Evaluation of five peanut (Arachis hypogaea) genotypes to identify drought responsive mechanisms utilising candidate-gene approach

Genome-Wide Association Analysis Identified Quantitative Trait Loci (QTLs) Underlying Drought-Related Traits in Cultivated Peanut (Arachis hypogaea L.)

Drought is a destructive abiotic stress that affects all critical stages of peanut growth such as emergence, flowering, pegging, and pod filling. The development of a drought-tolerant variety is a sustainable strategy for long-term peanut production. The U.S. mini-core peanut germplasm collection was evaluated for drought tolerance to the middle-season drought treatment phenotyping for pod weight, pod count, relative water content (RWC), specific leaf area (SLA), leaf dry matter content (LDMC), and drought rating. A genome-wide association study (GWAS) was performed to identify minor and major QTLs. A total of 144 QTLs were identified, including 18 significant QTLs in proximity to 317 candidate genes. Ten significant QTLs on linkage groups (LGs) A03, A05, A06, A07, A08, B04, B05, B06, B09, and B10 were associated with pod weight and pod count. RWC stages 1 and 2 were correlated with pod weight, pod count, and drought rating. Six significant QTLs on LGs A04, A07, B03, and B04 were associated with RWC stages 1 and 2. Drought rating was negatively correlated with pod yield and pod count and was associated with a significant QTL on LG A06. Many QTLs identified in this research are novel for the evaluated traits, with verification that the pod weight shared a significant QTL on chromosome B06 identified in other research. Identified SNP markers and the associated candidate genes provide a resource for molecular marker development. Verification of candidate genes surrounding significant QTLs will facilitate the application of marker-assisted peanut breeding for drought tolerance.

Transcriptome and Co-expression Network Analyses Reveal Differential Gene Expression and Pathways in Response to Severe Drought Stress in Peanut (Arachis hypogaea L.)

Drought is one of the major abiotic stress factors limiting peanut production. It causes the loss of pod yield during the pod formation stage. Here, one previously identified drought-tolerant cultivar, "L422" of peanut, was stressed by drought (35 ± 5%) at pod formation stage for 5, 7, and 9 days. To analyze the drought effects on peanut, we conducted physiological and transcriptome analysis in leaves under well-watered (CK1, CK2, and CK3) and drought-stress conditions (T1, T2, and T3). By transcriptome analysis, 3,586, 6,730, and 8,054 differentially expressed genes (DEGs) were identified in "L422" at 5 days (CK1 vs T1), 7 days (CK2 vs T2), and 9 days (CK3 vs T3) of drought stress, respectively, and 2,846 genes were common DEGs among the three-time points. Furthermore, the result of weighted gene co-expression network analysis (WGCNA) revealed one significant module that was closely correlated between drought stress and physiological data. A total of 1,313 significantly up-/down-regulated genes, including 61 transcription factors, were identified in the module at three-time points throughout the drought stress stage. Additionally, six vital metabolic pathways, namely, "MAPK signaling pathway-plant," "flavonoid biosynthesis," "starch and sucrose metabolism," "phenylpropanoid biosynthesis," "glutathione metabolism," and "plant hormone signal transduction" were enriched in "L422" under severe drought stress. Nine genes responding to drought tolerance were selected for quantitative real-time PCR (qRT-PCR) verification and the results agreed with transcriptional profile data, which reveals the reliability and accuracy of transcriptome data. Taken together, these findings could lead to a better understanding of drought tolerance and facilitate the breeding of drought-resistant peanut cultivars.

Association of differentially expressed R-gene candidates with leaf spot resistance in peanut (Arachis hypogaea L.)

Early leaf spot (ELS) and late leaf spot (LLS) are major fungal diseases of peanut that can severely reduce yield and quality. Development of acceptable genetic resistance has been difficult due to a strong environmental component and many major and minor QTLs. Resistance genes (R-genes) are an important component of plant immune system and have been identified in peanut. Association of specific R-genes to leaf spot resistance will provide molecular targets for marker-assisted breeding strategies. In this study, advanced breeding lines from different pedigrees were evaluated for leaf spot resistance and 76 candidate R-genes expression study was applied to susceptible and resistant lines. Thirty-six R-genes were differentially expressed and significantly correlated with resistant lines, of which a majority are receptor like kinases (RLKs) and receptor like proteins (RLPs) that sense the presence of pathogen at the cell surface and initiate protection response. The largest group was receptor-like cytoplasmic kinases (RLCKs) VII that are involved in pattern-triggered kinase signaling resulting in the production reactive oxygen species (ROS). Four R-genes were homologous to TMV resistant protein N which has shown to confer resistance against tobacco mosaic virus (TMV). When mapped to peanut genomes, 36 R-genes were represented in most chromosomes except for A09 and B09. Low levels of gene-expression in resistant lines suggest expression is tightly controlled to balance the cost of R-gene expression to plant productively. Identification and association of R-genes involved in leaf spot resistance will facilitate genetic selection of leaf spot resistant lines with good agronomic traits.

Identification of expressed R-genes associated with leaf spot diseases in cultivated peanut

Peanut (Arachis hypogaea L.) is an important food and oilseed crop worldwide. Yield and quality can be significantly reduced by foliar fungal diseases, such as early and late leaf spot diseases. Acceptable levels of leaf spot resistance in cultivated peanut have been elusive due to environmental interactions and the proper combination of QTLs in any particular peanut genotype. Resistance gene analogs, as potential resistance (R)-genes, have unique roles in the recognition and activation of disease resistance responses. Novel R-genes can be identified by searches for conserved domains such as nucleotide binding site, leucine rich repeat, receptor like kinase, and receptor like protein from expressed genes or through genomic sequences. Expressed R-genes represent necessary plant signals in a disease response. The goals of this research are to identify expressed R-genes from cultivated peanuts that are naturally infected by early and late spot pathogens, compare these to the closest diploid progenitors, and evaluate specific gene expression in cultivated peanuts. Putative peanut R-genes (381) were available from a public database (NCBI). Primers were designed and PCR products were sequenced. A total of 214 sequences were produced which matched to proteins with the corresponding R-gene motifs. These R-genes were mapped to the genome sequences of Arachis duranensis and Arachis ipaensis, which are the closest diploid progenitors for tetraploid cultivated peanut, A. hypogaea. Identification and association of specific gene-expression will elucidate potential disease resistance mechanism in peanut and may facilitate the selection of breeding lines with high levels of leaf spot resistance.

Characterization of small RNA populations in non-transgenic and aflatoxin-reducing-transformed peanut

Aflatoxin contamination is a major constraint in food production worldwide. In peanut (Arachis hypogaea L.), these toxic and carcinogenic aflatoxins are mainly produced by Aspergillus flavus Link and A. parasiticus Speare. The use of RNA interference (RNAi) is a promising method to reduce or prevent the accumulation of aflatoxin in peanut seed. In this study, we performed high-throughput sequencing of small RNA populations in a control line and in two transformed peanut lines that expressed an inverted repeat targeting five genes involved in the aflatoxin-biosynthesis pathway and that showed up to 100% less aflatoxin B₁ than the controls. The objective was to determine the putative involvement of the small RNA populations in aflatoxin reduction. In total, 41 known microRNA (miRNA) families and many novel miRNAs were identified. Among those, 89 known and 10 novel miRNAs were differentially expressed in the transformed lines. We furthermore found two small interfering RNAs derived from the inverted repeat, and 39 sRNAs that mapped without mismatches to the genome of A. flavus and were present only in the transformed lines. This information will increase our understanding of the effectiveness of RNAi and enable the possible improvement of the RNAi technology for the control of aflatoxins.