Past Research

Our current work in Drosophila involves characterizing the genotype-to-phenotype map, such as how the genotype builds the phenotype and how variation in the former creates the diversity in the latter. This work is interdisciplinary and involves molecular biologists, population geneticists, computational biologists, and statisticians, generating and analyzing large amounts of genome and transcriptome data to develop an intellectual framework to help elucidate the path from genotype to phenotype.

• Using Illumina technology we have obtained whole genome sequences for a wide range of Drosophila accessions of D. melanogaster and D. simulans. We have also generated transcriptome sequences from a large number of crosses between a set of inbred lines under different conditions, and collected data for different phenotypic traits.
• Using confocal microscopy and the Hybridization Chain Reaction (HCR), we tagged multiple mRNA transcripts for several eye development genes. We then used this spatial and expression data to compare the variation of these genes within and between species and sexes in the developmentally-synchronized larva of inbred lines of D. melanogaster and D. simulans. We are currently applying similar methods on fly brains to study the 3-dimensional and expression relationships of various genes involved in sex-specific neuron patterning within and between species.

Read a few of our recently published works:

• Kurmangaliyev YZ, Favorov AV, Osman NM, Lehmann KV, Campo D, Salomon MP, Tower J, Gelfand MS, Nuzhdin SV. Natural variation of gene models in Drosophila melanogaster. BMC Genomics. 2015. [PDF] [NCBI BioProject]
• Kao JY, Lymer S, Hwang SH, Sung A, Nuzhdin SV. Postmating reproductive barriers contribute to the incipient sexual isolation of the United States and Caribbean Drosophila melanogaster. Ecology and Evolution. 2015. [PDF] [NCBI BioProject]
• Kao JY, Zubair A, Salomon MP, Nuzhdin SV, Campo D. Population genomic analysis uncovers African and European admixture in Drosophila melanogaster populations from the south-eastern United States and Caribbean Islands. Molecular Ecology. 2015. [PDF] [NCBI BioProject]
• Campo D, Lehmann K, Fjeldsted C, Souaiaia, Kao J, Nuzhdin SV. Whole-genome sequencing of two North American Drosophila melanogaster populations reveals genetic differentiation and positive selection. Molecular Ecology. 2013. [PDF] [NCBI BioProject]

Chickpea is the world’s second most important pulse legume, with particular importance in the semi-arid tropics of sub-Saharan Africa and South Asia. Like the majority of cultivated legumes, chickpea has exceedingly narrow genetic and phenotypic diversity. This has consequences for breeding of climate-resilient crop varieties, because much of the historical phenotypic plasticity necessary to tolerate environmental extremes may have been lost through domestication. Thus breeding only within cultivated material will have steeply diminishing returns, and there is an urgent need for new sources of diversity.

Breeding for climate resilience as well as other high value traits will be greatly accelerated if we can expand the range of adaptations accessible to breeders. Towards this end, we are characterizing wild Cicer species from a representative range of environments; introducing wild diversity into phenology-normalized backgrounds so that it is amenable for trait assessment and breeding; characterizing the material by systematic phenotyping; developing a digital information network that explicitly identifies and quantifies the contributions of agronomically useful alleles; and developing improved chickpea varieties using an international consortium of chickpea breeders.

As important as single genotypes of model systems and forward genetics have been (and continue to be) for gene discovery, they are typically insufficient to inform us about the nature of standing genetic variation from which natural and human selection reshape organismal function. Bridging ecology and molecular biology by means of genomics and quantitative biology will permit identification and subsequent analysis of these evolutionarily active genes. We anticipate that the outcomes will include genes whose functions have not been identified in forward genetic screens. We anticipate describing the molecular genetic basis of long-standing, but poorly understood observations and questions.

Read a few of our recently published works characterizing our collection from Turkey, Russia, and Pakistan:

• von Wettberg EJB, Chang PL, Basdemir F, Carrasquilla-Garcia N, Balcha L, Moenga S, Sefara G, Greenlon A, Moriuchi K, Singh V, Cordeiro M, Noujdina N, Dinegde K, Sani S, Getahun T, Vance L, Bergmann E, Lindsay D, Mamo BE, Warschefsky E, Dacosta-Calheiros E, Marques E, Yilmaz M, Cakmak A, Rose J, Migneault A, Krieg C, Saylak S, Temel H, Friesen M, Siler E, Akhmetov Z, Ozelik H, Khalova J, Jan C, Gaur P, Yildirin M, Sharma H, Vadez V, Tesfaye K, Woldemedhin A, Bunyamin T, Aydogan A,  Bukun B, Penmetsa RV, Berger J, Kahraman A, Nuzhdin S, Cook DR. Ecology and genomics of an important crop wild relative as a prelude to agricultural innovation. Nature Communications. 2018. [PDF] [NCBI BioProject]
• Plekhanova E, Vishnyakova MA, Bulyntsev S, Chang PL, Carrasquilla-Garcia N, Negash K, Wettberg EV, Noujdina N, Cook DR, Samsonova MG, Nuzhdin SV. Genomic and phenotypic analysis of Vavilov’s historic landraces reveals the impact of environment and genomic islands of agronomic traits. Scientific Reports. 2017. [PDF] [NCBI BioProject]
• Sani SGAS, Chang PL, Zubair A, Munis MFH, Carrasquilla-Garcia N, Cordeiro M, Penmetsa RV, Nuzhdin SV, Cook DR, von Wettberg EJB. Genetic diversity, population structure, and genetic correlation with climatic variation in Chickpea (Cicer arietinum) landraces from Pakistan. The Plant Genome. 2017. [PDF] [NCBI BioProject]

• Palm oil is one of the highest consumed oil in the world, reaching three billion people in 150 countries. Although palm oil is primarily used for food, it is increasingly being used for industrial applications (i.e. biofuels, machine lubricants, soap etc.). Oil palm is the most efficient oil seed crop in the world—producing ten times more oil than other leading oilseed crops. Worldwide consumption of palm oil is predicted to double by 2050 and with limited agricultural land, there is a pressing need to improve commercial oil palm varieties. African origin E. guineensis is the current variety used for commercial breeding with a very limited genetic base. Low genetic diversity has been a major obstacle towards increasing crop yield and breeding other desirable traits. In addition to increasing oil yield, oil palm diseases are another major concern in the oil palm industry. Diseases such as fatal yellowing and lethal bud rot have swept through South America causing devastating damage to oil palm plantations. With limited genetic diversity, current commercial palms in South East Asia are highly susceptible to these diseases. Because many countries’ economies are dependent on palm oil, damage to oil palm plantations can cause serious economic losses. Identifying natural genetic variation in wild populations of oil palm will enable breeders to introduce favorable genetic variants into the current commercial palms. E. oleifera, a sister species of E. guineensis, possess genetic variation associated with disease resistance, higher quality of oils and smaller palms—traits that are not characteristic of E. guineensis. Since these two sister species readily hybridize, interspecific hybridization approach is a viable method to introgress favorable E. oleifera traits into the commercial E. guineensis varieties. In collaboration with the Malaysian Oil Palm Board (MPOB), wild oil palm populations sampled from Central and South America will be sequenced to identify natural genetic variants associated with traits of interest. Our group will use evolutionary principles and population genomic tools to optimize breeding programs to implement interspecies introgression of wild alleles into cultivated oil palm varieties.