Trait Diversity 

Leaf Architecture


In nature, different species exhibit remarkable diversity of leaf morphology, which is the result of adaptation to local environment for  optimization of photosynthesis.  Leaf shape, leaf size and leaf angle are important determinants of plant architecture, which significantly affect the photosynthetic potential. Big progress has been made in leaf development of Arabidopsis with mutants, however, little is known about the genetic basis of natural variation of leaf traits. In maize, different maize inbred lines show large natural variation in leaf traits. The NAM, designed to integrate the advantages of linkage analysis and association mapping, provide high resolution and statistical power to dissect complex quantitative traits. To dissect the genetic architecture of maize leaf, we collected the phenotypes for several important leaf traits in 5000 NAM lines in 12 environments across two years. Four questions in the context of genetic architecture will be deeply investigated:


  • What’s the genetic components controlling these important leaf traits? Whole genome joint linkage analysis will be conducted to identify the QTLs for these leaf traits. After projecting parental sequence to NAM, whole genome association analysis will dissect QTL to QTN.

  • Does QTL is shared among families? Do alleles at each QTL have different functional effects distributed across founders?

  • Are these leaf traits independently genetic controlled or genetic sharing to some extent?

  • To what extent Epistasis and G by E interaction contribute to phenotypic variation of leaf traits?

This project is led by Feng Tian, collaborating with Jianming Yu at Kansas State University.

Sweet Corn


What makes sweet corn taste so good?  It is a single base pair out of the three billion base pairs in the maize genome.  The mutant was recognized a century ago and called Sugary1 (Su1).  Several years ago Martha James identified the gene (Su1), and then Sherry Whitt collaborated with Bill Tracy to find the nucleotides that make sweet corn throughout the Americas (pdf)


The map indicates were the samples came from, excluding a few samples from the High Andes. It turned out that all of these sweet corns had mutations in the same gene - Su1.  But the mutations were in different positions in the same gene.  It appears that the Native Americans reselected for sweetness at least five times.

We also found that it was interesting that all North American sweet corns had mutations in same cleft of the isoamylase enzyme.  We speculate that mutations in this region allow the enzyme to still work during germination, but it still provides a sweet taste.

Stalk Strength


Lodging may be defined as rupture of the stalk below ear level. This phenomenon reduces yield 5-20% worldwide, raises drying costs, and exacerbates problems of volunteer plants emerging the following season. To address this issue, we have further elucidated the genetic architecture of stalk strength in maize using the Nested Association Mapping Population (NAM). Previous analyses of four biparental populations of F_2:3  families by Flint-Garcia et al. (2003) revealed the utility of rind penetrometer resistance (RPR) in phenotyping stalk strength as well as the complexity of its genetic architecture.  

Surveying the allelic diversity, and utilizing the statistical power andmarker density available in the twenty-five biparental populations of NAM, we have sought to confirm and supplement earlier analyses by implementing the same RPR phenotyping method.  Current data from a single evaluation environment have mapped eleven QTLs accounting for 30% of the phenotypic variance across the twenty-five recombinant inbred populations. All QTL are shared by more than four NAM populations and eight of the eleven possess a series of positive and negative alleles with respect to the B73. Future analyses to enhance our understanding of stalk strength include replicated evaluation and genome-wide association mapping of RPR to exploit historical recombination in NAM founders.

Vitamin A


Maize is essential to the diet of millions of people in the developing world. Consequently, vitamin A deficiency is prevalent since maize provides an insufficient amount of vitamin A. Around 17-30% of children in these developing regions suffer from complications that arise from vitamin A deficiency, such as xeropthalmia, which can result in blindness. Other health-related issues stemming from vitamin A deficiency affect another 250 million people. One solution for reducing the incidence of this form of micronutrient malnutrition is to develop maize lines with higher amounts of provitamin A. Several carotenoid compounds that naturally occur in maize (e.g., β-carotene) exhibit provitamin A activity. Humans convert provitamin A to vitamin A through digestion. Our research uses statistical methodologies such as association mapping to find genes that are associated with carotenoid compounds. Once these genes are discovered, breeders can use the relatively affordable method of marker-assisted selection to increase the amount of provitamin A activity. So far, two essential genes were identified and are published in Harjes et al. (2008) and Yan et al. (2010). The ultimate goal of this research is to find enough genes to develop lines of maize that have 15 micrograms of β-carotene per gram. This amount should provide the necessary daily levels of vitamin A for those who rely on maize for sustenance.

This is an NSF Plant Genome project (grant # 0922493) led by PI Dean DellaPenna, Co-PIs Torbert Rocheford, Edward Buckler, C. Robin Buell, and Key Collaborators Michael Gore and Jianbing Yan. For further information, please visit



Harjes, C. et al. Natural genetic variation in Lycopene epsilon cyclase tapped for maize biofortification. Science 319 (5861), 330-333 (2008).

Yan, J. et al. Rare genetic variation at Zea mays crtRB1 increases β-carotene in maize grain. Nature Genetics 42, 322-327 (2010).

Flowering Time


One of the most important traits for both wild and cultivated plants is the timing of the transition from vegetative to reproductive growth (flowering time), which needs to be controlled to avoid flowering under unfavorable conditions. This transition from vegetative to reproductive stage is affected by environmental cues and signals within the plant. Flowering time reflects the adaptation of a plant to its environment by tailoring vegetative and reproductive growth phases to local climatic effects. In an outcrossing species such as corn, Zea mays L., flowering time is a complex trait and controled by a large number of loci. The time required to mature varies widely in maize landraces, from 2 to 11 months. In addition, asynchrony of male and female flowering in maize may be adaptive in some cultivars, but can result in losses under drought conditions, especially in modern uniform varieties..

Maize is adapted to a range of environments, from the lowlands to the Andean highlands, and has been widely introduced worldwide into both temperate and tropical regions. Maize's genetic architecture for flowering time has evolved as its wild relatives adapted to distinct ecological zones in elevations differing by more than 3000 meters in Mexico; and then under both natural and artificial selection over the last 7,000 years, with especially intense selection over the past century. This genetic architecture has evolved under a predominantly outcrossing mating system in a species with little population differentiation.

Flowering time has been extensively studied in the predominantly self-fertilizing species Arabidopsis. Like maize, Arabidopsis grows across a wide range of latitudes and has flowering time controlled by the interaction of the photoperiod (light sensing and circadian rhythm), vernalization, and autonomous flowering and gibberellic acid-response pathways. In grasses, which include maize, wheat, and rices, some of the same genes are involved in flowering, but they have different functions.

Our study has shown that large differences in flowering time among inbred maize lines are not causes by a few genes of large effects, but by the cumulative effects of numerous QTLs, each with only a small impact on the trait. Selection may have favored a genetic architecture of additive small-effect QTLs, so that most offspring are likely to have partially synchronous flowering time to ensure fitness. So far, only one major maize flowering time QTL has been positionally cloned, vgt1 (Salvi et al., 2007). Our group is in the process of fine mapping to identify QTLs further.

Aluminum Tolerance 

Aluminum (Al) toxicity is a major constraint to maize productivity on acidic soils throughout the world. Phototoxic Al becomes soluble at pH < 5.5, inhibiting root growth and function, thus severely reducing yields. In countries where soil amelioration is not an economically feasible option, breeding maize for tolerance would provide an inexpensive, sustainable solution to the problem.

Allison Krill, a graduate student with our group, conducted a candidate gene association studies to dissect this pathway.  For this research she collaberated with Owen Hoekenga and Leon Kochian.

Nitrogen Metabolism


Nitrogen (N) is an essential nutrient to plant growth. Grain yields of maize and other important cereals are highly responsive to supplemental nitrogen. The useof N fertilizers has been dramatically increased during the last few decades. However, such high usage increases crop input costs, negatively impacts the environment by leaching the N fertilizers into the groundwater and volatizing them into the air as a greenhouse gas, and raises the energy requirement for crop production. Therefore, understanding genes controlling N uptake from soil, assimilation into amino acids, and N transport from vegetative source to reproductive sink tissues will help develop varieties with improved nitrogen use efficiency (NUE).

Nengyi Zhang is a postdoc leading this research. We collaborate with Drs. Steve Moose and Fred Below, University of Illinois at Urbana-Champaign to dissect the whole plant physiological aspects of NUE. With Dr. Mark Stitt, Max Planck Institute of Molecular Plant Physiology, Germany, we are collaborating to identify natural variation in nitrogen metabolism pathway at the enzyme and metabolite level.

This work is funded by a NSF project, Gene Discovery for Maize Responses to Nitrogen (NitroGENES).

Contact Us

Tel: 607-255-1809           


  • YouTube Social  Icon
  • Facebook
  • Twitter


175 Biotechnology Bldg  

Ithaca, NY 14853-2703