For this application, I had to submit the following: CV, one-page cover letter, three-page research statement, two-page teaching statement and one-page DEI statement. Figures and references are usually good to have in the statements but I have excluded them here out of convenience. Slides for the talks can be found here.

Cover Letter

Dear hiring manager,

I am applying to the position of Assistant Professor of Theoretical Plant Quantitative Geneticist (ID: XXXXXX) at the University of Nebraska-Lincoln. I find the position exciting as it offers a great opportunity to start a research group within a vibrant community of renowned faculty members in the Department of Agronomy and Horticulture. I appreciate the efforts by the Institute of Agriculture and Natural Resource in promoting interdisciplinary research programs surrounding the topics of genetic-by-environment interaction and breeding for climate resilience. Such research areas are important to address the current and future threats to food security due to climate change. I can contribute to the research progress through quantitative genetics and collaborations with others in different disciplines. I would like to demonstrate my leadership in delivering solutions to challenges in modern plant breeding, if given the opportunity to develop as an Assistant Professor.

I believe I would fit well in the Department of Agronomy and Horticulture because my research and teaching experience is directly relevant to the data-driven role in delivering quality research and education. I am keen to apply my skills in plant genetics, statistics, mentoring and teaching that I have developed in my academic research careers. I received my PhD in Genetics at the University of Wisconsin-Madison, and I am currently working as a postdoctoral researcher at the Scotland’s Rural College. I have experience working with various species, including maize (and teosinte), barley, wheat, red alga and purslane. I intend to utilize my liaison experience with collaborators, funders and stakeholders to deliver projects goals through an interdisciplinary effort within and across the Department. Overall, I would describe myself as a scientist who understands the technical details in biology, statistics and programming, as well as is able to translate the knowledge into mentoring and teaching.

Thank you very much for your time and consideration. I look forward to hearing back from you.

Regards, XXX

Research statement

I am a plant quantitative geneticist with a background in evolutionary genetics and a deep interest in interdisciplinary, collaborative research. I envision a research program aimed at improving pre-breeding for developing sustainable crop genetic resources that can be used to meet the needs for nutrition, climate resilience and economic development. This research program will bridge state-of-the-art approaches from the fields of quantitative genetics and various other areas of research. Some of these research areas (e.g. genomics, statistics, programming) will be developed internally, while some others will be developed through collaborations. Here, I will first present my research experience from my PhD and postdoctoral work, and then propose both short- and long-term research plans and visions.

In my PhD work at the University of Wisconsin-Madison, I studied the evolution of the genetic architecture of domestication traits in maize from its predecessor teosinte. I worked on several projects that focused on fine-mapping and characterization of domestication-associated quantitative trait loci (QTLs) and genes. These projects provided the opportunities to understand domestication at the level of individual genes in great depth, as well as the fine-scale interactions between them. Subsequently, I undertook a polygenic approach by quantifying the changes in the genetic variance for multiple traits in large populations of maize and teosinte. The results allowed me to evaluate the trade-offs and genetic constraints during maize domestication, which offered a renewed perspective on how ancient farmers were able to convert a wild, largely inedible grass into a major crop known as maize. Collectively, I view domestication as an evolutionary process that encompasses genetic changes at various scales (large versus small effects) and sources (standing versus novel variants) over a long period of time. Therefore, monogenic and polygenic models are ideal for studying domestication from contrasting angles.

In my postdoctoral work at the Scotland’s Rural College (SRUC), I shifted toward a more computational role with genetic diversity management in modern crops as the central theme. Much of my work revolved around statistical analyses of modern crop data and development of novel analytical tools for improving crop breeding. (1) I developed a new approach to genomic selection, known as Origin Specific Genomic Selection (OSGS), that provides a simple and straightforward method for introgressing novel diversity into breeding populations of any plant and animal species. I further demonstrated the utility of OSGS in a type of a Multi-Parental Population (MPP) called a Nested Association Mapping (NAM) population, which is a valuable genetic resource with untapped diversity from diverse accessions. (2) Given the limited diversity in modern crop varieties, the current Plant Variety Right (PVR) granting system of Distinctness, Uniformity and Stability (DUS) faces challenges in registering new crop varieties that are getting increasingly similar in morphologies. I undertook an investigation into the DUS system for the UK barley varieties and showed that the current system is obsolete and would benefit from using genomic markers for proper and fairer separation of varieties. (3) In line with the theme of genetic diversity, I developed the R/magicdesign package and magicdesignee Shiny app for simulating and testing population designs for Multi-parental Advanced Generation Inter Cross (MAGIC) populations, which are an MPP alternative to NAM with highly recombined genomes and novel haplotypes. (4) I also developed a selection mapping approach called Regression of ALLeles over Years (RALLY) that is geared toward identifying selection signature on genomic regions in modern crop populations by simply modeling the changes in allele frequencies as a logistic distribution. (5) Lastly, I am currently exploring the use of variance-controlling QTL (vQTL) for mapping genetical and non-genetical interactions and investigating the possible phantom epistasis observed in modern wheat hybrids.

To align with the focus of agriculture in Nebraska and wider areas, I am open to using any major crop (e.g. maize, soybean, wheat) or minor crop as a research model. In the short term, I intend to utilize my broad experience in quantitative genetics, programming and practical activities (e.g. growing plants and making crosses) to establish a research program with two parallel strands of work. The first strand will be fully computational and will involve statistical analyses of publicly available and simulated datasets. The second strand will involve population development for the purpose of downstream experimental validation and delivery of novel elite germplasm. I opt for this strategy to grow the research group by using the first strand to provide a direct and immediate pathway to producing relevant research outcomes like publications and grant applications. The second strand is intended to boost the research outcomes at a later stage and support the momentum as the research group grows. An additional benefit to this strategy is to ensure that the group members receive holistic research training in lab, desk, greenhouse and field. An example of how the short-term plan can be executed in the above mentioned strategy is described in the following three specific aims:

Aim 1: multivariate extension of Origin Specific Genomic Selection (OSGS). In its current form, OSGS has only been tested on single traits and a pair of parents at any time5. While this is an important piece of its proof of concept, further follow-up is needed to better deploy OSGS in pre-breeding practices. For example, selection for yield alone in elite-exotic crosses is insufficient as there is a need to consider adaptation traits like flowering time, plant height and stress tolerance. Therefore, I intend to extend OSGS to multivariate OSGS (mvOSGS) which can incorporate multiple traits and parents in the prediction model. I will test mvOSGS on publicly available and simulated Multi-Parental Population (MPP) datasets by applying an origin-based partitioning of genomic marker effects to pre-existing multi-trait genomic prediction (GP) models. There are three possible options for addressing multiple traits: (1) fit individual trait into single-trait Ridge Regression Best Linear Unbiased Prediction (RR-BLUP) models using the R/rrBLUP package and combine the origin-based prediction results for all traits, which is a quick but likely wrong model as it ignores covariances among traits; (2) fit multi-trait Elastic Net (EN) model using the R/glmnet package; (3) fit multi-trait genomic BLUP (G-BLUP) model using the R/sommer package and extract the multi-trait marker effects through linear transformation. OSGS is straightforward in bi-parental populations because the parental genotypes can be matched directly to the biallelic genomic markers. However, this can be extended for populations with more than two parents by using either (1) a parental haplotype matrix instead of standard genotype matrix or (2) an additional parental probabilities matrix. The use of haplotype over genotype matrix in GP is comparable and may improve the prediction accuracies under specific circumstances. The second method is similar but with the parental origin accounted after the GP model is fitted. Regardless of which methods is used, favorable parental markers can be identified similar to OSGS, which can then be used to compute the estimated breeding values (EBVs) specific to each parent.

Aim 2: expansion of the R/magicdesign package. The current version of R/magicdesign has a strong focus on its core utility, which is to design and test MAGIC crossing schemes through simulation. To date, the package has been used to create MAGIC crossing schemes for barley, ryegrass and oilseed rape. As its usage increases, features such as founder selection and crosses’ genotypes might be useful addition to the package. Because the founders determine the available diversity in any MAGIC population, the founders can be chosen as a subset from a full list of accessions that would maximize the diversity as measured from either genomic markers or phenotypic traits, or a combination of both. Examples of diversity measures include Manhattan distance, Jaccard index, fixation index (FST, QST) and site frequency spectrum (SFS). The founders can be chosen individually or as a set of individuals with greatest diversity using the simulated annealing method as previously demonstrated in maize. If individuals’ genotypes are available at any given generation, these can be used to identify individuals or combination of individuals with maximum unique recombinant haplotypes for use in subsequent crosses. Without these genotypes, the individuals are chosen at random for crosses and some may inevitably end up redundant by chance. By leveraging information from the genotypes, we can minimize the number of crosses and produce MAGIC recombinant inbred lines (RILs) that are diverse and distinct. Reduced crossing work also creates room for additional founders.

Aim 3: construction of elite-exotic and nested MAGIC populations. In parallel, MPPs like MAGIC populations can be developed using a combination of elite and exotic parents. Unlike NAM and NAM-like populations where the elite and exotic alleles are restricted to each bi-parental sub-population, alleles from multiple elite and exotic parents can segregate within a single MAGIC population. With the help of R/magicdesign, ideal crossing schemes for MAGIC populations can be easily constructed. Within a primary elite-exotic MAGIC population, further sub-populations with only crosses among the exotic parents can be extracted. The exotic-only MAGIC population can be directly compared against the elite-exotic MAGIC population to identify which is the better strategy for improving genetic gain in agronomic traits from exotic parents in pre-breeding program. However, there is a limit to such genetic gain from a standard quantitative genetic approach due to biological properties such as linkage disequilibrium and recombination coldspots. Possible solutions to this include generating novel recombinations via gene editing, and introducing parental lines with mutations in key recombination genes such as rec8. Aside from the pre-breeding purpose, these MAGIC populations can also be used in other research areas such as trait mapping and genetic-by-environment testing. Therefore, these populations are valuable resources for initiating collaborations with other researchers. In the long term, acquiring grant funding will be essential to maintain a sustainable research group and thus will be the primary focus. I will write grant applications using preliminary and published results from experimental and in silico studies, as well as through collaborations with partners of complementary expertise. Collaboration is the bread and butter of research. A good collaboration goes a long way toward encouraging research creativity, broadening the group’s research topics and reaching out further to global audiences. As one who has undergone traditional academic career pathway, I understand and treasure the value of good research training. For example, members of the research group will be given training in areas that are unfamiliar to them. This can be provided internally either by the group leader or experienced members, or externally through courses and workshops. Over the lifespan of the research group, many of the members are likely to be transient and thus it is important to consider each individual’s research goal and career choice in their training, regardless of whether they are postdoctoral researchers, graduate students or technicians. Lastly, just like any other living organism, fostering a healthy research group will be the key to growing the group expertise and contributing better to the university and society.

Teaching statement

Education is a life-long process that plays an important role in shaping who we are. As a member of the academia, I strive to deliver quality education in undergraduate and graduate courses, as well as research mentoring. This commitment is reflected in how I applied my teaching philosophies in the past opportunities. My formal teaching experience began as a Teaching Assistant (TA) for an undergraduate course in General Genetics at the University of Wisconsin (UW) - Madison. As a TA, my primary responsibility was to provide support to the students in understanding lecture materials through discussions. I was invited as a guest lecturer for the section on “IBD, IBS, Genetic Distance, Population Structure”, which is part of the XXIII International Master in Plant Genetics, Genomics and Breeding. The Master program was organized by CIHEAM Zaragoza in Spain and it had about 30 students with strong background and interest in applied genetics and plant breeding. More recently, I was guest lecturing a section on “Conventional and Advanced Breeding Methods” in a 4th year undergraduate class (Genetic Improvement of Crops). The class is organized by the University of Edinburgh under their Global Academy of Agriculture and Food Security program. Aside from the conventional teaching experience, I had directly and indirectly mentored 14 undergraduate students for various research projects at the UW-Madison.

I am excited to bring my teaching experience to the undergraduate and graduate programs at the University of Nebraska-Lincoln. My diverse research background offers an immediate relevance to teaching courses in Plant Biology major and Agronomy & Horticulture graduate degree. I can teach in any area related to plant breeding and quantitative genetics, including theories and applications of genetics, genomics, statistics, programming, agriculture, experimental designs and crop legislation system. I can adapt my teaching to a wide-array of settings including large lecture-based and small discussion-based courses using offline and/or online methods. In the same previously described course on “Genetic Improvement of Crops”, I was involved in its curriculum development. I intend to bring my experience in updating and developing curricula to your department.

My teaching philosophies are heavily shaped by my experience in diverse environments over the years. Born to a family of teachers, I was surrounded by years of opportunities to learn from the experienced. There, I grasped the importance of learning by examples and “practice makes perfect”. During my time as an undergraduate at the Indiana University Bloomington (IUB), I found the joy of learning in a liberal arts college with an abundance of course options to choose from. I took advantage of the freedom by enrolling in two separate Bachelor degrees in Biotechnology and Mathematics. It was critical to be able to adapt to various courses such as Organic Chemistry and Invertebrate Zoology in the morning, followed by Architecture and Differential Equations in the afternoon. While the topics are likely to be less divergent within the Department of Agronomy and Horticulture, new scientific knowledge has been emerging at a fast pace over the recent years. For example, genomic selection did not exist until two decades ago and gene editing with CRISPR-cas9 only came around a decade ago. To keep up with the expanding knowledge, I intend to borrow the holistic liberal arts approach to teach one to learn so the students will leave the classrooms with practical skills to acquire new knowledge instead of being crammed with only facts like “mitochondrion is the powerhouse of the cell”.

I intend to deliver my core teaching philosophy of training students to learn using three approaches: adaptation, analogy and assessment. (1) I strive to adapt the teaching style and course contents according to the overall needs, and if possible, down to individual needs. Everyone is unique. As a good educator, it is important to provide the space for everyone to develop their own learning styles that match their strengths. For example, I have encountered different preferences in reading a scientific literature as some may prefer to focus on the figures while others may prefer to focus on the texts. A good figure conveys the experimental results clearly while a good paragraph brings out the authors’ narrative of the results. Just as how one prefers to read an original book while another prefers to watch a movie adaptation, there is not one approach that is superior over the other. (2) Good analogies are effective education tools because they allow us to use prior knowledge to understand unfamiliar topics. Analogies make the topics more relatable and attractive, which in turn provide a clearer framework for the students to understands and evaluates. For example, “genotype imputation” can be hard to grasped by people who are not acquainted to the field. However, it can be drawn in parallel to many things that we do in daily life, such as guessing whether the rain will continue or stop based on current cloud cover and wind direction. The commonality between “genotype imputation” and its analogy is about making predictions based on observed and related information. (3) Aside from the routine uses in tracking students’ learning progress and assigning grades, assessments are valuable tools for educators to gauge students’ needs and interests, especially in a large lecture-based class. Assessment outcomes can be circulated within a feedback loop to adjust the teaching pace and develop an adaptive course plan that matches the students’ progress. I find that a combination of quick assessments (e.g. clicker questions, weekly quizzes and surveys) and post-mortems to be an effective approach in troubleshooting any learning issues or misconceptions, as well as identifying areas of interests that are not included in the syllabus. Using all three envisioned teaching approaches, I strive to cultivate a comfortable and enjoyable learning environment for every student.

My past teaching experience has demonstrated and refined my teaching philosophies over the years. As a TA, I gave short recaps of the lectures and led the discussion sessions. I maintained two-way communications by assessing the students’ understanding of lecture materials through short questions and providing them with flexible opportunities to ask questions in class and emails. I made myself available for the students outside of office hours, which was especially beneficial for students who were shy to ask in class or when the mid-term examinations were approaching. Later, I was invited to deliver online lectures for a Master program due to the travel restrictions at the height of the pandemic. This experience was more challenging than usual because of the lack of visual interactions between the students and me. To circumvent the challenge, I offered options for the students to speak out or type their questions in the chat boxes or emails. I relied on analogous examples to simplify complicated topics to familiar grounds. These teaching slides took longer time to make, but the effort was rewarding as it helped the students to understand better and think from various angles. In the practical sessions, we had computational analyses in R. To ensure that everyone was up to the same speed, I divided the analyses into multiple small sections so I could walk the students through carefully. In the take-home exercise, I wrote a few short answer questions to help guide the students along their analyses in R. I focused on the justifications for their answers as a way to get the students thinking and understanding how the analyses work. I also offered assistance in debugging codes through chat boxes and emails. I was excited to find the lecture materials useful in the students’ own research projects as they came with questions on analyzing their datasets. Building on my teaching experience and philosophies, I intend to give my best to deliver quality education in the Department of Agronomy and Horticulture.

Diversity, Equity and Inclusion (DEI) statement

When I first left my home country for college, I feared of not being able to fit in only to find that I was showered with warm welcome by the communities in Bloomington, IN. I met with kind neighbors who offered directions and rides, and friendly strangers on the streets who greeted passers-by. I participated in many local activities such as furniture giveaway, picnic, apple picking and Thanksgiving dinner. These activities were organized by the Bloomington International Students Ministries (BISM) as part of their goals in welcoming global diversity. These overwhelming receptions helped me greatly in adapting to the American culture and highlighted the importance of diversity, equity and inclusion (DEI) in creating a comfortable space for everyone. In return, I am constantly seeking out opportunities to promote DEI as shown in my past and future commitments.

I had many opportunities to contribute toward DEI when I was a graduate student at the University of Wisconsin-Madison. During the six years in my PhD, I directly and indirectly mentored 14 undergraduate students from various backgrounds, of which 6 were women, 3 were non-White minorities, and 2 were non-Americans. The students started out as research assistants to fulfill their research credits, and continued with their projects either for multiple semesters or until they graduated. As a research mentor, I encouraged and assisted them in making scientific presentations. The students participated in regular lab meetings and end-of-semester meeting to present their works. The students also presented in the undergraduate research symposiums and contributed in publications. These efforts were important, especially to the minorities, in engaging the students with broader research and career development. Apart from the students, I helped two visiting professors and a postdoctoral researcher in settling down after coming from halfway across the globe. I assisted them in finding housing, setting up utilities, and navigating through the university administrations.

Going forward, I aspire to further strengthen my commitments in promoting DEI at multiple levels including my research group, department and university. To cultivate diversity at work, it is important to keep the door open to various minority groups in science, including, but not limited to, women, persons of color, LGBT+, disabled and first generation students. In addition to having open doors, there is also a need to enable the paths for diversity to exist across all work levels. I strive to uphold equity at work by ensuring that everyone is given sufficient support to achieve fair and equal outcomes. This process can be challenging as it requires careful consideration of everyone’s background and not every disadvantage is apparent. Keys to safeguarding inclusion lies within good communications and cultural exchange. Being inclusive provides a sense of belonging to everyone and a better understanding of each other. Overall, diversity, equity and inclusion are inseparable as they go hand-in-hand toward creating a shared platform for everyone to shine.

Here, I am extending my multi-cultural experience that spans three continents toward building my plans for promoting DEI. D: I intend to remove the recruitment barrier into research and education by reaching out to various communities through outreach programs. Outreach can nurture scientific interest in kids from various minority backgrounds and bridge the gaps in higher education. I will join a DEI committee to contribute through a team effort. Recruitment for my research group members will be advertised in multiple platforms (e.g. job boards, career fairs, social media and emails) to reach out to a diverse pool of candidates. I will provide academic and career support to everyone through advices and opportunities in trainings and grants. E: I plan to deliver a fair education to every student. Some students may suffer from various disadvantages due to their backgrounds. I strive to be an observant educator who can identify and address the students’ needs. To achieve a fair recruitment process, I will evaluate not only the candidates’ research interest and abilities, but also consider any shortcomings that they might have faced. I: I will be flexible in engaging the students and establish a curriculum that avoids fitting the students into a box so that everyone can develop their own learning styles. As a research group leader, I will be accommodating to individuals’ needs for parental leaves, family care, health care (including mental health), preparation for examinations, vacations and others. I will ensure sufficient cover support on research projects and protect the ownership of each group member in their projects. I will also encourage inclusive social events to build a healthy and positive research community.

Modesty and humility are important values in building a DEI-friendly environment. I will continue to improve my flexibility and willingness to listen to everyone, and step up for others as needed. As the DEI standards evolve over time, I am offering my best to keep up with the changes and uphold the highest standards of DEI.