Genome Wide Association Study in Maize

The rapid development in genome-wide genotyping techniques promises to improve the power of association mapping and significantly refine our understanding of the genetic architecture of complex quantitative traits. We have built up a maize association mapping panel containing more than 500 diverse maize inbred lines which has been genotyped by using Maize 50K SNP chip and deep RNA sequencing technology. Totally, 1.06 million high quality maize SNPs were obtained covering about 60% of the annotated genes in B73 genome (1, 2). Large scale eQTL (1) and QTL mapping including fatty acids (2), flowering time (3) and metabolic traits (4) and so on were performed. Many functional genes and loci were identified and validated that potentially can be used for molecular breeding. A new model called A-D test (5) was also developed that is more powerful and working better especially for rare alleles. In the presentation, we will report the detail and discuss the challenges and opportunities for whole genome wide association studies in plants.

 Reference:

1. Fu et al. RNA sequencing reveals the complex regulatory network in the maize kernel. Nat Commun, 4:2832

2. Li et al. Genome-wide association study dissects the genetic architecture of oil biosynthesis in maize kernels. Nature Genetics, 2013, 45: 43-50

3. Yang et al. CACTA-like transposable element inZmCCTattenuated photoperiod sensitivity and accelerated the postdomestication spread of maize. Proc Natl Acad Sci U S A, 2013, 110: 16969-16974 

4. Wen et al. Metabolome-based genome-wide association study of maize kernel leads to novel biochemical insights. Nat Commun, 2014, 5: 3438.

5. Yang et al. Genome Wide Association Studies using a new nonparametric model reveal the genetic architecture of 17 agronomic traits in an enlarged maize association panel. Plos Genet, 2014, 10(9): e1004573.