For this application, I had to submit the following: CV, one-page cover letter, two-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 Search Committee,

I am applying to the position of Assistant Professor – Small Grains Breeder (ID: XXXXXX) at the North Carolina State University (NCSU). 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 Crop and Soil Sciences. I appreciate your interest in continuing the excellent research and breeding programs in small grains. I am eager to explore small grains genetics and breeding from various innovative angles surrounding the use of novel breeding strategies with genomic and/or phenomic selection. These research areas are valuable toward delivering higher rate of genetic gains in breeding programs and developing new cultivars that are better at tackling the threats to food security due to climate change. I can contribute to the research and breeding progress through quantitative genetics and collaborations with others in different disciplines. I would like to demonstrate my leadership in delivering elegant solutions to various challenges in modern small grains breeding, if given the opportunity to develop as an Assistant Professor.

I believe I would fit well in the Department of Crop and Soil Sciences because my research, teaching and collaboration experience is directly relevant to the data-driven role in delivering quality research, education and service. I am excited to apply my skills in plant genetics, statistics, mentoring and teaching that I have developed in my graduate and postdoctoral careers. 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, teaching and communication.

I have attached the additional documents here because the online submission system does not have an upload option for them. I hope this is alright and sorry for the inconvenience.

Page 2-3: Research statement.
Page 4-5: Teaching statement.
Page 6: Diversity, equity and inclusion statement.

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 strong interest in interdisciplinary, collaborative research. I am trained in maize evolutionary genetics and modern crop breeding during my graduate and postdoctoral careers, respectively. I am excited to apply modern quantitative genetics and other disciplines in small grains breeding at the North Carolina State University (NCSU). Sustainable crop improvement in quality, yield and stress tolerance is essential to meet the growing needs for climate resilience, nutrition and economy. Here, I will describe my past research work and propose a research program that will contribute to NCSU and wider community such as the SunGrains Breeding Cooperative.

During my PhD training 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 in several projects on fine-mapping and characterization of domestication quantitative trait loci (QTLs) and genes. These projects led me 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 variances for multiple traits in maize and teosinte. The results demonstrated 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. Thus, oligogenic and polygenic models are ideal for studying domestication from contrasting angles. In my postdoctoral work at the Scotland’s Rural College, I examined crop breeding from the angle of genetic diversity management in modern crops. My research work revolved around statistical analyses of modern crop data and development of novel analytical tools. (1) I developed the Origin Specific Genomic Selection (OSGS) approach to introgress novel diversity into modern breeding populations. Its utility was demonstrated in the barley Nested Association Mapping (NAM) population. (2) I evaluated the Plant Variety Rights (PVR) system of Distinctness, Uniformity and Stability (DUS) by comparing the pre-existing morphological approach to a more efficient genomic approach. (3) I built the R/magicdesign package and magicdesignee Shiny app for designing and testing crossing schemes in Multi-parental Advanced Generation Inter Cross (MAGIC) populations. (4) I developed the Regression of ALLeles over Years (RALLY) method to detect selection signature in breeding populations by modeling the changes in allele frequencies as a logistic distribution. (5) I am now developing a novel approach for mapping genetical and non-genetical interactions as variance-controlling QTLs (vQTLs), investigating phantom epistasis in modern wheat hybrids, establishing a purslane production system in vertical farm, applying genomic selection in mutation breeding, and improving the statistical models in crop variety trials.

I am proposing for a research group with focuses on delivering improved cultivars in small grains breeding and designing innovations in breeding programs. Based on the USDA statistics for 2022, small grains such as wheat, barley, oats, triticale and rye contributed up to 6% of the total crop production value in NC, and winter wheat ranked fifth with a production value of $202 million. Innovative breeding and research efforts are essential to sustain the commercial needs for small grains production. As elucidated previously, I have a broad research experience in quantitative genetics, domestication, genomic selection, plant variety registration, simulation, software and method development. My research background is deeply connected to plant breeding, and thus provides me with a clear understanding of the breeding process including selection, genetic gain, field trials and cultivar registration. Genetic gain (deltaG) in any breeding program is measured as the selection response in the breeder’s equation per unit time, and can be expressed as deltaG = sigma_a*i*r⁄t. The terms on the right side are additive genetic variation (sigma_a), selection intensity (i), selection accuracy (r) and breeding cycle time (t). This equation lends us a clear framework to conceptualize the various angles to increase genetic gain. I plan to take on the role in leading the small grains breeding programs at NCSU, and continue to explore opportunities in improving small grains breeding programs as outlined in the following three Research Areas (RA).

RA1: application of two-part strategy in small grains breeding. Conventional breeding strategy involves crossing the parents and selecting for high performing progeny over many field trials. Novel recombinations between the parents provide the genetic gains in breeding programs. A simulation study has shown that higher genetic gains can be achieved by decoupling the programs into Population Improvement (PI) and Product Development (PD). PI involves crossing the superior genotypes as predicted from Genomic Selection (GS), while PD involves field trials, phenotypic selection and GS model training. The reason for higher genetic gains is because PI can be done in greenhouses where multiple generations per year are possible. The benefits of this two-part strategy warrant an experimental validation, which will be done in parallel to the pre-existing breeding programs. Additional genetic gains can be obtained by applying speed breeding in PI to grow up to five generations per year of winter wheat and barley. However, the GS prediction accuracy is likely to decline as the genetic relationship between PI genotypes and PD training population decreases. We will optimize the trade-offs in this approach by simulation.

RA2: cultivar development with Origin Specific Genomic Selection (OSGS). In many breeding programs, GS and Marker Assisted Selection (MAS) are routinely used to select superior individuals and introgress novel favorable alleles, respectively. However, the allelic origins are intractable in GS and polygenic traits are unmanageable in MAS, leaving a gap in situation where introgression of polygenic traits is desired. Tolerances to abiotic stresses like drought, heat and salinity are examples of traits that are polygenic in nature but may not be readily present in the breeding populations. These traits are where OSGS can be advantageous. As an extended form of GS, OSGS accounts for the parental origins and thus allows us to select desirable parental contributions in any breeding population. We can use OSGS to transfer favorable alleles from donor parents to develop cultivars with higher stress tolerance while maintaining high yields and other important breeding traits. There is still room for improving OSGS as it is limited to single trait in bi-parental population. This project creates an opportunity to develop multivariate OSGS (mvOSGS) where multiple traits and parents can be evaluated together in the model. We will test mvOSGS in simulated and real data from the breeding populations.

RA3: evaluation of Phenomic Selection (PS) in breeding programs. As its name suggests, PS is similar to GS except that PS derives the relationship for prediction from the endophenotypes (phenome) instead of molecular markers (genome). Phenome can be near infrared spectra, satellite image, transcriptome, proteome or metabolome. Phenome accumulates complex interaction between the genome and environment, and may therefore serve as better predictor than the genome for some traits. The current research in PS indicates mixed results and offers many opportunities to identify ways to apply PS in breeding programs. First, we will develop a method for simulating the phenome so PS can be tested in silico. This method will build on existing approach (e.g. R/AlphaSimR) in simulating the genome, breeding values and phenotypes for making informed breeding decisions. Second, we will obtain the marker and phenomic data from breeding populations, and compare the performance of GS and PS across all target traits. We can quantify phenomic variance similar to how genetic/genomic variance is calculated in the GS model. Third, we will score the phenome across all developmental time points ranging from germination to harvest. While the post-flowering phenome is less useful for deciding on crosses, the results will elucidate the phenome-phenotype relationship over time.

My plans for a successful research program involve research, dissemination, funding, collaboration, engagement and training. I intend to use my broad research experience to formulate clear research directions for the group. There will be practical opportunities in greenhouse, field and basic laboratory work, as well as analytical opportunities in statistics, simulation and programming. The research outcomes will be disseminated through publications, talks, posters, websites and outreach participation. These outputs will be crucial in supporting grant applications to secure extramural funding and sustain the growth of the research group. Our research and grant applications will be assisted by collaboration with partners of complementary expertise to encourage creativity and broaden our research topics. Given the applied nature of breeding, engagement with various stakeholders such as seed industries, farmers and consumers is essential to guide our breeding direction. I highly value a strong training component in my research group for everyone to achieve research excellence and independence. There will be training opportunities in conducting research, presenting results, teaching classes, writing/reviewing manuscripts, writing grants, building collaboration and liaising with stakeholders. A good training is the key to building capacity in a research group that can better contribute to the university, industry 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. I am excited to demonstrate my teaching commitment in both undergraduate and graduate level courses at the North Carolina State University (NCSU) and the Department of Crop and Soil Sciences. My diverse research background offers an immediate relevance to teaching courses in the undergraduate major of Crop and Soil Sciences, especially in the specialty areas of Agronomy and Crop Biotechnology. The same relevance applies to the graduate degree in Crop Science. 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. If needed, I can contribute to the development of new courses in relevant areas too. I can adapt my teaching to a wide-array of settings including large lecture-based and small discussion-based courses using offline/online methods.

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 undergraduate time at the Indiana University Bloomington (IUB), I indulged myself in a variety of class options and enrolled in two majors in Biotechnology and Mathematics. It was critical to be able to adapt to different classes such as Organic Chemistry and Invertebrate Zoology in the morning, followed by Architecture and Differential Equations in the afternoon. In a lesser extent, topics taught within a class can be variable and are constantly evolving to incorporate new and fast emerging scientific knowledge. For examples, 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 topics, 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 plan 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 to whether focus on the figures or 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 similarity here is about making predictions from 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.

Over the years, I have demonstrated and refined my teaching philosophies in the several teaching opportunities. In 2013, I began my first formal teaching experience as a Teaching Assistant (TA) for an undergraduate course in General Genetics at the University of Wisconsin (UW) - Madison. My primary responsibility was to provide support to the students in understanding lecture materials through discussions. I gave short recaps of the lectures and led the discussion sessions. I maintained two-way communications by assessing the students’ understanding through short questions and providing them with flexible opportunities to ask questions anytime in class, emails and face-to-face meeting. Later in 2021, I was invited as a guest lecturer for the XXIII International Master in Plant Genetics, Genomics and Breeding organized by CIHEAM Zaragoza in Spain. Specifically, I was tasked to deliver 8 hours of lecture and practical for the section on “IBD, IBS, Genetic Distance, Population Structure”. Due to the ongoing pandemic and travel restrictions, the entire section was conducted online. This experience was more challenging than usual because of the lack of visual interactions between the students and me. To circumvent the challenge, I requested the students to speak out anytime or type their questions in the chat boxes or emails. In the practical sessions, we had computational analyses in R. To keep everyone up to speed, I divided the analyses into multiple small sections to walk the students through carefully and debug as needed. In the take-home exercise, I wrote a few short answer questions to help guide the students along their analyses in R. The questions were focused on the answers’ justifications as a way to stimulate the students into thinking critically and understanding how the analyses worked. I was excited to find the teaching materials useful in the students’ own research projects as they came with questions on analyzing their datasets. Recently in 2022, I served as a guest lecturer for the 4th year undergraduate class in Genetic Improvement of Crops organized by the University of Edinburgh. The class was offered as an elective for students who were enrolled in the Global Academy of Agriculture and Food Security program. I delivered 5 hours of lecture and practical for sections on “Conventional and Advanced Breeding Methods” and “Plant Variety Rights”. Guest lecturing can be challenging because there is a limited time to know the students and adapt the class materials to their background. For example, in contrary to what I was previously told, I learned in a practical session that the students did not have a strong knowledge of programming in R. Upon realizing that, I made an impromptu adjustment to spend extra time in teaching the students on how to use R before diving further into the initial plan in data analysis. Building on my teaching philosophies and experience, I strive to give my best to deliver quality education in the Department of Crop and Soil Sciences at NCSU.

My research mentoring approach generally takes the forms as described in Figure X. First, the mentees and I discuss and identify their interests in the available project options. After that, I describe the relevant background knowledge, demonstrate the process and explain the steps. I try to leave them to work independently while checking in occasionally and making myself available for help. It is important to emphasize that “failure is OK and we can troubleshoot together”. I give positive reinforcement as a way to recognize their hard work and perseverance. The training cycle continues into the subsequent parts of the project. It is important for me to provide enough support without being negligent so that the mentees can develop their projects’ ownerships. I view mentoring as a process for the mentees to achieve independence and excellence in research.

My PhD projects led me to 14 direct and indirect undergraduate research mentorship. In Fall 2015, I worked with a visiting scholar and an undergraduate to investigate a QTL for the maize prolificacy trait (number of ears on a branch) and found a different allele that was selected during domestication. In Summer 2016, I worked with a visiting undergraduate to test for interactions in staminate ear (spikelet sex) QTLs and identified significant interactions with the major domestication gene, teosinte branched1 (tb1). I mentored several undergraduates to work on semi-high-throughput seed imaging, germination test and data analysis. I contributed in the development of a comprehensive undergraduate research training experience using the teosinte nested association mapping (teoNAM) population. All participating students worked on independent research projects from start to finish, including field trial management, trait phenotyping, data curation, QTL mapping and result presentation. The undergraduates presented their results in meetings, symposiums and the Maize Genetics Conference in 2017. All research projects resulted in four journal publications and two chapters in my PhD dissertation with contributing undergraduates as co-authors. I plan to bring my research mentoring approach and build on my experience to deliver a strong research and teaching program with holistic training at NCSU.

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 committed to promoting DEI wherever possible.

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, especially those who lacked in prior experience. The students presented their work in lab meetings, symposiums and conferences, as well as 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. I strongly believe that DEI values are essential for maintaining a productive research group and delivering quality education.