Article

Marker-Assisted Selection for Drought Resistance in Wheat: A Review of Recent Advances

Authors: Atul Madhao Pradhan, Mouli Paul, İlhan Subaşi, Akash Singh, Virendra Singh

Journal Name: Plant Science Archives

DOI: https://doi.org/10.51470/PSA.2022.7.1.09

Keywords: Marker-Assisted Selection, Drought Resistance, Wheat, Genetic Mapping, QTL

Abstract

Marker-Assisted Selection [MAS] has revolutionized the field of crop breeding by facilitating the targeted selection of traits that improve drought resistance in wheat [Triticum aestivum L.]. Given the increasing impacts of climate change and water scarcity, ensuring the development of drought-tolerant wheat varieties is vital for global food security. This review comprehensively examines recent advances in MAS for drought resistance, including the identification of key quantitative trait loci [QTLs] associated with drought-tolerance traits such as root architecture, osmotic adjustment, and stomatal conductance. The advent of next-generation sequencing [NGS] and the discovery of single nucleotide polymorphisms [SNPs] have contributed to more precise marker development and application in breeding programs. Case studies of successful breeding initiatives employing MAS and its integration with genomic selection and CRISPR-based gene-editing technologies are highlighted. The article also delves into the challenges of MAS implementation, including marker validation, genotype-environment interactions, and economic barriers. Strategies for overcoming these challenges, such as leveraging multi-location trials and enhanced bioinformatics tools, are discussed. Finally, the review anticipates future trends, advocating for a holistic approach combining MAS with genome-wide association studies [GWAS] and advanced phenotyping to accelerate the breeding of drought-resistant wheat varieties.

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1. Introduction

Wheat [Triticum aestivum L.] is one of the most widely grown and consumed staple crops, providing a critical source of nutrition and calories for billions of people around the world [1]. However, the increasing prevalence of drought due to climate change poses a significant threat to global wheat production and food security [2]. Drought stress leads to reduced yields and lower crop quality, making the development of drought-resistant wheat varieties a priority for agricultural research [46]. Marker-Assisted Selection [MAS] has emerged as an effective breeding tool to address this challenge by enabling precise and accelerated selection for drought tolerance traits [3]. MAS facilitates the identification and selection of key genetic markers associated with drought resistance, thereby improving the efficiency and success rate of breeding programs [18, 24]. This review focuses on the principles, recent advances, challenges, and future directions of MAS in wheat breeding, specifically for enhancing drought resistance.

2. Principles of Marker-Assisted Selection

MAS is a modern breeding technique that uses molecular markers to track the presence of desirable genes within a plant’s genome [3]. Unlike traditional breeding, which relies solely on phenotypic selection and can be influenced by environmental conditions, MAS enables the direct selection of specific genetic traits [27].

Overview of MAS and How It Differs from Traditional Breeding

Traditional breeding for drought resistance involves crossbreeding varieties and selecting offspring based on their ability to thrive under drought conditions. This method, although effective, is time-consuming and often influenced by external environmental factors, making the results less predictable [30]. MAS, on the other hand, uses molecular markers such as single nucleotide polymorphisms [SNPs] and simple sequence repeats [SSRs] to identify specific genetic loci associated with drought resistance [3, 14]. These markers help breeders select plants that carry the desired traits without waiting for phenotypic expression under drought conditions.

Types of DNA Markers Used [e.g., SNPs, SSRs]

The most commonly used DNA markers in MAS include:

  • SNPs [Single Nucleotide Polymorphisms]: Variations at a single nucleotide position in the DNA sequence, providing high-resolution mapping of traits [14, 28].
  • SSRs [Simple Sequence Repeats]: Short, repeating sequences of DNA that are highly polymorphic and useful for genetic mapping [15].
  • RFLPs [Restriction Fragment Length Polymorphisms]: Older marker systems still used in some MAS applications for identifying larger genetic variations [6, 30].

The Process of Using MAS in Wheat Breeding

MAS begin with the identification of QTLs linked to traits of interest [7]. Breeders use molecular markers to screen breeding populations and select individuals with the desired QTLs. These selected plants are then crossed to develop new varieties that combine multiple drought-resistance traits [35, 37].

3. Recent Advances in MAS for Drought Resistance

Recent advancements in MAS have significantly improved the ability of researchers to identify and utilize genetic markers linked to drought resistance [24, 29].

3.1 Identification of Key QTLs

Definition and Significance of QTLs
QTLs are segments of DNA that correlate with variation in a phenotypic trait, such as drought tolerance. Identifying QTLs linked to drought resistance is crucial for MAS as they provide specific targets for marker development [23, 45].

Notable QTLs Related to Drought Resistance in Wheat
Researchers have identified several QTLs associated with traits such as root depth, osmotic adjustment, and stomatal regulation. For example, QTLs located on chromosomes 2B and 4A have been linked to enhanced root architecture, which allows for better water uptake [7, 9, 12].

Examples of Recent Studies
Recent studies have mapped QTLs associated with deep root systems, which contributed to higher drought resilience in wheat varieties [45, 38]. Other notable work has identified QTLs linked to osmotic regulation and efficient water use [17].

3.2 Genomic Tools and Technologies

Role of Next-Generation Sequencing [NGS] in MAS
NGS has been a game-changer in the field of MAS, enabling rapid sequencing of the entire genome and facilitating the identification of SNPs [5, 17]. This technology has improved the resolution of genetic mapping and made it easier to pinpoint loci associated with drought tolerance [29].

Application of GWAS for Trait Discovery
GWAS has emerged as a complementary tool to MAS. It involves scanning the entire genome to find associations between genetic markers and phenotypic traits across a population [19, 22]. Recent studies have used GWAS to identify additional drought-resistance genes that were previously unknown [8, 41].

Integration of High-Throughput Phenotyping
The use of high-throughput phenotyping allows for the simultaneous evaluation of multiple traits in large populations [16, 31]. Combining phenotyping with MAS enhances the accuracy of QTL mapping and helps breeders better understand the relationship between genotype and phenotype [13, 48].

3.3 Case Studies of Successful Breeding Programs

Summary of Case Studies
The CIMMYT breeding program is a prime example of MAS success, having released drought-tolerant wheat varieties by leveraging QTLs linked to water-use efficiency and root structure [10, 34]. Another significant case is the collaboration between international research centers that integrated MAS with conventional breeding techniques to develop high-yielding, drought-resistant wheat varieties [3, 42].

Comparative Analysis of MAS Approaches
Programs that combined MAS with other genomic tools, such as NGS and GWAS, reported higher success rates in developing drought-tolerant cultivars compared to those relying solely on traditional methods [41, 22].

4. Challenges in Implementing MAS for Drought Resistance

Marker Validation Across Diverse Environments
One of the significant challenges in MAS is validating markers across different environmental conditions [4, 32]. Markers that show strong associations with drought tolerance in one environment may not be as effective in another due to genotype-environment interactions [6, 27].

Limitations in Genetic Diversity and Trait Heritability
The narrow genetic base in some breeding populations limits the effectiveness of MAS. Moreover, drought resistance is often a polygenic trait, making it difficult to identify all contributing QTLs [30, 24].

Economic and Infrastructural Challenges
The implementation of MAS in developing regions is often hindered by limited funding and technological infrastructure [21, 36]. Addressing these challenges requires investments in training, facilities, and international collaboration [4, 46].

Solutions and Ongoing Strategies
Efforts to overcome these challenges include conducting multi-location trials and using marker-assisted recurrent selection [MARS] to increase genetic diversity [11, 20]. Public-private partnerships have also proven beneficial for funding MAS programs in resource-limited areas [34, 39].

5. MAS in Combination with Other Breeding Strategies

5.1 Genomic Selection

Explanation of Genomic Selection and Its Synergy with MAS
Genomic selection [GS] predicts breeding values using genome-wide marker data, making it possible to select for multiple traits simultaneously [18]. Combining GS with MAS allows for more precise selection and shorter breeding cycles [26].

Case Studies Showing the Effectiveness of Combining MAS and GS
Breeding programs that employed both MAS and GS reported significant improvements in yield stability and drought tolerance [8, 41]. Integrating these strategies has led to the development of varieties with enhanced root traits and higher water-use efficiency [26].

5.2 CRISPR/Cas9 and Gene Editing

Overview of CRISPR Technology and Its Application in Drought Resistance
CRISPR/Cas9 has opened new avenues for directly modifying genes associated with drought tolerance [25, 39]. This technology allows for the precise editing of QTLs to enhance or introduce drought-resistance traits [50].

Potential for Integrating Gene Editing with MAS
The integration of CRISPR with MAS can accelerate the development of drought-tolerant wheat varieties by enabling targeted improvements at specific loci [7, 39].

6. Future Perspectives

Emerging Trends in MAS Research and Technology
Future MAS research will likely involve more extensive use of multi-omics approaches, integrating genomics, transcriptomics, and proteomics for a more comprehensive understanding of drought resistance [29, 48].

Potential Benefits of Integrating AI and Machine Learning for Data Analysis
Artificial intelligence [AI] and machine learning can analyze large genomic datasets more efficiently, identifying complex patterns and potential markers faster than traditional methods [33, 48].

The Role of Global Collaborations in Advancing MAS Research
Collaborative efforts involving international research institutions and private companies will be crucial for advancing MAS and related technologies [42, 34]. Joint projects can facilitate the sharing of genetic resources and data, enhancing breeding programs worldwide [10, 46].

Speculation on Upcoming Breakthroughs and Innovative Practices
The future may see the development of predictive models that incorporate environmental variables to enhance the reliability of MAS [48]. Additionally, the integration of MAS with precision agriculture tools could lead to more sustainable and targeted breeding practices [40].

7. Conclusion

MAS have proven to be a transformative tool in the breeding of drought-resistant wheat varieties. Recent advances in genetic mapping, QTL identification, and the integration of genomic tools have made MAS more effective than ever before. However, challenges such as marker validation and economic barriers persist, necessitating continued research and international cooperation. The future of MAS lies in its combination with genomic selection, CRISPR technology, and AI-driven data analysis to accelerate the breeding of resilient wheat varieties. Sustained investment in MAS research will be essential to support global food security in the face of climate change.

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