Bioinformatics Genetics Genomics

Agrigenomics

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Agricultural genomics is the application of genomics in agriculture to improve the productivity and sustainability in crop and livestock production. It has and will continue to drive sustainable productivity and offer solutions to the mounting challenges of feeding the global population. Using modern technology, farmers, breeders, and researchers can easily identify the genetic markers linked to desirable traits, informing cultivation and breeding decisions.

Since the beginning of the century, our knowledge of genome composition and gene function has increased tremendously. The shift from single gene to whole genome analysis and the complete sequencing of higher eukaryotic genomes and transcriptomes offer the possibility to understand how all genes work together. These recent advancements have a great impact on agricultural research. Analyzing whole genomes of agricultural products will give further insights into evolutionary processes and how modern crops and livestock arose from their ancestors. 

With the combination of traditional and high-throughput sequencing platforms, there has been a tremendous increase in genomic resources available, including expressed sequence tags (ESTs), BAC end sequence, genetic sequence polymorphisms, gene expression profiling, whole-genome (re)sequencing, and genome-wide association studies. Given the emergence of genomic sequencing and expansion of bioinformatic tools, single gene study is shifting to whole-genome analysis, which offers a broader view of how all genes work together. Therefore, three reviews aimed to highlight recent advances in 

  • comparative genomics for plant breeding
  • transcriptome analysis for plant breeding
  • genotyping and marker-assisted breeding
  • recombinant DNA technology 

Comparative Genomics for Plant Breeding

The genome sequences for more than 55 plant species (mainly model plants, such as Arabidopsis, rice, and maize) have been produced. The 1000-plant initiative is underway. As a result, scientists are not totally dependent on genomic sequences of model plants. Almost every species-specific genome can be sequenced with affordable price and thus offer great opportunities for targeted crop breeding. Furthermore, genomics is playing a very crucial role in biodiversity conservation. Advanced genomics helps in identifying the segments of the genome responsible for adaptation. It can also improve our understanding of microevolution through a better understanding of natural selection, mutation, and recombination.

Predicting gene function only based on homology to others can sometimes be difficult. Thus, proteomics (the large-scale analysis of proteins) will greatly contribute to our understanding of gene function in the post genomic era. 

Transcriptome Analysis for Plant Breeding

In the absence of the complete genome sequence, transcriptome analysis would improve our understanding of gene function. A global transcriptome study reveals the gene responses to a particular biological condition at the genome level. 

Genotyping and Marker-Assisted Breeding

In addition to the generation of reference genome, high-throughput sequencing technology has facilitated resequencing of genomes of the same species but different accessions to identify genomic variation. The genotyping platforms have been used to generate large-scale marker segregation data on mapping populations and have led to comprehensive genetic maps. The genome sequence allows us to identify genome-wide molecular markers including functional markers, candidate genes, and predictive markers for breeding. Developing sensitive markers to select desirable ecotypes is critical in plant breeding. 

Molecular markers such as simple sequence repeats (SSR) and single nucleotide polymorphism (SNP) from genomic and transcriptomic studies are great resources in plant breeding, used for trait dissection and for enhancing precision in selecting functional genes. 

Genome-wide association study is another method to find the relationship between molecular markers and QTL based on linkage disequilibrium. Association mapping on founder parents and their derivatives can find some important QTL and favorable allelic variations, which can be further used for marker-assisted selection to produce more favorable varieties. 

Recombinant DNA Technology

Recombinant DNA technology is a milestone in plant science and crop breeding that can help to design almost any desirable characteristic by controlled targeted gene expression. One of the most powerful tools of recombinant DNA technology is CRISPR-Cas9-induced genome editing. 

Application

  • High-throughput PCR probes, reagents and instrumentation for marker assisted selection/breeding (MAS/B)
  • Genomic selection using SeqSNP targeted genotyping by sequencing
  • Sequencing, extraction and genotyping all-inclusive laboratory services
  • DNA extraction and purification chemistry and automation for NGS and microarray applications

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