Plant Comparative Genomics

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.