African soil properties and nutrients mapped at 30 m spatial resolution using two-scale ensemble machine learning.

Soil property and class maps for the continent of Africa were so far only available at very generalised scales, with many countries not mapped at all. Thanks to an increasing quantity and availability of soil samples collected at field point locations by various government and/or NGO funded projects, it is now possible to produce detailed pan-African maps of soil nutrients, including micro-nutrients at fine spatial resolutions. In this paper we describe production of a 30 m resolution Soil Information System of the African continent using, to date, the most comprehensive compilation of soil samples ([Formula: see text]) and Earth Observation data.

Revisiting the hetero-fertilization phenomenon in maize.

Development of a seed DNA-based genotyping system for marker-assisted selection (MAS) has provided a novel opportunity for understanding aberrant reproductive phenomena such as hetero-fertilization (HF) by observing the mismatch of endosperm and leaf genotypes in monocot species. In contrast to conventional approaches using specific morphological markers, this approach can be used for any population derived from diverse parental genotypes. A large-scale experiment was implemented using seven F(2) populations and four three-way cross populations, each with 534 to 1024 individuals.

Effects of the nanostructuring of gold films upon their thermal stability.

We report results relating to the thermal stability of nanoparticles and show a remarkable effect of nanostructuring of the metal. Au films are nanostructured by focused ion beam sputtering (FIB) to produce isolated areas of metal, which are imaged by atomic force microscopy (AFM). Images of the surface show that, if the islands are made small enough, the metal in the islands is lost by evaporation, whereas the nonfabricated areas outside are relatively stable and the nanoparticles remain present there.

Genetic characterization and linkage disequilibrium estimation of a global maize collection using SNP markers.

A newly developed maize Illumina GoldenGate Assay with 1536 SNPs from 582 loci was used to genotype a highly diverse global maize collection of 632 inbred lines from temperate, tropical, and subtropical public breeding programs. A total of 1229 informative SNPs and 1749 haplotypes within 327 loci was used to estimate the genetic diversity, population structure, and familial relatedness. Population structure identified tropical and temperate subgroups, and complex familial relationships were identified within the global collection.

Nucleotide diversity and molecular evolution of the PSY1 gene in Zea mays compared to some other grass species.

Phytoene synthase (PSY), which is encoded by the phytoene synthase 1 (PSY1) gene, is the first rate-limiting enzyme in the plant carotenoid biosynthetic pathway. In order to examine the genetic diversity and evolution pattern of PSY1 within the Andropogoneae, sequences of 76 accessions from 5 species (maize, teosinte, tripsacum, coix, and sorghum) of the Andropogoneae were tested, along with 4 accessions of rice (Oryza sativa L.) included as outliers.

Molecular characterization of global maize breeding germplasm based on genome-wide single nucleotide polymorphisms.

Characterization of genetic diversity is of great value to assist breeders in parental line selection and breeding system design. We screened 770 maize inbred lines with 1,034 single nucleotide polymorphism (SNP) markers and identified 449 high-quality markers with no germplasm-specific biasing effects. Pairwise comparisons across three distinct sets of germplasm, CIMMYT (394), China (282), and Brazil (94), showed that the elite lines from these diverse breeding pools have been developed with only limited utilization of genetic diversity existing in the center of origin.

Advances in maize genomics and their value for enhancing genetic gains from breeding.

Maize is an important crop for food, feed, forage, and fuel across tropical and temperate areas of the world. Diversity studies at genetic, molecular, and functional levels have revealed that, tropical maize germplasm, landraces, and wild relatives harbor a significantly wider range of genetic variation. Among all types of markers, SNP markers are increasingly the marker-of-choice for all genomics applications in maize breeding.

Isolation and characterization of novel microsatellite markers and their application for diversity assessment in cultivated groundnut (Arachis hypogaea).

Background: Cultivated peanut or groundnut (Arachis hypogaea L.) is the fourth most important oilseed crop in the world, grown mainly in tropical, subtropical and warm temperate climates. Due to its origin through a single and recent polyploidization event, followed by successive selection during breeding efforts, cultivated groundnut has a limited genetic background.

Association analysis of historical bread wheat germplasm using additive genetic covariance of relatives and population structure.

Linkage disequilibrium can be used for identifying associations between traits of interest and genetic markers. This study used mapped diversity array technology (DArT) markers to find associations with resistance to stem rust, leaf rust, yellow rust, and powdery mildew, plus grain yield in five historical wheat international multienvironment trials from the International Maize and Wheat Improvement Center (CIMMYT). Two linear mixed models were used to assess marker-trait associations incorporating information on population structure and covariance between relatives.

A database of annotated tentative orthologs from crop abiotic stress transcripts.

A minimal requirement to initiate a comparative genomics study on plant responses to abiotic stresses is a dataset of orthologous sequences. The availability of a large amount of sequence information, including those derived from stress cDNA libraries allow for the identification of stress related genes and orthologs associated with the stress response. Orthologous sequences serve as tools to explore genes and their relationships across species.

QTL mapping of grain length in rice (Oryza sativa L.) using chromosome segment substitution lines.

Chromosome segment substitution (CSS) lines have the potential for use in QTL fine mapping and map-based cloning. The standard t-test used in the idealized case that each CSS line has a single segment from the donor parent is not suitable for non-idealized CSS lines carrying several substituted segments from the donor parent. In this study, we present a likelihood ratio test based on stepwise regression (RSTEP-LRT) that can be used for QTL mapping in a population consisting of non-idealized CSS lines.

Laboratory Information Management Software for genotyping workflows: applications in high throughput crop genotyping.

Background: With the advances in DNA sequencer-based technologies, it has become possible to automate several steps of the genotyping process leading to increased throughput. To efficiently handle the large amounts of genotypic data generated and help with quality control, there is a strong need for a software system that can help with the tracking of samples and capture and management of data at different steps of the process. Such systems, while serving to manage the workflow precisely, also encourage good laboratory practice by standardizing protocols, recording and annotating data from every step of the workflow.

Development of ESTs from chickpea roots and their use in diversity analysis of the Cicer genus.

Background: Chickpea is a major crop in many drier regions of the world where it is an important protein-rich food and an increasingly valuable traded commodity. The wild annual Cicer species are known to possess unique sources of resistance to pests and diseases, and tolerance to environmental stresses. However, there has been limited utilization of these wild species by chickpea breeding programs due to interspecific crossing barriers and deleterious linkage drag.