| As a food, feed and industrial crop, maize is one of the most widely planted crops in the world, and also plays a prominent role in world food security. Some of the major agronomic traits directly or indirectly influenced maize production, so it is realistic meaningful to detect maize agronomic traits for maize high yield and sustainable production. We collected 700 elite inbred lines mainly from China and the US and all the lines were re-sequenced by the next generation sequencing technology. High density SNP makers were detected across the whole genome, the maize genome nucleotide diversity (π) and population differentiation (Fst) between subgroups were calculated. And also, genome wide association studies for 12 agronomic traits were performed. Additionally, we sequenced the transcriptome of the leaves above the primary ear in Zheng58 and Chang7-2 to identify expression difference genes under different genotypes and nitrogen conditions. The major results are as follows:1. About 66 million raw SNPs were got by re-sequenceing the association population based on the next generation sequencing technology. After filtered the SNPs with missing ratio more than 0.8, heterozygous ratio more than 0.1 and the heterozygous sites in the 6 deep sequenced lines (Zheng58,5003,8112,178,Chang7-2 and Mo 17), a total of ～20 million high quality SNPs were obtained. Whole genome π was calculated as 0.0062. Based on the source of the inbreds, we divided the population as three subgroups, Chinese lines、US-public lines and Ex-PVP lines, the Fst was 0.024 (Chinese lines-US-Publick),0.018(Chinese lines-Ex-PVP)'0.013 (US-Publick-Ex-PVP) between each of the two subgroups.2.12 agronomic traits were collected across two years and two locations, including 2 qualitative traits (cob color and silk color) and 10 quantitative traits. We then compared the phenotype data between Chinese lines the US lines. Interestingly,9 of the 10 quantitative traits showed a significant difference.3. After genotype missing sites imputation and minor allele frequency (MAF) selection,-9 million SNPs with MAF≥0.05 were used for the subsequent genome wide association studies. After the estimation of population kinship and population structure, we performed a genome wide association studies for the 12 agronomic traits by a compressed mix linear model. For the two qualitative traits, we successfully find the functional genes pl and rl for cob color and silk color. For the 10 quantitative traits,28 independent loci were obtained, and two of the 28 loci contain the ZCN8 and ZmMADS-box genes for flowering time. Based an additive model, the significant locis could explain ～16.2% of the phenotype variance on average.4. A total of 96 genes shown with significant genotype-environment interaction between genotypes and nitrogen conditions were identified. The functional analysis showed that the 96 genotype-environment interaction genes were most significantly enriched in "transcription factor activity", and of the identified transcription factors, the class of AP2/EREBP and WRKY families showed the most significant enrichment, suggesting that transcription factors may play important roles in nitrogen response under different genotypes and nitrogen conditions. |
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