Microsatellite Development and Application in Pigeonpea (<i>Cajanus cajan </i>(L.) Millsp.)

Pigeonpea is a major legume crop grown in the semi-arid tropics but has been relatively neglected in terms of genomic research. This study aimed at developing molecular markers as a basic requirement towards initiating marker assisted breeding techniques in pigeonpea. Simple Sequence Repeat (SSR) loci of pigeonpea were isolated by screening non-enriched (library A) and enriched (library B) partial genomic libraries with SSR probes. Positive clones were sequenced and primers designed for 152 microsatellite loci, 39 from library A and 113 from library B. Optimisation of reaction conditions was achieved for 51% and 65% of primers designed from library A and B, respectively. For the purpose of exploiting the transferability of SSRs across genera within the legume species, 220 soybean primers were tested in pigeonpea, 39 of which amplified interpretable bands. Nineteen out of 20 amplified primers from library A were polymorphic among 15 cultivated and 9 wild species. The diversity analysis revealed contrasted levels of variability within cultivated and wild accessions. A total of 98 alleles were detected at the 19 polymorphic loci with an average of 4.9 alleles per locus while the observed heterozygosity ranged from 0.17 – 0.80 with a mean of 0.42 per locus. Substantially less allelic variation (31 alleles) was observed within the cultivated species than across the wild species (92 alleles). Primers from library B were not tested for amplification in wild species but 35 out of the amplified 73 revealed polymorphism among 24 pigeonpea genotypes. The number of alleles detected ranged from 2 to 6 with a total of 110 alleles and an average of 3.1 alleles per locus. Only one of the 39 amplified soybean primers revealed polymorphism among 24 cultivated pigeonpea accessions. No significant relationship was detected between the class of repeats and heterozygosity values. AT and TG class of repeats were the most abundant di-nucleotide repeats in library A and B respectively while TAA and GAA were the most abundant trinucleotide repeats in both libraries. Protein database searches provided putative functions for 21 SSR-containing pigeonpea sequences that would be useful in functional marker development. UPGMA and MDS cluster analysis revealed genetic relationships among recently bred varieties, old varieties and wild accessions. Nine of the markers developed were polymorphic to the parental lines of a F6 Fusarium wilt RIL mapping population that had been developed by ICRISAT breeders. Analysis of allele segregation in the RIL population revealed that all the 9 SSRs segregated in the expected 1:1 ratio and were further tested for any possible linkage with a QTL for resistance to Fusarium wilt. All the polymorphic markers derived from this study are now being used for characterisation and evaluation of pigeonpea germplasm collection at the International Crops Research Institute for the Semi-Arid Tropics (ICRISAT) headquarters, India. SSRs provide a powerful tool for genomic studies and are recommended for systematic fingerprinting of pigeonpea germplasm

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

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. Results: We assembled a 1.02-Gb draft genome of S. aethiopicum, which contained predominantly repetitive sequences (78.9%). We annotated 37,681 gene models, including 34,906 protein-coding genes. Expansion of disease resistance genes was observed via 2 rounds of amplification of long terminal repeat retrotransposons, which may have occurred ∼1.25 and 3.5 million years ago, respectively. By resequencing 65 S. aethiopicum and S. anguivi genotypes, 18,614,838 single-nucleotide polymorphisms were identified, of which 34,171 were located within disease resistance genes. Analysis of domestication and demographic history revealed active selection for genes involved in drought tolerance in both “Gilo” and “Shum” groups. A pan-genome of S. aethiopicum was assembled, containing 51,351 protein-coding genes; 7,069 of these genes were missing from the reference genome. Conclusions: The genome sequence of S. aethiopicum enhances our understanding of its biotic and abiotic resistance. The single-nucleotide polymorphisms identified are immediately available for use by breeders. The information provided here will accelerate selection and breeding of the African eggplant, as well as other crops within the Solanaceae family

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 ‘Adapting Agriculture to Climate Change: Collecting, Protecting and Preparing Crop Wild Relatives’ (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 “Analysis of the Microbiomes of Naturally Fermented Foods Training Course”. 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 (ACA17–16) 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 “Adapting Agriculture to Climate Change: Collecting, Protecting and Preparing Crop Wild Relatives” (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