Proteome evaluation of homolog abundance patterns in Arachis hypogaea cv. Tifrunner

Background Cultivated peanut (Arachis hypogaea, AABB genome), an allotetraploid from a cross between A. duranensis (AA genome) and A. ipaensis (BB genome), is an important oil and protein crop with released genome and RNA-seq sequence datasets. These datasets provide the molecular foundation for studying gene expression and evolutionary patterns. However, there are no reports on the proteomic data of A. hypogaea cv. Tifrunner, which limits understanding of its gene function and protein level evolution. Results This study sequenced the A. hypogaea cv. Tifrunner leaf and root proteome using the tandem mass tag technology. A total of 4803 abundant proteins were identified. The 364 differentially abundant proteins were estimated by comparing protein abundances between leaf and root proteomes. The differentially abundant proteins enriched the photosystem process. The number of biased abundant homeologs between the two sub-genomes A (87 homeologs in leaf and root) and B (69 and 68 homeologs in leaf and root, respectively) was not significantly different. However, homeologous proteins with biased abundances in different sub-genomes enriched different biological processes. In the leaf, homeologs biased to sub-genome A enriched biosynthetic and metabolic process, while homeologs biased to sub-genome B enriched iron ion homeostasis process. In the root, homeologs with biased abundance in sub-genome A enriched inorganic biosynthesis and metabolism process, while homeologs with biased abundance in sub-genome B enriched organic biosynthesis and metabolism process. Purifying selection mainly acted on paralogs and homeologs. The selective pressure values were negatively correlated with paralogous protein abundance. About 77.42% (24/31) homeologous and 80% (48/60) paralogous protein pairs had asymmetric abundance, and several protein pairs had conserved abundances in the leaf and root tissues. Conclusions This study sequenced the proteome of A. hypogaea cv. Tifrunner using the leaf and root tissues. Differentially abundant proteins were identified, and revealed functions. Paralog abundance divergence and homeolog bias abundance was elucidated. These results indicate that divergent abundance caused retention of homologs in A. hypogaea cv. Tifrunner.

Chloroplast Phylogenomic Analyses Reveal a Maternal Hybridization Event Leading to the Formation of Cultivated Peanuts

Peanuts (Arachis hypogaea L.) offer numerous healthy benefits, and the production of peanuts has a prominent role in global food security. As a result, it is in the interest of society to improve the productivity and quality of peanuts with transgenic means. However, the lack of a robust phylogeny of cultivated and wild peanut species has limited the utilization of genetic resources in peanut molecular breeding. In this study, a total of 33 complete peanut plastomes were sequenced, analyzed and used for phylogenetic analyses. Our results suggest that sect. Arachis can be subdivided into two lineages. All the cultivated species are contained in Lineage I with AABB and AA are the two predominant genome types present, while species in Lineage II possess diverse genome types, including BB, KK, GG, etc. Phylogenetic studies also indicate that all allotetraploid cultivated peanut species have been derived from a possible maternal hybridization event with one of the diploid Arachis duranensis accessions being a potential AA sub-genome ancestor. In addition, Arachis monticola, a tetraploid wild species, is placed in the same group with all the cultivated peanuts, and it may represent a transitional species, which has been through the recent hybridization event. This research could facilitate a better understanding of the taxonomic status of various Arachis species/accessions and the evolutionary relationship among them, and assists in the correct and efficient use of germplasm resources in breeding efforts to improve peanuts for the benefit of human beings.

Peanut Germplasm Evaluation for Agronomic Traits and Disease Resistance under a Two-Season Cropping System in Taiwan

Cultivated peanut (Arachis hypogaea L.) is an important crop worldwide, and peanut germplasm is an important genetic resource for peanut breeding. The two-season cropping system is common in tropical and subtropical regions, which are the main peanut production areas. The weather in the two cropping seasons is usually distinct and makes germplasm evaluation challenging. In this study, random stratified sampling based on market type was applied to build a core collection. Comparisons between the original entire collection and core collection were conducted. Two seasons field trials were performed with additional three seasons rust resistance evaluation trials. Principal component analysis and genotype-by-trait biplots were utilized as selection tools. Which-won-where/what and stability plot relationships were determined to provide breeders with an easy and efficient method for selection. Rust resistance simple sequence repeat and single nucleotide polymorphism markers were used to screen the germplasm. Some resistant accessions showed susceptible phenotypes, indicating that under Taiwan’s environment, the favored rust physiological races are different from those of other areas. Some potential rust resistance lines were discovered and validated, which can survive under variable weather conditions in a two-season cropping system. A set of markers was developed for utilization for rust resistance screening in Taiwan.

Genome-Wide Identification and Expression Analysis of AP2/ERF Transcription Factor Related to Drought Stress in Cultivated Peanut (Arachis hypogaea L.)

APETALA2/ethylene response element-binding factor (AP2/ERF) transcription factors (TFs) have been found to regulate plant growth and development and response to various abiotic stresses. However, detailed information of AP2/ERF genes in peanut against drought has not yet been performed. Herein, 185 AP2/ERF TF members were identified from the cultivated peanut (A. hypogaea cv. Tifrunner) genome, clustered into five subfamilies: AP2 (APETALA2), ERF (ethylene-responsive-element-binding), DREB (dehydration-responsive-element-binding), RAV (related to ABI3/VP), and Soloist (few unclassified factors)). Subsequently, the phylogenetic relationship, intron–exon structure, and chromosomal location of AhAP2/ERF were further characterized. All of these AhAP2/ERF genes were distributed unevenly across the 20 chromosomes, and 14 tandem and 85 segmental duplicated gene pairs were identified which originated from ancient duplication events. Gene evolution analysis showed that A. hypogaea cv. Tifrunner were separated 64.07 and 66.44 Mya from Medicago truncatula L. and Glycine max L., respectively. Promoter analysis discovered many cis-acting elements related to light, hormones, tissues, and stress responsiveness process. The protein interaction network predicted the exitance of functional interaction among families or subgroups. Expression profiles showed that genes from AP2, ERF, and dehydration-responsive-element-binding subfamilies were significantly upregulated under drought stress conditions. Our study laid a foundation and provided a panel of candidate AP2/ERF TFs for further functional validation to uplift breeding programs of drought-resistant peanut cultivars.

Resistance to rust (Puccinia arachidis Speg.) identified in nascent allotetraploids cross-compatible with cultivated peanut (Arachis hypogaea L.)

Peanut rust, caused by Puccinia arachidis Speg., is a foliar disease that plagues peanut production along with early and late leaf spots, Passalora arachidicola (Hori) U. Braun and Nothopassalora personata (Berk. & M.A. Curtis) U. Braun, C. Nakash, Videira & Crous, respectively. Rust can cause up to 80% yield losses without control and is widespread in tropical countries but is also a sporadic problem in the United States. An integrative plant management strategy with rust resistant peanut cultivars is needed to decrease dependence on costly fungicides and increase yields for farmers who cannot afford or do not have access to fungicides. Only moderate levels of rust resistance have been found in cultivated peanut germplasm, but fortunately, high resistance to rust has been identified in wild Arachis species that can be introgressed into peanut cultivars. In this study, 16 diploid, wild Arachis species, five diploid, interspecific hybrids, 11 unique, allotetraploid interspecific hybrids, and two cultivated peanut controls were tested for resistance to rust. Resistance was evaluated in vitro by incubation time, susceptibility index (calculated based on the number of lesions of different diameters)/ leaf area, total number of lesions/ leaf area, and total number of sporulating lesions/ leaf area. All wild Arachis species tested were very highly resistant to rust, except for A. ipaënsis , the B-genome progenitor of cultivated peanut. Additionally, all interspecific hybrids and synthetic allotetraploids not produced with A. ipaënsis as a parent did not show symptoms for rust. Any of these nine synthetic allotetraploids, BatCor , BatDur 1, BatDur 2, BatSten 1, GregSten , MagCard , MagDio , MagDur , and ValSten 1 are recommended for progression to QTL mapping of rust resistance. These resistance QTLs can be pyramided into peanut cultivars to protect yields in the United States and to increase yields in tropical, developing countries for farmers that cannot afford, or do not have access to, costly fungicides.

Genetic diversity analysis of Korean peanut germplasm using 48 K SNPs ‘Axiom_Arachis’ Array and its application for cultivar differentiation

Cultivated peanut (Arachis hypogaea) is one of the important legume oilseed crops. Cultivated peanut has a narrow genetic base. Therefore, it is necessary to widen its genetic base and diversity for additional use. The objective of the present study was to assess the genetic diversity and population structure of 96 peanut genotypes with 9478 high-resolution SNPs identified from a 48 K ‘Axiom_Arachis’ SNP array. Korean set genotypes were also compared with a mini-core of US genotypes. These sets of genotypes were used for genetic diversity analysis. Model-based structure analysis at K = 2 indicated the presence of two subpopulations in both sets of genotypes. Phylogenetic and PCA analysis clustered these genotypes into two major groups. However, clear genotype distribution was not observed for categories of subspecies, botanical variety, or origin. The analysis also revealed that current Korean genetic resources lacked variability compared to US mini-core genotypes. These results suggest that Korean genetic resources need to be expanded by creating new allele combinations and widening the genetic pool to offer new genetic variations for Korean peanut improvement programs. High-quality SNP data generated in this study could be used for identifying varietal contaminant, QTL, and genes associated with desirable traits by performing mapping, genome-wide association studies.

Comprehensive Transcriptome Analyses Reveal Candidate Genes for Variation in Seed Size/Weight During Peanut (Arachis hypogaea L.) Domestication

Seed size/weight, a key domestication trait, is also an important selection target during peanut breeding. However, the mechanisms that regulate peanut seed development are unknown. We re-sequenced 12 RNA samples from developing seeds of two cultivated peanut accessions (Lines 8106 and 8107) and wild Arachis monticola at 15, 30, 45, and 60 days past flowering (DPF). Transcriptome analyses showed that ∼36,000 gene loci were expressed in each of the 12 RNA samples, with nearly half exhibiting moderate (2 ≤ FPKM < 10) expression levels. Of these genes, 12.2% (4,523) were specifically expressed during seed development, mainly at 15 DPF. Also, ∼12,000 genes showed significant differential expression at 30, 45, and/or 60 DPF within each of the three peanut accessions, accounting for 31.8–34.1% of the total expressed genes. Using a method that combined comprehensive transcriptome analysis and previously mapped QTLs, we identified several candidate genes that encode transcription factor TGA7, topless-related protein 2, IAA-amino acid hydrolase ILR1-like 5, and putative pentatricopeptide repeat-containing (PPR) protein. Based on sequence variations identified in these genes, SNP markers were developed and used to genotype both 30 peanut landraces and a genetic segregated population, implying that EVM0025654 encoding a PPR protein may be associated with the increased seed size/weight of the cultivated accessions in comparison with the allotetraploid wild peanut. Our results provide additional knowledge for the identification and functional research into candidate genes responsible for the seed size/weight phenotype in peanut.

Transcriptome Profile Reveals Drought-Induced Genes Preferentially Expressed in Response to Water Deficit in Cultivated Peanut (Arachis hypogaea L.)

Cultivated peanut (Arachis hypogaea) is one of the most widely grown food legumes in the world, being valued for its high protein and unsaturated oil contents. Drought stress is one of the major constraints that limit peanut production. This study’s objective was to identify the drought-responsive genes preferentially expressed under drought stress in different peanut genotypes. To accomplish this, four genotypes (drought tolerant: C76-16 and 587; drought susceptible: Tifrunner and 506) subjected to drought stress in a rainout shelter experiment were examined. Transcriptome sequencing analysis identified that all four genotypes shared a total of 2,457 differentially expressed genes (DEGs). A total of 139 enriched gene ontology terms consisting of 86 biological processes and 53 molecular functions, with defense response, reproductive process, and signaling pathways, were significantly enriched in the common DEGs. In addition, 3,576 DEGs were identified only in drought-tolerant lines in which a total of 74 gene ontology terms were identified, including 55 biological processes and 19 molecular functions, mainly related to protein modification process, pollination, and metabolic process. These terms were also found in shared genes in four genotypes, indicating that tolerant lines adjusted more related genes to respond to drought. Forty-three significantly enriched Kyoto Encyclopedia of Genes and Genomes pathways were also identified, and the most enriched pathways were those processes involved in metabolic pathways, biosynthesis of secondary metabolites, plant circadian rhythm, phenylpropanoid biosynthesis, and starch and sucrose metabolism. This research expands our current understanding of the mechanisms that facilitate peanut drought tolerance and shed light on breeding advanced peanut lines to combat drought stress.