Abstract：Abstract Molecular genetics and breeding of maize have been promoted and developed more efficiently, during the further study of maize genomics. The rapid development of the second generation sequencing technology possesses the characteristics of high throughput and low cost. Nowadays, more and more researchers began to conduct the population size of re-sequencing work, which promoted the analysis of maize genotype and the mining information of genetic variation. In this study, we constructed a recombination inbred line (RIL) mapping population crossed from two elite inbred lines of maize, X178 and NX531, consisting of 150 individuals. The library building and high-throughput sequencing of RIL population were conducted by genotype by sequencing method (GBS). Besides, the depth re-sequencing was applied for the two parents of the recombinant inbred lines, and the high throughput SNP markers of the populations were obtained. Using a sliding window method, the genotyping of the RIL population was carried out, and then the genetic linkage map was constructed based on bin markers. In order to verify the reliability of this map, the R/qtl packages and composite interval mapping (CIM) model was used for the mapping of QTLs responsible for nutritional quality traits of maize kernel. 5.0 × sequencing of the parents X178 and NX531 was performed, 881 259 high quality SNPs was obtained and there were polymorphisms between the parents. Based on the SNP between parents, a total of 1 842 109 SNP not only showed genotype homozygosity but also had the same genotype of one parental in the 150 lines of the RIL population. The minimum number of the SNP in one inbred line was 1 673, while the maximum number of the SNPs in one inbred lines was 20 403 and the mean SNP number in every inbred lines was 12, 281. After the screening, 124 RIL strain were chosen for further genotyping and the bin map containing 7 278 recombination bin were obtained. The maximum physical distance between two adjacent bins was 3.28 Mb, and the minimum physical distance was 80 kb, with the average of 277 kb. Among the bin makers, the physical length of 110 bin was more than 1 Mb, three more than 2 Mb. According to the genotyping of 7 278 restructuring bin markers and the information of each strain, a high density genetic linkage map was constructed by using R/qtl software. The total length of the genetic map was 2 569 cM, and the average genetic distance between adjacent bin markers was 0.35 cM. Besides, genetic distance of 35 restructuring bin markers was larger than 10 cM. Totally, 20 QTLs were identified for oil, lysine, protein and starch in the 2 years, locating on 8 chromosomes with exception of the chromosome 2 and 9. Each of these QTLs could explain 0.17% to 20.53% phenotypic variation, and 9 QTLs were more than 10% among them. Most of the QTLs were detected in single environment, indicating the significant interactions between QTL and environments. Therefore, this work could lay the foundation for the QTLs mapping and genes cloning of main agronomic.
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