8 research outputs found
Application of chloroplast phylogenomics to resolve species relationships within the plant genus Amaranthus
Amaranthus species are an emerging and promising nutritious traditional vegetable food source. Morphological plasticity and poorly resolved dendrograms have led to the need for well resolved species phylogenies. We hypothesized that whole chloroplast phylogenomics would result in more reliable differentiation between closely related amaranth species. The aims of the study were therefore: to construct a fully assembled, annotated chloroplast genome sequence of Amaranthus tricolor; to characterize Amaranthus accessions phylogenetically by comparing barcoding genes (matK, rbcL, ITS) with whole chloroplast sequencing; and to use whole chloroplast phylogenomics to resolve deeper phylogenetic relationships. We generated a complete A. tricolor chloroplast sequence of 150,027 bp. The three barcoding genes revealed poor inter- and intra-species resolution with low bootstrap support. Whole chloroplast phylogenomics of 59 Amaranthus accessions increased the number of parsimoniously informative sites from 92 to 481 compared to the barcoding genes, allowing improved separation of amaranth species. Our results support previous findings that two geographically independent domestication events of Amaranthus hybridus likely gave rise to several species within the Hybridus complex, namely Amaranthus dubius, Amaranthus quitensis, Amaranthus caudatus, Amaranthus cruentus and Amaranthus hypochondriacus. Poor resolution of species within the Hybridus complex supports the recent and ongoing domestication within the complex, and highlights the limitation of chloroplast data for resolving recent evolution. The weedy Amaranthus retroflexus and Amaranthus powellii was found to share a common ancestor with the Hybridus complex. Leafy amaranth, Amaranthus tricolor, Amaranthus blitum, Amaranthus viridis and Amaranthus graecizans formed a stable sister lineage to the aforementioned species across the phylogenetic trees. This study demonstrates the power of next-generation sequencing data and reference-based assemblies to resolve phylogenies, and also facilitated the identification of unknown Amaranthus accessions from a local genebank. The informative phylogeny of the Amaranthus genus will aid in selecting accessions for breeding advanced genotypes to satisfy global food demand.The Department of Science and Technology of South Africa, the National Research Foundation and the Professional Development Program of the Agricultural Research Council (ARC) in South Africa.https://link.springer.com/journal/2392019-04-01hj2018Forestry and Agricultural Biotechnology Institute (FABI)GeneticsPlant Production and Soil Scienc
From bits to bites: Advancement of the Germinate platform to support prebreeding informatics for crop wild relatives
Management and distribution of experimental data from prebreeding projects
is important to ensure uptake of germplasm into breeding and research programs.
Being able to access and share this data in standard formats is essential.
The adoption of a common informatics platform for crops that may have limited
resources brings economies of scale, allowing common informatics components
to be used across multiple species. The close integration of such a platform with
commonly used breeding software, visualization, and analysis tools reduces the
barrier for entry to researchers and provides a common framework to facilitate
collaborations and data sharing. This work presents significant updates to the
Germinate platform and highlights its value in distributing prebreeding data for
14 crops as part of the project âAdapting Agriculture to Climate Change: Collecting,
Protecting and Preparing Crop Wild Relativesâ (hereafter Crop Trust Crop
Wild Relatives project) led by the Crop Trust (https://www.cwrdiversity.org). The
addition of data on these species compliments data already publicly available in
Germinate. We present a suite of updated Germinate features using examples
from these crop species and their wild relatives. The use of Germinate within the
Crop TrustCropWildRelatives project demonstrates the usefulness of the system
and the benefits a shared informatics platform provides. These data resources
provide a foundation on which breeding and research communities can develop
additional online resources for their crops, harness new data as it becomes available,
and benefit collectively from future developments of the Germinate platform
Modelling illustrates that genomic selection provides new opportunities for intercrop breeding
Intercrop breeding programs using genomic selection can produce faster genetic
gain than intercrop breeding programs using phenotypic selection. Intercropping is
an agricultural practice in which two or more component crops are grown together.
It can lead to enhanced soil structure and fertility, improved weed suppression, and
better control of pests and diseases. Especially in subsistence agriculture, intercropping
has great potential to optimize farming and increase profitability. However, breeding
for intercrop varieties is complex as it requires simultaneous improvement of two or
more component crops that combine well in the field. We hypothesize that genomic
selection can significantly simplify and accelerate the process of breeding crops for
intercropping. Therefore, we used stochastic simulation to compare four different
intercrop breeding programs implementing genomic selection and an intercrop breeding
program entirely based on phenotypic selection. We assumed three different levels of
genetic correlation between monocrop grain yield and intercrop grain yield to investigate
how the different breeding strategies are impacted by this factor. We found that
all four simulated breeding programs using genomic selection produced significantly
more intercrop genetic gain than the phenotypic selection program regardless of the
genetic correlation with monocrop yield.We suggest a genomic selection strategy which
combines monocrop and intercrop trait information to predict general intercropping
ability to increase selection accuracy in the early stages of a breeding program and
to minimize the generation interval
Draft genome sequence of Solanum aethiopicum provides insights into disease resistance, drought tolerance, and the evolution of the genome
The African eggplant (Solanum aethiopicum) is a nutritious traditional vegetable used in many African countries, including Uganda and Nigeria. It is thought to have been domesticated in Africa from its wild relative, Solanum anguivi. S. aethiopicum has been routinely used as a source of disease resistance genes for several Solanaceae crops, including Solanum melongena. A lack of genomic resources has meant that breeding of S. aethiopicum has lagged behind other vegetable crops
Comparison of the microbial composition of African fermented foods using amplicon sequencing
Fermented foods play a major role in the diet of people in Africa, where a wide variety of raw materials
are fermented. Understanding the microbial populations of these products would help in the design of
specific starter cultures to produce standardized and safer foods. In this study, the bacterial diversity of
African fermented foods produced from several raw materials (cereals, milk, cassava, honey, palm sap,
and locust beans) under different conditions (household, small commercial producers or laboratory) in 8
African countries was analysed by 16S rRNA gene amplicon sequencing during the Workshop âAnalysis
of the Microbiomes of Naturally Fermented Foods Training Courseâ. Results show that lactobacilli
were less abundant in fermentations performed under laboratory conditions compared to artisanal or
commercial fermentations. Excluding the samples produced under laboratory conditions, lactobacilli
is one of the dominant groups in all the remaining samples. Genera within the order Lactobacillales
dominated dairy, cereal and cassava fermentations. Genera within the order Lactobacillales, and genera
Zymomonas and Bacillus were predominant in alcoholic beverages, whereas Bacillus and Lactobacillus
were the dominant genera in the locust bean sample. The genus Zymomonas was reported for the first
time in dairy, cereal, cassava and locust bean fermentations.The UK Biotechnology and Biological Sciences Research Council (BBSRC) via a
Global Challenge Research Fund Data and Resources award and Institute Strategic Programmes for Food
Innovation and Health (BB/R012512/1) and its constituent project BBS/E/F/000PR10343 and Gut Microbes and
Health (BB/R012490/1). M. D. was the beneficiary of a Clarin COFUND outgoing grants (ACA17â16) co-funded
by the 7th Work Package of the European Union, Marie Curie Actions and the FICyT Foundation.http://www.nature.com/srepam2020Consumer ScienceFood Scienc
From bits to bites: advancement of the germinate platform to support genetic resources collections and pre-breeding informatics for crop wild relatives
The efficient management and distribution of experimental data from pre-breeding projects is important to ensure uptake of valuable germplasm into breeding and research programmes. Being able to access and share this data in standard formats is essential in this process. The adoption of a common informatics platform for crops which may have limited resources brings economies of scale allowing common informatics components to be rolled out across multiple species. The close integration of such a platform with commonly used breeding software, visualization and analysis tools reduces the barrier for entry to researchers working on these data and provides a common framework to facilitate collaborations and data sharing. This work presents significant updates to the Germinate platform and highlights its value in distributing pre-breeding data for 14 crops as part of the project âAdapting Agriculture to Climate Change: Collecting, Protecting and Preparing Crop Wild Relativesâ (hereafter Crop Trust Crop Wild Relatives project) led by the Crop Trust (https://www.cwrdiversity.org). The addition of data on new crop species compliments data that are already publicly available on the platform. We present a suite of updated Germinate features using examples from these crop species and their wild relatives. The use of Germinate within the Crop Wild Relatives project demonstrates the usefulness of the system and the benefits that a shared informatics platform provides.These data resources provide a foundation on which breeding and research communities can develop additional online resources for their crops, harnessing new data as it becomes available, and benefiting collectively from future developments of the Germinate platform. Through this process Germinate will facilitate the utilization of plant genetic resources, including crop wild relatives. This article is protected by copyright. All rights reserve