Abstract
Understanding genetic characteristics can reveal the genetic diversity in maize and be used to explore evolutionary mechanisms and gene cloning. A high-density linkage map was constructed to determine recombination rates (RRs), segregation distortion regions (SDRs), and recombinant blocks (RBs) in two recombinant inbred line populations (RILs) (B73/By804 and Zong3/87-1) generated by the single seed descent method. Population B73/By804 containing 174 lines were genotyped with 198 simple sequence repeats (SSRs) markers while population Zong3/87-1 comprised of 175 lines, were genotyped with 210 SSR markers along with 1536 single nucleotide polymorphism (SNP) markers for each population, spanning 1526.7 cM and 1996.2 cM in the B73/By804 and Zong3/87-1 populations, respectively. The total variance of the RR in the whole genome was nearly 100 fold, and the maximum average was 10.43–11.50 cM/Mb while the minimum was 0.08–0.10 cM/Mb in the two populations. The average number of RB was 44 and 37 in the Zong3/87-1 and B73/By804 populations, respectively, whereas 28 SDRs were observed in both populations. We investigated 11 traits in Zong3/87-1 and 10 traits in B73/By804. Quantitative trait locus (QTLs) mapping of SNP+SSR with SNP and SSR marker sets were compared to showed the impact of different density markers on QTL mapping and resolution. The confidence interval of QTL Pa19 (FatB gene controlling palmitic acid content) was reduced from 3.5 Mb to 1.72 Mb, and the QTL Oil6 (DGAT1-2 gene controlling oil concentration) was significantly reduced from 10.8 Mb to 1.62 Mb. Thus, the use of high-density markers considerably improved QTL mapping resolution. The genetic information resulting from this study will support forthcoming efforts to understand recombination events, SDRs, and variations among different germplasm. Furthermore, this study will facilitate gene cloning and understanding of the fundamental sources of total variation and RR in maize, which is the most widely cultivated cereal crop.
Highlights
Maize (Zea mays L.) is an important crop used for food and feed while its production and consumption are the highest among cereal crops [1]
Type A mixing resulted in homozygous lines in later generations, and in-depth analysis revealed only a few recombination events
Type B contamination resulted in relatively high heterozygosity ratios in the recombinant inbred line populations (RILs) used in this study
Summary
Maize (Zea mays L.) is an important crop used for food and feed while its production and consumption are the highest among cereal crops [1]. It has recently gained additional interest as a renewable energy plant due to its high biomass potential. High-density single nucleotide polymorphism (SNP) markers are widely used for such investigations and are an effective tool for determining the genomic and genetic characteristics of maize [4]. Compared with traditional markers such as random amplified polymorphic DNAs (RAPDs), simple sequence repeats (SSRs), and restriction fragment length polymorphisms (RFLPs), SNPs are of higher density, cost effective, and yields more genetic information. The investigative utility of this large number of maize SNPs is enhanced because the cost of genotyping is decreasing steadily [6]
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