Research using Genstat
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.
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.
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.
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.
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.
Research using ASReml-SA
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.
Differences in milk composition associated with enteric methane emissions
Milk samples from sheep were analysed for fat, protein, lactose, somatic cell counts and detailed fatty acid composition. The sheep were from two lines each of 100 adult ewes, grazed together but differing by an average of 10% in enteric methane yield (g CH4/kg dry matter intake).
Cause of Death: Phytophthora or Flood? Effects of Waterlogging on Phytophthora medicaginis and Resistance of Chickpea (Cicer arietinum)
Chickpea production in Australia is constrained by both waterlogging and the root disease Phytophthora root rot (PRR). Soil saturation is an important pre-condition for significant disease development for many soil-borne Phytophthora spp. In wet years, water can pool in low lying areas within a field, resulting in waterlogging, which, in the presence of PRR, can result in a significant yield loss for Australian chickpea varieties.
New residual feed intake criterion for longitudinal data
Residual feed intake (RFI) is one measure of feed efficiency, which is usually obtained by multiple regression of feed intake (FI) on measures of production, body weight gain and tissue composition. If phenotypic regression is used, the resulting RFI is generally not genetically independent of production traits, whereas if RFI is computed using genetic regression coefficients, RFI and production traits are independent at the genetic level. The corresponding regression coefficients can be easily derived from the result of a multiple trait model that includes FI and production traits. However, this approach is difficult to apply in the case of multiple repeated measurements of FI and production traits. To overcome this difficulty, we used a structured antedependence approach to account for the longitudinality of the data with a phenotypic regression model or with different genetic and environmental regression coefficients [multi- structured antedependence model (SAD) regression model].
Climate-Resilient Dairy Cattle Production: Applications of Genomic Tools and Statistical Models
The current changing climate trend poses a threat to the productive efficacy and welfare of livestock across the globe. This review is an attempt to synthesize information pertaining to the applications of various genomic tools and statistical models that are available to identify climate-resilient dairy cows. The different functional and economical traits which govern milk production play a significant role in determining the cost of milk production. Thus, identification of these traits may revolutionize the breeding programs to develop climate-resilient dairy cattle. Moreover, the genotype–environment interaction also influences the performance of dairy cattle especially during a challenging situation. The recent advancement in molecular biology has led to the development of a few biotechnological tools and statistical models like next-generation sequencing (NGS), microarray technology, whole transcriptome analysis, and genome-wide association studies (GWAS) which can be used to quantify the molecular mechanisms which govern the climate resilience capacity of dairy cows. Among these, the most preferred option for researchers around the globe was GWAS as this approach jointly takes into account all the genotype, phenotype, and pedigree information of farm animals. Furthermore, selection signatures can also help to demarcate functionally important regions in the genome which can be used to detect potential loci and candidate genes that have undergone positive selection in complex milk production traits of dairy cattle. These identified biomarkers can be incorporated in the existing breeding policies using genomic selection to develop climate-resilient dairy cattle.
Research using ASReml-R
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.
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.
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.
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.
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.
Genotypic variation for lodging tolerance in spring wheat: wider and deeper root plates, a feature of low lodging, high yielding germplasm
Plant lodging reduces yield and quality of irrigated and rainfed spring wheats alike. Local and imported germplasm was screened to identify consistently higher-yielding genotypes with low plant lodging for the north-eastern Australian wheat belt. Using field level treatments, such as fertilisation and tactical overhead irrigation to consistently simulate scenarios leading to lodging in the target region, high reproducibility of lodging rankings was achieved in multi-environment experiments. In separate experiments in two years, detailed phenotyping of selected genotypes in field plots was implemented for traits underpinning stem and root type lodging. Multi-environment and phenotyping experiments ranked genotypes similarly in terms of lodging score. In the phenotyping experiments, root plate spread from field grown plants consistently emerged as a trait able to discriminate low lodging, high yielding germplasm from a multi-trait analysis quantifying genotypic correlations. If the root plate spread was greater than or equal to 5.5 cm, the lodging scores were small, and yield was high. Importantly, root plate spread phenotyped on plants growing at uniform planting density was found to be highly heritable (above 0.80), with a high genotypic correlation (0.80) across environments and strong association with structural rooting depth. A simplified phenotyping approach is discussed based on the main traits driving lodging tolerance and others routinely measured in breeding programs.
Research using CycDesigN
Experimental design in practice: The importance of blocking and treatment structures
Experimental design and analysis has evolved substantially over the last 100 years, driven to a large extent by the power and availability of the computer. To demonstrate this development and encourage the use of experimental design in practice, three experiments from different research areas are presented. In these examples multiple blocking factors have been employed and they show how extraneous variation can be accommodated and interpreted. The examples are used to discuss the importance of blocking and treatment structures in the conduct of designed experiments.
Augmented quasi-sudoku designs in field trials
Augmented designs play an important role in early-generation plant breeding when many varieties are tested and sufficient seeds are unavailable to permit each variety to be replicated more than once. The key idea is to include some replicated varieties to adjust for environmental heterogeneity and provide a good estimate of error. The simplest form of augmented design is constructed using randomized complete blocks for a few replicated varieties and augmenting each block with unreplicated varieties. This idea is readily extended to incomplete-block designs and row-column designs. A challenge is to ensure good coverage of the experimental field with replicated varieties. A problem with augmented row-column designs is that replicated variety plots may be clustered in parts of the field. One way to improve the evenness of replicated variety plot distribution is to use regions as a third blocking factor, formed by intersection of row groups (i.e. groups of adjacent rows) and column groups (i.e. groups of adjacent columns). First, a strategy to identify the numbers of regions, row groups, and column groups is proposed. Second, a general approach to search for augmented designs with three blocking factors for any numbers of unreplicated varieties and replicated varieties is presented. Finally, the algorithm is illustrated for common scenarios in plant breeding.
Factors responsible for yield improvement in new Gossypium hirsutum L. cotton cultivars
The factors responsible for yield progress can be analysed through yield determinant frameworks. These conceptual models consider factors such as crop growth dynamics, partitioning of vegetative and reproductive biomass and yield components to provide insights into the factors responsible for observed genetic gains and opportunities for future gains. The aim of this study was to use direct cultivar comparison to assess the rate of genetic gain in the CSIRO (Australia) cotton breeding program, and to understand how factors within a conceptual yield determinant framework relate to yield performance. Using field experimentation, yield progress of 16.1 kg lint ha−1 y−1 was observed in ten cultivars released between 1968 and 2012. This study identified that selection pressure has resulted in improvements in total dry matter (TDM), harvest index (HI), lint percentage and carbon assimilation. While gains have been made in these four parameters, improvements in lint yield have largely been driven by altering HI through increasing lint percentage. Although improvements have been made in TDM, the reproductive allocation of total biomass and the amount and efficiency of light capture has not been altered in modern cultivars. Future gains in lint yield will require the concurrent maintenance of harvest index while producing larger plants with more fruiting branches that capture more incident radiation with increased efficiency. As the collection of phenotype data such as biomass, boll number, boll size and radiation use efficiency at the scale required in a commercial breeding program is largely aspirational, we conclude in the short term improvements may be achieved through direct selection for yield. Future efforts should be placed in increasing early season growth rates, and in the longer term enhancing carbon assimilation rates. Importantly, due to trait associations and the effects of trade-offs between functional components, factors within a conceptual framework must not be considered in isolation.
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.