Genome-wide association studies reveal novel loci for resistance to groundnut rosette disease in the African core groundnut collection.

KEY MESSAGE: We identified markers associated with GRD resistance after screening an Africa-wide core collection across three seasons in Uganda Groundnut is cultivated in several African countries where it is a major source of food, feed and income. One of the major constraints to groundnut production in Africa is groundnut rosette disease (GRD), which is caused by a complex of three agents: groundnut rosette assistor luteovirus, groundnut rosette umbravirus and its satellite RNA. Despite several years of breeding for GRD resistance, the genetics of the disease is not fully understood. The objective of the current study was to use the African core collection to establish the level of genetic variation in their response to GRD, and to map genomic regions responsible for the observed resistance. The African groundnut core genotypes were screened across two GRD hotspot locations in Uganda (Nakabango and Serere) for 3 seasons. The Area Under Disease Progress Curve combined with 7523 high quality SNPs were analyzed to establish marker-trait associations (MTAs). Genome-Wide Association Studies based on Enriched Compressed Mixed Linear Model detected 32 MTAs at Nakabango: 21 on chromosome A04, 10 on B04 and 1 on B08. Two of the significant markers were localised on the exons of a putative TIR-NBS-LRR disease resistance gene on chromosome A04. Our results suggest the likely involvement of major genes in the resistance to GRD but will need to be further validated with more comprehensive phenotypic and genotypic datasets. The markers identified in the current study will be developed into routine assays and validated for future genomics-assisted selection for GRD resistance in groundnut.

A high-density linkage map of finger millet provides QTL for blast resistance and other agronomic traits.

Finger millet [Eleusine coracana (L.) Gaertn.] is a critical subsistence crop in eastern Africa and southern Asia but has few genomic resources and modern breeding programs. To aid in the understanding of finger millet genomic organization and genes underlying disease resistance and agronomically important traits, we generated a F2:3 population from a cross between E. coracana (L.) Gaertn. subsp. coracana accession ACC 100007 and E. coracana (L.) Gaertn. subsp. africana , accession GBK 030647. Phenotypic data on morphology, yield, and blast (Magnaporthe oryzae) resistance traits were taken on a subset of the F2:3 population in a Kenyan field trial. The F2:3 population was genotyped via genotyping-by-sequencing (GBS) and the UGbS-Flex pipeline was used for sequence alignment, nucleotide polymorphism calling, and genetic map construction. An 18-linkage-group genetic map consisting of 5,422 markers was generated that enabled comparative genomic analyses with rice (Oryza sativa L.), foxtail millet [Setaria italica (L.) P. Beauv.], and sorghum [Sorghum bicolor (L.) Moench]. Notably, we identified conserved acrocentric homoeologous chromosomes (4A and 4B in finger millet) across all species. Significant quantitative trait loci (QTL) were discovered for flowering date, plant height, panicle number, and blast incidence and severity. Sixteen putative candidate genes that may underlie trait variation were identified. Seven LEUCINE-RICH REPEAT-CONTAINING PROTEIN genes, with homology to nucleotide-binding site leucine-rich repeat (NBS-LRR) disease resistance proteins, were found on three chromosomes under blast resistance QTL. This high-marker-density genetic map provides an important tool for plant breeding programs and identifies genomic regions and genes of critical interest for agronomic traits and blast resistance.

Genetics and breeding for climate change in Orphan crops.

Climate change is rapidly changing how we live, what we eat and produce, the crops we breed and the target traits. Previously underutilized orphan crops that are climate resilient are receiving much attention from the crops research community, as they are often the only crops left in the field after periods of extreme weather conditions. There are several orphan crops with incredible resilience to biotic and abiotic stresses. Some are nutritious, while others provide good sources of biofuel, medicine and other industrial raw materials. Despite these benefits, orphan crops are still lacking in important genetic and genomic resources that could be used to fast track their improvement and make their production profitable. Progress has been made in generating draft genomes of at least 28 orphan crops over the last decade, thanks to the reducing cost of sequencing. The implementation of a structured breeding program that takes advantage of additional modern crop improvement tools such as genomic selection, speed breeding, genome editing, high throughput phenotyping and breeding digitization would make rapid improvement of these orphan crops possible, but would require coordinated research investment. Other production challenges such as lack of adequate germplasm conservation, poor/non-existent seed systems and agricultural extension services, as well as poor marketing channels will also need to be improved if orphan crops were to be profitable. We review the importance of breeding orphan crops under the increasing effects of climate change, highlight existing gaps that need to be addressed and share some lessons to be learned from major crops.

Draft genome sequence of Solanum aethiopicum provides insights into disease resistance, drought tolerance, and the evolution of the genome.

BACKGROUND: 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.

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.

Physical organization of mixed protease inhibitor gene clusters, coordinated expression and association with resistance to late blight at the StKI locus on potato chromosome III.

Protease inhibitors (PIs) play a role in plant defence against pests and pathogens as well as in plant development. Potato (Solanum tuberosum) contains abundant levels of diverse PIs. Most potato Kunitz-type inhibitor (KTI) genes map to the StKI locus on potato chromosome III, which is linked to a quantitative trait locus (QTL) for resistance to Phytophthora infestans. To elucidate the physical organization of PIs at the StKI locus, we screened bacterial artificial chromosome (BAC) libraries with KTI probes. Ten different clones were selected, sequenced and annotated. Of 100 putative genes, 22 corresponded to five PI classes. Expression analysis by quantitative real-time PCR (qRT-PCR) using PI class-specific primers in different tissues of the tetraploid potato cultivars 'Nikita' and 'Baltica' revealed different transcript levels, depending on PI type and genotype. During the compatible interaction with a complex race of P. infestans, four PI classes showed coordinated expression over 3 d after infection, a strong decrease in infected leaves and a transient induction in systemic leaves. Basal transcript levels in non-infected leaves differed strongly between the two genotypes examined. Two microsatellite markers located within the PI gene cluster were associated with resistance to P. infestans in a population of potato varieties and breeding clones.