Diversity and linkage disequilibrium features in a composite public/private dent maize panel: consequences for association genetics as evaluated from a case study using flowering time

Abstract

Recent progress in genotyping and resequencing techniques have opened new opportunities for deciphering quantitative trait variation by looking for associations between traits of interest and polymorphisms in panels of diverse inbred lines. Association mapping raises specific issues related to the choice of appropriate (i) panels and marker-densities and (ii) statistical methods to capture associations. In this study, we used a panel of 314 maize inbred lines from the dent pool, composed of inbred material from public institutes (113 inbred lines) and a private company (201 inbred lines). We showed that local LD was higher and genetic diversity lower in the material of private origin than in the public material. We compared the results obtained by different software for identifying population structure and computing relatedness among lines, and ran association tests for earliness related traits. Our results confirmed the importance of the mite polymorphism of Vgt1 on flowering time, but also showed that its effect can be captured by zmRap2.7 polymorphisms located 70 kb apart. We also highlighted associations with polymorphisms within genes putatively involved in lignin biosynthesis pathway, which deserve further investigations.

Adaptation of Maize to Temperate Climates: Mid-Density Genome-Wide Association Genetics and Diversity Patterns Reveal Key Genomic Regions, with a Major Contribution of the Vgt2 (ZCN8) Locus

“…According to the Hill and Weir model, LD dropped below 0.1 after 200 kb at the genome level and dropped to almost the background level at around 500 kb-1 Mb. This value was in the range of those reported in the literature for different types of panels [85], [86], [87], [88] and illustrates that linkage disequilibrium in maize has markedly increased as a result of domestication [1] and genetic improvement [2], [74], [89]. We observed that the extent of LD varied among chromosomes, i.e.…”

“…This value was in the upper range of those reported by other diversity analyses based on SNP genotyping, ranging from 0.27 to 0.39 [72], [73], [74], [75], [76]. Only eight percent of markers appeared to be monomorphic, showing that some rare alleles discovered with the Panzea panel used to build the 50K Illumina array were not represented in our panel.…”

“…100 kb on average along chromosome 1, between 140 and 200 kb on average along chromosomes 5, 6, 3 and 7, between 200 and 300 kb along chromosomes 9, 2, 4, 10 and 8, which suggests different selection pressures were involved. Note that this ranking apparently varies among populations [74], [89]. Extracting the variation due to population structure did not much change these trends, with an average decrease of around 150 kb instead of 198 kb.…”

Genomic selection helps accelerate popcorn population breeding

“…However, these values are not common and could be the result of the specific breeding processes to which this population has been submitted. Other studies with corn report the extent of LD to be low, with rapid decay over physical distances between locations, with a varying range in most cases between 0.5 and 7.0 kb (Remington et al., 2011; Truntzler et al., 2012).…”

A MITE Transposon Insertion Is Associated with Differential Methylation at the Maize Flowering Time QTLVgt1

“…One of the major flowering-time QTL, Vegetative to generative transition 1 ( Vgt1 ) (Phillips et al 1992; Vlăduţu et al 1999; Salvi et al 2002) on chromosome 8, corresponds to a ≈2-kb intergenic region upstream of an Ap2 -like flowering-time gene, ZmRap2.7 and appears to act as a cis -regulator of ZmRap2.7 expression (Salvi et al 2007). A maize–sorghum–rice evolutionarily conserved noncoding sequence (CNS) (Freeling and Subramaniam 2009) was identified within Vgt1 ; in early Vgt1 alleles, this CNS is interrupted by the insertion of a miniature transposon (MITE) belonging to the Tourist family (Salvi et al 2007), and this insertional polymorphism has been repeatedly identified as strongly associated with flowering time in independent studies (Salvi et al 2007; Ducrocq et al 2008; Buckler et al 2009; Hung et al 2012; Truntzler et al 2012). …”