Rice Genomics and Genetics 2024, Vol.15, No.4, 190-202 http://cropscipublisher.com/index.php/rgg 193 The first step in traditional hybrid breeding is the development of inbred lines. Inbreeding involves the self-pollination of rice plants over several generations to produce homozygous lines that are genetically uniform. These inbred lines serve as the parental lines for producing hybrids. The process of inbreeding helps to stabilize desirable traits and eliminate undesirable ones. However, it also results in inbreeding depression, where the progeny exhibit reduced vigor and performance due to the accumulation of deleterious alleles. Despite this drawback, inbreeding is crucial for creating pure lines that can be used in hybrid breeding programs (Virmani, 1996). Once stable inbred lines are developed, crossbreeding techniques are employed to produce hybrid varieties. Crossbreeding involves the controlled pollination of two genetically distinct inbred lines to produce F1 hybrids. These hybrids exhibit heterosis, manifesting in superior traits such as increased yield, improved resistance to diseases and pests, and enhanced stress tolerance. In rice, two main types of hybrid breeding systems are used: two-line and three-line systems. The two-line system involves the use of a male-sterile line and a maintainer line, while the three-line system includes a male-sterile line, a maintainer line, and a restorer line. The three-line system, pioneered by Yuan Longping in China, has been widely adopted due to its effectiveness in producing high-yielding hybrids. 3.2 Modern approaches in hybrid breeding Advancements in molecular biology and genomics have paved the way for modern hybrid breeding approaches, such as marker-assisted selection (MAS) and genomic selection. These methods enhance the efficiency and precision of breeding programs by leveraging genetic information. Marker-assisted selection (MAS) is a technique that uses molecular markers to identify and select desirable traits in breeding populations. By associating specific markers with traits of interest, breeders can screen for these markers in early generations, accelerating the breeding process and increasing the accuracy of selection. In rice, MAS has been successfully used to identify markers linked to key traits such as yield, disease resistance, and stress tolerance. For example, markers associated with the Sub1 gene, which confers submergence tolerance, have been used to develop flood-tolerant rice varieties (Xu et al., 2006). Similarly, markers linked to major QTLs for yield and grain quality have been employed to select superior parental lines and hybrids (Li et al., 2020). Genomic selection is a more advanced approach that uses genome-wide markers to predict the breeding value of individuals. Unlike MAS, which focuses on a few markers linked to specific traits, genomic selection considers the combined effects of all markers across the genome. This allows for the selection of individuals with the best overall genetic potential. Genomic selection involves the development of a training population with known phenotypes and genotypes. Statistical models are then used to estimate the effects of all markers and predict the performance of untested individuals. This approach has been shown to significantly improve the accuracy and efficiency of selection in rice breeding programs (Spindel et al., 2015). 3.3 Developing superior hybrid varieties The development of superior hybrid rice varieties involves several critical steps, including the assessment of combining ability and parental selection, as well as rigorous testing and evaluation of hybrid performance. Combining ability refers to the ability of parental lines to produce superior hybrids when crossed. It is assessed through diallel crosses, where multiple parental lines are crossed in all possible combinations, and the performance of the resulting hybrids is evaluated. General combining ability (GCA) indicates the average performance of a line when crossed with several other lines, while specific combining ability (SCA) reflects the performance of specific hybrid combinations. The selection of parental lines with high GCA and SCA is crucial for developing superior hybrids. This involves evaluating the genetic diversity and compatibility of potential parents, as well as their performance in various environments. Advanced molecular techniques, such as genome-wide association studies (GWAS), can also aid in identifying parental lines with desirable traits and high combining ability (Figure 1) (Huang et al., 2016).
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