Genetic analysis and characterization of a new maize association mapping panel for quantitative trait loci dissection

Abstract

Association mapping based on the linkage disequilibrium provides a promising tool to identify genes responsible for quantitative variations underlying complex traits. Presented here is a maize association mapping panel consisting of 155 inbred lines with mainly temperate germplasm, which was phenotyped for 34 traits and genotyped using 82 SSRs and 1,536 SNPs. Abundant phenotypic and genetic diversities were observed within the panel based on the phenotypic and genotypic analysis. A model-based analysis using 82 SSRs assigned all inbred lines to two groups with eight subgroups. The relative kinship matrix was calculated using 884 SNPs with minor allele frequency > or = 20% indicating that no or weak relationships were identified for most individual pairs. Three traits (total tocopherol content in maize kernel, plant height and kernel length) and 1,414 SNPs with missing data < 20% were used to evaluate the performance of four models for association mapping analysis. For all traits, the model controlling relative kinship (K) performed better than the model controlling population structure (Q), and similarly to the model controlling both population structure and relative kinship (Q + K) in this panel. Our results suggest this maize panel can be used for association mapping analysis targeting multiple agronomic and quality traits with optimal association model.

The Genetic Basis of Plant Architecture in 10 Maize Recombinant Inbred Line Populations

“…Additionally, 14 diverse elite inbred lines were selected from a diverse association mapping panel (Yang et al, 2010(Yang et al, , 2011 and were subject to RNA-seq experiments on kernels at 15 d after pollination (Fu et al, 2013), generating hundreds of thousands of SNP markers. Recombination bins and ultra-high-density linkage maps of the ROAM population were used to dissect the genetic factors underlying maize plant architecture as follows.…”

“…Differentially expressed genes were identified between RHLs with and without 600-kb target genomic substitutions. Additionally, association mapping of the target genomic region of qPH3 was performed using 1.03 million SNPs genotyped in a diverse Chinese association mapping panel with 505 inbred lines (Yang et al, 2010(Yang et al, , 2011(Yang et al, , 2014Li et al, 2013a). Furthermore, the haplotypes of all candidate genes in the 600-kb genomic region in all 14 parents were analyzed and compared.…”

Genome‐wide recombination dynamics are associated with phenotypic variation in maize

“…mexicana) (Supporting Information Table S1). Among the 16 maize parents, SK is an inbred line selfed from a landrace in Peru, and BK is an inbred line selfed from a landrace in the USA, whereas the others are from a diverse maize-association panel that was previously described (Yang et al, 2010). Each of the 11 RIL populations was derived from a single F 1 plant and was developed through self-pollination and single seed descent for at least six generations.…”

Simple sequence repeat-based association analysis of fruit traits in eggplant (Solanum melongena)

“…Association mapping has several advantages over traditional familybased linkage mapping, including shorter research time, higher mapping resolutions, and the ability to investigate a greater number of alleles (Flint-Garcia et al, 2005;Yu and Buckler, 2006;Yang et al, 2010). It was 1st applied to plant genetic mapping in maize (Zea mays L.) (Thornsberry et al, 2001), and LD mapping has now been conducted in many different plant species (Gupta et al, 2005), such as Arabidopsis thaliana Heynh.…”