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

Title 
Association mapping of maturity and plant height using SNP markers with the sorghum mini core collection 
Publication Type 
Journal Article 
Authors 
Upadhyaya HD, Wang Y-H, Gowda CLL, Sharma S 
Year of Publication 
2013 
Volume 
126 
Journal 
Theoretical and Applied Genetics 
Issue 
Pagination 
2003 - 2015 
Date Published 
8/2013 
ISSN 
1432-2242 
Keywords 
Association analysi, Linkage disequilibrium analysis, LUMINIDEPENDENS, maturity, Plant heigh, SbARF3, SbLAX4, SbMED12, SbPPR1, SbSUC9, Sorghum, sorghum breeding 
URL 
http://link.springer.com/article/10.1007/s00122-013-2113-x 
DOI 
10.1007/s00122-013-2113-x 
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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