Maize Genomics and Genetics 2024, Vol.15, No.4, 182-190 http://cropscipublisher.com/index.php/mgg 184 Figure 1 Pan-genome analysis of the gene space (Adopted from Hufford et al., 2021) Image caption: (A) Pan-genes categorized by annotation method and phylostrata; Genes annotated with evidence have mRNA support, whereas ab initio genes are predicted on the basis of DNA sequence alone; Genes within progressing phylostrata [species Z. mays (maize), tribe Andropogoneae, family Poaceae, kingdom Viridiplantae] are more conserved; (B) Number of pan-genes added with each additional genome assembly. Order of genomes being added into the pan-genome was bootstrapped 1000 times. Tropical lines include CML52, CML69, CML103, CML228, CML247, CML277, CML322, CML333, Ki3, Ki11, NC350, NC358, and Tzi8; temperate lines include B73, B97, Ky21, M162W, Ms71, Oh43, Oh7B, HP301, P39, and Il14H. (C) Proportion of pan-genes in the core, near-core, dispensable, and private fractions of the pan-genome. For (B) and (C), tandem duplicates were considered as a single pan-gene and coordinates were filled in when a gene was not annotated, but an alignment with>90% coverage and 90% identity was present within the correct homologous block; (D) Number of tissues with expression (reads per kilobase per million reads>1) for each gene in each genome on the basis of their pan-genome classification. Tissues in this analysis include root, shoot, V11 base, V11 middle, V11 tip, anther, tassel, and ear (Adopted from Hufford et al., 2021) 3 Methodologies in Gene Flow Studies 3.1 Genetic markers and molecular tools Genetic markers and molecular tools are fundamental in studying gene flow in maize. Techniques such as next-generation sequencing (NGS) have revolutionized the field by enabling rapid and comprehensive sequencing of plant genomes. For instance, the use of Illumina sequencing to analyze nearly complete genomes of Maize dwarf mosaic virus (MDMV) isolates has provided insights into genetic diversity and evolutionary relationships (Wijayasekara et al., 2021). Additionally, genotyping by target sequencing (GBTS) technology has been employed to develop low-density genotyping platforms, such as the 5.5 K SNP markers panel, which are crucial for genetic and molecular breeding studies (Ma et al., 2022). These tools facilitate the identification of genetic variations and the mapping of quantitative traits, thereby enhancing the understanding of gene flow dynamics in maize.
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