Abstract
Iron (Fe) is an essential micronutrient for humans, and iron deficiency is the most common micronutrient deficiency worldwide. Research on the genetic basis of iron concentration in maize kernels will provide guidance for the development of iron-rich crops, a major breeding goal to address iron deficiency. The maize Yellow Stripe 1 (ZmYS1) gene encodes a specific transporter that takes up Fe(III)-phytosiderophore complexes into roots. Here, we re-sequenced ZmYS1 gene in 88 elite maize inbred lines and detected the association between the nucleotide polymorphisms and micronutrient concentrations in maize kernels. Our analyses detected a total of 71 sequence variants in ZmYS1, including 61 single nucleotide polymorphisms (SNPs) and 10 insertions and deletions (indels), from the tested population. Fourteen haplotypes, which encode 13 different ZmYS1 proteins, are classified based on the polymorphism in the coding region. Numerous polymorphic sites in maize ZmYS1 locus were found in linkage disequilibrium (LD) that decay with increasing physical distance, and at least 14 recombination events have contributed to the LD and haplotype diversity of this gene. Additionally, our data show that a non-synonymous site in the ZmYS1 gene is associated with the maize kernel Fe concentration, and two other non-synonymous sites with Zinc (Zn) concentration. These findings suggest that the polymorphism in maize ZmYS1 locus may be used for biofortifying kernel mineral concentrations in maize breeding programs.
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Acknowledgments
This work was supported by grants from the National Program on the Development of Basic Research (2011CB100100), the Priority Academic Program Development of Jiangsu Higher Education Institutions, the National Natural Science Foundations (31391632, 31200943, and 31171187), the Natural Science Foundations of Jiangsu Province (BK2012261), the Natural Science Foundation of the Jiangsu Higher Education Institutions (14KJA210005), and the Innovative Research Team of Universities in Jiangsu Province.
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Supplementary Table 1
The maize inbred lines used in this study. (DOCX 22 kb)
Supplementary Table 2
The nucleotide polymorphisms and their positions in the maize ZmYS1 gene. (XLSX 58 kb)
Supplementary Table 3
Parameters of the nucleotide polymorphisms in 7 exons and 6 introns of the maize ZmYS1 gene. (DOCX 21 kb)
Supplementary Table 4
Distribution of haplotypes of the ZmYS1 gene in 88 inbred lines using both the full-length sequence and coding regions (DOCX 14 kb)
Supplementary Fig. 1
Sequence alignment of maize ZmYS1 proteins encoded by different CDS haplotypes. The haplotypes defined by the coding sequences of the gene ZmYS1 were used as the sequence names. Polymorphisms from inferred amino acids were indicated by boxes. (DOCX 3120 kb)
Supplementary Fig. 2
LD patterns across the whole locus of ZmYS1. (A) LD between pairs of ZmYS1 sequence polymorphic sites. (B) Decay of LD between pairs of ZmYS1 sequence informative polymorphisms. The regression coefficient b is 0.00545. (DOCX 443 kb)
Supplementary Fig. 3
Population structure of 88 maize inbred lines estimated using 3,072 SNPs. (A) Population structure of 88 maize inbred lines when k = 3. (B) Rate of change in the log probability of data between successive k values (Δk). (DOCX 48 kb)
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Yang, Z., Ma, S., Hu, Y. et al. Association Analysis of the Maize Gene ZmYS1 with Kernel Mineral Concentrations. Plant Mol Biol Rep 33, 1327–1335 (2015). https://doi.org/10.1007/s11105-014-0836-8
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DOI: https://doi.org/10.1007/s11105-014-0836-8