ABSTRACT
Multiple "omics" approaches have emerged as successful technologies for plant systems over the last few decades. Advances in next-generation sequencing (NGS) have paved a way for a new generation of different omics, such as genomics, transcriptomics, and proteomics. However, metabolomics, ionomics, and phenomics have also been well-documented in crop science. Multi-omics approaches with high throughput techniques have played an important role in elucidating growth, senescence, yield, and the responses to biotic and abiotic stress in numerous crops. These omics approaches have been implemented in some important crops including wheat (Triticum aestivum L.), soybean (Glycine max), tomato (Solanum lycopersicum), barley (Hordeum vulgare L.), maize (Zea mays L.), millet (Setaria italica L.), cotton (Gossypium hirsutum L.), Medicago truncatula, and rice (Oryza sativa L.). The integration of functional genomics with other omics highlights the relationships between crop genomes and phenotypes under specific physiological and environmental conditions. The purpose of this review is to dissect the role and integration of multi-omics technologies for crop breeding science. We highlight the applications of various omics approaches, such as genomics, transcriptomics, proteomics, metabolomics, phenomics, and ionomics, and the implementation of robust methods to improve crop genetics and breeding science. Potential challenges that confront the integration of multi-omics with regard to the functional analysis of genes and their networks as well as the development of potential traits for crop improvement are discussed. The panomics platform allows for the integration of complex omics to construct models that can be used to predict complex traits. Systems biology integration with multi-omics datasets can enhance our understanding of molecular regulator networks for crop improvement. In this context, we suggest the integration of entire omics by employing the "phenotype to genotype" and "genotype to phenotype" concept. Hence, top-down (phenotype to genotype) and bottom-up (genotype to phenotype) model through integration of multi-omics with systems biology may be beneficial for crop breeding improvement under conditions of environmental stresses.
ABSTRACT
Coconut (Cocos nucifera L.) is an important economic fruit and oil crop largely cultivated in humid and sub-humid tropical coastal zones worldwide. To date proteomic profile analysis of coconut under cold stress yet not been conducted. In order to understand the cold stress tolerance in coconut, the iTRAQ approach was employed to dissect proteomic response of two coconut varieties Hainan Tall, BenDi (BD) and Aromatic coconut, XiangShui (XS) under cold stress. Under cold treatment at (8 °C) for 2 days, 193 up and 134 down-regulated in BD (Cn-DB-0_VS_Cn-DB-2) and 140 up and 155 down-regulated DEPs in XS (Cn-XS-0_VS_Cn-XS-2) were identified. The 5 days post cold treatment also identified increased abundance of up-regulated proteins in BD compared to XS. The 5 days post treatment (dpt) depicted 172-up/127-down and 108-up/134-down accumulated proteins for BD (Cn-DB-0_VS_Cn-DB-5) and XS (Cn-XS-0_VS_Cn-XS-5) respectively. A total of 22, 12 and 14 DEP categories were enriched in biological process, cellular component and molecular function respectively in Gene Ontology (GO) analysis of two coconut varieties. Metabolic and biosynthesis of secondary metabolites pathways were highly enriched in KEGG pathway analysis of DEPs between two varieties. Twenty-two different functional classes revealed differentially expressed proteins in two varieties. Among those, four major categories involved in metabolism, stress response, photosynthesis and respiration related DEPs increased abundance in two varieties. However, general function perdition only (GFPO) and stress-responsive proteins were greatly up-regulated in BD than XS. Increased abundance of stress response related proteins up-regulation under cold stress suggested that BD is cold-tolerant variety. Collectively, iTRAQ-based coconut leaf proteomic analysis showed that XS (aromatic) coconut variety is cold-sensitive compared to BD (Hainan Tall) variety. This study provided a basis for further functional analyses to understand the molecular mechanisms of tropical crops adapting to cold stress. SIGNIFICANCE: Leaf proteomic approach determines the role of differentially expressed proteins (DEPs) under cold stress in crops. However, cold stress could damage the coconut fruit lead to decrease in crop yield during winter in China. Here, we report the first ever iTRAQ-based proteomic analysis of two coconut varieties in response to cold stress. The study identified the proteins involved in biosynthesis of secondary metabolites, photosynthesis, respiration, biotic and abiotic stresses under cold stress in two coconut varieties. Moreover, the increased abundance of stress-responsive and general function proteins in BD under cold stress suggested that Hainan Tall is cold-tolerant compared to aromatic coconut variety. Inhibition abundance of photosynthesis related proteins may reduce photodamage owing to the over energized state of thylakoid membrane lead to ROS generation during oxidative stress. This could be the reason for adaption of BD to low temperature stress. Nonetheless, further research may insight the mechanism involved in cold tolerance/sensitive in coconut in response to low temperature.
