Identifying and exploring significant genomic regions associated with soybean yield,seed fatty acids,protein and oil

Soybean [Glycine max (L.) Merrill] yield and seed fatty acids, protein, and oil content are important traits for which an improved understanding of significant genomic regions would be useful. To accomplish this, a soybean population consisting of 203 F5 derived recombinant inbred lines (RILs) was developed and genotyped with 11,633 polymorphic single nucleotide polymorphisms (SNPs). Each RIL was grown in a single plot at Knoxville, TN in 2010; followed by replicated, multi-location field trials in 2013 and 2014. The data from 2010, 2013, and 2014 were analyzed together in order to detect quantitative trait loci (QTL) for these traits, and 30 total QTLs were detected. Five QTLs are candidates for confirmed status and one QTL is a candidate for positional confirmation. Many of the genes with mutations in close proximity to the fatty acid QTLs are involved in biological processes for fatty acids and/or lipids and could be considered possible candidate genes. Similarly, genes with mutations in genomic regions near yield, protein, and oil QTLs were plentiful and may contribute to the variation observed in these traits. Except for yield and stearic acid, each trait displayed pleiotropic effects with other traits in this study. Notable are the pleiotropic effects for oleic and linolenic acid on chromosomes 9, 13, and 19. Overall, the findings from this research contribute new information to the genetic understanding of soybean yield and seed fatty acids, protein and oil content. This understanding will be useful in making trait improvements.     

Genotype by environment interactions (GEIs) for barley grain yield under salt stress condition

Changes in the relative genetic performance of genotypes across environments are referred to as genotype × environment interactions (GEIs). GEIs can affect barley breeding improvement for salt tolerance because it often complicates the evaluation and selection of superior genotypes. The present study evaluated the GEIs over 60 barley genotypes for yield components and grain yield in six salinity environments in North Delta, Egypt. Data were analyzed using the additive main effects and multiplicative interaction (AMMI) and Tai’s stability parameters. GEIs effects on yield explained 20.3, 20.1, 14.6, and 33.0% of the total variation besides, the first two principal components account for 67.3, 56.3, 64.3, and 83.7% of the explained variance in the four sets, respectively. Six genotypes namely G-4, G-7, G-20, G-34, G-36, and G-39 were found to be most stable and high yielding across environments (GY >2.00 t ha^-1), and located close to zero projection onto the AEC ordinate. Tai’s stability parameters demonstrated that these genotypes were more responsive to the environmental changes. The genotypes G-50 and G-53 showed perfect/static stability (α = -0.95, -0.91, respectively). In contrast, the genotype; G-36 had α = 0 and λ = 1.10, indicating parallel with the environmental effects followed by G-44. Overall, we found that GEIs for grain yield are highly significant in all sets, suggesting that responded differently across environments. This interaction may be a result of changes in genotypes’ relative performance across environments, due to their differential responses to various abiotic factors.     

Exploring diversity among rice germplasms based on their physiological traits responses to salinity

Salinity is one of the major abiotic stresses that severely effects rice production throughout the world. Previously, there have not been many studies which focused on studying diversity among rice germplasm based on specific physiological traits for salt tolerance. Our diversity study was based on physiological traits such as Na+ concentration, K⁺ concentration, K⁺/Na⁺ ratio, osmotic potential, and biomass which are major components determining salt tolerance. This study has systematically analyzed phenotypic data of 191 germplasms in two different salt concentrations apart from the control. The current study identified salt tolerant germplasms based on their response to a single physiological trait as well as a combination of different physiological traits. Some of the germplasm identified outperformed known salt tolerant cultivar Pokkali. This study identifies correlation among various physiological traits. The salt tolerant germplasms can be taken forward into developing better varieties by conventional breeding and exploring genes for salt tolerance.     

Geospatial delineation of South Korea for adjusted barley cultivation under changing climate

Determining effective measures to alleviate the impact of climate change on crops under various regional environments is one of the most urgent issues facing agriculture. In this study, geographic regions of South Korea for future-adjusted barley cultivation were outlined and the impact of climate change on barley production in the next 100 years was evaluated under two greenhouse gas concentration trajectory scenarios: the representative concentration pathway (RCP) 4.5 and RCP 8.5. To achieve our intended study goals, a geospatial crop simulation modeling (GCSM) scheme was formulated using CERES-barley model of Decision Support System for Agricultural Technology (DSSAT) crop model package version 4.6 to simulate grid-based geospatial crop yields. Two experiments were carried out at an open field to obtain model coefficients for the nation and at temperature gradient field chambers to evaluate the performance of the CERES-barley model under elevated temperature conditions. Suitable cultivation regions for three different types of barley (naked, hooded, and malting) under changing climate were projected to expand to the northern regions under both RCP 8.5 and RCP 4.5. However, they were projected to expand more rapidly under RCP 8.5 than those under RCP 4.5. Projected yields of four barley varieties were increased with a slow phase as year progressed under RCP 4.5 scenario. However, they were rapidly increased under RCP 8.5 scenario. It appears that geospatial variation in barley yield under changing climate can be effectively outlined. Therefore, GCSM system might be useful for determining impacts of climate change on geospatial variations of crops, potentially providing means to impede food insecurity.     

Allelic composition and associated quality traits of the <Emphasis Type="Italic">Glu-1</Emphasis> and <Emphasis Type="Italic">Glu-3</Emphasis> loci in selected modern Ethiopian durum wheat varieties

Gluten protein determines the processing quality of both durum wheat and bread wheat. The glutenin subunits compositions and associated quality traits of 20 Ethiopian durum wheat varieties were systematically analyzed using SDS-PAGE and Payne numbers. A total of 16 glutenin patterns were identified. At the Glu-A1 locus, all varieties scored the null allele. The predominant glutenin alleles at the Glu-B1 locus were Glu-B1b (7+8) and Glu-B1e (20). In Glu-3, the most abundant glutenin subunits were Glu-A3a and Glu-B3c. Based on the Payne scores, the varieties Yerer, Ginchi, Candate, and Foka were identified to have allelic composition suitable for pasta making. The cluster analysis using agglomerative hierarchical clustering (AHC) method classified the varieties into four similarity classes. Based on the findings of this experiment, suggestions were made for allelic composition improvement through introgression of superior alleles from known Glu-1 and Glu-3 sources.     

Identification and validation of cold responsive microRNAs of <Emphasis Type="Italic">Hevea brasiliensis</Emphasis> using high throughput sequencing

Cold stress is one of the major abiotic factors that influence the productivity and geographical distribution of many agriculturally important crops like Hevea brasiliensis. Cultivation of H. brasiliensis in India is being extended to northeastern regions, where low temperature during winter adversely affects its survival, growth, and productivity. Developing cold-tolerant genotypes is a primary requisite to maximize the productivity under such challenging environmental conditions. However, lack of methods for early evaluation of cold tolerance in the newly developed clones and the extensive time required for assessing their tolerance in the field are major constraints for clonal selection. The present study was initiated with an objective to identify and characterize cold stress responsive miRNAs from H. brasiliensis that show stronger association with cold tolerance. Next generation sequencing using Illumina HiSeq method revealed the expression of 21 and 29 conserved miRNA (from clone RRIM 600) families in cold-stressed and control samples, respectively. Forty-two novel miRNAs were identified from this study. Upon differential expression analysis, eight conserved miRNAs were found commonly expressed in both the samples. When expression analyses were performed subsequently with six selected miRNAs in two Hevea clones (viz. RRII 105 and RRIM 600), miR169 showed a strong association with cold tolerance. miRNAs such as miR482 and miR159 also exhibited association with cold tolerance. This study suggests the possibility of employing these miRNAs as markers for cold tolerance after validation in more number of genotypes with varying levels of cold tolerance.     

Efficiency of SNP and SSR-based analysis of genetic diversity,population structure,and relationships among cowpea (<Emphasis Type="Italic">Vigna unguiculata</Emphasis> (L.) Walp.) germplasm from East Africa and IITA inbred lines

The extent of genetic diversity and relatedness of cowpea germplasm from East Africa are poorly understood. A set of 13 microsatellites (SSR) and 151 single nucleotide polymorphisms (SNPs) markers were applied to assess the levels of genetic diversity in a sample of 95 accessions of local cowpea germplasm and inbred lines of Vigna unguiculata. The average genetic diversity (D), as quantified by the expected heterozygosity, was higher for SSR loci (0.52) than for SNPs (0.34). The polymorphic information content was 0.48 for SSR and 0.28 for SNP while the fixation index was 0.095 for SSR and 0.15 for SNPs showing moderate differentiation and high gene flow among cowpea accessions from East African countries. The results of data analysis of both SSR and SNP markers showed similar clustering patterns suggesting a substantial degree of association between origin and genotype. Principal coordinate analysis (PCoA) with SSR and SNP markers showed that accessions were grouped into two and three broad groups across the first two axes, respectively. Our study found that SNP markers were more effective than SSR in determining the genetic relationship among East African local cowpea accessions and IITA inbred lines. Based on this analysis, five local cowpea accessions Tvu-13490, Tvu-6378, Tvu-13448, Tvu-16073, and 2305675 were identified to be tightly clustered sharing several common alleles with the drought tolerant variety Danila when analyzed with SSR and SNP markers. The findings will assist and contribute to future genetic diversity studies aimed at the genetic improvement of local Eastern Africa cowpea accessions for improved overall agronomic performance in general and breeding for drought tolerant in particular.     

Effects of carbohydrate source and polyethylene glycol on maturation and germination of somatic embryos in walnut (<Emphasis Type="Italic">Juglans regia</Emphasis> L.)

Low efficiency of somatic embryo maturation, germination, and conversion to plantlets is a major problem in many species including J. regia L. Germination efficiency of somatic embryos is very low in walnut. In this study, effects of two carbohydrate sources, sucrose and maltose (each at 3% and 6%), and two kinds of PEG (4000 and 6000) (each at four levels of 1.5%, 3%, 5% and 7.5%) on maturation and germination of walnut embryos were tested. The number of somatic embryos increased conspicuously on medium containing PEG. Furthermore, higher levels of PEG-4000 (7.5%) could remarkably enhance the morphogenesis of somatic embryos and the number of embryos produced. PEG-4000 stimulated somatic embryo maturation of walnut. This stimulatory effect was dependent on the carbohydrate source used. Sucrose in combination with PEG-4000 produced 50% of cotyledonary and normal somatic embryos. Different concentrations of PEG were effective on the number of embryos with a shoot meristem. PEG-4000 7.5% and sucrose 3.0% produced the highest rate (50.0%) of normal shooting embryos. However, PEG (4000, 6000) and maltose caused an unfavorable effect and increased the frequency of abnormal shaped somatic embryos.     

Chemical and Non-Chemical Thinning Treatments Influence Berry Growth and Composition of <Emphasis Type="Italic">Cv.</Emphasis> Shiraz Wine Grape (<Emphasis Type="Italic">V. vinifera</Emphasis> L.)

Yield management is important subject in modern grape growing and winter pruning and cluster thinning treatments were used for yield control. Standard cluster thinning is generally labor intensive and expensive method and grape growers try to new methods, which are alternative to cluster thinning for reducing berry set. The goal of the present research was to investigate the effects of chemical thinning treatments such as ethephon (ETH), gibberellic acid (GA₃), naphthalene acetic acid (NAA) and non-chemical thinning treatments such as early leaf removal (ELR) and standard cluster thinning (SCT) on decreasing grape yield and enhancing berry composition of cv. Shiraz. In this study, percentages of berry set of cv. Shiraz were decreased by both chemical and non-chemical thinning treatments compared to Control. The results from these two different thinning methods shown certainly significant differences in berry composition of cv. Shiraz. Eventually, the best results in improved quality characteristics of cv. Shiraz were obtained from ELR treatment and treatments of ELR, ETH, GA_3, NAA and SCT successively resulted in considerable enhancements in quality attributes of cv. Shiraz.     

Determination of Energy Input-Output Analysis in Plum (<Emphasis Type="Italic">Prunus domestica</Emphasis> L.) Production

The aim of this research is to compose the energy input-output analysis of plum in Nevsehir province in Turkey. This research was conducted at the plum cultivating facilities during the 2015–2016 production seasons in Nevsehir province of Central Anatolian Region in Turkey. The agricultural input energies and output energies used in plum cultivation were calculated to determine the energy input-output analysis. According to the research findings, the energy inputs in plum cultivation were calculated respectively 3920?MJ ha^?1 (44.99%) chemical fertilizers energy, 1618.91?MJ ha^?1 (18.58%) diesel fuel energy, 1125.85?MJ ha^?1 (12.92%) chemicals energy, 1069.20?MJ ha^?1 (12.27%) machinery energy, 723.24?MJ ha^?1 (8.30%) human labour energy and 255?MJ ha^?1 (2.93%) irrigation water energy. Production output plum yield were calculated as 12,112.50?MJ ha^?1. The energy output/input ratio, specific energy, energy usage efficiency and net energy calculations were calculated respectively as 1.39, 1.37?MJ kg^?1, 0.73?kg MJ^?1 and 3400.30?MJ ha^?1.