Breeding of plant based protein crops (mung bean and urd bean) using USDA germplasm

Mungbean (Vigna radiata) L. Wilczek and Urdbean (Vigna mungo) are important pulse crops worldwide. They are commonly referred to as green gram and black gram. They were produced in America in the 1830’s as Chickasaw pea. Most of the mungbean production in the US is currently in Oklahoma; however, small portion is also grown in Kansas, California, Tennessee, Kentucky, and Texas.

Mungbean and urdbean are short-season (60-90 days) legume crops with good drought tolerance. These crops are used as a food crop particularly for a plant-based protein diet; and from an agronomic perspective, it is useful as a cover crop, a rotational crop, and a double crop. The attractive features of this crop as a food crop are its neutral taste, versatility in applications, high nutrition value, and easy digestibility. Additionally, there is a rapidly growing market demand.

This project was initiated in 2017, and since inception has involved numerous farmers in multiple states and processing companies nationally to set up breeding and research objectives. Approximately 3,000 mungbean and 300 urdbean accessions were obtained from the United States Department of Agriculture (USDA) germplasm collection bank, Griffin, GA, USA. These lines underwent extensive field evaluations in Iowa; and 482 mungbean and 30 urdbean lines with production potential were selected for further research and development. Based on these results and yield testing, new varieties will be recommended to farmers. The 482 mungbean lines were sent for genome sequencing to correlate regions in the genome with specific traits, to identify genes responsible for the traits of interest and SNP markers linked to the trait of interest, so targeted breeding can be done. Examples of traits that were phenotyped included days to flowering, plant height, days to maturity, seed weight, plant growth habit, seed quality, diseases, and pest resistance. Our first paper and its results can be seen here: https://acsess.onlinelibrary.wiley.com/doi/full/10.1002/csc2.20322. Currently, several breeding populations are undergoing advancement and selection to develop new varieties for the US farmers.

Our work suggests that mungbean farming will easily fit in the current mid-west agricultural production system, including no major equipment changes by soybean farmers. More research is needed to understand agronomic practices including standardization of seed rate, planting dates, and crop rotation; food quality trait research on seed protein and other functional characteristics; identification and mitigation strategies of diseases and insect-pests; and genomics and phenomics tools for breeding strategies.

RII Track-2 FEC: Genome Engineering to Sustain Crop Improvement (GETSCI)

Improved and practical crop breeding tools are required to meet the increasing demands of a growing global population and to overcome the sudden and variable stresses, made worse, by climate change. This project brings together researchers from the University of Hawai’i at Manoa and Iowa State University to develop an efficient, robust genome engineering toolkit that can be used to speed the generation of resilient crops adapted to a changing environment. Reproductive barriers are a major bottleneck that limits the genetic diversity available for crop improvement. Tropical maize germplasm is a rich source of genetic diversity but its flowering behavior in temperate regions precludes its broad use for maize improvement. To access this diversity, our two institutions formed a collaboration that integrates our strengths in tropical plant biology and transformation (Hawai’i) with maize transformation, genome engineering, and breeding (Iowa). Our goals are to establish a rapid and efficient genetic transformation platform and to develop improved genome editing tools to reprogram the flowering behavior of high-yielding tropical maize lines allowing their incorporation into any maize breeding program. Both Hawai’i and Iowa will gain a valuable new capability in genetic transformation and genome engineering which will transform the types of crop research possible at both institutions. Expected impacts from this project will help address food security and economic weaknesses in Hawai’i, by allowing for the development of new tropical crop breeding industries. In Iowa, access to gene-edited temperate-adapted tropical germplasm will move maize improvement into the next era of genome-optimized breeding. Workforce capacity will be increased by engaging underrepresented students, particularly Native Hawai’ians and Pacific Islanders, in diverse aspects of genome engineering research, by the exchange of undergraduates between partner institutions to prepare a globally competitive, multiculturally, and socially responsible workforce, and by creating opportunities for improved science communication skills through training sessions, workshops, and engagement with the community to communicate the value and safety of these new tools.

Critical to our future is maintaining the rate of genetic improvement of the crops that feed us and sustain our economy. But the sudden and increasingly severe stresses caused by climate change limit the pace of improvement. Advances in genome engineering offer rapid solutions by enabling precise and targeted reprogramming of molecular networks to improve crop performance. The rich genetic diversity in tropical maize is largely underutilized for maize improvement because tropical lines are photoperiod sensitive and flower late in the long-days of temperate growing regions. To access this diversity, we formed a collaboration between the University of Hawai’i at Manoa (UH Manoa) and Iowa State University (ISU), which integrates strengths in tropical plant system biology and transformation (UH Manoa) with maize transformation, genome engineering, and breeding (ISU). Our goal is to use gene editing to suppress the photoperiod response in elite, high-yielding tropical maize to promote earlier flowering. These edited tropical lines can then be used to enhance any maize breeding program. Our objectives are to (1) establish an efficient, germplasm-independent maize transformation platform, (2) develop a facile, tractable genome editing toolkit to suppress the photoperiod response in six tropical inbreds, (3) analyze photoperiod network function in genome edited tropical lines, and (4) improve skills in communicating the value and safety of these new genome engineering tools.
The outcomes from this project include new tropical maize transformation capabilities at both jurisdictions, genome editing reagents for modulating flowering in maize, six elite tropical inbreds adapted to temperate breeding programs, a mechanistic understanding of the response to reprogramming the flowering network, and improved skills to communicate the value of this technology in professional and public contexts. Broader impacts expected from this project include opening this technology to academic labs, that can build research capacity by allowing genome engineering of diverse crops. Democratizing these tools are expected to speed breeding advancements, sustain crop improvement efforts, and spur economic growth. Both Hawai’i and Iowa will gain a valuable new capability in maize transformation and genome engineering, and will transform the types of crop research possible at both institutions. In Hawai’i, this project will help address food security and economic weaknesses revealed by the pandemic, by allowing for development of new tropical crop breeding industries. In Iowa, access to gene-edited temperate-adapted tropical germplasm moves maize improvement into the next era of genome-optimized breeding. Workforce capacity will be increased by engaging underrepresented students, particularly Native Hawai’ians and Pacific Islanders, in diverse aspects of genome engineering research, by the exchange of undergraduates between partner institutions to prepare a globally competitive, multiculturally, and socially responsible workforce, and by creating opportunities for improved science communication skills through training sessions, workshops, and engagement with the community to communicate the value and safety of these new tools.

Genetic networks regulating structure and function of the maize shoot apical meristem

The shoot apical meristem (SAM) is responsible for development of all above ground organs in the plant. SAM structure and function correlates with agronomically-important adult traits in the maize plant, and is also affected by planting density and shade stresses induced by agricultural environments. The ultimate goal of this project is to increase understanding of the regulatory networks controlling SAM structure and function and the responses of these networks to environmental stresses. The specific objectives are to: 1) describe the SAM allometric space in maize and its relatives using nanoscale computer tomographic scanning to provide 3-dimensional images of the phenotypic diversity of SAM structure and identify adult plant traits correlated with SAM structure; 2) identify differentially expressed genes in SAM size/shape outliers and mutants with abnormal SAM structures and generate a co-expression network of key genes implicated during SAM structure and function; 3) perform quantitative genetic analyses to identify specific variations within genes that correlate with variations in SAM structure/function and adult plant traits, and test functions of 40 key genes using reverse genetic aaproaches; 4) analyze the shade avoidance response and its effects on SAM structure and function; and 5) investigate epigenetic changes of SAM functional domains in response to shade avoidance using novel protocols that distinguish the stem cell organizing regions from the organogenic domains in the maize SAM.

These studies will provide the framework for scientific training and the public release of original data. Undergraduates at Truman State University, a small liberal arts institution, will be trained in morphological and LM-RNAseq analyses of maize mutants. REU students and undergraduates enrolled in Plant Physiology courses at Cornell University will participate in physiological experiments. This project will generate extensive transcriptomic data and vector constructs for tissue-specific epigenetic analyses which will be available to the scientific research community. Molecular markers and phenotypic data for diverse maize lines will be supplied to Panzea (http://www.panzea.org/). Genetic mapping associations, physiological shade-avoidance response data, transcriptomic and phenotypic data will be curated at MaizeGDB (http://www.maizegdb.org/), and seed stocks for maize shoot mutants and SAM size variants will be released through the Maize Genetics Cooperation Stock Center (http://maizecoop.cropsci.uiuc.edu/).