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They attributed this to the high level of LD among the diverse maize lines used in their study.
To examine the extent of natural variation for SAM architecture, we examined 27 diverse inbred maize lines used as parents in the maize NAM population (Yu et al. 2008).
The maize lines used in this study were derived from the UniformMu population, a Mutator line with the mutable bz1-mum9 anthocyanin biosynthetic gene introgressed into the W22 genetic background (McCarty et al. 2005).
Specifically in the case of the two maize lines used in this work, a previous study indicates that S1587-17 produces higher levels of ROS under Al stress, while ROS production remains constant in Cat100-6 [ 41].
The maize lines used in this study were inbred lines LC (a color converted W22 line), A188, H99, and a flavonol-deficient conditionally male-sterile line " white pollen" (genotype: whp/whp, c2/c2; [ 22]) and its corresponding fertile wild type line (whp/whp, C2/C2 or whp/whp, C2/c2).
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The present study aimed to characterize subtropical maize lines using high-quality SNPs distributed throughout the genome.
Yan et al., 2009 [ 22], genotyping 632 maize lines using 1,229 SNP markers, showed that the LD (r) between markers increased with increasing MAF threshold, especially in the case of very close SNP pairs (0 10 kb).
Our results indicate that prediction of the performance of inbred maize lines using GBS data combined with pedigree information outperforms the prediction accuracy of pedigree-based methods and, at a minimum, can yield prediction accuracies comparable to those obtained with low-density to mid-density SNP arrays.
This number exceeds the largest number of NUMTs previously observed in a maize line using FISH, which was 19 NUMTs in the nonstiff stalk line Oh43 (Lough et al. 2008).
(DOCX 153 kb) Additional file 4: Analysis of the population structure within the set of 300 maize inbred lines used for the GWAS study.
We characterized subtropical elite maize breeding lines using a large number of high-quality SNPs.
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