Genetic properties of 240 maize inbred lines and identity-by-descent segments revealed by high-density SNP markers

Abstract

Characterization of the genetic properties of maize inbred lines is beneficial not only for increasing knowledge of genetic diversity, but also for maize breeding. In the present study, a panel of 240 maize inbred lines commonly used in China, including three foundation parents Dan340, Mo17, and Huangzao4, and their derivatives, was genotyped using the MaizeSNP50 BeadChip, which contains 56,110 single-nucleotide polymorphism (SNP) markers. As a result, 40,757 SNPs with unique physical positions were successfully recalled in this panel with an average coverage of 50 kb per SNP. Five subgroups including Lan, LRC, PB, Reid, and SPT were inferred using 4000 SNPs with minor allele frequency C0.200, a result that was largely consistent with the pedigree information for these 240 inbred lines. With a cutoff value of r 2 \ 0.100, linkage disequilibrium (LD) decay distances along the ten chromosomes of maize ranged from 397 to 819 kb, with an average of 643 kb. A subtotal of 26, 35, and 23 identity-by-descent segments, which were longer than both the average LD decay distance on the corresponding chromosomes and the local LD decay distance of r 2 \ 0.100, were identified in the Dan340, Huangzao4, and Mo17 derivatives, respectively. Three lower peaks for Tajima's D overlapped with three major quantitative trait loci (qkrn7, scmv1, and qHS2.09) in these derivatives. Elucidating the genetic properties of this panel provides information for investigating the genetic architecture of agronomic traits and heterotic grouping during maize breeding.

Exploring Identity-By-Descent Segments and Putative Functions Using Different Foundation Parents in Maize

“…In Chinese maize breeding, more than 40 elite lines and 80 hybrids have been derived from HZS [6]. Liu et al [7] used three FPs of Dan340, HZS, and Mo17 and 23 relevant derivatives to explore the IBD segments in different FP lines and their descendants and identified 26, 25, and 23 IBD regions, respectively. In this paper, among the FP lines of B73, Mo17, 207, and HZS and their relevant descendants, 128 conservative genetic regions were determined to be identical (Fig 2), which may account for some common phenotypes that were improved during the maize breeding process due to the common corn breeding objectives of high yield, good quality, wide adaptation and strong stress tolerance [12].…”

“…For each group, genetic diversity (GD) was evaluated using 43,252 SNPs in PowerMarker V3.25 [37] and was defined as the probability that two alleles randomly chosen from the test sample were different [18]. SNPs with a GD of zero were defined as tag loci with no variation, as widely used in the identification of conserved regions [5, 7]. Then, comparisons between lines were performed by slide window in one given FP group, with a window size of 25 kilobases (kb) before and after each tag SNP.…”

“…These lines are defined as foundation parents (FPs) and play no-alternative roles in historical and current maize breeding programs. Understandably, some important genomic segments are often retained during the formation of FPs and their descendants under selection [7]. Such segments contain the same ancestral origins and are defined as identity-by-descent (IBD) regions [8], which have been demonstrated to be powerful in relatedness evaluation and mapping of genetic loci associated with phenotypic variations in animal and human research [9–11].…”

Transcriptomes of early developing tassels under drought stress reveal differential expression of genes related to drought tolerance in maize

“…After treatment, when plants had reached the floral organ differentiation stage Ji 81162 LRC S 525×Ye 107 -1.56 1) The inbred lines are mainly used for hybrids parents in breeding programs of China. The heterotic group and pedigree were induced by high-density SNP markers from Liu et al (2015), and the evaluation for drought tolerance was inferred by the selection index (SI) value from Hao et al (2011). And the SI value is higher, the more drought-tolerant for this line.…”

“…However, the metabolic pathways involved and the reasons that drought stress results in male sterility are still not clearly understood. In the present study, we used RNA-Seq to explore drought-induced gene expression in early developing tassels from 10 inbred lines, which selected from five heterotic groups of China (Liu et al 2015) with different drought resistance (Hao et al 2011), under both well-watered and drought-stressed conditions. The goal of the present study was to identify transcripts that were differentially expressed under drought stress, explore the important gene networks and metabolic pathways induced by drought in early developing tassels, and propose transcriptional and other mechanisms of drought-induced male sterility in maize.…”