Field Crop 2024, Vol.7, No.6, 325-333 http://cropscipublisher.com/index.php/fc 326 2 Advances in Genetic Marker Research in Cotton 2.1 Historical development of genetic marker technologies The development of genetic marker technologies in cotton has evolved significantly over the years. Initially, traditional breeding methods were the primary approach for cotton improvement, but these methods were limited by their time-consuming nature and the need for extensive field trials (Figure 1) (Kushanov et al., 2021). The introduction of molecular markers revolutionized cotton breeding by enabling the identification and utilization of DNA polymorphisms. Early marker systems included Restriction Fragment Length Polymorphism (RFLP) and Random Amplified Polymorphic DNA (RAPD), which laid the groundwork for more advanced techniques (Shehzad et al., 2017). The sequencing of cotton genomes, such as G. raimondii and G. hirsutum, further propelled the development of genetic markers by providing a comprehensive understanding of the cotton genome (Sabev et al., 2020). Figure 1 Marker-assisted selection in comparison with conventional breeding (Adopted from Kushanov et al., 2021) Image caption: P1 and P2, parental genotypes, F1, first generation hybrid, Fn, hybrid progeny obtained from first generation by self-pollination, and BCn, backcross generations (Adopted from Kushanov et al., 2021) 2.2 Commonly used genetic markers in cotton breeding In cotton breeding, several types of genetic markers are commonly used, including simple sequence repeats (SSRs) and single nucleotide polymorphisms (SNPs). SSR markers are valued for their high polymorphism and ease of use in genetic diversity studies and DNA fingerprinting (Wu et al., 2020; Kuang et al., 2022). They have been instrumental in constructing linkage maps and conducting QTL analysis for traits such as fiber quality and yield (Sabev et al., 2020). SNP markers, on the other hand, offer high-throughput genotyping capabilities and are increasingly used for genome-wide association studies and genomic selection (Ashrafi et al., 2015; Hulse-Kemp et al., 2015). The development of SNP arrays, such as the CottonSNP63K, has provided a standardized resource for high-density genetic mapping and trait dissection. 2.3 Advances in high-throughput sequencing and marker discovery Recent advances in high-throughput sequencing technologies have significantly enhanced marker discovery in cotton. Techniques such as genotyping-by-sequencing (GBS) and specific locus amplified fragment sequencing (SLAF-seq) have enabled the rapid identification of SNP markers across the cotton genome (Fan et al., 2018). These technologies facilitate the construction of high-density genetic maps, which are crucial for precise QTL mapping and marker-assisted selection (Wang et al., 2015; Zhang et al., 2016). The use of transcriptome
RkJQdWJsaXNoZXIy MjQ4ODYzNA==