Genome‐Wide Association Study for Nine Plant Architecture Traits in Sorghum

• Published in: The plant genome Vol. 9; no. 2; pp. 1 - 14
• Main Authors: Zhao, Jing, Mantilla Perez, Maria B., Hu, Jieyun, Salas Fernandez, Maria G.
• Format: Journal Article
• Language: English
• Published: United States Crop Science Society of America 01.07.2016; John Wiley & Sons, Inc; Wiley
• Subjects: Agricultural production; Barley; Biomass; Chromosome 7; Corn; Gene polymorphism; Genes; Genetic engineering; Genome, Plant - genetics; Genome-Wide Association Study; Genomes; Genomics; Genotype & phenotype; Genotyping; Germplasm; Gibberellins; Leaf angle; Leaves; Phenotype; Phenotypes; Phenotypic variations; Polymorphism, Single Nucleotide; Power; Quantitative trait loci; Quantitative Trait Loci - genetics; Rice; Seeds; Seeds - genetics; Single-nucleotide polymorphism; Sorghum; Sorghum - anatomy & histology; Sorghum - genetics
• ISSN: 1940-3372; 1940-3372
• DOI: 10.3835/plantgenome2015.06.0044

Core Ideas The 101 SNPs were associated with at least one of nine plant architecture traits KS3 gene was associated with variation in seed number GA2ox5 gene included in a significant region on chromosome 9 controlling plant height Novel genomic regions were associated with stem circumference and internode number Novel genomic regions were associated with tiller number, panicle exsertion, and length Sorghum [Sorghum bicolor (L) Moench], an important grain and forage crop, is receiving significant attention as a lignocellulosic feedstock because of its water‐use efficiency and high biomass yield potential. Because of the advancement of genotyping and sequencing technologies, genome‐wide association study (GWAS) has become a routinely used method to investigate the genetic mechanisms underlying natural phenotypic variation. In this study, we performed a GWAS for nine grain and biomass‐related plant architecture traits to determine their overall genetic architecture and the specific association of allelic variants in gibberellin (GA) biosynthesis and signaling genes with these phenotypes. A total of 101 single‐nucleotide polymorphism (SNP) representative regions were associated with at least one of the nine traits, and two of the significant markers correspond to GA candidate genes, GA2ox5 (Sb09 g028360) and KS3 (Sb06 g028210), affecting plant height and seed number, respectively. The resolution of a previously reported quantitative trait loci (QTL) for leaf angle on chromosome 7 was increased to a 1.67 Mb region containing seven candidate genes with good prospects for further investigation. This study provides new knowledge of the association of GA genes with plant architecture traits and the genomic regions controlling variation in leaf angle, stem circumference, internode number, tiller number, seed number, panicle exsertion, and panicle length. The GA gene affecting seed number variation (KS3, Sb06 g028210) and the genomic region on chromosome 7 associated with variation in leaf angle are also important outcomes of this study and represent the foundation of future validation studies needed to apply this knowledge in breeding programs.