Molecular Plant Breeding 2024, Vol.15, No.5, 220-232 http://genbreedpublisher.com/index.php/mpb 225 consistent, the specific set of transcribed genes varied significantly among the lines (Hansey et al., 2012). This variation in gene expression, coupled with the presence of novel transcripts in some lines but not others, indicates that polymorphism within genes can contribute to phenotypic diversity and adaptation. 4.3 Diversity in maize germplasm resources Maize germplasm resources exhibit a remarkable level of genetic diversity, which is crucial for crop improvement and adaptation to different environments. A global germplasm collection, including 527 inbred lines with tropical, subtropical, and temperate backgrounds, revealed broad phenotypic diversity and complex genetic relatedness among the lines. This diversity is reflected in the presence of numerous SNPs, with 926 SNPs having minor allele frequencies of ≥0.1 used to estimate genetic diversity and relatedness (Yang et al., 2011). The maize pan-genome, which includes genes present in every individual (core) and genes in a subset of individuals (dispensable), further highlights the extent of genetic diversity in maize. Transcriptome sequencing of 503 maize inbred lines identified 8 681 representative transcript assemblies (RTAs), with 16.4% expressed in all lines and 82.7% expressed in subsets of the lines (Hirsch et al., 2014). This dynamic nature of the maize genome suggests that a substantial portion of genetic variation lies outside the single reference genome, emphasizing the importance of exploring diverse germplasm resources for crop improvement. High-throughput SNP genotyping platforms, such as the GoldenGate assay, have been instrumental in characterizing genetic diversity in maize. A custom GoldenGate assay containing 1 536 SNPs was used to genotype a panel of 154 diverse inbred lines, revealing a high level of polymorphism and providing valuable insights into the genetic structure of maize populations (Yan et al., 2010). Such tools are essential for conducting association mapping studies and understanding the genetic basis of complex traits in maize. The distribution patterns of nucleotide polymorphism in maize are influenced by various factors, including recombination rates, selection pressures, and the dynamic nature of the maize genome. The extensive genetic diversity present in maize germplasm resources provides a rich foundation for crop improvement and adaptation to diverse environments. 5 Influence of Nucleotide Polymorphism on Maize Crop Traits 5.1 Impact on stress resistance traits Nucleotide polymorphisms play a significant role in enhancing maize's resistance to various environmental stresses. For instance, a genome-wide association study (GWAS) identified several single-nucleotide polymorphisms (SNPs) associated with alkaline stress tolerance in maize seedlings. This study revealed nine SNPs and their associated candidate genes that significantly contribute to alkaline tolerance, which is crucial for improving maize growth in salt-alkalized soils (Li et al., 2022). Additionally, another study focused on drought and aflatoxin resistance in maize hybrids in sub-tropical regions. This research identified ten quantitative trait variants for grain yield, plant height, and other agronomic traits under both irrigated and non-irrigated conditions, demonstrating the potential of genetic diversity to improve stress resistance in maize breeding programs (Farfan et al., 2015). Moreover, a study on the genetic architecture of stalk lodging resistance-related traits in maize identified 423 significant quantitative trait nucleotides (QTNs) associated with stem diameter, stalk bending strength, and rind penetrometer resistance. These traits are crucial for improving lodging resistance, which directly impacts maize’s ability to withstand environmental stresses such as strong winds and heavy rains (Zhang et al., 2018). Collectively, these findings underscore the importance of nucleotide polymorphisms in enhancing maize's resilience to various environmental stresses, thereby contributing to more stable and sustainable crop production. 5.2 Impact on yield-related traits Nucleotide polymorphisms also significantly influence yield-related traits in maize. A study on the genetic analysis of tropical quality protein maize (QPM) germplasm revealed that both additive and non-additive genetic effects are important for the inheritance of grain yield and other agronomic traits under both stress and non-stress
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