Benjamin Blackman, Professor

Closed (1) Functional Genetics of Sunflower and Monkeyflower

Applications for fall 2021 are now closed for this project.

In order to test the function of specific genes or the impact of genetic variants on phenotype, genetic manipulation is required. The aim of the project is to assist with development and implementation of methods for genetic transformation of sunflower and monkeyflower, the two main study systems in the lab. These methods will help extend the lab's capabilities and in doing so allow us to study our traits of interest (flowering time regulation, solar tracking, floral pigmentation) with a greater level of mechanistic understanding and rigor.

The undergraduate will learn sterile technique and methods for plant tissue culture in the process of implementing and troubleshooting genetic transformation methods for sunflower and monkeyflower. Specific tasks may include media preparation; transgene development; preparation of bacterial cultures; preparation, selection, and culture of plant explants; nucleic acid extraction; and genotyping of transformed or edit-carrying plants. The student is invited to participate in weekly Blackman lab group meetings as well.

Day-to-day supervisor for this project: Ryan Nasti, Post-Doc

Weekly Hours: 9-11 hrs

Closed (2) Genetics of Adaptation in Monkeyflowers

Applications for fall 2021 are now closed for this project.

A major focus of our lab is identifying how genetic and phenotypic variation that has evolved among plant populations adapts plants to their local climates and habitats. Understanding how these adaptations to climate variation across space have evolved will help us understand mechanisms by which plants can evolve to cope with a changing climate over time and thus know what subsets of natural variation are most important to conservation efforts. We are studying the genetics of local adaptation in two monkeyflower species, Mimulus guttatus and Mimulus laciniatus.

We also have ongoing projects related to the genetics of natural variation in a specific trait, photoperiodic flowering in Mimulus guttatus. Populations of this species will only flower at times of year when days are sufficiently long, but the threshold day length varies with elevation such that populations at high elevation (i.e., areas with later starting springs) require longer day lengths than populations at low elevation. We have identified several regions of the genome involved in divergence in this trait between high and low elevation populations, and following large field studies with our collaborators this and in previous summers, we will be exploring how these genomic regions help to adapt populations to their local environments through their impacts on flowering, additional phenotypes, and overall plant fitness in native seasonal habitats.

We are also pursuing projects to examine how Mimulus guttatus populations have adapted to unique soil conditions (copper mine tailings and calcium-poor serpentine soils). This coming term we will be advancing transgenic experiments to test the roles that specific genes might play in helping populations that inhabit these soils thrive there as well as testing gene expression differences among populations.

On another front, we are pursuing studies how populations of Mimulus laciniatus differ in how the environment experienced by parental plants influences offspring phenotypes and why this variation could be adaptive.

The undergraduate researchers will grow, care for, and cross monkeyflowers as part of our efforts to scoring of germination, flowering, leaf shape, and other traits of plants under controlled conditions or in the greenhouse. Some of this work will be remote, as some traits can be scored from collected images. They will collect tissue for DNA or RNA extraction and may also be involved with some combination of DNA isolation and genotyping. The student is encouraged to join weekly Blackman lab group meetings as well.

Day-to-day supervisor for this project: Allie Gaudinier, Post-Doc

Qualifications: Students with strong interests in plant-environment interaction, genetics, evolution, and ecology will find the experience most rewarding. Attention to detail and good record keeping skills are essential. The student should be comfortable and enthusiastic about working in greenhouse and growth chamber conditions for extended periods, and they will be expected to follow guidelines for safely doing so.

Weekly Hours: 6-8 hrs

Related website: http://nature.berkeley.edu/blackmanlab

Closed (3) Natural Variation in Developmental Timing and Morphology in Sunflower

Applications for fall 2021 are now closed for this project.

Flowering and reproduction are highly regulated processes in composite plants like sunflower which produce disks that are clusters of many individual flowers. Environmental cues like light and temperature interact with the circadian clock regulate what time of the season buds first start to develop, and the same integration of internal and external signals likely occurs as new whorls individual florets open daily to present pollen and receptive stigmas at reproductive maturity. We are working to understand the molecular mechanisms underlying this process by mapping genetic changes segregating among cultivated sunflower lines that alter the timing of these events. To do so and to obtain information about pollinator visitation, we are collecting time-lapse video data for a large genetic mapping cross of wild sunflowers that we are growing in this year in Davis. Students will be involved in scoring these images for traits, and while the fieldwork is still ongoing, there may be opportunities to assist with data collection and other aspects of the project in the field depending on their schedule. There is also potential opportunity for students who have savvy with machine learning / image analysis / pattern recognition software to develop methods for automated scoring of these data.

The undergraduate researchers will contribute to the scoring of floral time-lapse image data collected in the field. The students may also have the opportunity to score additional traits on sunflowers out in field conditions or be involved in DNA extractions of tissue collected for genotyping. They may also develop methods for automated image analysis of pollinator visitation. The student is encouraged to join weekly Blackman lab group meetings as well.

Day-to-day supervisor for this project: Srinidhi Holalu, Post-Doc

Qualifications: Students with strong interests in plant-environment interaction, evolution, and ecology will find the experience most rewarding. Attention to detail and good record keeping skills are essential. The student should be comfortable and enthusiastic about intermittently working in greenhouse, growth chamber, or field conditions for extended periods, and they will be expected to follow guidelines for safely doing so. Students with experience in image analysis / machine learning / computer programming and interested in applying or developing tools for pollinator visitation video scoring should note that in their applications.

Weekly Hours: 6-8 hrs

Related website: http://nature.berkeley.edu/blackmanlab

Closed (4) Genetics of Floral Pigmentation Patterns

Applications for fall 2021 are now closed for this project.

During floral development, patterns of pigment are painted on to the petals of many plants, and these pigments often serve to attract and direct bee pollinators toward pollen and nectar rewards. We have found several natural variants affecting the nectar guide pigmentation patterns of the common monkeyflower in both the visible and UV spectrums, and we are pursuing genetic studies to determine what specific molecular changes have occurred to disrupt these patterns. In doing so, we hope to learn more about the mechanisms that specify where and when petal cells develop pigmentation and the ecological processes that maintain variation in these patterns in nature.

The student will grow monkeyflower populations for trait mapping, score pigmentation phenotypes, conduct pollinations to do further genetic crosses, and harvest tissue and seed. The student may also be involved in examining patterns of candidate gene expression as well as progress and characterization of lines where candidate genes have been targeted with RNAi or CRISPR/Cas9 gene editing. Attention to detail and good record keeping are essential. Experience with plant husbandry is desirable. The student will also be invited to participate in weekly Blackman lab group meetings., Staff Researcher

Qualifications: Students with strong interests in evolution, development, and genetics will find the experience most rewarding. Attention to detail and good record keeping skills are essential. The student should be comfortable and enthusiastic about working in greenhouse and growth chamber conditions for extended periods, and they will be expected to follow guidelines for safely doing so.

Weekly Hours: 6-8 hrs