Legume Genomics and Genetics 2024, Vol.15, No.6, 291-302 http://cropscipublisher.com/index.php/lgg 297 Additionally, genomic resources such as whole-genome sequences and high-throughput marker genotyping platforms have facilitated the discovery of markers and genes for drought tolerance, further supporting the implementation of MAS in soybean breeding programs (Valliyodan et al., 2016). 6.2 Key successes and challenges in these programs The application of MAS in soybean breeding programs has yielded several notable successes. One significant achievement is the identification and validation of QTLs associated with drought tolerance, which has enabled the development of soybean varieties with improved drought resilience. For instance, the identification of QTLs on chromosomes 1, 2, 7, 10, 14, 19, and 20 has provided valuable targets for MAS, facilitating the breeding of drought-tolerant soybean cultivars (Dhungana et al., 2021). Moreover, the use of context-specific MAS (CSM) has demonstrated significant yield gains in elite soybean populations, with selected sublines showing up to 5.8% higher yields compared to their mother lines (Sebastian et al., 2010). Despite these successes, several challenges remain in the implementation of MAS for drought tolerance in soybean. One major challenge is the complexity of drought tolerance as a trait, which involves multiple genes and environmental interactions. This complexity can make it difficult to achieve consistent improvements across different genetic backgrounds and environmental conditions. For example, the performance of MAS-derived populations can vary substantially across different genetic backgrounds, highlighting the need for careful characterization of donor alleles within elite backgrounds before implementing MAS-based breeding (Singh et al., 2022). Another challenge is the cost and resource requirements associated with MAS. While advances in genotyping technologies have made MAS more feasible, the initial investment in developing and validating markers can be substantial. Additionally, the integration of MAS with conventional breeding methods requires careful planning and coordination to ensure the successful introgression of target traits. 7 Case Study: Marker-Assisted Selection for Drought Tolerance in Soybean 7.1 Detailed description of a specific MAS breeding program or case study In this case study, we focus on a Marker-Assisted Selection (MAS) breeding program aimed at improving drought tolerance in soybean. The program utilized a high-yielding but drought-sensitive cultivar, 'Zhonghuang 35', and a drought-tolerant cultivar, 'Jindou 21', to develop F6:9 Recombinant Inbred Lines (RILs). The primary goal was to identify Quantitative Trait Loci (QTL) associated with drought tolerance traits, such as plant height and seed weight per plant, and to use these markers to accelerate the breeding of drought-tolerant soybean varieties (Ren et al., 2020). 7.2 Methodology: selection of markers, phenotyping, and genotyping approaches The methodology involved several key steps. Selection of Markers: Specific locus amplified fragment sequencing (SLAF-Seq) technology was employed to construct a high-density genetic map containing 8 078 SLAF markers distributed across 20 soybean chromosomes. This map facilitated the identification of QTL associated with drought tolerance traits. Phenotyping: Field tests were conducted under two conditions: irrigation and drought. Plant height and seed weight per plant were used as indicators of drought tolerance. These phenotypic traits were measured to assess the performance of the RILs under both conditions (Ren et al., 2020). Genotyping: The genetic map was used to perform Additive-Inclusive Composite Interval Mapping (ICIM-ADD) to identify QTL. This approach allowed for the precise localization of QTL on the soybean genome, which were then linked to the phenotypic traits measured during the field tests (Sreenivasa et al., 2020). 7.3 Results: identification of key markers and their impact on drought tolerance The study identified a total of 23 QTL related to drought tolerance. Key findings include seven QTL (qPH2, qPH6, qPH7, qPH17, qPH19-1, qPH19-2, and qPH19-3) were associated with plant height and were located on chromosomes 2, 6, 7, 17, and 19. Five QTL (qSWPP2, qSWPP6, qSWPP13, qSWPP17, and qSWPP19) were linked to seed weight per plant and were found on chromosomes 2, 6, 13, 17, and 19. Three common QTL (qPH6/qSWPP6, qPH17/qSWPP17, and qPH19-3/qSWPP19) were identified for both plant height and seed
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