Comparative SNP and Haplotype Analysis Reveals a Higher Genetic Diversity and Rapider LD Decay in Tropical than Temperate Germplasm in Maize

Abstract

Understanding of genetic diversity and linkage disequilibrium (LD) decay in diverse maize germplasm is fundamentally important for maize improvement. A total of 287 tropical and 160 temperate inbred lines were genotyped with 1943 single nucleotide polymorphism (SNP) markers of high quality and compared for genetic diversity and LD decay using the SNPs and their haplotypes developed from genic and intergenic regions. Intronic SNPs revealed a substantial higher variation than exonic SNPs. The big window size haplotypes (3-SNP slide-window covering 2160 kb on average) revealed much higher genetic diversity than the 10 kb-window and gene-window haplotypes. The polymorphic information content values revealed by the haplotypes (0.436–0.566) were generally much higher than individual SNPs (0.247–0.259). Cluster analysis classified the 447 maize lines into two major groups, corresponding to temperate and tropical types. The level of genetic diversity and subpopulation structure were associated with the germplasm origin and post-domestication selection. Compared to temperate lines, the tropical lines had a much higher level of genetic diversity with no significant subpopulation structure identified. Significant variation in LD decay distance (2–100 kb) was found across the genome, chromosomal regions and germplasm groups. The average of LD decay distance (10–100 kb) in the temperate germplasm was two to ten times larger than that in the tropical germplasm (5–10 kb). In conclusion, tropical maize not only host high genetic diversity that can be exploited for future plant breeding, but also show rapid LD decay that provides more opportunity for selection.

Identification and validation of genomic regions influencing kernel zinc and iron in maize

“…We found an average LD decay ( r 2  = 0.2) across the whole genome close to 6 kb in the panel. This is in accordance with several previous studies (Yan et al 2009; Lu et al 2011; Romay et al 2013; Zhang et al 2016) employing tropical and sub-tropical maize. This rapid LD decay in the panel is reflective of the genetic diversity of the tropical/subtropical maize germplasm used in this study.…”

“…A significant correlation between grain Zn and Fe concentrations was also reported in wheat (Velu et al 2011), rice (Kabir et al 2003), pearl millet (Velu et al 2008; Gupta et al 2009) and sorghum (Kumar et al 2009). This suggests that these traits might have some common genetic mechanisms leading to their accumulation in grains.…”

Population genomics of the eastern cottonwood (Populus deltoides)

“…The LD extent observed in P. deltoides is advantageous for the successful implementation of genomewide association studies (GWAS) in this species, methodology that relies on LD between causative and tested markers to identify genomic regions associated with a trait or variable of interest (Platt, Vilhjálmsson, & Nordborg, 2010). LD levels observed in this population when using common markers are sufficiently high for GWAS to be successful (e.g., Fahrenkrog et al., 2017), but also low enough to achieve high resolution (Lu et al., 2011). In this population, linkage mapping is thus likely to be more effective for common markers, variants that most GWAS methods have also higher power to detect.…”

Genetic diversity and population structure of Bambara groundnut (Vigna subterranea (L.) Verdc.): synopsis of the past two decades of analysis and implications for crop improvement programmes

“…The use of molecular markers to assess genetic diversity in landraces, breeding lines, varieties, wild relatives and mutant populations to aid breeding decisions in major crops such as rice (Oryza sativa L.) (Zhang et al 2011;Choudhary et al 2013), maize (Zea mays L.) (Lu et al 2011;Wen et al 2012), soya bean (Glycine max (L.) Merr.) (He et al 2012) and cowpea (Vigna unguiculata (L.) Walp.)…”