Plant Gene and Trait 2025, Vol.16, No.1, 15-22 http://genbreedpublisher.com/index.php/pgt 17 Figure 1 Genes with primary and secondary effects of the quantitative trait of interest are captured by trait-specific (FAST) SNP markers associated to RNA-seq in molecular plant breeding (Adopted from Fu et al., 2017) 4 Practice of Marker-Assisted Breeding 4.1 Basic principles and workflow of marker-assisted selection (MAS) The principle of marker-assisted selection (MAS) is to identify DNA markers related to a certain target trait, and then use these markers to track these traits in the breeding population (Bonnett et al., 2004). The advantage of this method is that without waiting for the plants to grow and then observing their performance, those plants with good genes can be selected in advance, thereby accelerating the breeding process. The general process is to first identify the markers related to traits, then verify whether these markers are reliable, and then apply them to the breeding program to select disease-resistant, high-yielding or high-quality plants (Xu and Crouch, 2008). 4.2 Practical applications of marker-assisted selection inSapindus breeding MAS technology can be used in the breeding of Sapindus to improve some important traits such as oil content, disease resistance and growth rate. Breeders can identify plants with target genes more quickly through DNA markers and then carry out selection and breeding. Hasan et al. (2021) found that this method has been successfully applied in other crops to enhance traits such as drought resistance and insect resistance, indicating that it also has great application potential in Sapindus breeding. However, the practical application of MAS in Sapindus has just begun at present, and more studies are needed to identify the stable traits and marker correspondence suitable for Sapindus (Liu, 2024). 4.3 Performance of MAS technology in enhancing breeding efficiency and reliability Through this technology, breeders can select individuals with target traits in advance when plants are not fully grown, thereby accelerating the entire breeding process. The effect of MAS largely depends on whether the relationship between markers and traits is stable. However, MAS still encounters some challenges when dealing with traits controlled by multiple genes (Thavamanikumar et al., 2013). Kumawat et al. (2020) demonstrated in their study that MAS can enhance the accuracy of selection and the genetic gain of breeding, indicating its potential to help improve efficiency in the breeding of Sapindus. 5 Gene-Trait Association Analysis inSapindus Breeding 5.1 Statistical models and tools for marker-trait association analysis The mixed linear model (MLM) in TASSEL software is widely used in Sapindus breeding research and it works well in identifying the association between ISSR markers and fruit traits. Sun et al. ’s research in 2018(a) identified 18 ISSR loci, which were related to 13 fruit traits, including seed oil content and saponin yield. Principal component analysis (PCA) and correlation analysis are also often used to evaluate the trait differences among different plants, which is very helpful for determining which populations are suitable for correlation analysis (Neale and Savolainen, 2004).
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