Molecular diversity of RNA-2 genome segments in pecluviruses causing peanut clump disease in West Africa and India

The complete nucleotide sequence of RNA-2 genome segments of four isolates of Peanut clump virus (PCV) and two isolates of Indian peanut clump virus (IPCV) were determined. Comparisons among the complete RNA-2 sequences of six isolates from this study and two published earlier, revealed a high degree of variability in size (between 4290 and 4652 nucleotides) and nucleotide sequence identities (between 58% and 79%). Amino acid sequence alignments of the five open reading frames (ORF) showed that ORF 4, which encodes the second of the triple gene block proteins, is highly conserved (90 to 98% identical) whereas the protein encoded by ORF 2, whose function is unknown, is less conserved (25 to 60% identical). The coat protein of the eight isolates showed amino acid identities between 37% and 89% and contained several conserved residues. Phylogenetic comparisons, based on complete RNA-2 sequences, revealed that the eight isolates grouped into two distinct clusters with no geographical distinction between PCV and IPCV isolates. Phylogenetic tree topologies for individual ORFs showed an overall similarity with that obtained from entire RNA-2 sequences, although the relative positions of individual isolates vary within each cluster. The results indicate that there is substantial divergence among the RNA-2 genomes of pecluviruses and suggest that different proteins have evolved differently, possibly due to different selection pressures

Groundnut Production Guide for Uganda: Recommended Practices for Farmers

Groundnut is one of the staple crops in the Uganda rich in protein, oil and essential minerals. The crop is increasingly becoming a cash crop and both production area and productivity are increasing. This is evident by the significant expansion of the industry in Uganda and with spillovers in the neighbouring countries. The end-users’ preferences of groundnuts vary and are dynamic. The crop also suffers from numerous pests and diseases and erratic weather that affect production. The National Groundnuts Improvement Programme responded to these challenges by developing groundnuts varieties to meets these challenges. The manual contains valuable scientific information about crop management topics such as land preparation, varietal selection, seed management, crop protection and postharvest management under Ugandan conditions. The appendices contain a catalogue of groundnut varieties released since 1966 with their yields and botanical classifications. This is in addition to the summarized poster of recommended practices at major growth stages covering pre- and post harvest operations The manual is carefully written in comprehensible language while making no scientific compromises. I believe that this production manual will become an essential source of ideas and information for any farmer, extension staff, and researchers interested in cultivating groundnuts in Uganda. NARO as a leader of quality agricultural research and development in the country and the region furnishes the users with practical technologies and the accompanying packages. Publication of this production manual is thus timely, and will help the wide spectrum of industry stakeholders (agricultural researchers, extension people, smallholder producers, agricultural consultants and commercial producers) by providing information on best management practices that will improve groundnut productivity and quality. I sincerely thank the development partners for their contribution towards the production of this manual. The management of NARO applauds this effort by the authors and hope that the messages in the manual reach the intended users as we strive towards a sustainable quality groundnut production and productivity, and improvement of livelihoods

Spatiotemporal Separation of Groundnut Rosette Disease Agents

Analysis by triple-antibody sandwich enzyme-linked immunosorbent assay of groundnut samples from fields in two seasons from different regions of Malawi showed the absence of groundnut rosette assistor virus (GRAV) from some plants showing groundnut rosette disease symptoms and the presence of GRAV in some symptomless plants. Viruliferous Aphis craccivora collected from fields transmitted either GRAV alone, groundnut rosette virus (GRV) with its satellite RNA (sat RNA), or all three agents together, in different proportions. More plants became infected with all three agents when increasing numbers of potentially viruliferous aphids were used per plant, suggesting a dosage response. Electrical penetration graph studies of aphid stylet activities indicated successful transmission of GRV and its sat RNA during both the "stylet pathway phase" and salivation into sieve elements, whereas GRAV was transmitted only during the latter phase. Aphids transmitted all three agents together only during the salivation phase. Reverse-transcriptase polymerase chain reaction testing of viruliferous aphids and of inoculated plants revealed no correlation between the presence of all three agents in prospective aphid vectors and their simultaneous transmission to groundnut plants. These results show that separation of the groundnut rosette disease agents occurs over time and space

Sequence Diversity Within the Three Agents of Groundnut Rosette Disease

Sequence diversity was examined in the coat protein (CP) gene of Groundnut rosette assistor virus (GRAV), the overlapping open reading frames (ORFs) 3 and 4 of Groundnut rosette virus (GRV), and the satellite RNA (sat-RNA) of GRV obtained from field isolates from Malawi and Nigeria. These three agents cause groundnut rosette disease, a major disease of groundnut in sub-Saharan Africa (SSA). Sequence analysis showed that the GRAV CP gene was highly conserved (97 to 99%) independent of its geographic source. The nucleotide sequence of the overlapping ORFs 3 and 4 of GRV was highly conserved (98 to 100%) from isolates within a geographic region but less conserved (88 to 89%) between isolates from the two distinct geographic regions. Phylogenetic analysis of the overlapping ORFs 3 and 4 show that the GRV isolates cluster according to the geographic region from which they were isolated, indicating that Malawian GRV isolates are distinct from Nigerian GRV isolates. Similarity within the sat-RNA sequences analyzed ranged from 88 to 99%. Phylogenetic analysis also showed clustering within the sat-RNA isolates according to country of origin, as well as within isolates from two distinct regions of Malawi. Because the GRAV CP sequence is highly conserved, independent of the geographic source of the GRAV isolates, the GRAV CP sequence represents the most likely candidate to use for pathogen-derived resistance in groundnut and may provide effective protection against groundnut rosette disease throughout SSA

Current status of groundnut improvement in Uganda

In Uganda, groundnut (Arachis hypogaea L) is the second most important legume after beans. Groundnuts is cultivated on nearly 260,000 ha, representing 24.6% of the total arable land. On-farm pod yields are low, averaging 800 kg/ha of dry pods, compared to on-station potential yields of 3,000kg/ha. Sales from current production could potentially generate $344 million to the producers who are largely small-scale farmers. The yield gaps are attributed to a combination of biotic, abiotic, cultural and political factors. Since the 1920s, research efforts have released 24 varieties, the most recent commercial varieties being the Serenut 1-14 series. These varieties have overcome some of the mentioned production constraints. However, varied growing agroecologies, land tenure systems, diverse market preferences, and emerging stresses call for continuous research. Current research agenda includes breeding for high oleic, leafminer resistance, confectionery, aflatoxin tolerance, drought tolerance, early to medium maturing varieties, high yielding, and rosette disease resistant varieties. We have initiated Marker Assisted Selection for high oleic breeding and adopted BMS for Digitalization of data capture, management, analyses and storage. Recently developed regeneration protocol will aid in introgressing additional traits across taxa. The bimodal rainfall pattern and active hybridization programme increases our breeding cycles. To date, the groundnut breeding program has an active breeding pipeline frequently releasing varieties and lines which have already been shared with National Programs across Africa, Haiti and the USA with many additional National Programs making requests. We have strong partnerships in Research and Development among the African Countries, USAID, ICRISAT, and BMGF

Groundnut rossette: A virus disease affecting groundnut production in Sub-Saharan Africa

Groundnut (peanut, Arachis hypogaea L.) is cultivated in the semiarid tropical and subtropical regions of nearly 100 countries on six continents between 40°N and 40°S (Fig. 1). For people in many developing countries, groundnuts are the principal source of digestible protein (25 to 34%), cooking oil (44 to 56%), and vitamins like thiamine, riboflavin, and niacin (65)..

Peanut yellow spot virus: A distinct tospovirus species based on serology and nucleic acid hybridisation

Nucleocapsids of peanut yellow spot virus (PYSV), purified from peanut (= groundnut) plant tissue, contained a protein with a molecular mass of 29 kDa. In ELISA and immuno-blot analysis the virus did not react with tomato spotted wilt virus (TSWV), Impatiens necrotic spot virus (INSV) and peanut bud necrosis virus (PBNV) antisera. PYSV contained three RNA species, a large (L) RNA (c.8900 nucleotides), a medium (M) RNA (c.4800 nucleotides) and a small (S) RNA (c.3000 nucleotides), similar to other tospoviruses. In addition, a fourth RNA species of approximately 1800 nucleotides was also present in purified preparations. Hybridisation analysis under high stringency conditions revealed no hybridisation between PYSV RNAs and cDNA probes representing the nucleocapsid (N) gene, the glycoprotein (GP) gene and the 3' half of the RNA polymerase gene of PBNV. PYSV genomic RNAs also failed to hybridise with cDNA probes from the GP genes of TSWV and INSV. In reciprocal tests, the cDNA clones of PYSV S and M RNAs did not hybridise with any of the PBNV RNAs. Based on the absence of serological relationships between PYSV and PBNV, TSWV and INSV and lack of nucleotide homology based on hybridisation studies between the PYSV RNAs and cDNA clones from PBNV, TSWV and INSV, PYSV should be considered as a distinct species of the genus Tospovirus under a new serogroup, putatively designated ‘V

Registration of ICG 12991 peanut germplasm line

ICG 12991 is a short duration (90–110 d to maturation), drought-tolerant, spanish-type peanut (Arachis hypogaea L. subsp. fastigiata Waldron var. vulgaris Harz.) germplasm line (Reg. no. GP-122, PI 639691) with a high level of field resistance to groundnut rosette disease (Naidu et al., 1999a; Subrahmanyam et al., 2000). Groundnut rosette disease results from a synergism of three agents: Groundnut rosette assistor virus (GRAV, a luteovirus), Groundnut rosette virus (GRV, an umbravirus), and a satellite RNA (sat RNA) of GRV. ICG 12991 was originally collected from a farmer’s field in south India in 1988. In 1994, ICRISAT introduced ICG 12991 into Malawi for evaluation during a germplasm screening program for resistance to groundnut rosette disease and early leaf spot disease (caused by Cercospora arachidicola S. Hori). Subsequently, ICG 12991 was released in Malawi as ‘Baka’ in 2001 and in Uganda as ‘Serenut 4T’ in 2002, following extensive testing and distribution by the national programs of each country. Resistance to groundnut rosette disease in ICG 12991 is due to aphid resistance, not due to resistance to the virus complex (Naidu et al., 1999b)

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

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