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

Deciphering peanut complex genomes paves a way to understand its origin and domestication

Peanut (Arachis) is a key oil and protein crop worldwide with large genome. The genomes of diploid and tetraploid peanuts have been sequenced, which were compared to decipher their genome structures, evolutionary, and life secrets. Genome sequencing efforts showed that different cultivars, although Bt homeologs being more privileged in gene retention and gene expression. This subgenome bias, extended to sequence variation and point mutation, might be related to the long terminal repeat (LTR) explosions after tetraploidization, especially in At subgenomes. Except that, whole-genome sequences revealed many important genes, for example, fatty acids and triacylglycerols pathway, NBS-LRR (nucleotide-binding site-leucine-rich repeats), and seed size decision genes, were enriched after recursive polyploidization. Each ancestral polyploidy, with old ones having occurred hundreds of thousand years ago, has thousands of duplicated genes in extant genomes, contributing to genetic novelty. Notably, although full genome sequences are available, the actual At subgenome ancestor has still been elusive, highlighted with new debate about peanut origin. Although being an orphan crop lagging behind other crops in genomic resources, the genome sequencing achievement has laid a solid foundation for advancing crop enhancement and system biology research of peanut.

Deciphering evolutionary dynamics of WRKY genes in Arachis species

BACKGROUND

Cultivated peanut (Arachis hypogaea), a progeny of the cross between A. duranensis and A. ipaensis, is an important oil and protein crop from South America. To date, at least six Arachis genomes have been sequenced. WRKY transcription factors (TFs) play crucial roles in plant growth, development, and response to abiotic and biotic stresses. WRKY TFs have been identified in A. duranensis, A. ipaensis, and A. hypogaea cv. Tifrunner; however, variations in their number and evolutionary patterns across various Arachis spp. remain unclear.

RESULTS

WRKY TFs were identified and compared across different Arachis species, including A. duranensis, A. ipaensis, A. monticola, A. hypogaea cultivars (cv.) Fuhuasheng, A. hypogaea cv. Shitouqi, and A. hypogaea cv. Tifrunner. The results showed that the WRKY TFs underwent dynamic equilibrium between diploid and tetraploid peanut species, characterized by the loss of old WRKY TFs and retention of the new ones. Notably, cultivated peanuts inherited more conserved WRKY orthologs from wild tetraploid peanuts than their wild diploid donors. Analysis of the W-box elements and protein-protein interactions revealed that different domestication processes affected WRKY evolution across cultivated peanut varieties. WRKY TFs of A. hypogaea cv. Fuhuasheng and Shitouqi exhibited a similar domestication process, while those of cv. Tifrunner of the same species underwent a different domestication process based on protein-protein interaction analysis.

CONCLUSIONS

This study provides new insights into the evolution of WRKY TFs in Arachis spp.

Crop Proteomics under Abiotic Stress: From Data to Insights

Food security is a major challenge in the present world due to erratic weather and climatic changes. Environmental stress negatively affects plant growth and development which leads to reduced crop yields. Technological advancements have caused remarkable improvements in crop-breeding programs. Proteins have an indispensable role in developing stress resilience and tolerance in crops. Genomic and biotechnological advancements have made the process of crop improvement more accurate and targeted. Proteomic studies provide the information required for such targeted approaches. The crosstalk among cellular components is being analyzed by subcellular proteomics. Additionally, the functional diversity of proteins is being unraveled by post-translational modifications during abiotic stress. The exploration of precise cellular responses and the networking among different cellular organelles help in the prediction of signaling pathways and protein-protein interactions. High-throughput mass-spectrometry-based protein studies are now possible due to incremental advancements in mass-spectrometry techniques, sample protocols, and bioinformatic tools as well as the increasing availability of plant genome sequence information for multiple species. In this review, the key role of proteomic analysis in identifying the abiotic-stress-responsive mechanisms in various crops was summarized. The development and availability of advanced computational tools were discussed in detail. The highly variable protein responses among different crops have provided a wide avenue for molecular-marker-assisted genetic buildup studies to develop smart, high-yielding, and stress-tolerant varieties to cope with food-security challenges.