BackgroundExploring genetic differentiation and genomic variation is important for both the utilization of heterosis and the dissection of the genetic bases of complex traits.MethodsWe integrated 1857 diverse maize accessions from America, Africa, Europe and Asia to investigatetheir genetic differentiation, genomic variation using 43,252 high-quality single-nucleotide polymorphisms(SNPs),combing GWAS and linkage analysis strategy to exploring the function of relevant genetic segments.ResultsWe uncovered many more subpopulations that recently or historically formed during the breeding process. These patterns are represented by the following lines: Mo17, GB, E28, Ye8112, HZS, Shen137, PHG39, B73, 207, A634, Oh43, Reid Yellow Dent, and the Tropical/subtropical (TS) germplasm. A total of 85 highly differentiated regions with a DEST of more than 0.2 were identified between the TS and temperate subpopulations. These regions comprised 79 % of the genetic variation, and most were significantly associated with adaptive traits. For example, the region containing the SNP tag PZE.108075114 was highly differentiated, and this region was significantly associated with flowering time (FT)-related traits, as supported by a genome-wide association study (GWAS) within the interval of FT-related quantitative trait loci (QTL). This region was also closely linked to zcn8 and vgt1, which were shown to be involved in maize adaptation. Most importantly, 197 highly differentiated regions between different subpopulation pairs were located within an FT- or plant architecture-related QTL.ConclusionsHere we reported that 700–1000 SNPs were necessary needed to robustly estimate the genetic differentiation of a naturally diverse panel. In addition, 13 subpopulations were observed in maize germplasm, 85 genetic regions with higher differentiation between TS and temperate maize germplasm, 197 highly differentiated regions between different subpopulation pairs, which contained some FT- related QTNs/QTLs/genes supported by GWAS and linkage analysis, and these regions were expected to play important roles in maize adaptation.Electronic supplementary materialThe online version of this article (doi:10.1186/s12870-015-0646-7) contains supplementary material, which is available to authorized users.

ABSTRACT. Maize (Zea mays L.) is one of the most important cereal crops worldwide, and increasing the grain yield and biomass has been among the most important goals of maize production. The plant architecture can determine the grain yield and biomass to some extent; however, the genetic basis of the link between the plant architecture and grain yield/biomass is unclear. In this study, an immortal F 9 recombinant inbred line population, derived from the cross Mo17 x Huangzao4, was used to detect quantitative trait loci (QTLs) for 3 traits associated with plant architecture under two nitrogen regimes: plant height, ear height, and leaf number. As a result, 8 and 10 QTLs were identified under the high nitrogen regime and low nitrogen regime, respectively. These QTLs mapped to chromosomes 1 (six QTLs), 2 (one QTL), 3 (one QTL), 7 (two QTLs), and 9 (eight QTLs), and had different genetic distances to their closest markers, ranging from 0 to 22.0 cM, explaining 4.7 to 20.5% of the phenotypic variance. Because of an additive effect, 9 and 9 could make the phenotypic values of traits increase and decrease to some extent, respectively. These results are beneficial for understanding the genetic basis of agronomic traits associated with plant architecture and for performing marker-assisted selection in maize breeding programs.

ABSTRACT. The ear leaf is one of the most important leaves in maize (Zea mays); it affects plant morphology and yield. To better understand its genetic basis, we examined ear leaf length, ear leaf width, and ear leaf area for quantitative trait locus (QTL) mapping in a recombinant inbred line population under two nitrogen regimes. Nine QTLs, on chromosomes 1 (one), 2 (one), 3 (one), 4 (three), 7 (one), and 8 (two), were mapped under the high nitrogen regime, which explained phenotypic variation ranging from 5.4 to 14.8%. Under the low nitrogen regime, 7 QTLs were located on chromosomes 1 (one), 4 (two), 7 (one), and 8 (three), which accounted for phenotypic variation ranging from 5.5 to 20.5%. These QTLs had different mapping intervals to their nearest markers, ranging from 0.3 to 21.0 cM. Due to additive effects, 3 and 13 QTLs can cause phenotypic values of these traits to increase or decrease to some extent, respectively. This information will help understand the genetic basis of ear leaf formation and will be useful for developing marker-assisted selection in maize-breeding projects.

ABSTRACT. Days to silking (DTS) is one of the most important traits in maize (Zea mays).To investigate its genetic basis, a recombinant inbred line population was subjected to high and low nitrogen (N) regimes to detect quantitative trait loci (QTLs) associated with DTS. Three QTLs were identified under the high N regime; these explained 25.4% of the phenotypic variance. Due to additive effects, the QTL on chromosome 6 increased DTS up to 0.66 days; while the other two QTLs mapped on chromosome 9 (one linked with Phi061 and the other linked with Nc134) decreased DTS 0.89 and 0.91 days, respectively. Under low N regime, two QTLs were mapped on chromosomes 6 and 9, which accounted for 25.9% of the phenotypic variance. Owing to additive effects, the QTL on chromosome 6 increased DTS 0.67 days, while the other QTL on chromosome 9 decreased it 1.48 days. The QTL on chromosome 6, flanked by microsatellite markers Bnlg1600 and Phi077, was detected QTL identification for days to silking in maize under both N regimes. In conclusion, we identified four QTLs, one on chromosome 6 and three on chromosome 9. These results contribute to our understanding of the genetic basis of DTS and will be useful for developing marker-assisted selection in maize breeding programs.

ABSTRACT. Kernel number per ear (KNE) is one of the most important yield-related agronomic traits in maize (Zea mays). To clarify its genetic basis, we made a quantitative trait locus (QTL) analysis of KNE in a recombinant inbred line population derived from lines Mo17 and Huangzao4, under two nitrogen (N) regimes. Seven QTLs, on chromosomes 4, 6 and 9, were mapped under the high N regime, which explained phenotypic variation ranging from 5.03 to 15.49%. Under the low N regime, three QTLs were located on chromosomes 6 and 9, which accounted for phenotypic variation ranging from 8.54 to 12.21%. These QTLs had different mapping intervals to their nearest markers, ranging from 0 to 16.5 cM. According to the chromosome positions and genetic effects of these QTLs, only seven QTLs for KNE were identified in our experiment, out of which three were found under both N regimes, on chromosomes 6 (one) and 9 (two); the other four were mapped only under the high N regime, on chromosomes 4 (three) and 6 (one). This information could be useful for developing marker-assisted selection in maize-breeding projects.

ABSTRACT. Ear weight is one of the most important agronomic traits considered necessary in maize (Zea mays L.) breeding projects. To determine its genetic basis, a population consisting of 239 recombinant inbred lines, derived from the cross Mo17 x Huangzao4, was used to detect quantitative trait loci (QTLs) for ear weight under two nitrogen regimes. Under a high nitrogen fertilization regime, one QTL was identified in chromosome bin 2.08-2.09, which explained 7.46% of phenotypic variance and an increase in ear weight of about 5.79 g, owing to an additive effect. Under a low nitrogen regime, another QTL was identified in chromosome bin 1.10-1.11; it accounted for 7.11% of phenotypic variance and a decrease of 5.24 g in ear weight, due to an additive effect. Based on comparisons with previous studies, these two QTLs are new loci associated with ear weight in maize. These findings contribute to our knowledge about the genetic basis of ear weight in maize.

Grain rate (GR) is a very important trait in maize (Zea mays L.) breeding program related to yield. To realize its genetic basis, a recombinant inbred line (RIL) population and different nitrogen (N) regimes were used to map the quantitative trait loci (QTLs) for GR in maize. As a result, two QTLs were identified under high N regime and could explain a total of 14.84% of phenotypic variance. Due to additive effect, the QTL on chromosome 6 could decrease 0.029 of GR, while the QTL on chromosome 9 could increase 0.0203 of GR. Under low N regime, one QTL was mapped on chromosome 6 and could account for 9.52% of phenotypic variance, and owning to additive effect, the QTL could make GR decrease by 0.0234. The result in comparison with previous studies showed that the three QTLs in this present study were new quantitative loci associated with GR in maize. These results were beneficial for understanding the genetic basis of GR in maize.

Nitrogen (N) deficiency will severely affect many metabolic pathways and physiological progresses during maize (Zea mays L.) growth and change of anthesis-silking interval (ASI) is one of the most serious consequences. To realize the genetic basis of ASI, a recombinant inbred line (RIL) population consisting of 239 RILs, derived from the cross between Mo17 and Huangzao4, was used to identify the quantitative trait loci (QTLs) controlling ASI under different N environments. As a result, 6 QTLs were detected under high N environment on chromosome 3, 6, 7 and 8 and could explain total 53.67% of phenotypic variance. While, under low N environment, only 3 QTLs were identified on chromosome 6, 7 and 8, and they could account for total 31.87% of phenotypic variance. The two QTLs Qasihn6-1 and Qasihn3-1, identified under high N environment, were quite near to their linked marker Phi077 and Bnlg197, respectively, with less than 1 cM of genetic distance. These results are beneficial for understanding the genetic basis of ASI in maize.Key words: Maize (Zea mays L.), recombinant inbred line (RIL), quantitative trait locus (QTL), anthesis-silking interval (ASI), nitrogen environment.