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.

Comparison of SNP Calling Pipelines and NGS Platforms to Predict the Genomic Regions Harboring Candidate Genes for Nodulation in Cultivated Peanut.

Cultivated peanut (Arachis hypogaea L.) forms root nodules to enable a symbiotic relationship with rhizobia for biological nitrogen fixation. To understand the genetic factors of peanut nodulation, it is fundamental to genetically map and clone the genes involved in nodulation. For genetic mapping, high throughput genotyping with a large number of polymorphic markers is critical. In this study, two sets of sister recombinant inbred lines (RILs), each containing a nodulating (Nod+) and non-nodulating (Nod-) line, and their Nod+ parental lines were extensively genotyped. Several next generation sequencing (NGS) methods including target enrichment sequencing (TES), RNA-sequencing (RNA-seq), genotyping by sequencing (GBS), and the 48K Axiom Arachis2 SNP array, and various analysis pipelines were applied to identify single nucleotide polymorphisms (SNP) among the two sets of RILs and their parents. TES revealed the largest number of homozygous SNPs (15,947) between the original parental lines, followed by the Axiom Arachis2 SNP array (1,887), RNA-seq (1,633), and GBS (312). Among the five SNP analysis pipelines applied, the alignment to A/B genome followed by HAPLOSWEEP revealed the largest number of homozygous SNPs and highest concordance rate (79%) with the array. A total of 222 and 1,200 homozygous SNPs were polymorphic between the Nod+ and Nod- sister RILs and between their parents, respectively. A graphical genotype map of the sister RILs was constructed with these SNPs, which demonstrated the candidate genomic regions harboring genes controlling nodulation across the whole genome. Results of this study mainly provide the pros and cons of NGS and SNP genotyping platforms for genetic mapping in peanut, and also provide potential genetic resources to narrow down the genomic regions controlling peanut nodulation, which would lay the foundation for gene cloning and improvement of nitrogen fixation in peanut.

Identification of QTLs for resistance to leaf spots in cultivated peanut (Arachis hypogaea L.) through GWAS analysis.

KEY MESSAGE: Two QTLs on ChrB09 significantly associated with both early and late leaf spots were identified by genome-wide association study in the US peanut mini-core collection. Early leaf spot (ELS) and late leaf spot (LLS) are two serious peanut diseases in the USA, causing tens of millions of dollars of annual economic losses. However, the genetic factors underlying resistance to those diseases in peanuts have not been well-studied. We conducted a genome-wide association study for the two peanut diseases using Affymetrix version 2.0 SNP array with 120 genotypes mainly coming from the US peanut mini-core collection. A total of 46 quantitative trait loci (QTLs) were identified with phenotypic variation explained (PVE) from 10.19 to 24.11%, in which eighteen QTLs are for resistance to ELS and 28 QTLs for LLS. Among the 46 QTLs, there were four and two major QTLs with PVE higher than 16.99% for resistance ELS and LLS, respectively. Of the six major QTLs, five were located on the B sub-genome and only one was on the A sub-genome, which suggested that the B sub-genome has more potential resistance genomic regions than the A sub-genome. In addition, two genomic regions on chromosome B09 were found to provide significant resistance to both ELS and LLS. A total of 74 non-redundant genes were identified as resistance genes, among which, twelve candidate genes were in significant genomic regions including two candidate genes for both ELS and LLS, and other ten candidate genes for ELS. The QTLs and candidate genes obtained from this study will be useful to breed peanuts for resistances to the diseases.