How Can Gwas Be Used In Plant Breeding?

Genome-wide association studies (GWAS) have become a valuable tool for investigating complex traits, particularly in plant breeding. Advances in genomic technology have fueled the development of GWAS in plants, which has had even greater success than those in humans. In an ecological framework, mapping tools can be used to separate functional genetic variation from the genetic basis of phenotypic variation.

GWAS and genomic prediction (GP) are extensively employed to accelerate genetic gain and identify QTL in plant breeding. Plant breeding has a long history of developing new varieties that ensure the food security of the human population. More deep analysis for detected causative loci by GWAS, such as haplotype-based analysis, is crucial for genomics-assisted crop breeding.

GWAS has become one of the most powerful tools available to geneticists to identify the genomic loci controlling traits of plants. Linking phenotypes and genotypes to identify genetic architectures that regulate important traits is crucial for plant breeding and the development of plant species. For example, GWAS has identified single-nucleotide polymorphisms (SNPs) and population structure that can explain up to 45 of the phenotypic variation in flowering time.

GWAS involves testing genetic variants across the genomes of many individuals of a population to identify genotype-phenotype association. It has transformed from a promising new tool to a powerful, ubiquitous technique for understanding complex traits in plants.

GWAS has been successfully applied to define the causative allele(s)/loci that can be used in breeding crops for adaptation and yield. Overall, GWAS is a powerful approach to identify the genetic factors underlying intraspecific phenotypic variations and contribute to the advancement of agricultural genetics.

What are the main applications of plant breeding?

Plant breeding aims to increase crop yield, raise plants with desired characteristics, develop disease-resistant crops, and develop plants that can tolerate extreme environmental stress. It involves manipulating plant qualities to create new varieties with desired traits. Plants with higher qualities are selected and crossed to obtain plants with desired quality, resulting in a population with improved traits.

What is the purpose of the GWAS?

Genome-wide association studies (GWAS) are a method used to compare genomes from different individuals to identify genetic markers linked to a specific disease phenotype or risk. The Division of Cancer Research uses GWAS to study various cancers and exposures and survival. Researchers use fine-mapping and deep sequencing techniques to identify functional variants responsible for disease risk and the biological mechanisms involved. Large-scale consortial arrangements enable rapid replication of positive findings using independent data sets.

This collaborative infrastructure allows for the quantification of risks associated with specific gene variants and exposures, and subset analyses to uncover gene-gene and gene-environment interactions. This collaboration presents an opportunity for cancer research to advance while leveraging economies of scale. NCI also partners with other NIH institutes to investigate complex diseases and traits, including diabetes, cardiovascular, neurological disorders, obesity, and smoking behaviors.

What is the application of GWAS in plant breeding?

Genome-wide association studies (GWAS) have become a powerful tool for understanding complex genotype-phenotype associations across various species, particularly maize. Maize, known for its extensive genetic diversity and rapid linkage disequilibrium, has made significant advancements by identifying numerous genetic loci and potential genes associated with complex traits, including responses to abiotic and biotic stress. These discoveries have the potential to enhance adaptability and yield through effective breeding strategies.

However, the impact of environmental stress on crop growth and yield is evident in various agronomic traits, making understanding the complex genetic basis of these traits paramount. This review delves into current and future prospects for yield, quality, and environmental stress resilience in maize, addressing challenges encountered during genomic selection and molecular breeding. The integration of omics, including genomics, transcriptomics, proteomics, metabolomics, epigenomics, and phenomics, has enriched our understanding of intricate traits in maize, enhancing environmental stress tolerance and maize production. GWAS provides robust support for delving into the genetic mechanism underlying complex traits in maize and enhancing breeding strategies.

What is genome-wide association studies in plants?

GWAS, or genome-wide association studies, is a powerful tool that uses phenotypic and genotypic variations within plant species to identify favorable alleles associated with desired traits. In maize research, GWAS has been extensively applied to investigate the relationship between genetic markers and phenotypic traits. The first GWAS in maize was conducted in 2008, targeting the identification of SNPs that significantly affect the oleic acid content in kernels by utilizing 8590 loci in 553 elite inbred lines. Since then, GWAS have undergone notable advancements and become a common technique for uncovering genotype–phenotype relationships in maize.

Previous studies have successfully identified candidate genes responsive to both biotic and abiotic stresses in maize, providing valuable insights. GWAS have enabled the discovery of numerous putative candidate genes associated with various traits in maize, further enhancing our understanding of its genetic architecture. GWAS allow for the fine mapping of quantitative trait loci (QTL) using a diverse maize population, confronting a huge number of historical recombination events that may result in rapid LD decay.

GWAS in maize are characterized by the rapid LD decay due to the crop’s diverse genotypic and phenotypic characteristics compared to other species. Some genes do not segregate independently because the two loci involved are located on the same chromosome. LD strength between two SNPs is often quantified using the ‘r 2 ‘ estimate, if r 2 values are below 0. 2 indicating co-inheritance and two SNPs are present on the same QTL. Lower levels of LD enable higher-resolution association mapping, emphasizing loci significantly associated with the interested trait.

Maize, with its abundant marker density and high-density genotyping technologies, is an ideal cereal crop for GWAS. This method has recently emerged as a critical approach for studying natural variation and mapping quantitative traits, enabling the detailed exploration of genetic architecture in maize.

What is the role of gene technology in plant breeding?

Molecular biology and genetic engineering are revolutionizing agriculture by transferring foreign genes into plant cells, similar to how plant breeders combine genes to create improved crops. This approach offers several advantages, such as specificity and the potential for selecting valuable traits from any organism. For example, research is underway on the transfer of genes for nitrogen fixation from bacteria to plants or herbicide resistance from weeds to crop plants.

If successful, these techniques could be used to design plants that are hardier, higher yielding, more nutritious, or less expensive to produce, such as those that require fewer pesticides, fungicides, or fertilizers. Additionally, they could thrive in marginal conditions, such as soils that are too salty, too acidic, too wet, or too dry.

However, the genetic engineering of plants is still in its infancy, and fundamental questions remain about their feasibility. Researchers have demonstrated for the first time that a foreign gene can be successfully inserted into a plant and made to function. Extensive research is needed before these techniques can be used in practical crop improvement schemes. Molecular biologists must identify agriculturally important genes, search for vectors to carry foreign genes into plant cells, and develop reliable methods for regenerating plants from single cells in culture. Additionally, little is known about how plants will respond to the introduction of foreign genes, such as yield or vigor.

What is the application of microarray in plant breeding?

DNA microarray technology is a crucial tool in functional genomics, allowing for large-scale and genome-wide acquisition of quantitative biological information from multiple samples. It is fabricated and assayed using two main approaches: in situ synthesis of oligonucleotides (oligonucleotide microarrays) or deposition of pre-synthesized DNA fragments (cDNA microarrays). The main applications of microarrays include gene expression monitoring and DNA variation analyses for mutation identification and genotyping.

In plant science, microarrays are used to examine various biological issues, such as the circadian clock, plant defense, environmental stress responses, fruit ripening, phytochrome A signalling, seed development, and nitrate assimilation. New insights are gained into molecular mechanisms coordinating metabolic pathways, regulatory, and signaling networks. The value of microarray technology to our understanding of living processes depends on the amount of data generated and its clever exploration and integration with other biological knowledge from complementary functional genomics tools for profiling the genome, proteome, metabolome, and phenome.

What is genomic prediction in plant breeding?

Genetic prediction (GP) is a data-driven method widely used to accelerate genetic gain in plant-breeding programs. It has been widely accepted and used in various studies. The use of cookies on this site is governed by copyright © 2024 Elsevier B. V., its licensors, and contributors. All rights are reserved for text and data mining, AI training, and similar technologies. Open access content is licensed under Creative Commons terms.

What are the methods used in GWAS?

The procedures for DNA extraction, genotype quality control, variant calling, exclusions, imputation of genotypes, adjustment for ancestry and population stratification, GWAS analysis, reporting and annotation, and post-GWAS analyses and procedures are discussed in a study by several researchers.

What is the role of genomics in plant breeding?

The increasing human population under climate change conditions requires new, multidisciplinary approaches to plant breeding. Recent technological innovations, such as rapid sequencing technologies and genomics, have revolutionized the science of plant breeding, allowing for detailed analysis of plant genomes and dissection of genetic basis of agronomic traits. Genomics is now at the core of crop improvement, identifying genetic variation underlying differences in phenotypes, identifying additional sources of variation and novel traits, and characterization of molecular pathways involved in biotic and abiotic stress tolerance.

Genome editing technologies, particularly CRISPR/Cas9, have opened new routes of fast and precise genome modification, promising rapid translation of knowledge from the lab to the field. This allows selective modification of Known genes controlling important traits, allowing for manipulation of phenotypes. In recent years, several genome edited crop plants entered final stages of commercialization in the United States, including drought and salt-tolerant soybean, Camelina with increased oil content, and waxy corn.

In conclusion, genomic approaches have the potential to develop climate change resilient crops, addressing the urgent need for crop plant improvement and the rapid advancements in technology.

What is the difference between GWAS and NGS?

Frontotemporal Dementia (FTD) is a focal neurodegenerative disease causing early-onset dementia. Current knowledge about risk loci and causative mutations of FTD is primarily derived from genetic linkage analysis, candidate gene studies, Genome-Wide Association Studies (GWAS), and Next-Generation Sequencing (NGS) applications. Linkage studies of large FTD pedigrees have led to the identification of causal mutations in different genes, such as C9orf72, MAPT, and GRN genes, which explain the majority of cases with a high family history of the disease.

GWAS and NGS have contributed to understanding the genetic picture of FTD, identifying common genetic variants with a modest risk effect in genes related to the endo-lysosomal pathway, immune response, and neuronal survival. On the other hand, NGS has allowed the identification of rare variants with a strong risk effect in known FTD-associated genes and genes involved in the endo-lysosomal pathway and immune response.

Both approaches have demonstrated that several genes are associated with multiple neurodegenerative disorders, including FTD. The genetic picture of FTD is becoming more clear, and novel key molecular processes are emerging. This will help move toward prevention and therapy for this incurable disease. FTD is now considered a common form of early-onset dementia, with a mean age of presentation under 65 years old.

What is genome-wide selection plant breeding?

Genomic selection (GS) is a promising approach that uses molecular genetic markers to design novel breeding programs and develop new markers-based models for genetic evaluation. In plant breeding, GS provides opportunities to increase genetic gain of complex traits per unit time and cost. The cost-benefit balance was an important consideration for GS to work in crop plants. The availability of genome-wide high-throughput, cost-effective, flexible markers, having low ascertainment bias, suitable for large population sizes, and both model and non-model crop species with or without the reference genome sequence was the most important factor for its successful and effective implementation in crop species.

Next-generation sequencing (NGS) technologies have provided novel SNP genotyping platforms, especially genotyping by sequencing, which have changed the entire scenario of marker applications and made the use of GS a routine work for crop improvement in both model and non-model crop species. NGS-based genotyping has increased genomic-estimated breeding value prediction accuracies over other established marker platforms in cereals and other crop species, making the dream of GS true in crop breeding. To harness the true benefits from GS, these marker technologies will be combined with high-throughput phenotyping for achieving the valuable genetic gain from complex traits.

Plant breeding has been and will continue to remain the major driving force for science-based productivity enhancements in major food, feed, and industrial crops. Conventional and marker-assisted breeding (MAB) are the two approaches used to accomplish plant breeding. Conventional breeding involves hybridization between diverse parents and subsequent selection over a number of generations to develop improved crop variety. However, conventional breeding has several limitations such as requiring a long period to develop crop variety, high environmental noise, and less effectiveness for complex and low heritable traits.

GS estimates the genetic worth of the individual based on a large set of marker information distributed across the whole genome, and it is not based on few markers like MAS. The GEBVs allow us to predict individuals that will perform better and are suitable either as a parent in hybridization or for next-generation advancement of the breeding program.