Triticeae Genomics and Genetics, 2024, Vol.15, No.3, 137-151 http://cropscipublisher.com/index.php/tgg 139 The evolution of genetic mapping techniques from early morphological markers to high-density SNP arrays has significantly advanced our understanding of the genetic architecture of complex traits in wheat. These advancements have important implications for wheat breeding and the development of high-yielding, resilient wheat varieties. 3 Methodologies in High-Density Genetic Mapping 3.1 Molecular markers Molecular markers are pivotal in high-density genetic mapping, providing the necessary resolution to identify genetic variations associated with key traits. 3.1.1 Simple sequence repeats (SSRs) Simple Sequence Repeats (SSRs), also known as microsatellites, are short, repetitive DNA sequences that are highly polymorphic and distributed throughout the genome. SSR markers have been extensively used in wheat genetic mapping due to their high level of polymorphism, co-dominant inheritance, and reproducibility. For instance, a study evaluated 20 wheat lines using eight SSR markers, revealing significant genetic diversity and identifying specific alleles associated with high-yielding varieties (Tahir et al., 2022). 3.1.2 Single nucleotide polymorphisms (SNPs) Single Nucleotide Polymorphisms (SNPs) are the most abundant type of genetic variation in the genome. SNP arrays, such as the Wheat 660 K SNP array, have been developed to facilitate high-throughput genotyping. This array contains a high percentage of genome-specific SNPs with reliable physical positions, making it a valuable tool for marker-assisted selection and genomic studies in wheat (Sun et al., 2020). SNP markers have been used to construct high-density genetic maps and identify quantitative trait loci (QTLs) for various traits, including grain protein content and starch properties (Guo et al., 2020). 3.1.3 Diversity arrays technology (DArT) Diversity Arrays Technology (DArT) is a microarray-based method that detects DNA polymorphisms without the need for sequence information. DArT markers have been used to generate high-density genetic maps and identify QTLs for important agronomic traits in wheat. This technology provides a cost-effective and efficient approach for genotyping large populations and has been successfully applied in wheat breeding programs (Jadon et al., 2023). 3.2 Mapping populations 3.2.1 Recombinant inbred lines (RILs) Recombinant Inbred Lines (RILs) are developed by repeated selfing of F2 individuals, leading to homozygous lines that are ideal for genetic mapping. RIL populations have been used to construct high-density genetic maps and identify QTLs for various traits in wheat. For example, a study on QTL (quantitative trait loci) mapping for wheat quality traits using a high-density genetic map (Guo et al., 2020). The research team used recombinant inbred lines (RILs) derived from a cross between 'Tainong 18' and 'Linmai 6' to analyze the genetic control of protein content, sedimentation value, dough rheological properties, falling number, and starch pasting properties. Over three years of field trials, a total of 106 QTLs related to 13 quality traits were detected, distributed across 21 chromosomes (Figure 1). The study found that some QTLs exhibited high stability and frequency, which can be used for subsequent fine mapping of QTLs and identification of candidate genes, providing valuable information for marker-assisted breeding. 3.2.2 Double haploids (DH) Double Haploids (DH) are produced through the doubling of haploid cells, resulting in completely homozygous lines in a single generation. DH populations are valuable for genetic mapping due to their high level of homozygosity and rapid development. Double haploid (DH) technology plays a crucial role in the localization of quantitative trait loci (QTL) and breeding applications for various crops, significantly improving breeding efficiency and accelerating the development of new varieties. Recent studies have shown that DH populations have been widely used for the localization of QTLs for traits such as iron and zinc concentration and protein
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