Molecular Plant Breeding 2024, Vol.15, No.1, 8-14 http://genbreedpublisher.com/index.php/mpb 10 For example, in barley breeding, the paper “Advanced Backcross QTL Analysis in Barley (Hordeum vulgare L.)” demonstrated how to use assisted-marker backcrossing technology to transfer yield-related QTLs from wild barley donors to superior receptors (Pillen et al., 2003). In addition, the study “Population Structure and Breeding Patterns of 145 US Rice Cultivars Based on SSR Marker Analysis” used SSR molecular marker technology to confirm the lineage of 145 US rice germplasm resources, providing accurate genetic background information for breeding work (Lu et al., 2005). 3.2 Application of linkage maps in analyzing complex traits The application of linkage maps in Breeding 3.0 plays a crucial role in analyzing complex traits. By constructing a linkage map, we can reveal the association between traits and loci, and identify key genes that control traits. The analysis of the gene-trait association is crucial for the selection and optimization of breeding objectives. In Breeding 3.0, we use higher resolution linkage mapping technologies such as high-density SNP chips and genome sequencing to more accurately locate and identify genes related to complex traits. The paper “Dissection of Complex Traits in Crop Plants: A Plea for Multiparental Populations” (Plant, Cell&Environment, 2004) proposed the importance of using multi parent populations to construct linkage maps to analyze complex traits in crop plants (Lander and Schork, 2006). In maize breeding, the study “Genome Wide Association Studies Using a New Nonparametric Model Reveal the Genetic Architecture of 17 Agronomic Traits in an Enlarged Maize Association Panel” (Plos Genetics, 2014) conducted a genome-wide association study using high-density SNP markers in maize, showcasing the genetic structure of 17 agronomic traits (Yang et al., 2014). 3.3 Technological progress and application of high-throughput genotyping High throughput genotyping technology has made significant progress and application in breeding 3.0. Through high-throughput genotyping technology, we can quickly and accurately analyze large-scale genetic variations. These technologies include SNP chips, genome-wide association study, and whole genome sequencing. Through these technologies, we can screen candidate genes related to agronomic traits in natural populations and accelerate the breeding process. The technological progress of high-throughput genotyping provides more comprehensive and in-depth genetic information for breeding work, thereby improving the accuracy and efficiency of breeding. For example, the “The 3000 Rice Genomes Project” (GigaScience, 2014) used high-throughput genotyping technology to comprehensively sequence 3 000 rice genomes, revealing the diversity and genetic variation of the rice genome. In wheat breeding, the study “Genome-Wide Association Study Reveals Novel Genes Associated with Culm Cellulose Content in Bread Wheat (Triticum aestivumL.)” (BMC Plant Biology, 2017) analyzed the stem cellulose content of 288 different wheat varieties and conducted genome-wide association studies (GWAS), revealing new genes related to wheat stem cellulose content. Another paper, “Genome-wide Association Mapping of Black Point Reaction in Common Wheat (Triticum aestivum L.)” (BMC Plant Biology, 2017), conducted a genome-wide association study (GWAS) on black point of wheat through high-density 90 K and 660 K single nucleotide polymorphisms (SNP) analysis. The black points of 166 elite wheat varieties was evaluated in five environments, and 25 unique loci were identified, which were distributed on multiple chromosomes and explained 7.9% to 18.0% of phenotypic variations (Liu et al., 2017). Based on the above statements, the methodology of Breeding 3.0 includes optimized assisted-marker backcrossing and pedigree confirmation technologies, the application of linkage maps to analyze complex traits, and the technological progress and application of high-throughput genotyping technology. The development of these methods enables us to select and optimize breeding materials more accurately, providing more genetic information and tools for plant breeding. 4 The Advantages and Applications of Breeding 3.0 4.1 Precision and efficiency in integrating genetic and genomic data A significant advantage of Breeding 3.0 is its ability to integrate genetic and genomic data, thereby improving the accuracy and efficiency of breeding. For example, in tomato breeding, The study “Efficiency of Genomic Selection for Tomato Fruit Quality” (Molecular Breeding, 2016) demonstrated the accuracy of genome selection
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