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Plant Comparative Genomics PI: Jennifer Hawkins Overview: Our research is focused on understanding the underlying molecular evolutionary processes that contribute to phenotypic diversity, particularly those processes pertaining to genome structure and affecting gene expression. By combining the power of comparative genomics with bioinformatics, we use mass data sets from large-scale sequencing projects to elucidate genetic and epigenetic differences among closely related organisms with the primary goal of relating these molecular differences to phenotype. Some specific interests in the lab include the underlying genetics that contribute to hybrid vigor, hybridization barriers, and domestication. Cis-effects on gene expression variation in maize To explore the relationship between genomic context and gene expression, we are using 454 sequencing technology to quantify the cis-effects on variation in allelic gene expression for eight of the thirteen genes in the Bz1-Sh1 region in several maize inbred line crosses. Interestingly, the most significant expression variation is concentrated around a defined recombination hotspot. An ear from the selfing of a hybrid showing both types of recombinant kernels. Parental genotypes: (sh1, bz1) – bronze colored and excessively shrunken kernels. (Sh1, Bz1) – purple colored kernels with small indention. Recombinant genotypes: sh1, BZ1 – purple colored with excessively shrunken kernel as indicated by upper recombinant arrow. Sh1, bz1 – bronze colored kernel with small indention as indicated by lower recombinant arrow. D4201 (Sh1-B73/ Bz1-B73) In W22 HAWKINS LAB PEOPLE Jennifer Hawkins Vivian Delgado Michael Carlise Chelsea Bradshaw Lindsey Coffield Diana Black Sorghum as a model for evolutionary genetic studies Sorghum, one of the world’s major grain crops, is an African genus of about 25 species of grasses distributed throughout tropical and subtropical regions. We have constructed a recombinant inbred line (RIL) population of approximately 250 plants from a single S. bicolor x S. propinquum cross for use in evolutionary genetic analyses aimed at relating Sorghum genes to their function. The plants will be used in a wide range of studies from the evolution of traits involved in domestication, weediness and invasiveness, and the genomic impact of hybridization on genome architecture and gene expression. Sorghum bicolor x S. propinquum hybrid parent shown on the left with a small population of RILs on the right. Recombination HOTSPOT D4202 (sh1-W22/ bz1-W22) In W22 D4204 (sh1/bz1) B73 D5156 (Sh1/Bz1) In W22 D4204 (sh1/bz1) B73 D4205 (Sh1/Bz1) BMS Colored lines indicate the extent of expression bias toward the parental alleles indicated on the left. Gray genes were excluded from the analysis, either because they contained no SNP between parental lines (mainly for D4204xD4205) or for other technical reasons. The greatest expression bias was detected in the recombination hotspot located between tac6058 and stc1. Green = leaf; Orange = root; Yellow = ear; and Purple = tassel. Jasmine Freeman Dhanushya Ramachandran Not pictured: Courtney Saporito The RIL population displays tremendously high levels of phenotypic variation due to parental divergence. The offspring from the same generation can vary wildly in height, total biomass, drought tolerance, seed set, day-length dependence, and fitness, making them ideal models for allelic interactions. The individual (plant!) pictured here grew to this height in just three months.