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Association mapping of maturity and plant height using SNP markers with the sorghum mini core collection

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An Erratum to this article was published on 04 May 2014

Abstract

Plant height and maturity are two critical traits in sorghum breeding. To develop molecular tools and to identify genes underlying the traits for molecular breeding, we developed 14,739 SNP markers used to genotype the complete sorghum [Sorghum bicolor (L.) Moench] mini core collection. The collection was evaluated in four rainy and three post-rainy season environments for plant height and maturity. Association analysis identified six marker loci linked to height and ten to maturity in at least two environments with at least two SNPs in each locus. Of these, 14 were in close proximity to previously mapped height/maturity QTL in sorghum. Candidate genes for maturity or plant height close to the marker loci include a sugar transporter (SbSUC9), an auxin response factor (SbARF3), an FLC and FT regulator (SbMED12), and a photoperiod response gene (SbPPR1) for maturity and peroxidase 53, and an auxin transporter (SbLAX4) for plant height. Linkage disequilibrium analysis showed that SbPPR1 and SbARF3 were in regions with reduced sequence variation among early-maturing accessions, suggestive of past purifying selection. We also found a linkage disequilibrium block that existed only among the accessions with short plant height in rainy season environments. The block contains a gene homologous to the Arabidopsis flowering time gene, LUMINIDEPENDENS (LD). Functional LD promotes early maturity while mutation delays maturity, affecting plant height. Previous studies also found reduced sequence variations within this gene. These newly-mapped SNP markers will facilitate further efforts to identify plant height or maturity genes in sorghum.

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Acknowledgments

We thank Patricia E. Klein, Robert R. Klein, and A. Millie Burrell for reviewing and the two reviewers for their suggestions to improve the manuscript. The study was supported in part by the International Crops Research Institute for the Semi-Arid Tropics and the University of Louisiana at Lafayette.

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The authors declare that they have no conflict of interest.

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Experiments conducted for this study comply with the current laws of India and the United States.

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  1. Gene Bank, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, 502 324, Andhra Pradesh, India

    Hari D. Upadhyaya, C. L. L. Gowda & Shivali Sharma

  2. Department of Biology, University of Louisiana at Lafayette, Lafayette, LA, 70504, USA

    Yi-Hong Wang

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  1. Hari D. Upadhyaya
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  2. Yi-Hong Wang
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  3. C. L. L. Gowda
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Correspondence to Yi-Hong Wang.

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Communicated by A. E. Melchinger.

H. D. Upadhyaya and Y.-H. Wang have contributed equally to this work.

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Upadhyaya, H.D., Wang, YH., Gowda, C.L.L. et al. Association mapping of maturity and plant height using SNP markers with the sorghum mini core collection. Theor Appl Genet 126, 2003–2015 (2013). https://doi.org/10.1007/s00122-013-2113-x

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