
Plant breeding programs are often used to improve varieties through creating diverse agronomic traits. During a breeding program, a lot of genetic diversities are created in the genome after different generations through homologous recombination. Genome sequencing technology has revolutionized the discovery of genes and molecular markers associated with diverse agronomic traits in crop improvement programs. Genomic research is now in the peak of success, thus creating new opportunities for crop improvement modern sequencing technology is now capable of sequencing thousands to millions of bases per run. Modern sequencing technologies enable the sequencing of different cultivars with small to complex genomes at a reasonable time and cost. These massive data can be used to identify important agronomic traits of crops such as fruit color, size, ripening, flowering time adaptation, grain yield, and quality maintenance. In addition, they can be used to develop crop varieties. This mini-review is focused on the role of genome sequencing in genomic research and plant breeding for crop improvements.
Plant breeding is a natural way to create genetic variation among individuals of species in order to obtain desired characteristics. It is important to ensure that the world food demand is met by developing new varieties with improved crop qualities, including high yield, tolerance to various environmental stresses (drought, cold, salinity, flood, etc.), and resistance to various insects, fungi, bacteria, and viruses. Breeding programs can develop crop varieties with these qualities. One major technique in plant breeding is by crossing between two closely related individuals to produce new crop varieties or lines with desirable properties. A successful breeding program largely depends on homologous recombination to exchange genetic information between chromosomes during meiosis, thus creating genetic diversity and hybrid plants with desired characteristics. These genomic changes in individuals could be associated with phenotype changes, including different colors of plants or fruits, size, grain yields, tolerance to various stresses, male sterility in plants, and different disease resistance. Phenotypic variations through domestication from one region to other regions are also associated with different agricultural species. Analysis of DNA sequence variations in candidate genes based on morphological phenotypes is a good way to identify causal genes for these traits. Many studies have reported genome-wide evaluations for different breeding varieties or lines of plants with strong genetic diversity across different chromosomal regions in association with different phenotypic changes (Lam
Modern sequencing technology is a great tool for identifying the genetic diversity in hybrid plants, especially for discovering genes and developing molecular markers associated with diverse agronomic traits of crops. Recent advances in genome sequencing technology have made it possible to sequence thousands to millions of bases per run within a short time at a low cost so that millions of molecular markers can be developed for different crop species. In addition, they can be used to identify agronomically important genes. Complete reference genome sequences are now available for several agronomic important crop species, making it relatively easy to rapidly identify candidate genes or detect genetic variation during breeding events (Goff
The sequencing technology was invented at the early 1970s. The first complete genome of Bacteriophage
Roche (454) sequencing was launched to the market in 2005 as the first high-throughput next-generation DNA sequencing technology. It is based on pyrosequencing also known as sequencing by-synthesis. In this method, single fragments of DNA are hybridized to an array of capture bead that contains all necessary reagents for polymerase chain reaction (PCR) amplification of individually bound template. The bead also contains enzymes so that fluorescence can be generated through consumption of inorganic phosphate. During sequencing, one pyro-phosphate is released from each nucleotide. The released pyrophosphate is detected by an enzymatic luminometric inorganic pyrophosphate detection assay through creating a light signal during the transformation of PPi into adenosine triphosphate (ATP) by ATP sulfurylase (Ronaghi
After the launch of Roche (454) sequencing, another high-throughput reversible terminator sequencing technology that was released to the market was Illumina (Solexa) sequencing using the sequencing-by-synthesis concept (Bentley
SOLiD sequencing platform was invented as the third high-throughput next generation sequencing system. It was jointly developed by Harvard Medical School and Howard Hughes Medical Institute (Shendure
The first complete plant genome (the model plant
Sequenced genome of crops can be used to improve crop varieties in different ways, including the discovery of molecular markers, identification of agronomical important traits, and the transfer of these traits into elite varieties. Modern sequencing technology and sequenced genomes provide great opportunities to plant breeders for efficient marker assisted breeding, selection of quantitative trait locus (QTL), and management of genomic resources within a short time frame.
The main advantage of genome sequence is the development of molecular markers that can be used to distinguish different species or varieties or cultivars to find possible elite variety. Molecular markers are developed based on genomic variations between individuals. The discovery of millions of novel genetic markers through genome sequencing is revolutionizing plant genomic research and crop improvements. Different types of molecular markers are now being widely used for analyzing genomic diversity in plants and for their development (Henry 2001; Phillips and Vasil 2001). Among these markers, single nucleotide polymorphisms (SNPs) are the most abundant ones due to their availability in the genomes of different populations. SNP markers are now widely used for the analysis of population structure, association mapping, selection of QTL, and/or evolutionary studies. Due to technological advances, thousands to millions of SNP markers are now available for each plant species. Whole genome sequencing is the best way to find genetic diversity and molecular markers in a population and gain a better understanding about the relationship between genotypic and phenotypic changes. Chen
A QTL is a region of DNA or locus associated with a particular phenotype. QTLs typically contain genes that control the phenotype. Generally, a single phenotypic trait is determined by many genes. Therefore, many QTLs are associated with a single trait. By using complete genome sequencing data, it is possible to make QTL map so that it is easy to identify reasons behind phenotypic variations among individuals. High density molecular markers developed from sequenced genome can be used to rapidly map agronomical important traits and identify candidate genes within a region of interest. Lam
Abiotic stress is a stress to plants caused by non-living factors such as environmental and non-biological factors, including drought, flood, temperature, salt, radiation, and chemicals. On the other hand, biotic stress is caused by living organisms such as fungi, bacteria, viruses, insects, parasites, and weeds. Due to technological advances, researchers can now focus more on the development of crop varieties tolerant to different stresses. It is relatively easier to develop different stress tolerance varieties if the reference genome of important crop is available. Once the rice genome becomes available, researchers have identified a gene called
Several genes involved in stress responses related to drought, heat, flooding, salinity, and pathogen defense were identified by transcriptome analysis for two switchgrass ecotypes: lowland variety AP13 and upland variety VS16 (Fiedler
The wild grass species
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