Quantitative trait loci analysis of phenotypic traits and principal components of maize tassel inflorescence architecture

Maize tassel inflorescence architecture is relevant to efficient production of F₁ seed and yield performance of F₁ hybrids. The objectives of this study were to identify genetic relationships among seven measured tassel inflorescence architecture traits and six calculated traits in a maize backcross population derived from two lines with differing tassel architectures, and identify Quantitative Trait Loci (QTL) involved in the inheritance of those tassel inflorescence architecture traits. A Principal Component (PC) analysis was performed to examine relationships among correlated traits. Traits with high loadings for PC1 were branch number and branch number density, for PC2 were spikelet density on central spike and primary branch, and for PC3 were lengths of tassel and central spike. We detected 45 QTL for individual architecture traits and eight QTL for the three PCs. For control of inflorescence architecture, important QTL were found in bins 7.02 and 9.02. The interval phi034—ramosa1 (ral) in bin 7.02 was associated with six individual architecture trait QTL and explained the largest amount of phenotypic variation (17.3%) for PC1. Interval bnlg344–phi027 in bin 9.02 explained the largest amount of phenotypic variation (14.6%) for PC2. Inflorescence architecture QTL were detected in regions with candidate genes fasciated ear2, thick tassel dwarf1, and ral. However, the vast majority of QTL mapped to regions without known candidate genes, indicating positional cloning efforts will be necessary to identify these genes.     

An ultra-high density bin-map for rapid QTL mapping for tassel and ear architecture in a large F2 maize population

Background

Understanding genetic control of tassel and ear architecture in maize (Zea mays L. ssp. mays) is important due to their relationship with grain yield. High resolution QTL mapping is critical for understanding the underlying molecular basis of phenotypic variation. Advanced populations, such as recombinant inbred lines, have been broadly adopted for QTL mapping; however, construction of large advanced generation crop populations is time-consuming and costly. The rapidly declining cost of genotyping due to recent advances in next-generation sequencing technologies has generated new possibilities for QTL mapping using large early generation populations.

Results

A set of 708 F₂ progeny derived from inbreds Chang7-2 and 787 were generated and genotyped by whole genome low-coverage genotyping-by-sequencing method (average 0.04×). A genetic map containing 6,533 bin-markers was constructed based on the parental SNPs and a sliding-window method, spanning a total genetic distance of 1,396 cM. The high quality and accuracy of this map was validated by the identification of two well-studied genes, r1, a qualitative trait locus for color of silk (chromosome 10) and ba1 for tassel branch number (chromosome 3). Three traits of tassel and ear architecture were evaluated in this population, a total of 10 QTL were detected using a permutation-based-significance threshold, seven of which overlapped with reported QTL. Three genes (GRMZM2G316366, GRMZM2G492156 and GRMZM5G805008) encoding MADS-box domain proteins and a BTB/POZ domain protein were located in the small intervals of qTBN5 and qTBN7 (~800 Kb and 1.6 Mb in length, respectively) and may be involved in patterning of tassel architecture. The small physical intervals of most QTL indicate high-resolution mapping is obtainable with this method.

Conclusions

We constructed an ultra-high-dentisy linkage map for the large early generation population in maize. Our study provides an efficient approach for fast detection of quantitative loci responsible for complex trait variation with high accuracy, thus helping to dissect the underlying molecular basis of phenotypic variation and accelerate improvement of crop breeding in a cost-effective fashion.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-433) contains supplementary material, which is available to authorized users.     

Class II tassel seed mutations provide evidence for multiple types of inflorescence meristems in maize (Poaceae)

The tassel seed mutations ts4 and Ts6 of maize cause irregular branching in its inflorescences, tassels, and ears, in addition to feminization of the tassel due to the failure to abort pistils. A comparison of the development of mutant and wild-type tassels and ears using scanning electron microscopy reveals that at least four reproductive meristem types can be identified in maize: the inflorescence meristem, the spikelet pair meristem, the spikelet meristem, and the floret meristem. ts4 and Ts6 mutations affect the fate of specific reproductive meristems in both tassels and ears. ts4 mutants fail to form spikelet meristems from spikelet pair meristems. Ts6 mutants are delayed in the conversion of certain spikelet meristems into floret meristems. Once floret meristems are established in both of these mutants, they form florets that appear normal but fail to undergo pistil abortion in the tassel. The abnormal branching associated with each mutant is suppressed at the base of ears, permitting the formation of normal, fertile spikelets. The classification of the different types of reproductive meristems will be useful in interpretation of gene expression patterns in maize. It also provides a framework for understanding meristem functions that can be varied to diversify inflorescence architectures in the Gramineae.     

QTL mapping analysis of plant height and ear height of maize (Zea mays L.)

Genetic map containing 103 microsatellite loci obtained on 200 F2 plants derived from the cross R15 x 478 was used for quantitative trait loci (QTL) mapping in maize. QTL were characterized in a population of 200 F2:4 lines, derived from selfing the F2 plants, and were evaluated with two replications in two environments. QTL determinations were made from the mean of these two environments. Plant height (PH) and ear height (EH) were measured. Using composite interval mapping (CIM) method, a total of 14 distinct QTLs were identified: nine for PH and five for EH. Additive, partial dominance, dominance, and overdominance actions existed among all detected QTL affecting plant height and ear height. The QTL explained 78.27% of the phenotypic variance of PH and 41.50% of EH. The 14 QTLs displayed mostly dominance or partial dominance gene action and mapped to chromosomes 2, 3, 4, 8 and 9.     

Genetic analysis and major QTL detection for maize kernel size and weight in multi-environments

Key Message

Twelve major QTL in five optimal clusters and several epistatic QTL are identified for maize kernel size and weight, some with pleiotropic will be promising for fine-mapping and yield improvement.

Abstract

Kernel size and weight are important target traits in maize (Zea mays L.) breeding programs. Here, we report a set of quantitative trait loci (QTL) scattered through the genome and significantly controlled the performance of four kernel traits including length, width, thickness and weight. From the cross V671 (large kernel) × Mc (small kernel), 270 derived F_2:3 families were used to identify QTL of maize kernel-size traits and kernel weight in five environments, using composite interval mapping (CIM) for single-environment analysis along with mixed linear model-based CIM for joint analysis. These two mapping strategies identified 55 and 28 QTL, respectively. Among them, 6 of 23 coincident were detected as interacting with environment. Single-environment analysis showed that 8 genetic regions on chromosomes 1, 2, 4, 5 and 9 clustered more than 60 % of the identified QTL. Twelve stable major QTLs accounting for over 10 % of phenotypic variation were included in five optimal clusters on the genetic region of bins 1.02–1.03, 1.04–1.06, 2.05–2.07, 4.07–4.08 and 9.03–9.04; the addition and partial dominance effects of significant QTL play an important role in controlling the development of maize kernel. These putative QTL may have great promising for further fine-mapping with more markers, and genetic improvement of maize kernel size and weight through marker-assisted breeding.     

A new QTL for resistance to Fusarium ear rot in maize

Understanding the inheritance of resistance to Fusarium ear rot is a basic prerequisite for an efficient resistance breeding in maize. In this study, 250 recombinant inbred lines (RILs) along with their resistant (BT-1) and susceptible (N6) parents were planted in Zhengzhou with three replications in 2007 and 2008. Each line was artificially inoculated using the nail-punch method. Significant genotypic variation in response to Fusarium ear rot was detected in both years. Based on a genetic map containing 207 polymorphic simple sequence repeat (SSR) markers with average genetic distances of 8.83?cM, the ear rot resistance quantitative trait loci (QTL) were analyzed by composite interval mapping with a mixed model (MCIM) across the environments. In total, four QTL were detected on chromosomes 3, 4, 5, and 6. The resistance allele at each of these four QTL was contributed by resistant parent BT-1, and accounted for 2.5-10.2% of the phenotypic variation. However, no significant epistasis interaction effect was detected after a two-dimensional genome scan. Among the four QTL, one QTL with the largest effect on chromosome 4 (bin 4.06) can be suggested to be a new locus for resistance to Fusarium ear rot, which broadens the genetic base for resistance to the disease and can be used for further genetic improvement in maize-breeding programs.     

Inheritance of inflorescence architecture in sorghum

The grass inflorescence is the primary food source for humanity, and has been repeatedly shaped by human selection during the domestication of different cereal crops. Of all major cultivated cereals, sorghum [Sorghum bicolor (L.) Moench] shows the most striking variation in inflorescence architecture traits such as branch number and branch length, but the genetic basis of this variation is little understood. To study the inheritance of inflorescence architecture in sorghum, 119 recombinant inbred lines from an elite by exotic cross were grown in three environments and measured for 15 traits, including primary, secondary, and tertiary inflorescence branching. Eight characterized genes that are known to control inflorescence architecture in maize (Zea mays L.) and other grasses were mapped in sorghum. Two of these candidate genes, Dw3 and the sorghum ortholog of ramosa2, co-localized precisely with QTL of large effect for relevant traits. These results demonstrate the feasibility of using genomic and mutant resources from maize and rice (Oryza sativa L.) to investigate the inheritance of complex traits in related cereals.Electronic Supplementary Material Supplementary material is available to authorised users in the online version of this article at .     

QTL mapping of resistance to Fusarium ear rot using a RIL population in maize

Fusarium ear rot is a prevalent disease in maize, reducing grain yields and quality. Resistance breeding is an efficient way to minimize losses caused by the disease. In this study, 187 lines from a RIL population along with the resistant (87-1) and susceptible (Zong 3) parents were planted in Zhengzhou and Beijing with three replications in years 2004 and 2006. Each line was artificially inoculated using the nail-punch method. Significant genotypic variation in response to Fusarium ear rot was detected in both years. Based on a genetic map containing 246 polymorphic SSR markers with average genetic distances of 9.1 cM, the ear-rot resistance QTL were firstly analyzed by composite interval mapping (CIM). Three QTL were detected in both Zhengzhou and Beijing in 2004; and three and four QTL, respectively, were identified in 2006. The resistant parent contributed all resistance QTL. By using composite interval mapping and a mixed model (MCIM), significant epistatic effects on Fusarium ear rot as well as interactions between mapped loci and environments were observed across environments. Two QTL on chromosome 3 (3.04 bin) were consistently identified across all environments by the two methods. The major resistant QTL with the largest effect was flanked by markers umc1025 and umc1742 on chromosome 3 (3.04 bin), explaining 13–22% of the phenotypic variation. The SSR markers closely flanking the major resistance QTL will facilitate marker-assisted selection (MAS) of resistance to Fusarium ear rot in maize breeding programs.     

Genetics of tassel branch number in maize and its implications for a selection program for small tassel size

Summary Tassel branch numbers of six crosses of maize (Zea mays L.) were analyzed to determine inheritance of this trait. Generation mean analyses were used to estimate genetic effects, and additive and nonadditive components of variance were calculated and evaluated for bias due to linkage. Both narrow-sense and broad-sense heritabilities were estimated. Additive genetic variance estimates were significant in five of the six crosses, whereas estimates of variance due to nonadditive components were significant in only three crosses. Additionally, estimates of additive variance components usually were larger than corresponding nonadditive components. There was no evidence for linkage bias in these estimates. Estimates of additive genetic effects were significant in four of six crosses, but significant dominance, additive × additive and additive × dominance effects also were detected. Additive, dominance, and epistatic gene action, therefore, all influenced the inheritance of tassel branch number, but additive gene action was most important. Both narrow-sense and broadsense heritability estimates were larger than those reported for other physiological traits of maize and corroborated conclusions concerning the importance of additive gene action inferred from analyses of genetic effects and variances. We concluded that selection for smalltasseled inbreds could be accomplished most easily through a mass-selection and/or pedigree-selection system. Production of a small-tasseled hybrid would require crossing of two small-tasseled inbreds. We proposed two genetic models to explain unexpected results obtained for two crosses. One model involved five interacting loci and the other employed two loci displaying only additive and additive × additive gene action.Journal Paper No. J-9231 of the Iowa Agriculture and Home Economics Experiment Station, Ames, Iowa 50011. Project No. 2152     

Mapping QTLs and meta-QTLs for two inflorescence architecture traits in multiple maize populations under different watering environments

Drought significantly affects the architectural development of maize inflorescence, which leads to massive losses in grain yield. However, the genetic mechanism for traits involved in inflorescence architecture in different watering environments, remains poorly understood in maize. In this study, 19 QTLs for tassel primary branch number (TBN) and ear number per plant (EN) were detected in 2 F_2:3 populations under both well-watered and water-stressed environments by single environment mapping with composite interval mapping (CIM); 11/19 QTLs were detected under water-stressed environments. Moreover, 21 QTLs were identified in the 2 F_2:3 populations by joint analysis of all environments with a mixed linear model based on composite interval mapping (MCIM), 11 QTLs were involved in QTL × environment interactions, seven epistatic interactions were identified with additive by additive/dominance effects. Remarkably, 12 stable QTLs (sQTLs) were simultaneously detected by single environment mapping with CIM and joint analysis through MCIM, which were concentrated in ten bins across the chromosomes: 1.05_1.07, 1.08_1.10, 2.01_2.04, 3.01, 4.06, 4.09, 5.06_5.07, 6.05, 7.00, and 7.04 regions. Twenty meta-QTLs (mQTLs) were detected across 19 populations under 51 watering environments using a meta-analysis, and 34 candidate genes were predicted in corresponding mQTLs regions to be involved in the regulation of inflorescence development and drought resistance. Therefore, these results provide valuable information for finding quantitative trait genes and to reveal the genetic mechanisms responsible for TBN and EN under different watering environments. Furthermore, alleles for TBN and EN provide useful targets for marker-assisted selection to generate high-yielding maize varieties.     

QTL mapping and epistasis analysis of brace root traits in maize

Root architecture is a major factor influencing root lodging, which limits greater yield stability at high planting density. Total brace root tier number (TBRTN) and effective brace root tier number (EBRTN) are the two most important root architecture traits influencing root lodging. However, the genetic mechanisms that underlie these traits remain poorly understood. In this study, quantitative trait loci (QTL) for TBRTN and EBRTN were mapped using a set of 201 recombinant inbred lines (RILs) and 278 immortalized F2 (IF2) populations derived from these RILs, which were evaluated in three environments. Ten QTL in the RILs and 15 QTL in the IF2 population were detected. In the two populations, we identified two coincident major QTL for TBRTN and a single identical major QTL for EBRTN. The QTL for TBRTN showed the largest additive effect, accounting for 16.36 and 17.88% of the phenotypic variance in the RILs and IF2 population, respectively. Additional epistatic effects were identified for all the maize chromosomes, except for chromosome 4. Most epistatic effects involved pairs of loci that were on different chromosomes. At the same time, we found loci that interacted simultaneously with several other loci to affect expression of the traits, which was particularly evident in the IF2 population. For example, qTAR1-2 interacted simultaneously with qTAR2-1, qTAR3-1, qTAR5-1, and qITAR8-2 to affect the expression of TBRTN. Therefore, a complex network controlling the traits was found in maize. These results provide useful information for understanding the molecular mechanisms controlling root architecture.     

Clonal analysis of corn plant development. I. The development of the tassel and the ear shoot

The development of the tassel and the ear shoot has been investigated in corn (Zea mays L.). X irradiation of dry kernels and seedlings heterozygous for anthocyanin markers or for factors altering tassel and ear morphology results in the formation of clones (sectors) from cells of the apical meristem. Most tassels develop from 4 +/- 1 cells of the mature embryo. The expression of ramosa-1, tunicate, tassel seed-6, and vestigial is cell autonomous in the tassel. These genes act late in development and modify the developmental fate or decision of an individual clone and not of the whole group of cells producing a tassel. The ear shoot develops from lineages of one to three cells derived each from the L-I (outmost cell layer) and L-II (second cell layer) of the apical meristem. Typically the clones start in the ear shoot (in the husks and possibly in the cob), extend upward in an internode, continue along the margin of the leaf sheath or leaf blade at the node above, and terminate in this or the next higher leaf. The separation of lineages for ear shoot and internode occurs in the period around 13 days after sowing. The analysis of clonal boundaries shows that a small number of embryonic cells become isolated in their developmental capacity. This commitment process appears to be analogous to the process of compartmentation in the imaginal disks of fruit flies. The extent of proliferation of individual cells within a group of highly flexible and any particular clone does not generate a specific part of a tassel or an ear shoot. There must be cellular communication between various clones so that the overall size and morphology of an organ remain normal and more or less fixed. Thus the process of development in plants is also highly regulative in nature and shares many features in common with development in fruit flies.