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Research using Genstat

Environmental Science

Litter layer and earthworms as an indicator of coffee production in the coffee and pine based agroforestry system

Critical support for successful coffee-based agroforestry production is the amount of litter input and the activity of macro-organisms. The purpose of this study was to analyze the relationship between the amount of litter on the soil surface, the population of earthworms, and the growth and production of coffee. The research was conducted between June 2019 and March 2020 at the Universitas Brawijaya Forest, East Java, Indonesia.

Plant

Mineral Fertilization Influences the Growth, Cryptolepine Yield, and Bioefficacy of Cryptolepis sanguinolenta (Lindl.) Schlt.

Cryptolepis sanguinolenta (Lindl.) Schlt., the main source of cryptolepine alkaloid, is intensively exploited in the wild to treat malaria and Lyme disease. In this study, the influence of four inorganic fertilizers (supplying N, P, K, or NPK) and four growth periods (3, 6, 9, and 12 months after transplanting) on the herb’s root biomass, cryptolepine content and yield, and biological activities were investigated in a pot and field trial.

Animal Science

The effect of perennial and annual wheat forages, fed with or without lucerne, on the fatty acid profile and oxidative status of lamb meat

The current study investigated the fatty acid profile and oxidative status of the meat from lambs that were fed a novel perennial wheat or a conventional annual wheat, either as a cereal monoculture or lucerne biculture. Twelve lambs were assigned to each of the four dietary treatments (48 lambs in total) and held within individual pens for the duration of the 28 day feeding study. Lambs were slaughtered and the longissimus lumborum (LL) and semimembranosus (SM) muscles analysed. The independent effect of wheat type on fatty acid concentrations was negligible.

Animal

Automated Monitoring of Panting for Feedlot Cattle: Sensor System Accuracy and Individual Variability

Panting is considered a robust animal response indicator of heat stress; however, continuous visual monitoring is impractical on a commercial scale. Current thermal indices are good predictors of heat stress at a herd level but have limited application at the individual level. The automated monitoring of heat stress responses of individual cattle based on animal response and environmental parameters are required for strategic management and genetic selection. We validated an ear tag-based sensor for the monitoring of panting in cattle and determined the individual variability in panting duration for heat stress events, comparing with existing thermal indices. Sensors were able to monitor differences in cattle panting due to breed, coat colour, and individual variability. High variation in panting responses between and within genotype and coat category highlights the opportunity for targeted heat amelioration based on breed and coat colour grouping of animals, and selection within breeds and types for heat resilience.

Agricultural System

The agronomic and economic viability of innovative cropping systems to reduce Fusarium head blight and related mycotoxins in wheat

The effective control of Fusarium head blight (FHB) in wheat, mainly caused by the toxigenic fungus Fusarium graminearum, has a significant impact on food safety worldwide. As maize is one of the main hosts of F. graminearum, the risk of infection by this plant pathogen is highest when wheat is grown after maize and infected crop residues are not buried through ploughing.

General Research

Nature

SynGAP isoforms exert opposing effects on synaptic strength

Alternative promoter usage and alternative splicing enable diversification of the transcriptome. Here we demonstrate that the function of Synaptic GTPase-Activating Protein (SynGAP), a key synaptic protein, is determined by the combination of its amino-terminal sequence with its carboxy-terminal sequence. 5′ rapid amplification of cDNA ends and primer extension show that different N-terminal protein sequences arise through alternative promoter usage that are regulated by synaptic activity and postnatal age. Heterogeneity in C-terminal protein sequence arises through alternative splicing.

Research using CycDesigN

Plant

Stability of Single-Parent Gene Expression Complementation in Maize Hybrids upon Water Deficit Stress

Heterosis is the superior performance of F1 hybrids compared with their homozygous, genetically distinct parents. In this study, we monitored the transcriptomic divergence of the maize (Zea mays) inbred lines B73 and Mo17 and their reciprocal F1 hybrid progeny in primary roots under control and water deficit conditions simulated by polyethylene glycol treatment.

Plant

Extensive tissue-specific transcriptomic plasticity in maize primary roots upon water deficit

Water deficit is the most important environmental constraint severely limiting global crop growth and productivity. This study investigated early transcriptome changes in maize (Zea mays L.) primary root tissues in response to moderate water deficit conditions by RNA-Sequencing. Differential gene expression analyses revealed a high degree of plasticity of the water deficit response.

Experimental design

Experiments in Rectangular Areas: Design and Randomization

Agricultural experiments are often laid out in a rectangle in 3—5 replicates. Is it better to use a standard randomized complete-block design in rows, or a complete-block design in rows but with restricted randomization, or an efficient row-column design? These approaches differ in the variance of the estimator of a difference between two treatments, and in the bias of the estimator of that variance, as well as in the mechanics of constructing the design and analyzing the data.

Row-Column Designs

Optimal Nested Row-Column Designs with Specified Components

We consider nested row-column designs where each of the row and column component designs is specified. For the case that each of the component designs has second-order balance, we define such a nested row-column design to be special if it is generally balanced, with the smallest possible number of canonical treatment contrasts having the lower canonical efficiency factor in both components. We show that if any special row-column design exists then it is A-optimal over all nested row-column designs with the given components.

Randomization

An Evaluation of Super-Valid Restricted Randomization

Designs exhibiting super-valid restricted randomization have been proposed as alternatives to efficient row–column designs in situations where the column variance component is small. This paper examines some existing uniformity data and results from two field variety trial programs and concludes that in these situations efficient row–column designs are to be preferred.

Experimental design

Random Generation and Selection of One- and Two-Dimensional Designs for Experiments on Blocks of Natural Size

Many incomplete block design strategies have been devised to improve the efficiency of experiments. However, the constraints imposed by these designs can be unrealistic because natural blocks may not be all the same size or there may be no conventional designs for required treatment, replication, block and plot combinations. In addition, because of similar constraints, two-dimensional block designs--the so called row-column designs--are used less frequently than the occurrence of conditions where their use would result in greater experimental efficiency.

Research using ASReml-R

Plant

Identification of Climate and Genetic Factors That Control Fat Content and Fatty Acid Composition of Theobroma cacao L. Beans

The main ingredients of chocolate are usually cocoa powder, cocoa butter, and sugar. Both the powder and the butter are extracted from the beans of the cacao tree (Theobroma cacao L.). The cocoa butter represents the fat in the beans and possesses a unique fatty acid profile that results in chocolate’s characteristic texture and mouthfeel. Here, we used a linkage mapping population and phenotypic data of 3,292 samples from 420 progeny which led to the identification of 27 quantitative trait loci (QTLs) for fatty acid composition and six QTLs for fat content.

Plant

Genome-wide association studies for yield component traits in a macadamia breeding population

Breeding for new macadamia cultivars with high nut yield is expensive in terms of time, labour and cost. Most trees set nuts after four to five years, and candidate varieties for breeding are evaluated for at least eight years for various traits. Genome-wide association studies (GWAS) are promising methods to reduce evaluation and selection cycles by identifying genetic markers linked with key traits, potentially enabling early selection through marker-assisted selection. This study used 295 progeny from 32 full-sib families and 29 parents (18 phenotyped) which were planted across four sites, with each tree genotyped for 4113 SNPs.

Disease

Impact of Small Vessel Disease Progression on Long-term Cognitive and Functional Changes After Stroke

The severity of white matter hyperintensities (WMH) at presentation with stroke is associated with poststroke dementia and dependency. However, WMH can decrease or increase after stroke; prediction of cognitive decline is imprecise; and there are few data assessing longitudinal interrelationships among changing WMH, cognition, and function after stroke, despite the clinical importance.

Plant

Yield dissection models to improve yield: a case study in tomato

Yield as a complex trait may either be genetically improved directly, by identifying QTLs contributing to yield, or indirectly via improvement of underlying components, where parents contribute complementary alleles to different components. We investigated the utility of two yield dissection models in tomato for identifying promising yield components and corresponding QTLs. In a harvest dissection, marketable yield was the product of number of fruits and individual fruit fresh weight. In a biomass dissection, total yield was the product of fruit fresh-dry weight ratio and total fruit dry weight.

Health

Gut microbiome heritability is nearly universal but environmentally contingent

Relatives have more similar gut microbiomes than nonrelatives, but the degree to which this similarity results from shared genotypes versus shared environments has been controversial. Here, we leveraged 16,234 gut microbiome profiles, collected over 14 years from 585 wild baboons, to reveal that host genetic effects on the gut microbiome are nearly universal. Controlling for diet, age, and socioecological variation, 97% of microbiome phenotypes were significantly heritable, including several reported as heritable in humans. Heritability was typically low (mean = 0.068) but was systematically greater in the dry season, with low diet diversity, and in older hosts. We show that longitudinal profiles and large sample sizes are crucial to quantifying microbiome heritability, and indicate scope for selection on microbiome characteristics as a host phenotype.

Plant Science

Extensive variation within the pan-genome of cultivated and wild sorghum

Sorghum is a drought-tolerant staple crop for half a billion people in Africa and Asia, an important source of animal feed throughout the world and a biofuel feedstock of growing importance. Cultivated sorghum and its inter-fertile wild relatives constitute the primary gene pool for sorghum. Understanding and characterizing the diversity within this valuable resource is fundamental for its effective utilization in crop improvement. Here, we report analysis of a sorghum pan-genome to explore genetic diversity within the sorghum primary gene pool. We assembled 13 genomes representing cultivated sorghum and its wild relatives, and integrated them with 3 other published genomes to generate a pan-genome of 44,079 gene families with 222.6 Mb of new sequence identified. The pan-genome displays substantial gene-content variation, with 64% of gene families showing presence/absence variation among genomes. Comparisons between core genes and dispensable genes suggest that dispensable genes are important for sorghum adaptation. Extensive genetic variation was uncovered within the pan-genome, and the distribution of these variations was influenced by variation of recombination rate and transposable element content across the genome. We identified presence/absence variants that were under selection during sorghum domestication and improvement, and demonstrated that such variation had important phenotypic outcomes that could contribute to crop improvement. The constructed sorghum pan-genome represents an important resource for sorghum improvement and gene discovery.

Plant Science

Copy number variation of Ppd-B1 is the major determinant of heading time in durum wheat

Heading time is an important adaptive trait in durum wheat. In hexaploid wheat, Photoperiod-1 (Ppd) loci are essential regulators of heading time, with Ppd-B1 conferring photoperiod insensitivity through copy number variations (CNV). In tetraploid wheat, the D-genome Ppd-D1 locus is absent and generally, our knowledge on the genetic architecture underlying heading time lacks behind that of bread wheat.

Research using ASReml-SA

Aquaculture

Analysis of hybrid combining ability for growth and multiple stress tolerance traits in the Pacific white shrimp, Litopenaeus vannamei

To identify optimal mating combinations for Litopenaeus vannamei, a linear mixed model was used to estimate the general combining ability (GCA) and specific combining ability (SCA) for growth and multiple stress tolerance [high salt (35‰), low pH (6 ± 0.1), and high ammonia nitrogen (70 mg/L) co-stress] traits in 47 combinations of L. vannamei. The results showed that the SCA in the parents played a dominant role in the offspring traits. The highest GCAs were observed for females of strain O and males of strain B (0.602 and 8.889, respectively), indicating that the dams of strain O and sires of strain B could be used as maternal and paternal lines to increase multiple stress resistance in the next generation. The growth traits of the hybrid combination strain G♂ × strain H♀ exhibited the highest degree of heterosis (9.838%–46.518%) and a generally high SCA (0.643–8.596) among all mating combinations.

Genetics

Complex Traits and Candidate Genes: Estimation of Genetic Variance Components Across Modes of Inheritance

Large-effect loci—those discovered by genome-wide association studies or linkage mapping—associated with key traits segregate amidst a background of minor, often undetectable genetic effects in both wild and domesticated plants and animals. Accurately attributing mean differences and variance explained to the correct components in the linear mixed model (LMM) analysis is important for both selecting superior progeny and parents in plant and animal breeding, but also for gene therapy and medical genetics in humans.

Plant

Unraveling the Genetic Basis of Key Agronomic Traits of Wrinkled Vining Pea (Pisum sativum L.) for Sustainable Production

Estimating the allelic variation and exploring the genetic basis of quantitatively inherited complex traits are the two foremost breeding scenarios for sustainable crop production. The current study utilized 188 wrinkled vining pea genotypes comprising historical varieties and breeding lines to evaluate the existing genetic diversity and to detect molecular markers associated with traits relevant to vining pea production, such as wrinkled vining pea yield (YTM100), plant height (PH), earliness (ERL), adult plant resistance to downy mildew (DM), pod length (PDL), numbers of pods per plant (PDP), number of peas per pod (PPD), and percent of small wrinkled vining peas (PSP).

Aquaculture

Genetic parameters and genotype by environment interaction in a unique Indonesian hybrid tilapia strain selected for production in brackish water pond culture

Recurrent farming failures due to disease outbreaks have driven Indonesian shrimp farmers to develop co-culture between shrimp and tilapia. For this reason the Research Institute for Fish Breeding (RIFB) Indonesia has started to develop a fast-growing tilapia with good growth over a range of fluctuating salinities in brackish water ponds. A freshwater nucleus and evaluation breeding program is the simplest strategy to implement, but requires knowledge on the extent of genotype by environment (GxE) interaction between fresh and brackish water environments.

Genetics

Performance of Swedish Warmblood fragile foal syndrome carriers and breeding prospects

Warmblood fragile foal syndrome (WFFS) is a monogenetic defect caused by a recessive lethal missense point mutation in the procollagen‐lysine, 2‐oxoglutarate 5‐dioxygenase 1 gene (PLOD1, c.2032G>A). The majority of homozygous WFFS horses are aborted during gestation. Clinical signs of affected horses include fragile skin, skin and mucosa lacerations, hyperextension of the articulations, and hematomas. In spite of its harmful effect, a relatively high frequency of WFFS carriers has been found in Warmblood horses, suggesting a heterozygote advantage.

Explore Research Papers

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Research papers

Research using Genstat

READ MORE

Litter layer and earthworms as an indicator of coffee production in the coffee and pine based agroforestry system

READ MORE

Mineral Fertilization Influences the Growth, Cryptolepine Yield, and Bioefficacy of Cryptolepis sanguinolenta (Lindl.) Schlt.

READ MORE

The effect of perennial and annual wheat forages, fed with or without lucerne, on the fatty acid profile and oxidative status of lamb meat

READ MORE

Automated Monitoring of Panting for Feedlot Cattle: Sensor System Accuracy and Individual Variability

READ MORE

The agronomic and economic viability of innovative cropping systems to reduce Fusarium head blight and related mycotoxins in wheat

General Research

READ MORE

SynGAP isoforms exert opposing effects on synaptic strength

Research using CycDesigN

READ MORE

Stability of Single-Parent Gene Expression Complementation in Maize Hybrids upon Water Deficit Stress

READ MORE

Extensive tissue-specific transcriptomic plasticity in maize primary roots upon water deficit

READ MORE

Experiments in Rectangular Areas: Design and Randomization

READ MORE

Optimal Nested Row-Column Designs with Specified Components

READ MORE

An Evaluation of Super-Valid Restricted Randomization

READ MORE

Random Generation and Selection of One- and Two-Dimensional Designs for Experiments on Blocks of Natural Size

Research using ASReml-R

READ MORE

Identification of Climate and Genetic Factors That Control Fat Content and Fatty Acid Composition of Theobroma cacao L. Beans

READ MORE

Genome-wide association studies for yield component traits in a macadamia breeding population

READ MORE

Impact of Small Vessel Disease Progression on Long-term Cognitive and Functional Changes After Stroke

READ MORE

Yield dissection models to improve yield: a case study in tomato

READ MORE

Gut microbiome heritability is nearly universal but environmentally contingent

READ MORE

Extensive variation within the pan-genome of cultivated and wild sorghum

READ MORE

Copy number variation of Ppd-B1 is the major determinant of heading time in durum wheat

Research using ASReml-SA

READ MORE

Analysis of hybrid combining ability for growth and multiple stress tolerance traits in the Pacific white shrimp, Litopenaeus vannamei

READ MORE

Complex Traits and Candidate Genes: Estimation of Genetic Variance Components Across Modes of Inheritance

READ MORE

Unraveling the Genetic Basis of Key Agronomic Traits of Wrinkled Vining Pea (Pisum sativum L.) for Sustainable Production

READ MORE

Genetic parameters and genotype by environment interaction in a unique Indonesian hybrid tilapia strain selected for production in brackish water pond culture

READ MORE

Performance of Swedish Warmblood fragile foal syndrome carriers and breeding prospects