ResearchPad - agronomy https://www.researchpad.co Default RSS Feed en-us © 2020 Newgen KnowledgeWorks <![CDATA[An improved 7K SNP array, the C7AIR, provides a wealth of validated SNP markers for rice breeding and genetics studies]]> https://www.researchpad.co/article/elastic_article_14581 Single nucleotide polymorphisms (SNPs) are highly abundant, amendable to high-throughput genotyping, and useful for a number of breeding and genetics applications in crops. SNP frequencies vary depending on the species and populations under study, and therefore target SNPs need to be carefully selected to be informative for each application. While multiple SNP genotyping systems are available for rice (Oryza sativa L. and its relatives), they vary in their informativeness, cost, marker density, speed, flexibility, and data quality. In this study, we report the development and performance of the Cornell-IR LD Rice Array (C7AIR), a second-generation SNP array containing 7,098 markers that improves upon the previously released C6AIR. The C7AIR is designed to detect genome-wide polymorphisms within and between subpopulations of O. sativa, as well as O. glaberrima, O. rufipogon and O. nivara. The C7AIR combines top-performing SNPs from several previous rice arrays, including 4,007 SNPs from the C6AIR, 2,056 SNPs from the High Density Rice Array (HDRA), 910 SNPs from the 384-SNP GoldenGate sets, 189 SNPs from the 44K array selected to add information content for elite U.S. tropical japonica rice varieties, and 8 trait-specific SNPs. To demonstrate its utility, we carried out a genome-wide association analysis for plant height, employing the C7AIR across a diversity panel of 189 rice accessions and identified 20 QTLs contributing to plant height. The C7AIR SNP chip has so far been used for genotyping >10,000 rice samples. It successfully differentiates the five subpopulations of Oryza sativa, identifies introgressions from wild and exotic relatives, and is useful for quantitative trait loci (QTL) and association mapping in diverse materials. Moreover, data from the C7AIR provides valuable information that can be used to select informative and reliable SNP markers for conversion to lower-cost genotyping platforms for genomic selection and other downstream applications in breeding.

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<![CDATA[Optimizing planting geometry for barley-Egyptian clover intercropping system in semi-arid sub-tropical climate]]> https://www.researchpad.co/article/elastic_article_14568 Intercropping legumes with cereals has been a common cropping system in short-season rainfed environments due to its increased productivity and sustainability. Intercropping barley (Hordeum vulgare L.) with Egyptian clover (Trifolium alexandrinum L.) could increase the grain yield of barley and improve resource use efficiency of the intercropping system. However, non-optimum planting geometry has been a hurdle in the adaptation of barley-based cropping systems. This study was aimed at optimizing the planting geometry, and assess the productivity and profitability of barley-Egyptian clover intercropping system. Ten different planting geometries, differing in number of rows of barley, width and number of irrigation furrows and planting method were tested. Intercropping barley with Egyptian clover improved 56–68% grain yield of barley compared with mono-cropped barley. Barley remained dominant crop in terms of aggressiveness, relative crowding coefficient and competitive ratio. The amount of water used was linearly increased with increasing size of barley strip from 3 to 8 rows. The highest water use efficiency (4.83 kg/cf3) was recorded for 8-row barley strip system with 120 cm irrigation furrows compared to rest of the planting geometries. In conclusion, 8-rows of barley planted on beds with Egyptian clover in 120 cm irrigation furrows had the highest net income and cost benefit ratio. Therefore, it is recommended that this planting geometry can be used for better economic returns of barley-Egyptian clover intercropping system. However, barley strips with >8 rows were not included in this study, which is limitation of the current study. Therefore, future studies with >8 barley rows in strip should be conducted to infer the economic feasibility and profitability of wider barley strips.

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<![CDATA[Use of multiple traits genomic prediction, genotype by environment interactions and spatial effect to improve prediction accuracy in yield data]]> https://www.researchpad.co/article/elastic_article_14474 Genomic selection has been extensively implemented in plant breeding schemes. Genomic selection incorporates dense genome-wide markers to predict the breeding values for important traits based on information from genotype and phenotype records on traits of interest in a reference population. To date, most relevant investigations have been performed using single trait genomic prediction models (STGP). However, records for several traits at once are usually documented for breeding lines in commercial breeding programs. By incorporating benefits from genetic characterizations of correlated phenotypes, multiple trait genomic prediction (MTGP) may be a useful tool for improving prediction accuracy in genetic evaluations. The objective of this study was to test whether the use of MTGP and including proper modeling of spatial effects can improve the prediction accuracy of breeding values in commercial barley and wheat breeding lines. We genotyped 1,317 spring barley and 1,325 winter wheat lines from a commercial breeding program with the Illumina 9K barley and 15K wheat SNP-chip (respectively) and phenotyped them across multiple years and locations. Results showed that the MTGP approach increased correlations between future performance and estimated breeding value of yields by 7% in barley and by 57% in wheat relative to using the STGP approach for each trait individually. Analyses combining genomic data, pedigree information, and proper modeling of spatial effects further increased the prediction accuracy by 4% in barley and 3% in wheat relative to the model using genomic relationships only. The prediction accuracy for yield in wheat and barley yield trait breeding, were improved by combining MTGP and spatial effects in the model.

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<![CDATA[Effect of internal surface structure of the north wall on Chinese solar greenhouse thermal microclimate based on computational fluid dynamics]]> https://www.researchpad.co/article/Nf5b70015-c0ce-4e08-9dc5-5525c2c91d69

Chinese solar greenhouses are unique facility agriculture buildings and widely used in northeastern China, providing a favorable requirement for crop growth. The north wall configurations play an essential role in heat storage and thermal insulation and directly affect the management of the internal environment. This research is devoted to further improve the thermal performance of the greenhouse and explore the potential of the north wall. A mathematical model was designed to investigate the concave-convex wall configurations based on computational fluid dynamics. Four passive heat-storage north walls were analyzed by using the same constituent materials, including a plane wall, a vertical wall, a horizontal wall and an alveolate wall. The numerical model was validated by experimental measurements. The temperature distributions of the north walls were examined and a comparative analysis of the heat storage-release capabilities was carried out. The results showed that the heat-storage capacity of the north wall is affected by the surface structure. Moreover, the critical factor influencing the air temperature is the sum of the heat load released by the wall and the energy increment of greenhouse air. The results suggested that the alveolate wall has preferable thermal accumulation capacity. The concave-convex wall configurations have a wider range of heat transfer performance along the thickness direction, while the plane wall has a superior thermal environment. This study provides a basic theoretical reference to rationally design the internal surface structures of the north wall.

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<![CDATA[The role of embryo contact and focal adhesions during maternal recognition of pregnancy]]> https://www.researchpad.co/article/5c8823f5d5eed0c484639429

Maternal recognition of pregnancy (MRP) in the mare is an unknown process. In a non-pregnant mare on day 14 post-ovulation (PO), prostaglandin F (PGF) is secreted by the endometrium causing regression of the corpus luteum. Prior to day 14, MRP must occur in order to attenuate secretion of PGF. The embryo is mobile throughout the uterus due to uterine contractions from day of entry to day 14. It is unknown what signaling is occurring. Literature stated that infusing oil or placing a glass marble into the equine uterus prolongs luteal lifespan and that in non-pregnant mares, serum exosomes contain miRNA that are targeting the focal adhesion (FA) pathway. The hypothesis of this study is embryo contact with endometrium causes a change in abundance of focal adhesion molecules (FA) in the endometrium leading to decrease in PGF secretion. Mares (n = 3/day) were utilized in a cross-over design with each mare serving as a pregnant and non-pregnant (non-mated) control on days 9 and 11 PO. Mares were randomly assigned to collection day and endometrial samples and embryos were collected on the specified day. Biopsy samples were divided into five pieces, four for culture for 24 hours and one immediately snap frozen. Endometrial biopsies for culture were placed in an incubator with one of four treatments: [1] an embryo in contact on the luminal side of the endometrium, [2] beads in contact on the luminal side of the endometrium, [3] peanut oil in contact on the luminal side of the endometrium or [4] the endometrium by itself. Biopsies and culture medium were frozen for further analysis. RNA and protein were isolated from biopsies for PCR and Western blot analysis for FA. PGF assays were performed on culture medium to determine concentration of PGF. Statistics were performed using SAS (P ≤ 0.05 indicated significance). The presence of beads on day 9 impacted samples from pregnant mares more than non-pregnant mares and had very little impact on day 11. Presence of oil decreased FA in samples from pregnant mares on day 9. On day 11, oil decreased FA abundance in samples from non-pregnant mares. Embryo contact caused multiple changes in RNA and protein abundance in endometrium from both pregnant and non-pregnant mares. The PGF secretion after 24 hours with each treatment was also determined. On day 9, there was no change in PGF secretion compared to any treatments. On day 11, presence of peanut oil increased PGF secretion in samples from non-pregnant mares. In samples from non-pregnant mares, presence of an embryo decreased PGF secretion compared to control samples from non-pregnant mares. Results revealed that while beads and peanut oil may impact abundance of FA RNA and protein in endometrial samples, it does not appear to impact PGF secretion. Conversely, embryo contact for 24 hours with endometrium from a non-pregnant mare causes a decrease in PGF secretion. These results suggest that it is not just contact of any substance/object causing attenuation of PGF secretion, but the embryo itself is necessary to decrease PGF secretion.

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<![CDATA[Combining biophysical parameters, spectral indices and multivariate hyperspectral models for estimating yield and water productivity of spring wheat across different agronomic practices]]> https://www.researchpad.co/article/5c897762d5eed0c4847d2b85

Manipulating plant densities under different irrigation rates can have a significant impact on grain yield and water use efficiency by exerting positive or negative effects on ET. Whereas traditional spectral reflectance indices (SRIs) have been used to assess biophysical parameters and yield, the potential of multivariate models has little been investigated to estimate these parameters under multiple agronomic practices. Therefore, both simple indices and multivariate models (partial least square regression (PLSR) and support vector machines (SVR)) obtained from hyperspectral reflectance data were compared for their applicability for assessing the biophysical parameters in a field experiment involving different combinations of three irrigation rates (1.00, 0.75, and 0.50 ET) and five plant densities (D1: 150, D2: 250, D3: 350, D4: 450, and D5: 550 seeds m-2) in order to improve productivity and water use efficiency of wheat. Results show that the highest values for green leaf area, aboveground biomass, and grain yield were obtained from the combination of D3 or D4 with 1.00 ET, while the combination of 0.75 ET and D3 was the best treatment for achieving the highest values for water use efficiency. Wheat yield response factor (ky) was acceptable when the 0.75 ET was combined with D2, D3, or D4 or when the 0.50 ET was combined with D2 or D3, as the ky values of these combinations were less than or around one. The production function indicated that about 75% grain yield variation could be attributed to the variation in seasonal ET. Results also show that the performance of the SRIs fluctuated when regressions were analyzed for each irrigation rate or plant density specifically, or when the data of all irrigation rates or plant densities were combined. Most of the SRIs failed to assess biophysical parameters under specific irrigation rates and some specific plant densities, but performance improved substantially for combined data of irrigation rates and some specific plant densities. PLSR and SVR produced more accurate estimations of biophysical parameters than SRIs under specific irrigation rates and plant densities. In conclusion, hyperspectral data are useful for predicting and monitoring yield and water productivity of spring wheat across multiple agronomic practices.

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<![CDATA[Options for calibrating CERES-maize genotype specific parameters under data-scarce environments]]> https://www.researchpad.co/article/5c75ac02d5eed0c484d07ff4

Most crop simulation models require the use of Genotype Specific Parameters (GSPs) which provide the Genotype component of G×E×M interactions. Estimation of GSPs is the most difficult aspect of most modelling exercises because it requires expensive and time-consuming field experiments. GSPs could also be estimated using multi-year and multi locational data from breeder evaluation experiments. This research was set up with the following objectives: i) to determine GSPs of 10 newly released maize varieties for the Nigerian Savannas using data from both calibration experiments and by using existing data from breeder varietal evaluation trials; ii) to compare the accuracy of the GSPs generated using experimental and breeder data; and iii) to evaluate CERES-Maize model to simulate grain and tissue nitrogen contents. For experimental evaluation, 8 different experiments were conducted during the rainy and dry seasons of 2016 across the Nigerian Savanna. Breeder evaluation data were also collected for 2 years and 7 locations. The calibrated GSPs were evaluated using data from a 4-year experiment conducted under varying nitrogen rates (0, 60 and 120kg N ha-1). For the model calibration using experimental data, calculated model efficiency (EF) values ranged between 0.88–0.94 and coefficient of determination (d-index) between 0.93–0.98. Calibration of time-series data produced nRMSE below 7% while all prediction deviations were below 10% of the mean. For breeder experiments, EF (0.58–0.88) and d-index (0.56–0.86) ranges were lower. Prediction deviations were below 17% of the means for all measured variables. Model evaluation using both experimental and breeder trials resulted in good agreement (low RMSE, high EF and d-index values) between observed and simulated grain yields, and tissue and grain nitrogen contents. It is concluded that higher calibration accuracy of CERES-Maize model is achieved from detailed experiments. If unavailable, data from breeder experimental trials collected from many locations and planting dates can be used with lower but acceptable accuracy.

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<![CDATA[Does picture background matter? Peopleʼs evaluation of pigs in different farm settings]]> https://www.researchpad.co/article/5c6c75c8d5eed0c4843d0185

Pictures of farm animals and their husbandry systems are frequently presented in the media and are mostly connected to discussions surrounding farm animal welfare. How such pictures are perceived by the broader public is not fully understood thus far. It is presumable that the animalsʼ expressions and body languages as well as their depicted environment or husbandry systems affect public perception. Therefore, the aim of this study is to test how the evaluation of a picture showing a farmed pig is influenced by portrayed attributes, as well as participants’ perceptions of pigs’ abilities in general, and if connection to agriculture has an influence. In an online survey, 1,019 German residents were shown four modified pictures of a pig in a pen. The pictures varied with regards to facial expression and body language of the pig (ʽhappyʼ versus ʽunhappyʼ pig) and the barn setting (straw versus slatted floor pen). Respondents were asked to evaluate both the pen and the welfare of the pig. Two Linear Mixed Models were calculated to analyze effects on pig and pen evaluation. For the pictures, the pen had the largest influence on both pig and pen evaluation, followed by the pigʼs appearance and participants’ beliefs in pigs’ mental and emotional abilities, as well as their connection to agriculture. The welfare of both the ʽhappyʼ and the ʽunhappyʼ pig was assessed to be higher in the straw setting compared to the slatted floor setting in our study, and even the ʽunhappy pigʼ on straw was perceived more positively than the ʽhappy pigʼ on slatted floor. The straw pen was evaluated as being better than the slatted floor pen on the pictures we presented but the pens also differed in level of dirt on the walls (more dirt in the slatted floor pen), which might have influenced the results. Nevertheless, the results suggest that enduring aspects of pictures such as the husbandry system influence perceptions more than a momentary body expression of the pig, at least in the settings tested herein.

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<![CDATA[Oil palm plantations in Peninsular Malaysia: Determinants and constraints on expansion]]> https://www.researchpad.co/article/5c76fde3d5eed0c484e5afe5

Agricultural expansion is one of the leading causes of deforestation in the tropics and in Southeast Asia it is predominantly driven by large-scale production for international trade. Peninsular Malaysia has a long history of plantation agriculture and has been a predominantly resource-based economy where expanding plantations like those of oil palm continue to replace natural forests. Habitat loss from deforestation and expanding plantations threatens Malaysian biodiversity. Expanding industrial plantations have also been responsible for drainage and conversions of peatland forests resulting in release of large amounts of carbon dioxide. The demand for palm oil is expected to increase further and result in greater pressures on tropical forests. Given Malaysia’s high biophysical suitability for oil palm cultivation, it is important to understand patterns of oil palm expansion to better predict forest areas that are vulnerable to future expansion. We study natural forest conversion to industrial oil palm in Peninsular Malaysia between 1988 and 2012 to identify determinants of recent oil palm expansion using logistic regression and hierarchical partitioning. Using maps of recent conversions and remaining forests, we characterize agro-environmental suitability and accessibility for the past and future conversions. We find that accessibility to previously existing plantations is the strongest determinant of oil palm expansion and is significant throughout the study period. Almost all (> 99%) of the forest loss between 1988 and 2012 that has been converted to industrial oil palm plantations is within 1 km from oil palm plantations that have been established earlier. Although most forest conversions to industrial oil palm have been in areas of high biophysical suitability, there has been an increase in converted area in regions with low oil palm suitability since 2006. We find that reduced suitability does not necessarily restrict conversions to industrial oil palm in the region; however, lack of access to established plantations does.

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<![CDATA[Introgression of peanut smut resistance from landraces to elite peanut cultivars (Arachis hypogaea L.)]]> https://www.researchpad.co/article/5c67306ad5eed0c484f37ac6

Smut disease caused by the fungal pathogen Thecaphora frezii Carranza & Lindquist is threatening the peanut production in Argentina. Fungicides commonly used in the peanut crop have shown little or no effect controlling the disease, making it a priority to obtain peanut varieties resistant to smut. In this study, recombinant inbred lines (RILs) were developed from three crosses between three susceptible peanut elite cultivars (Arachis hypogaea L. subsp. hypogaea) and two resistant landraces (Arachis hypogaea L. subsp. fastigiata Waldron). Parents and RILs were evaluated under high inoculum pressure (12000 teliospores g-1 of soil) over three years. Disease resistance parameters showed a broad range of variation with incidence mean values ranging from 1.0 to 35.0% and disease severity index ranging from 0.01 to 0.30. Average heritability (h2) estimates of 0.61 to 0.73 indicated that resistance in the RILs was heritable, with several lines (4 to 7 from each cross) showing a high degree of resistance and stability over three years. Evidence of genetic transfer between genetically distinguishable germplasm (introgression in a broad sense) was further supported by simple-sequence repeats (SSRs) and Insertion/Deletion (InDel) marker genotyping. This is the first report of smut genetic resistance identified in peanut landraces and its introgression into elite peanut cultivars.

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<![CDATA[Genetic diversity and population structure of Miscanthus lutarioriparius, an endemic plant of China]]> https://www.researchpad.co/article/5c5df329d5eed0c484580de8

Miscanthus lutarioriparius is a native perennial Miscanthus species of China, which is currently used as raw material of papermaking and bioenergy crop. It also has been considered as a promising eco-bioindustrial plant, which can offer raw material and gene for the biomass industry. However, lack of germplasm resources and genetic diversity information of M. lutarioriparius have become the bottleneck that prevents the stable and further development of the biomass industry. In the present study, genetic diversity of 153 M. lutarioriparius individuals nine populations was studied using 27 Start Codon Targeted (SCoT) markers. High polymorphic bands (97.67%), polymorphic information content (0.26) and allele number (1.88) showed SCoT as a reliable marker system for genetic analysis in M. lutarioriparius. At the species, the percentage of polymorphic loci [PPL] was 97.2%, Nei’s gene diversity [H] was 0.36, Shannon index [I] was 0.54 and Expected Heterozygosity [He] was 0.56. Genetic variation within populations (84.91%) was higher than among populations (15.09%) based on analysis of molecular variance (AMOVA). Moderate level of genetic differentiation was found in M. lutarioriparius populations (Fst = 0.15), which is further confirmed by STRUCTURE, principal coordinates analysis (PCoA) and an unweighted pair group method with arithmetic mean (UPGMA) analysis that could reveal a clear separation between groups of the north and south of Yangtze River. The gene flow of the populations within the respective south and north of Yangtze River area was higher, but lower between the areas. There was no obvious correlation between genetic distance and geographic distance. The breeding systems, geographical isolation and fragmented habitat of M. lutarioriparius may be due to the high level of genetic diversity, moderate genetic differentiation, and the population, structure. The study further suggests some measure for conservation of genetic resources and provides the genetic basis for improving the efficiency of breeding based on the results of diversity analysis.

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<![CDATA[Investigating changes within the handling system of the largest semi-captive population of Asian elephants]]> https://www.researchpad.co/article/5c5ca28dd5eed0c48441e603

The current extinction crisis leaves us increasingly reliant on captive populations to maintain vulnerable species. Approximately one third of Asian elephants (Elephas maximus) are living in semi-captive conditions in range countries. Their relationship with humans stretches back millennia, yet elephants have never been fully domesticated. We rely on the expertise of traditional handlers (mahouts) to manage these essentially wild animals, yet this profession may be threatened in the modern day. Here, we study the handling system of semi-captive timber elephants in Myanmar; the largest global semi-captive population (~5 000). We investigate how recent changes in Myanmar may have affected the keeping system and mahout-elephant interactions. Structured interviews investigated changes to mahout attitude and experience over the last two decades, as perceived by those who had worked in the industry for at least 10 years (n = 23) and as evaluated in current mahouts (n = 210), finding mahouts today are younger (median age 22yrs), less experienced (median experience 3yrs), and change elephants frequently, threatening traditional knowledge transfer. Mahout-elephant interactions manifested as 5 components (‘job appreciation’; ‘experience is necessary’; ‘human-elephant interaction’; ‘own knowledge’; ‘elephant relationship’), according to Principal Components Analysis. Experienced mahouts and mahouts of bulls and younger elephants were more likely to agree that ‘experience is necessary’ to be a mahout. Mahouts with difficult elephants scored lower on ‘human-elephant interaction’ and a mahout’s perception of their ‘own knowledge’ increased with more experience. Our finding of change in terms of mahout experience, age and commitment in the largest semi-captive elephant population suggests need for formal training and assessment of impacts on elephant welfare; these are findings applicable to thousands of elephants under similar management.

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<![CDATA[Evolution of SSR diversity from wild types to U.S. advanced cultivars in the Andean and Mesoamerican domestications of common bean (Phaseolus vulgaris)]]> https://www.researchpad.co/article/5c5ca2f4d5eed0c48441ee62

Progress in common bean breeding requires the exploitation of genetic variation among market classes, races and gene pools. The present study was conducted to determine the amount of genetic variation and the degree of relatedness among 192 selected common bean advanced cultivars using 58 simple-sequence-repeat markers (SSR) evenly distributed along the 11 linkage groups of the Phaseolus reference map. All the lines belonged to commercial seed type classes that are widely grown in the USA and include both dry bean and snap beans for the fresh and processing markets. Through population structure, principal components analyses, cluster analysis, and discriminant analysis of principal components (DAPC), Andean and Mesoamerican genotypes as well as most American commercial type classes could be distinguished. The genetic relationship among the commercial cultivars revealed by the SSR markers was generally in agreement with known pedigree data. The Mesoamerican cultivars were separated into three major groups—black, small white, and navy accessions clustered together in a distinct group, while great northern and pinto clustered in another group, showing mixed origin. The Andean cultivars were distributed in two different groups. The kidney market classes formed a single group, while the green bean accessions were distributed between the Andean and Mesoamerican groups, showing inter-gene pool genetic admixture. For a subset of 24 SSR markers, we compared and contrasted the genetic diversity of the commercial cultivars with those of wild and domesticated landrace accessions of common bean. An overall reduction in genetic diversity was observed in both gene pools, Andean and Mesoamerican, from wild to landraces to advanced cultivars. The limited diversity in the commercial cultivars suggests that an important goal of bean breeding programs should be to broaden the cultivated gene pool, particularly the genetic diversity of specific commercial classes, using the genetic variability present in common bean landraces.

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<![CDATA[Culturally modified trees or wasted timber: Different approaches to marked trees in Poland’s Białowieża Forest]]> https://www.researchpad.co/article/5c52182ed5eed0c4847976a4

Studies of past forest use traditions are crucial in both understanding the present state of the oldest European forests, and in guiding decisions on future forest conservation and management. Current management of Poland’s Białowieża Forest (BF), one of the best-preserved forests of the European lowlands, is heavily influenced by anecdotal knowledge on forest history. Therefore, it is important to gain knowledge of the forest’s past in order to answer questions about its historical administration, utilisation, and associated anthropogenic changes. Such understanding can then inform future management. This study, based on surveys in Belarussian and Russian archives and a preliminary field survey in ten forest compartments of Białowieża National Park, focuses on culturally-modified trees (CMTs), which in this case are by-products of different forms of traditional forest use. Information about the formation of the CMTs can then be used to provide insight into former forest usage. Two types of CMTs were discovered to be still present in the contemporary BF. One type found in two forms was of 1) pine trees scorched and chopped in the bottom part of the trunk and 2) pine trees with carved beehives. A second type based on written accounts, and therefore known to be present in the past (what we call a ‘ghost CMT’), was of 3) lime-trees with strips of bark peeled from the trunk. Written accounts cover the period of transition between the traditional forest management (BF as a Polish royal hunting ground, until the end of the eighteenth century) and modern, “scientific” forestry (in most European countries introduced in the second half of the nineteenth century). These accounts document that both types of CMTs and the traditional forest uses responsible for their creation were considered harmful to “rational forestry” by the nineteenth-century forest administration. Thus the practices which created CMTs were banned and the trees gradually removed from the forest. Indeed, these activities drew the attention of forest administrators for several decades, and in our view delayed the introduction of new, timber-oriented, forest management in the BF.

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<![CDATA[Criteria for evaluating molecular markers: Comprehensive quality metrics to improve marker-assisted selection]]> https://www.researchpad.co/article/5c478c38d5eed0c484bd0df6

Despite strong interest over many years, the usage of quantitative trait loci in plant breeding has often failed to live up to expectations. A key weak point in the utilisation of QTLs is the “quality” of markers used during marker-assisted selection (MAS): unreliable markers result in variable outcomes, leading to a perception that MAS products fail to achieve reliable improvement. Most reports of markers used for MAS focus on markers derived from the mapping population. There are very few studies that examine the reliability of these markers in other genetic backgrounds, and critically, no metrics exist to describe and quantify this reliability. To improve the MAS process, this work proposes five core metrics that fully describe the reliability of a marker. These metrics give a comprehensive and quantitative measure of the ability of a marker to correctly classify germplasm as QTL[+]/[–], particularly against a background of high allelic diversity. Markers that score well on these metrics will have far higher reliability in breeding, and deficiencies in specific metrics give information on circumstances under which a marker may not be reliable. The metrics are applicable across different marker types and platforms, allowing an objective comparison of the performance of different markers irrespective of the platform. Evaluating markers using these metrics demonstrates that trait-specific markers consistently out-perform markers designed for other purposes. These metrics also provide a superb set of criteria for designing superior marker systems for a target QTL, enabling the selection of an optimal marker set before committing to design.

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<![CDATA[Screening dietary biochanin A, daidzein, equol and genistein for their potential to increase DHA biosynthesis in rainbow trout (Oncorhynchus mykiss)]]> https://www.researchpad.co/article/5c478c8bd5eed0c484bd2fbe

Plant oil utilization in aquafeeds is still the most practical option, although it decreases the content of the nutritionally highly valuable omega-3 fatty acids eicosapentaenoic acid (20:5n-3, EPA) and docosahexaenoic acid (22:6n-3, DHA) in fish. Phytoestrogens and their metabolites are putatively able to affect genes encoding proteins centrally involved in the biosynthesis of EPA and DHA due to their estrogenic potential. Thus, the aim of the study was to screen the potential of the phytoestrogens to stimulate the biosynthesis of EPA and DHA in rainbow trout (Oncorhynchus mykiss). Additionally, the potential effects on growth performance, nutrient composition and hepatic lipid metabolism in rainbow trout were investigated. For that, a vegetable oil based diet served as a control diet (C) and was supplemented with 15 g/kg dry matter of biochanin A (BA), daidzein (DA), genistein (G) and equol (EQ), respectively. These five diets were fed to rainbow trout (initial body weight 83.3 ± 0.4 g) for 52 days. Growth performance and nutrient composition of whole body homogenates were not affected by the dietary treatments. Furthermore, feeding EQ to rainbow trout significantly increased DHA levels by +8% in whole body homogenates compared to samples of fish fed the diet C. A tendency towards increased DHA levels in whole body homogenates was found for fish fed the diet G. Fish fed diets BA and DA lacked these effects. Moreover, EQ and G fed fish showed significantly decreased hepatic mRNA steady state levels for fatty acyl desaturase 2a (delta-6) (fads2a(d6)). In contrast, carnitine palmitoyl transferases 1 (cpt1) hepatic mRNA steady state levels and hepatic Fads2a(d6) protein contents were not affected by the dietary treatment. In conclusion, when combined with dietary vegetable oils, equol and genistein seem to stimulate the biosynthesis of DHA and thereby increase tissue DHA levels in rainbow trout, however, only to a moderate extent.

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<![CDATA[Tofu and fish oil independently modulate serum lipid profiles in rats: Analyses of 10 class lipoprotein profiles and the global hepatic transcriptome]]> https://www.researchpad.co/article/5c605a43d5eed0c4847ccc8f

Soy protein and fish oil are food components that decrease the risk of cardiovascular disease. Previous studies demonstrated that these food components reduced serum cholesterol levels and suppressed hepatic lipogenesis. However, the underlying mechanisms of action of these food components remain unclear. Ten classes of serum lipoprotein profiles showed that dietary tofu, a soybean curd, suppressed cholesterol absorption, while fish oil reduced most of the lipoprotein classes in rats. Tofu and fish oil both halved the level of the lipoprotein class LAC1 (LDL-anti-protease complex), a 15-nm LDL-anti-protease complex, which is speculated to be a cause of atherosclerosis. Moreover, a global transcriptome analysis revealed that tofu inhibited the mRNA expression of genes involved in hepatic lipogenesis, while fish oil stimulated that of genes related to fatty acid degradation. Therefore, tofu and fish oil independently regulate lipid metabolism. The decrease observed in LAC1 may have been due to reduced cholesterol absorption in the tofu diet group and the interference of lipogenesis via the activation of polyunsaturated fatty acid detoxification in the fish oil group.

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<![CDATA[Characterization and performance of castor bean lineages and parents at the UFRB germplasm bank]]> https://www.researchpad.co/article/5c3d0120d5eed0c48403885a

The objective of this work was to characterize 203 lineages and five parents of Ricinus communis L. from the germplasm bank at the Federal University of Recôncavo da Bahia (UFRB), which was established by the Genetic Improvement and Biotechnology Program (NBIO) at the Center for Agrarian, Environmental and Biological Sciences. The study used 35 morpho-agronomic descriptors, proposed by the Ministry of Agriculture, Livestock and Supply, and 12 quantitative descriptors suggested by NBIO. The experiment was conducted in a randomized block design, composed of four blocks, in the experimental field at UFRB in 2014. The frequency and entropy level of the qualitative descriptors were estimated with the Renyi procedure, and an analysis of variance was used for the quantitative descriptors. The analyses were made with the statistical program R. Of the qualitative morpho-agronomic descriptors evaluated, 22.86% had a high level of entropy (above 1.0), and all 12 quantitative descriptors showed significant differences. This indicates genetic variability in the germplasm bank and a satisfactory performance for most of the descriptors evaluated, as well as the possibility of direct and indirect use of the lineages and parents in genetic improvement programs of the species.

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<![CDATA[Topical essential fatty acid oil on wounds: Local and systemic effects]]> https://www.researchpad.co/article/5c390bafd5eed0c48491dd3a

Background

The use of medicinal plants and their derivatives is increasing, and approximately one-third of all traditional herbal medicines are intended for wound treatment. Natural products used in these treatments include vegetable oils, which are rich in essential fatty acids. Once in contact with an ulcerative surface, the oil reaches the blood and lymphatic vessels, thus eliciting systemic effects.

Objective

This study evaluated the local and possible systemic effects of essential fatty acids (sunflower oil) applied topically to rat wounds.

Methods

Cutaneous punch wounds (6 mm) were produced on the dorsa of 30 rats. Saline (SS), mineral oil (MO) or essential fatty acid (EFA) solutions were applied topically. Healing was evaluated after 2, 4 and 10 days (n = 5 per group) by visual and histological/morphometric examination, second harmonic generation (SHG) microscopy, and cytokine and growth factor quantification in the scar tissue (real-time PCR) and in serum (ELISA).

Results

MO/EFA-treated animals had higher IGF-1, leptin, IL-6 and IFN-γ mRNA expression and lower serum IL-6 levels than the control (SS/MO) animals. SHG analysis showed no difference in collagen density between the animals treated with MO and EFA.

Conclusion

EFA treatment induces topical (observed by local IGF-1, leptin, IL-6 and IFN-γ production) and systemic effects, lowering IL-6 levels in the serum. As the oil is widely used to shorten ulcer healing time, studies are needed to evaluate the treatment safety and possible undesired effects.

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<![CDATA[Correlations between growth and wool quality traits of genetically divergent Australian lambs in response to canola or flaxseed oil supplementation]]> https://www.researchpad.co/article/5c37b7c4d5eed0c484490c47

The correlations between growth and wool traits in response to canola and flaxseed oil supplementation were evaluated in Australian prime lambs. Sixty dual-purpose prime lambs including purebred Merino and crossbred lambs were allocated to one of five treatments of lucerne hay basal diet supplemented with isocaloric and isonitrogenous wheat-based pellets. Treatments were: no oil inclusion (Control); 2.5% canola oil; 5% canola oil; 2.5% flaxseed oil and 5% flaxseed oil, with lamb groups balanced by breed and gender. Each lamb was daily supplemented with 1kg of pellets and had free access to lucerne hay and water throughout the 7-week feeding trial, after a 3-week adaptation. Individual animal basal and supplementary pellet feed intakes were recorded daily, while body conformation traits, body condition scores and liveweights were measured on days 0, 21, 35 and 49. The lambs were dye-banded on the mid-side and shorn before commencing the feeding trial and mid-side wool samples were collected from the same dye-banded area of each lamb at the end of the experiment. Correlations between wool quality traits and lamb performance were non-significant (P>0.05). Oil supplementation had no detrimental effect on lamb growth and wool quality traits (P > 0.05). Gender significantly affected wither height gain and fibre diameter. There were significant interactions between oil supplementation and lamb breed on chest girth. The correlations between clean fleece yield (CFY) and other wool quality traits were moderate ranging from 0.29 to 0.55. Moderate to high correlations between fibre diameter (FD) and other wool quality traits were detected (0.46–0.99) with the strongest relationship between FD and wool spinning fineness (SF). The relationship between CFY and wool comfort factor (CF) were positive, while negative relationships between CFY and the others were observed. A combination of 5% oil supplementation and genetics is an effective and strategic management tool for enhancing feed efficiency and growth performance without negative effects on wool quality in dual-purpose lamb production. This is a good outcome for dual-purpose sheep farmers. It essentially means the absorbed nutrients in supplemented lambs yielded good growth performance without any detrimental impact on wool quality; a win-win case of nutrient partitioning into the synthesis of muscle and wool without compromising either traits.

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