Transcriptomic analyses reveal the expression and regulation of genes associated with resistance to early leaf spot in peanut.

OBJECTIVE: Early leaf spot (ELS) caused by Cercospora arachidicola (Hori) is a serious foliar disease in peanut worldwide, which causes considerable reduction of yield. Identification of resistance genes is important for both conventional and molecular breeding. Few resistance genes have been identified and the mechanism of defense responses to this pathogen remains unknown. RESULTS: We detected several genes involved in disease resistance to ELS through transcriptome analysis. Using RNA-seq technology, one hundred thirty-three differentially expressed genes (DEGs) were identified between resistant and susceptible lines. Among these DEGs, coiled coil-nucleotide binding-leucine rich repeat (NLR) type resistance genes were identified as duplicated R genes on the chromosome B2. Peanut phytoalexin deficient 4 (PAD4) regulator of effector-triggered immunity mediated by NLR resistance proteins and polyphenol oxidase (PPO) genes play important roles in early leaf spot resistance. Our study provides the useful information on plant response to C. arachidicola infection in peanut. The results suggest that a few major genes and several factors mediate the resistance to ELS disease, showing the characteristics of quantitative trait in defense responses.

Comparison of Arachis monticola with Diploid and Cultivated Tetraploid Genomes Reveals Asymmetric Subgenome Evolution and Improvement of Peanut.

Like many important crops, peanut is a polyploid that underwent polyploidization, evolution, and domestication. The wild allotetraploid peanut species Arachis monticola (A. monticola) is an important and unique link from the wild diploid species to cultivated tetraploid species in the Arachis lineage. However, little is known about A. monticola and its role in the evolution and domestication of this important crop. A fully annotated sequence of ≈2.6 Gb A. monticola genome and comparative genomics of the Arachis species is reported. Genomic reconstruction of 17 wild diploids from AA, BB, EE, KK, and CC groups and 30 tetraploids demonstrates a monophyletic origin of A and B subgenomes in allotetraploid peanuts. The wild and cultivated tetraploids undergo asymmetric subgenome evolution, including homoeologous exchanges, homoeolog expression bias, and structural variation (SV), leading to subgenome functional divergence during peanut domestication. Significantly, SV-associated homoeologs tend to show expression bias and correlation with pod size increase from diploids to wild and cultivated tetraploids. Moreover, genomic analysis of disease resistance genes shows the unique alleles present in the wild peanut can be introduced into breeding programs to improve some resistance traits in the cultivated peanuts. These genomic resources are valuable for studying polyploid genome evolution, domestication, and improvement of peanut production and resistance.

Identification of groundnut (Arachis hypogaea) SSR markers suitable for multiple resistance traits QTL mapping in African germplasm

Background This study aimed to identify and select informative Simple Sequence Repeat (SSR) markers that may be linked to resistance to important groundnut diseases such as Early Leaf Spot, Groundnut Rosette Disease, rust and aflatoxin contamination. To this end, 799 markers were screened across 16 farmer preferred and other cultivated African groundnut varieties that are routinely used in groundnut improvement, some with known resistance traits. Results The SSR markers amplified 817 loci and were graded on a scale of 1 to 4 according to successful amplification and ease of scoring of amplified alleles. Of these, 376 markers exhibited Polymorphic Information Content (PIC) values ranging from 0.06 to 0.86, with 1476 alleles detected at an average of 3.7 alleles per locus. The remaining 423 markers were either monomorphic or did not work well. The best performing polymorphic markers were subsequently used to construct a dissimilarity matrix that indicated the relatedness of the varieties in order to aid selection of appropriately diverse parents for groundnut improvement. The closest related varieties were MGV5 and ICGV-SM 90704 and most distant were Chalimbana and 47-10. The mean dissimilarity value was 0.51, ranging from 0.34 to 0.66. Discussion Of the 376 informative markers identified in this study, 139 (37%) have previously been mapped to the Arachis genome and can now be employed in Quantitative Trait Loci (QTL) mapping and the additional 237 markers identified can be used to improve the efficiency of introgression of resistance to multiple important biotic constraints into farmer-preferred varieties of Sub-Saharan Africa.

Development and characterization of BAC-end sequence derived SSRs, and their incorporation into a new higher density genetic map for cultivated peanut (Arachis hypogaea L.).

BACKGROUND: Cultivated peanut (Arachis hypogaea L.) is an important crop worldwide, valued for its edible oil and digestible protein. It has a very narrow genetic base that may well derive from a relatively recent single polyploidization event. Accordingly molecular markers have low levels of polymorphism and the number of polymorphic molecular markers available for cultivated peanut is still limiting. RESULTS: Here, we report a large set of BAC-end sequences (BES), use them for developing SSR (BES-SSR) markers, and apply them in genetic linkage mapping. The majority of BESs had no detectable homology to known genes (49.5%) followed by sequences with similarity to known genes (44.3%), and miscellaneous sequences (6.2%) such as transposable element, retroelement, and organelle sequences. A total of 1,424 SSRs were identified from 36,435 BESs. Among these identified SSRs, dinucleotide (47.4%) and trinucleotide (37.1%) SSRs were predominant. The new set of 1,152 SSRs as well as about 4,000 published or unpublished SSRs were screened against two parents of a mapping population, generating 385 polymorphic loci. A genetic linkage map was constructed, consisting of 318 loci onto 21 linkage groups and covering a total of 1,674.4 cM, with an average distance of 5.3 cM between adjacent loci. Two markers related to resistance gene homologs (RGH) were mapped to two different groups, thus anchoring 1 RGH-BAC contig and 1 singleton. CONCLUSIONS: The SSRs mined from BESs will be of use in further molecular analysis of the peanut genome, providing a novel set of markers, genetically anchoring BAC clones, and incorporating gene sequences into a linkage map. This will aid in the identification of markers linked to genes of interest and map-based cloning.

Development of trinucleotide (GGC)n SSR markers in peanut (Arachis hypogaea L)

Cultivated peanut (Arachis hypogaea L.) is an oilseed crop of economic importance. It is native to South America, and it is grown extensively in the semi-arid tropics of Asia, Africa, and Latin America. Given an extremely narrow genetic base, efforts are being made to develop simple sequence repeat (SSR) markers to provide useful genetic and genomic tools for the peanut research community. A SSR-enriched library to isolate trinucleotide (GGC)n SSRs in peanut was constructed. A total of 143 unique sequences containing (GGC)n repeats were identified. One hundred thirty eight primer pairs were successfully designed at the flanking regions of SSRs. A suitable polymerase was chosen to amplify these GC-rich sequences. Although a low level of polymorphism was observed in cultivated peanut by these new developed SSRs, a high level of transferability to wild species would be beneficial to increasing the number of SSRs in wild species.