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

Upadhyaya, H D and Wang, Y H and Gowda, C L L and Sharma, S (2013) Association mapping of maturity and plant height using SNP markers with the sorghum mini core collection. TAG Theoretical and Applied Genetics, 126 (8). pp. 2003-2015. ISSN 1432-2242

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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

Item Type: Article
Divisions: RP-Grain Legumes
CRP: CGIAR Research Program on Dryland Cereals
Uncontrolled Keywords: SNP markers, Sorghum, Mini core collection, Plant materials
Subjects: Mandate crops > Sorghum
Others > Genetics and Genomics
Depositing User: Mr Siva Shankar
Date Deposited: 13 May 2013 06:23
Last Modified: 19 Oct 2016 04:56
Official URL:
Acknowledgement: 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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