Genome-wide and gene-based association mapping for rice eating and cooking characteristics and protein content.
Xiaoqian WangYunlong PangJian ZhangZhichao WuKai ChenJauhar AliGuoyou YeJianlong XuZhikang LiPublished in: Scientific reports (2017)
Rice eating and cooking quality and protein content (PC) are important properties affecting consumers' preferences, nutrition and health. Linkage QTL mapping and association studies are usually applied to genetically dissect related traits, which could be further facilitated by high density SNP markers and gene annotation based on reference genome to rapid identify candidate genes associated with interested traits. Here, we carried out an association study for apparent amylose content (AC), gel consistency (GC), gelatinization temperature (GT) and PC evaluated in two environments using a diverse panel of 258 accessions from 3 K Rice Genome Project. Wide phenotypic variations were observed in this panel. Genome-wide association study using 22,488 high quality SNPs identified 19 QTL affecting the four traits. Combining gene-based association study and haplotype analyses plus functional annotation allowed us to shortlist nine candidate genes for four important QTL regions affecting AC, GC and GT, including two cloned genes (Wx and ALK), and seven novels. The research suggested that GWAS and gene-based association analysis followed by haplotype analysis is an effective way to detect candidate genes. The identified genes and QTL provided valuable sources for future functional characterization and genetic improvement of rice eating and cooking quality and PC.
Keyphrases
- genome wide
- high density
- dna methylation
- copy number
- healthcare
- gene expression
- public health
- quality improvement
- high resolution
- drinking water
- risk assessment
- genome wide identification
- genome wide association
- protein protein
- human immunodeficiency virus
- hepatitis c virus
- rna seq
- quantum dots
- binding protein
- current status
- hiv infected
- social media
- small molecule
- magnetic resonance imaging
- contrast enhanced
- gas chromatography