Pigeons: a novel GUI software for analysing and parsing high density heterologous oligonucleotide microarray probe level data

Genomic DNA-based probe selection by using high density oligonucleotide arrays has recently been applied to heterologous species (Xspecies). With the advent of this new approach, researchers are able to study the genome and transcriptome of a non-model or an underutilised crop species through current state-of-the-art microarray platforms. However, a software package with a graphical user interface (GUI) to analyse and parse the oligonucleotide probe pair level data is still lacking when an experiment is designed on the basis of this cross species approach. A novel computer program called Pigeons has been developed for customised array data analysis to allow the user to import and analyse Affymetrix GeneChip® probe level data through XSpecies. One can determine empirical boundaries for removing poor probes based on genomic hybridisation of the test species to the Xspecies array, followed by making a species-specific Chip Description File (CDF) file for transcriptomics in the heterologous species, or Pigeons can be used to examine an experimental design to identify potential Single-Feature Polymorphisms (SFPs) at the DNA or RNA level. Pigeons is also focused around visualization and interactive analysis of the datasets. The software with its manual (the current release number version 1.2.1) is freely available at the website of the Nottingham Arabidopsis Stock Centre (NASC)

Preanthesis biomass accumulation of plant and plant organs defines yield components in wheat

The preanthesis period in wheat is critical for growth of plant organs including leaves, stems, spikes and roots. However, the roles of the preanthesis biomass accumulation of plant and plant organs in yield determination are only partially elucidated, and the underlying genetic basis remains largely unknown. This study aimed to understand the physiological and genetic relationships between preanthesis biomass accumulation and yield determination. In a mapping population of bread wheat (Triticum aestivum ‘Forno’) and its relative spelt (Triticum spelta ‘Oberkulmer’) contrasting for biomass, the dry weight of above-ground whole shoots and different organs, and leaf area, were analysed at GS39 (full flag leaf emergence) and anthesis. Yield components (thousand grain weight, grains per spike, final shoot biomass and grain weight per spike) and plant height were measured at maturity, followed by identification of quantitative trait loci (QTL) for all above traits. Field experiments were carried out in UK in 2011–2012 and 2012–2013 seasons, each using a randomised complete block design with three replicates. The results showed that there was a significant variation in biomass and its partitioning to organs at different stages. Consistent with the previous findings, stem water soluble carbohydrates and spike dry weight at anthesis contributed to thousand grain weight and grains per spike, respectively. In addition, this study revealed many other traits positively associated with one or more yield components, including biomass and leaf area at GS39, leaf and structural stem growth as well as whole shoot biomass at anthesis, and higher dry matter accumulation and crop (and spike) growth rates between the two stages. Increasing shoot biomass by removing other tillers at GS39 led to higher grain number and grain weight per spike. These results indicate the importance of the preanthesis growth of plant and plant organs for yield determination. Plant height was only weakly correlated with final biomass at maturity so it is possible to produce high-biomass genotypes without increasing plant height. Genetic analysis revealed 193 QTL associated with biomass and biomass-related traits. Frequent QTL coincidences between biomass and yield traits were observed, mainly on chromosomes 2B, 3A, 4A, 4B, 5A, 6A and 7B, indicating pleiotropy or tight gene linkages, consistent with their phenotypic associations. The preanthesis biomass traits associated with yield components and the underlying QTL, would facilitate the trait-based physiological and molecular breeding in wheat

Identifying seedling root architectural traits associated with yield and yield components in wheat

Background and Aims: Plant roots growing underground are critical for soil resource acquisition, anchorage and plant-environment interactions. In wheat (Triticum aestivum), however, the target root traits to improve yield potential still remain largely unknown. This study aimed to identify traits of seedling root system architecture (RSA) associated with yield and yield components in 226 recombinant inbred lines (RILs) derived from a cross between the bread wheat Triticum aestivum ‘Forno’ (small, wide root system) and spelt Triticum spelta ‘Oberkulmer’ (large, narrow root system). Methods: A ‘pouch and wick’ high-throughput phenotyping pipeline was used to determine the RSA traits of 13-d-old RIL seedlings. Two field and one glasshouse experiments were carried out to investigate the yield, yield components and phenology, followed by identification of quantitative trait loci (QTL). Key Results: There was substantial variation in RSA traits between genotypes. Seminal root number and total root length were both positively associated with grains m-2, grains per spike, above-ground biomass m-2, and grain yield. More seminal roots and longer total root length were also associated with delayed maturity and extended grain filling, likely to be a consequence of more grains being defined before anthesis. Additionally, the maximum width of the root system displayed positive relationships with spikes m-2, grains m-2, and grain yield. Ten RILs selected for longest total roots exhibited the same effects on yield and phenology as described above, compared to the ten lines with shortest total roots. Genetic analysis revealed 38 QTL for the RSA, and QTL coincidence between the root and yield traits were frequently observed, indicating tightly linked genes or pleiotropy, which concurs with the results of phenotypic correlation analysis. Conclusions: Based on the results from the Forno × Oberkulmer population, it is proposed that vigorous early root growth, particularly more seminal roots and longer total root length, is important to improve yield potential, and should be incorporated into wheat ideotypes in breeding

Triple GPS Localization

The purpose of this thesis is to increase the positional accuracy of Global Position System (GPS) modules using an artificial intelligence algorithm. Three basic and identical GPS modules were setup in an equilateral triangle formation with side lengths of one meter. The triangle was placed in four separate locations where approximately 700 GPS data points were collected per GPS module. The data was then analyzed and tested using a Gaussian distribution. In the best-case scenario, the Triple GPS Localization algorithm was able to improve the localization accuracy by 82%. This shows that utilizing a machine-learning algorithm can improve the positional accuracy of any GPS module

Genomic selection strategies to increase genetic gain in tea breeding programs

Tea [Camellia sinensis (L.) O. Kuntze] is mainly grown in low‐ to middle‐income countries (LMIC) and is a global commodity. Breeding programs in these countries face the challenge of increasing genetic gain because the accuracy of selecting superior genotypes is low and resources are limited. Phenotypic selection (PS) is traditionally the primary method of developing improved tea varieties and can take over 16 yr. Genomic selection (GS) can be used to improve the efficiency of tea breeding by increasing selection accuracy and shortening the generation interval and breeding cycle. Our main objective was to investigate the potential of implementing GS in tea‐breeding programs to speed up genetic progress despite the low cost of PS in LMIC. We used stochastic simulations to compare three GS‐breeding programs with a Pedigree and PS program. The PS program mimicked a practical commercial tea‐breeding program over a 40‐yr breeding period. All the GS programs achieved at least 1.65 times higher genetic gains than the PS program and 1.4 times compared with Seed‐Ped program. Seed‐GSc was the most cost‐effective strategy of implementing GS in tea‐breeding programs. It introduces GS at the seedlings stage to increase selection accuracy early in the program and reduced the generation interval to 2 yr. The Seed‐Ped program outperformed PS by 1.2 times and could be implemented where it is not possible to use GS. Our results indicate that GS could be used to improve genetic gain per unit time and cost even in cost‐constrained tea‐breeding programs

Carpel size, grain filling, and morphology determine individual grain weight in wheat

Individual grain weight is a major yield component in wheat. To provide a comprehensive understanding of grain weight determination, the carpel size at anthesis, grain dry matter accumulation, grain water uptake and loss, grain morphological expansion, and final grain weight at different positions within spikelets were investigated in a recombinant inbred line mapping population of bread wheat (Triticum aestivum L.)×spelt (Triticum spelta L.). Carpel size, grain dry matter and water accumulation, and grain dimensions interacted strongly with each other. Furthermore, larger carpels, a faster grain filling rate, earlier and longer grain filling, more grain water, faster grain water absorption and loss rates, and larger grain dimensions were associated with higher grain weight. Frequent quantitative trait locus (QTL) coincidences between these traits were observed, particularly those on chromosomes 2A, 3B, 4A, 5A, 5DL, and 7B, each of which harboured 16−49 QTLs associated with >12 traits. Analysis of the allelic effects of coincident QTLs confirmed their physiological relationships, indicating that the complex but orderly grain filling processes result mainly from pleiotropy or the tight linkages of functionally related genes. After grain filling, distal grains within spikelets were smaller than basal grains, primarily due to later grain filling and a slower initial grain filling rate, followed by synchronous maturation among different grains. Distal grain weight was improved by increased assimilate availability from anthesis. These findings provide deeper insight into grain weight determination in wheat, and the high level of QTL coincidences allows simultaneous improvement of multiple grain filling traits in breeding

Root foraging capacity in bambara groundnut (Vigna subterranea (L.) Verdc.) core parental lines depends on the root system architecture during the pre-flowering stage

© 2020 by the authors. Licensee MDPI, Basel, Switzerland. Characterizing the morphological variability in root system architecture (RSA) during the sensitive pre-flowering growth stage is important for crop performance. To assess this variation, eight bambara groundnut single genotypes derived from landraces of contrasting geographic origin were selected for root system architecture and rooting distribution studies. Plants were grown in a polyvinyl chloride (PVC) column system under controlled water and nutrient availability in a rainout shelter. Days to 50% plant emergence was characterized during the first two weeks after sowing, while taproot length (TRL), root length (RL), root length density (RLD), branching number (BN), branching density (BD) and intensity (BI), surface area (SA), root volume (RV), root diameter (RDia), root dry weight (RDW), shoot dry weight (SDW), and shoot height (SH) were determined at the end of the experiment, i.e., 35 days after emergence. Genotypes S19-3 and DipC1 sourced from drier regions of sub-Saharan Africa generally had longer taproots and greater root length distribution in deeper (60 to 90 cm) soil depths. In contrast, bambara groundnut genotypes from wetter regions (i.e., Gresik, Lunt, and IITA-686) in Southeast Asia and West Africa exhibited relatively shallow and highly branched root growth closer to the soil surface. Genotypes at the pre-flowering growth stage showed differential root foraging patterns and branching habits with two extremes, i.e., deep-cheap rooting in the genotypes sourced from dry regions and a shallow-costly rooting system in genotypes adapted to higher rainfall areas with shallow soils. We propose specific bambara groundnut genotype as donors in root trait driven breeding programs to improve water capture and use efficiency

Image-based 3D canopy reconstruction to determine potential productivity in complex multi-species crop systems

Background and Aims: Intercropping systems contain two or more species simultaneously in close proximity. Due to contrasting features of the component crops, quantification of the light environment and photosynthetic productivity is extremely difficult. However it is an essential component of productivity. Here, a low-tech but high resolution method is presented that can be applied to single and multi-species cropping systems, to facilitate characterisation of the light environment. Different row layouts of an intercrop consisting of Bambara groundnut (Vigna subterranea (L.) Verdc.) and Proso millet (Panicum miliaceum) have been used as an example and the new opportunities presented by this approach have been analysed. Methods: Three-dimensional plant reconstruction, based on stereocameras, combined with ray-tracing was implemented to explore the light environment within the Bambara groundnut-Proso millet intercropping system and associated monocrops. Gas exchange data was used to predict the total carbon gain of each component crop. Key Results: The shading influence of the tall Proso millet on the shorter Bambara groundnut results in a reduction in total canopy light interception and carbon gain. However, the increased leaf area index (LAI) of Proso millet, higher photosynthetic potential due to the C4 pathway and sub-optimal photosynthetic acclimation of Bambara groundnut to shade means that increasing the number of rows of millet will lead to greater light interception and carbon gain per unit ground area, despite Bambara groundnut intercepting more light per unit leaf area. Conclusions: Three-dimensional reconstruction combined with ray tracing provides a novel, accurate method of exploring the light environment within an intercrop that does not require difficult measurements of light interception and data-intensive manual reconstruction, especially for such systems with inherently high spatial possibilities. It provides new opportunities for calculating potential productivity within multispecies cropping systems; enables the quantification of dynamic physiological differences between crops grown as monoculture and those within intercrops or; enables the prediction of new productive combinations of previously untested crops

A cross-species gene expression marker-based genetic map and QTL analysis in bambara groundnut

Bambara groundnut (Vigna subterranea (L.) Verdc.) is an underutilised legume crop, which has long been recognised as a protein-rich and drought-tolerant crop, used extensively in Sub-Saharan Africa. The aim of the study was to identify quantitative trait loci (QTL) involved in agronomic and drought-related traits using an expression marker-based genetic map based on major crop resources developed in soybean. The gene expression markers (GEMs) were generated at the (unmasked) probe-pair level after cross-hybridisation of bambara groundnut leaf RNA to the Affymetrix Soybean Genome GeneChip. A total of 753 markers grouped at an LOD (Logarithm of odds) of three, with 527 markers mapped into linkage groups. From this initial map, a spaced expression marker-based genetic map consisting of 13 linkage groups containing 218 GEMs, spanning 982.7 cM (centimorgan) of the bambara groundnut genome, was developed. Of the QTL detected, 46% were detected in both control and drought treatment populations, suggesting that they are the result of intrinsic trait differences between the parental lines used to construct the cross, with 31% detected in only one of the conditions. The present GEM map in bambara groundnut provides one technically feasible route for the translation of information and resources from major and model plant species to underutilised and resource-poor crops