Pattern and variation in simple sequence repeat (SSR) at different genomic regions and its implications to maize evolution and breeding

• DOI: 10.1186/s12864-023-09156-0
• Publication Date: 2023-03-21T12:03:06Z
• Authors: Meiqi Zhao; Guoping Shu; Yanhong Hu; Gangqiang Cao; Yibo Wang
• Keywords: Intergenic region; Repeated sequence

Repetitive DNA sequences accounts for over 80% of maize genome. Although simple sequence repeats (SSRs) account only 0.03% the genome, they have been widely used in genetic research and breeding as highly informative codominant markers. The genome-wide distribution polymorphism SSRs are not well studied due to lack high-quality genome data.In this study, using data from de novo-sequenced genomes five representative inbred lines, we revealed that were more densely present telomeric region than centromeric region, abundant genic intergenic sequences. On sequences, tri- hexanucleotide motifs CDS some mono- dinucleotide UTR Median length chromosomal density both narrowly range-bound, with median 14-18 bp average 3355.77 bp/Mbp. LTR-RTs < 0.4 Mya had higher SSR (4498-4992 bp/Mbp). genome-specific motif-specific studied. Their potential applications discussed.We found different was nearly constant. regions much regions. In addition, at evolutionary ages varied a narrow range. their LTR-RT carriers evolved an equal rate. All these observations indicated under control yet unknown forces. chromosome region-specific polymorphisms observed supported notion invaluable resource developing gene markers molecular breeding.