to growers. The objective of this study was to determine the stability of selected soybean genotypes with regards to the agronomic traits, high yield and nodule formation. Field experiments were conducted under dryland conditions during the 2007/2008 and 2008/2009 growing seasons at the University of Limpopo’s experimental farm (Syferkuil) and at a farmer’s field at Gabaza community, Mopani District near Tzaneen. Ten selected soybean cultivars were evaluated under a randomised complete block design with three replications. Stability was assessed via joint regression and superiority analyses. Significant differences were found for genotypes, environments and genotype by environment interactions. Stability analysis after Eberhart and Russell’s model suggested that the genotypes showed marked differences to environmental changes. The cultivar superiority measure for seed yield indicated that variety Clark was the most stable genotype with an average yield of 5235 kg/ha, followed by L81-4858 and Barc-2 that provided average yield of 4839 kg/ha and 4582 kg/ha, respectively. In terms of number of nodules Magoye was observed to be stable with average of five nodules per plant. Cultivar Barc-2 was found stable for number of active nodules with an average of 3.17 active nodules per plant. Most of the genotypes performed better at Syferkuil than at Gabaza. In general Barc-2 was found stable for yield and other agronomic traits considered in this study. This variety could be suitable for large scale production in these or other similar environments in Limpopo Province.

O elevado valor sócioeconômico da soja é atribuído, em grande parte, à combinação muito favorável de altos teores de proteína e óleo, juntamente com níveis adequados de produtividade de grãos. Porém, existe uma alta correlação negativa entre os teores de proteína e óleo, fato que dificulta o melhoramento simultâneo destes caracteres. Além disso, também existe tendência de correlação negativa e moderada entre o teor de proteína e a produtividade de grãos. Existem evidências de que a seleção para densidade da semente pode promover ganhos indiretos simultâneos no teor de proteína e na produtividade de grãos. Assim, os principais objetivos deste trabalho foram: a) estimar parâmetros genéticos relacionados com a herança da densidade da semente; b) avaliar a eficiência da seleção para densidade da semente no melhoramento do teor de proteína e da produtividade de grãos. Para o estudo de herança foram utilizados quatro cruzamentos diferentes: USP98-06.011.10 x Abura, MSOY 8001 x Abura, USP98-06.027.03 x Biloxi e USP98-06.009.01 x PI 239.235, sendo que os parentais e as plantas F2 foram avaliados durante a safra 2006/07. Já para avaliar as respostas correlacionadas à seleção para densidade da semente foram delineados três experimentos distintos: Experimento Inicial, no qual foram avaliadas 520 progênies F7:6, durante a safra 2005/06; Experimento Densidade, em que foram avaliadas 100 progênies F8:6 selecionadas para densidade da semente; Experimento Alimentos, em que foram avaliadas 100 progênies F8:6 selecionadas para soja tipo alimento. Os dois últimos experimentos foram realizados durante a safra 2006/07, e as progênies avaliadas neles foram selecionadas dentre as 520 progênies F7:6 do Experimento Inicial. Os resultados permitiram chegar as seguintes conclusões: a) existe ampla variabilidade genética para densidade da semente; b) a herdabilidade no sentido amplo para este caráter é baixa quando estimada na geração F2, mas em geração avançada de endogamia atinge valor alto; c) a herança genética é aditiva e, assim, o caráter não manifesta heterose; d) existe correlação moderada e positiva da densidade da semente com a produtividade de grãos e o teor de proteína e, por outro lado, a correlação entre a densidade da semente e o teor de óleo é negativa; e) é possível identificar genótipos tipo alimento com médias altas de produtividade de grãos e teor de proteína; f) a seleção para aumentar a densidade da semente é eficiente no melhoramento simultâneo do teor de proteína e da produtividade de grãos, permitindo a obtenção de genótipos com alta produtividade de proteína; g) a seleção para reduzir a densidade da semente não promove aumentos significativos do teor de óleo. / The high socioeconomic importance of soybean is mainly attributed to its much favorable combination of high protein and oil contents, together with appropriate levels of seed yield. However, there is a high negative correlation between protein and oil contents, fact that difficult the simultaneous breeding of these traits. Besides, also there is tendency of negative and moderate correlation between protein content and seed yield. There are evidences that the selection for seed density can promote indirect responses in protein content and seed yield, simultaneously. The main objectives of this work were: a) to estimate genetic parameters related to inheritance of seed density; b) to evaluate the efficiency of selection for seed density in breeding protein content and seed yield. In the inheritance study, four different crosses were used: USP98-06.011.10 x Abura, M-SOY 8001 x Abura, USP98-06.027.03 x Biloxi e USP98-06.009.01 x PI 239.235. The parents and F2 plants were evaluated during the 2006/07 season. For evaluating the correlated responses to selection for seed density three different experiments were designed: the Initial Experiment, in which were evaluated 520 F7:6 progenies, during the 2005/06 season; the Seed Density Experiment, in that were evaluated 100 F8:6 progenies selected for seed density; and the Food Soybean Experiment, in that were evaluated 100 F8:6 progenies selected for food type soybean. The last two experiments were accomplished during the 2006/07 season, and the progenies were selected among the 520 F7:6 progenies of the Initial Experiment. The results allowed the following conclusions: a) there is genetic variability for seed density; b) the broad sense heritability for seed density is low in F2 and high in advanced generations; c) the genetic inheritance is additive, because this, there is no heterosis for seed density; d) there is moderate and positive correlation of seed density with seed yield and protein content, but the correlation between seed density and oil content is negative; e) is possible to identify food type genotypes with high means of seed yield and protein content; f) the selection to increase seed density is efficient in breeding protein content and seed yield simultaneously, obtaining genotypes with high protein yield; g) the selection to reduce seed density promote no significant increases of oil content.

A study was conducted to determine the responses of 10 selected soybean (Glycine max L.) genotypes to potassium silicate (KSi) and Trichoderma harzianum (Eco-T®) applications. Preliminary studies involving two independent experiments were conducted under controlled conditions at the University of KwaZulu-Natal during 2010. Potassium silicate at three concentrations (0, 200 and 250ppm) were applied twice weekly over a period of four months to the genotypes laid out in a randomized complete block design. Subsequently, a field experiment was conducted at Ukulinga Research Farm of the University of KwaZulu-Natal, Pietermaritzburg during 2010/2011 to investigate the responses of the genotypes to KSi at 0 and 200ppm, with and without(Eco-T®) seed treatment. This experiment was set out in a randomized complete block design with three replications. Data collected included number of days to 50% flowering, number of days to 50% maturity, plant height, number of pods per plant, number of seeds per pod, 100 seed weight, root mass, shoot mass, seed yield and harvest index. The total number of root nodules formed and the number of active nodules were determined at end of the field experiment. In most cases a decrease was noted in total nodule formation as well as a decrease in the number of active nodules that formed. In the controlled environments there was a significant interaction between genotype and KSi concentrations for all measured traits. In most cases KSi applied at 200ppm was more successful in enhancing growth, improving seed yield and resulted in high harvest indices. The genotypes that produced the highest seed yield and harvest index in these environments were Williams and Barc-2 at 200ppm KSi. Results from correlation analysis revealed that harvest index and seed yields were generally positively associated with plant height, number of pods per plant and 100 seed weight, which in turn were the traits that contributed to most of the variation to seed yield and harvest index as revealed in the principle component analysis (PCA). The field experiment revealed a significant interaction between genotype x KSi x Eco-T®. Potassium silicate applied at 200ppm with Eco-T® usually promoted growth, seed yield and high harvest indices for all the genotypes. The PCA showed seed yield and harvest index were the traits that contributed to most of the variation. Genotypes Williams, LS6161R, Magoye and Barc-2 were the best seed yielders with the highest harvest indices that responded strongly to the combined use of KSi and Eco-T® under field conditions. Genetic comparison of the ten soybean genotypes with eight microsatellite markers revealed the close genetic relationship between Williams, LS6161 R and Magoye. A link between Barc-2 and Williams was noted by the common parent Clark. Therefore, for these genotypes, the application of KSi at 200 ppm with Eco-T® under field conditions effectively increased seed yield, ranging from 0.45 to 65.26% for some genotypes when compared to the control. An increase was also noted for other agronomic traits and harvest index. / Thesis (M.Sc.)-University of KwaZulu-Natal, Pietermaritzburg, 2012.