Molecular Plant Breeding 2025, Vol.16, No.1, 13-23 http://genbreedpublisher.com/index.php/mpb 18 of ORF5+ (killer) and ORF4+ (partner) causes endoplasmic reticulum (ER) stress. ORF3+ (protector) prevents ER stress and produces normal gametes, but ORF3− cannot prevent ER stress, resulting in premature programmed cell death and leads to embryo-sac abortion. Preferential transmission of ORF3+ gametes results in segregation distortion in the progeny (Figure 2). Figure 2 Schematic representation of the killer-protector system in an indica-japonica hybrid regulated by the S5 locus. (A) A genetic model depicting the process of megaspore formation and effects of the three genes, where 3+, 3-, 4+, 4-, 5+, and 5- represent ORF3+, ORF3-, ORF4+, ORF4-, ORF5+, and ORF5-, respectively, and colored blocks and circles represent the proteins. In the megaspore mother cell and daughter cells immediately after meiotic division, killing would not occur because of the presence of ORF3+. Killing would occur in the daughter cell carrying ORF3- and ORF4+ at a later stage of megaspore development. (B) Hypothetical molecular processes involving ER-stress and PCD. bZIP50-S, spliced bZIP50; ER, endoplasmic reticulum; PM, plasma membrane (Adapted from Yang et al., 2012) The impact of linkage drag on agronomic traits can be significant, often resulting in reduced yield, poor grain quality, or susceptibility to diseases. For example, the deletion in the qSW5 gene, which is associated with increased grain size, also highlights how changes in DNA regulating agronomically important traits can be linked with other undesirable traits due to linkage drag (Shomura et al., 2008). Additionally, the study on recombination patterns in tomato, which shares similarities with rice, found that loss of recombination hotspots due to domestication can lead to linkage drag, affecting the overall genetic diversity and agronomic performance (Fuentes et al., 2021). 5.2 Strategies to mitigate linkage drag Marker-assisted selection (MAS) is a powerful tool to mitigate linkage drag by allowing breeders to select for specific genetic markers associated with desirable traits while avoiding those linked with undesirable ones. The identification of QTLs (Quantitative Trait Loci) controlling domestication-related traits in rice provides a basis for MAS. For instance, the study (Xiong et al.1999) identified 44 QTLs associated with various traits, which can be used in MAS to selectively breed for beneficial traits while minimizing linkage drag. This approach can significantly enhance the efficiency of breeding programs by reducing the co-inheritance of undesirable traits. Increasing recombination rates and employing gene editing technologies are other effective strategies to break linkage drag. Recombination can be enhanced through the use of wild relatives or induced mutations to create new genetic variations. The study on recombination patterns in tomato suggests that understanding the dynamics of recombination hotspots can help in designing strategies to increase recombination in specific genomic regions, thereby reducing linkage drag (Fuentes et al., 2021). Additionally, gene editing technologies like CRISPR/Cas9 offer precise tools to directly modify or remove undesirable genes linked with beneficial traits. This can be particularly useful in overcoming the limitations posed by linkage drag in traditional breeding methods.
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