Recipient Organization
TEXAS A&M UNIVERSITY
750 AGRONOMY RD STE 2701
COLLEGE STATION,TX 77843-0001
Performing Department
Soil & Crop Sciences
Non Technical Summary
Summary:Rice is cultivated worldwide and a staple food for nearly half of humanity. The United States is a major rice exporter, with nearly half of its rice production being exported. Rice in the U.S. is primarily produced by five states in the South: Arkansas, Louisiana, Mississippi, Missouri and Texas, as well as California. Texas rice production contributes to about 5% to 7% of the rice supply in the US, with more than 95% being long grain rice for domestic and export markets. This totals nearly $160 million in production value and contributed about $500 million to $600 million to the economy of Texas. However, increasing problems in rice cultivation have been faced by Texas rice farmers and rice growers around the world. Water shortages in some parts of the state have brought about uncertainty in rice cultivation.Attempts by farmers to plant as early as possible in the spring can sometimes lead to increased exposure to early?season cold temperatures and ultimately slow down the growth of rice crops, which in turns affects rice yields. Weeds have also been a major problem, even with the widespread use of herbicides and non-chemical measures. Globally, rice production must increase to keep up with population growth and world food security challenges to feed nine billion people by 2050 (Godfray et al., 2010). With limited available land and water for cultivation expansion, the bulk of future increases has to be achieved from intensification of cultivation. Further, global rice cultivation is facing ever-growing challenges, such as abiotic and biotic stresses, that may worsen from increasingly volatile climatic conditions. Abiotic stresses, such as drought, flooding, heat, UV radiation, cold, and salinity, threaten rice production and food security around the globe. This problem is often accompanied by the onset of diseases and insects that further make rice cultivation more vulnerable. Plateauing yields are another challenge facing the future of rice cultivation, along with the need to improve grain quality for better milling and end-user preferences for the premium rice markets.Legume crops are well suited for the sustainable production of nutritious foods due to their contribution to soil health from nitrogen fixation and their many benefits for human nutrition and health (Maphosa and Jideani 2017); however, most legumes have not yet benefited from advanced breeding methods, including genome editing and related technologies. Cultivated peanut (Arachis hypogea L.) is planted on 28.52 million ha with a total yield of 45.95 million tons (FAOSTAT 2020) and is distinguished by high oil content with a large percentage of oleic acid. Peanut contributes more than $4 billion to the Unites States economy yearly and Americans spend nearly $800 million a year on peanut butter; meanwhile, peanuts are also one of the key ingredients in many snacks consumed in the US. Peanuts in the U.S. are mainly grown in the seven states, e.g. Georgia, Texas, Alabama, North Carolina, Florida, Virginia and Oklahoma. Peanut production, however, was often hampered by diseases including leafspot, stem rot and pod rot, insects and abiotic stresses, such as drought, and weed invasion. Improvements of production costs, nutrition and overall quality have also been important issues. Food allergies are also on the rise, including allergy to peanuts products, which in the U.S. affects 2% to 10% children. Despite its global importance, peanut breeding is still largely conventional, with limited success to date with genome editing applications. Cowpea (Vigna unguiculata), a native of Sub-Sahara Africa, has a number of advantages over other legumes with respect to sustainable production, due to its abiotic stress-tolerance, ability to grow on low-nutrient soils, and 60 to 70-day maturity compared to 120 to 140 days of other pulses (Singh 2014, 2016). Additionally, cowpea is a diploid species with a relatively small genome, but having a low efficiency for genetic transformation, thus serving as an excellent model to optimize regeneration and gene editing technologies for the legumes. To realize the full potential of peanut and cowpea as sustainable sources of highly nutritious foods, it is necessary to develop technologies to enable rapid molecular breeding in these crops, with potential future application across various legume crops.This project will use molecular genetics tools towards improving rice andlegumes. These strategies include using diverse or exotic germplasm in ourresearch to identify novel genes/alleles through DNA maker-trait association, genome-wide gene expression studies to identify genes/pathways associated with the traits of interest,and/or genome editing by cutting the target genomic sequence to either abolish the function of the gene to validateits function or to replace the specific gene with a better one to improve the traits of interest.This project will work towards the following goals: (i) to help stabilize yield production of rice and legumes both in Texas and globally; (ii) to improve the quality and nutrition of rice grains and legumes as premium market in the U.S. and globally; and (iii) to identify and optimize advanced technologies to speed up rice and legume improvement.
Animal Health Component
50%
Research Effort Categories
Basic
50%
Applied
50%
Developmental
0%
Goals / Objectives
Goals:(i) To help stabilize yield production of rice and legumes both in Texas and globally; (ii) to improve the quality and nutrition of rice grains and legumes for the premium market in the U.S. and globally; and (iii) to identify and optimize advanced technologies to speed up rice and legume improvement.Objectives:To help stabilize yield production of rice and legumes both in Texas and globally:Research needs to be implemented to better understand the molecular genetic and physiological mechanisms affecting yield and yield stability under stress, including exploring novel variation to introduce yield-enhancing and stress tolerance alleles, for rice and key legumes such as peanuts and cowpea.To improve the quality and nutrition of rice grains and legumes for the premium market in the U.S. and globally: Different aspects of grain quality traits need to be further investigated for improving the premium quality of U.S rice, including physical and sensory properties and enhanced nutrition. At the same time, peanuts are also a nutrient-rich food, containing essential nutrients; enhancement of these compounds will add further value to peanut-based products and increase the nutritional value of peanuts.To identify and optimize advanced technologies to speed up rice and legume improvement: More research is needed to optimize new crop improvement techniques, such as genomics-assisted breeding and CRISPR/Cas-based gene editing, for rice and legumes.
Project Methods
Methods:Exploring and characterizing novel genetic diversity: Until now, only a small fraction of the wealth of crop germplasm diversity held in the world's germplasm repositories has been explored. But this trend is expected to change with the advances of high-throughput genotyping and next generation sequencing technologies. Natural diversity, including wild species relatives held in the germplasm repositories, is essential to improving crop production, grain/product quality and nutrition, and different abiotic and biotic stresses aggravated by the adversity of climate change. One of the strategies that can be used to take advantage of the advances of genomic technologies and the wealth of rice natural diversity is using genome-wide association studies (GWAS), which identifies marker-trait associations across the genome. This strategy will be used complementary with the bi-parental QTL mapping strategy. Whenever possible, high throughput phenotyping and genotyping will be performed. Compatible software will be used to analyze the data.Novel sources of genetic diversity will be explored to provide new genetic donors, including landraces and wild relatives, to facilitate the identification and transfer of important genes to elite breeding lines. QTL and or candidate genes of the selected traits of interest will be identifiedand further explored.Applying genome editing and related activities: Genome editing is a powerful tool to manipulate a genome in a precise manner. It can be used to elucidate the function by knocking out the gene or to 'replace' alleles with a superior allele. One of the genome techniques is the CRISPR-Cas9 (clustered regularly interspaced short palindromic repeats) system where a guide RNA is used to recognize a specific sequence and recruit the nuclease Cas9 to make targeted changes in the gene of interest. This system has many advantages over other genome editing methods, including the simplicity and low cost of synthesizing new guide RNAs, increased specificity of cleavage sites, and the ability to simultaneously edit multiple loci.Once key genes and alleles have been identified, valuable information on their function can be gained by knocking out and replacing alleles using CRISPR/Cas9. Ultimately, genome editing can also be used to rapidly combine key alleles into elite breeding lines to accelerate the process of crop improvement.Exploring more efficient genome editing strategies and transgene-delivery systems: Although simple gene knockouts are now routine with CRISPR/Cas9 through error-prone non-homologous end joining (NHEJ) repair, more powerful applications, such as precision edits and allele replacements, are much more difficult to achieve due to the low frequency of homology-directed repair (HDR) in plants. However, an alternative method is prime editing, which employs a Cas9 nickase (nCas9) fused to an engineered reverse transcriptase (RT), and programmed with a prime editing guide RNA (pegRNA) that both specifies the target site and encodes the desired edit (Anzalone et al. 2019). Nanotechnologies have also been recently used as delivery agents for gene modification, including carbon nanotubes and carbon dots (Demirer et al. 2019; Doyle et al. 2019). First, these techniques will be optimized in rice first and then similar technologies can be further tested and optimized in peanut and cowpea and/or other legumes, to enable routine and precise gene editing for crop improvement. Additionally, legume transformation protocol needs to be optimized by working together with the TAMU crop transformation group.