Source: BRIGHAM YOUNG UNIVERSITY submitted to NRP
IMPROVING QUINOA PRODUCTIVITY THROUGH THE USE OF WILD RELATIVES AND INDUCED VARIATION
Sponsoring Institution
National Institute of Food and Agriculture
Project Status
ACTIVE
Funding Source
AFRI COMPETITIVE GRANT
Reporting Frequency
Annual
Accession No.
1022158
Grant No.
2020-67014-30867
Cumulative Award Amt.
$500,000.00
Proposal No.
2018-06307
Multistate No.
(N/A)
Project Start Date
May 1, 2020
Project End Date
Dec 31, 2025
Grant Year
2020
Program Code
[A1141]- Plant Health and Production and Plant Products: Plant Breeding for Agricultural Production
Recipient Organization
BRIGHAM YOUNG UNIVERSITY
775 WIDSTOE BUILDING
PROVO,UT 84602
Performing Department
Plant and Wildlife Sciences
Non Technical Summary
Quinoa is a nutritious Andean grain that has dramatically increased in international popularity over the past decade. Unfortunately, quinoa was domesticated at high elevations in the Titicaca Basin of the Andean Altiplano and therefore doesn't grow well in lowland tropical, subtropical, and warm-season temperate production environments, including those found in the U.S. In order to improve quinoa production in the U.S. and throughout the world, new varieties are needed that are able to tolerate the new stresses that quinoa will undoubtedly encounter as its cultivation spreads. The long-term goal of this project is to introduce new genetic diversity into quinoa for the enhancement of U.S. and international quinoa breeding programs. To do this, we will take two general approaches: first, cross quinoa with wild relatives that already grow well throughout the U.S. in regions in which quinoa does not grow well; and second, induce mutations in quinoa that can help create new variation in traits of interest. These new quinoa materials with increased genetic diversity will be distributed to breeders and growers who can use them to develop new quinoa varieties that are adapted to environments in which quinoa does not currently grow well.
Animal Health Component
90%
Research Effort Categories
Basic
10%
Applied
90%
Developmental
0%
Classification

Knowledge Area (KA)Subject of Investigation (SOI)Field of Science (FOS)Percent
20215991080100%
Knowledge Area
202 - Plant Genetic Resources;

Subject Of Investigation
1599 - Grain crops, general/other;

Field Of Science
1080 - Genetics;
Goals / Objectives
The overall goal of this project is to produce new genetic variation that can be used to improve quinoa production domestically and internationallyObjective 1. Development and distribution of interspecific populations capturing natural diversity from wild relatives. This will involve assessing the genetic and phenotypic diversity in our set of ~200 C. berlandieri accessions, selecting 10 representative accessions for crossing with quinoa, advancing the resulting populations, and distributing the populations to domestic and international collaborators.2. Development and analysis of an induced mutant population for quinoa. This will involve treating quinoa seeds with the chemical mutagen EMS, advancing the mutant lines to the M3 generation, and sequencing mutant lines to identify mutations.3. Outreach to promote use of the enhance germplasm. This will involve creating a public database of genetic and phenotypic information from quinoa and interspecific crosses, and hosting a genomics workshop to teach necessary genomics analysis skills to potential users of our materials.
Project Methods
We will perform crosses between C. berlandieri and quinoa. To select accessions of C. berlandieri that best represent the genetic and phenotypic diversity of the 200 accessions, we will first assess genetic diversity through re-sequencing of the 200 accessions. Specifically, we will harvest young leaf tissue from all accessions, extract DNA from each accession, prepare Illumina sequencing libraries, and perform sequencing to a depth of ~10X coverage. We will then map sequencing reads to the reference quinoa genome and identify sequence variants in each accession, and use this data to calculate genetic diversity. This data will be primarily used for the selection of diverse accessions to be used for the crosses proposed. Moreover, the full genome re-sequencing data of all accession will be made publicly available to enable other researchers to identify and request accessions with variation in their genes of interest.While growing plants for DNA extraction and genotyping, we will also record data for morphological traits, including earliness; plant, panicle and seed color; panicle morphology; growth habit; and height. We will then use this phenotypic data, together with the genotypic data, to select 10 accessions that represent the genetic and phenotypic diversity of the larger panel.We will perform interspecific crosses using an approach we have used successfully in the past which involves placing C. berlandieri and heat-sensitive quinoa in a custom tent. High temperatures within the tent kill pollen from quinoa but not from C. berlandieri, facilitating the pollination of quinoa by C. berlandieri. We will cross each of the 10 selected C. berlandieri accessions with three quinoa accessions: PI 614886 (the reference genome accession, representing the coastal ecotype), Real (also a sequenced accession, representing the Salares ecotype from the high plains of Bolivia), and 0654 (representing the highland ecotype). In the event that we are unable to successfully cross with any of these quinoa varieties, we will concurrently perform crosses with a small number of additional varieties that can be used as backups. This will result in the development of 30 new interspecific populations, in addition to the populations that we have already generated.We will advance approximately 100 individuals from each population to the F5 generation using single-seed descent. To prevent cross pollination we will cover the seed head of each line with a pollination bag. These populations will then be distributed to breeding programs in the U.S. and throughout the world, including at Washington State University, University of Nevada-Reno, Utah State University, University of Minnesota, Vietnam National University of Agriculture, Universidad National Agraria La Molina, Universidad Autonoma Gabriel Rene Moreno, Institut Agronomique et Veterinaire Hassan II, King Abdullah University of Science and Technology, Lilongwe University of Agriculture and Natural Resources, Pontificia Universidad Catolica de Chile, and National Agricultural Research and Extension Institute. These researchers have agreed to collect and report data for several morphological traits, which will then be made publicly available.We performed preliminary work to identify an appropriate concentration of EMS for mutagenesis in quinoa. We treated approximately 12,000 quinoa seeds of the reference genome accession PI 614886 with 2.0% EMS, and 12,000 seeds with 2.5% EMS, in order to ensure a mix of mutant lines that have sufficient but not excessive mutations. EMS-treated seeds are growing in greenhouses at Brigham Young University. We will continue this initial mutagenesis step by harvesting M2 seed from approximately 2,000 M1 plants.We have observed several abnormal phenotypes in the M1 plants, suggesting that the initial mutagenesis treatment was successful. To perform an initial quantification of the mutagenesis rate, we will plant six seeds from each of 24 segregating M2 families and will perform exome capture sequencing from these plants. Specifically, we will extract DNA from each plant individually and then pool the DNA from all six plants for each M2 family, resulting in 24 DNA samples. We will use exome capture probes which we have already designed with Roche Sequencing in order to capture the exome of each pooled sample, which we will then sequence with Illumina sequencing to a depth of ~10X. This small pilot sequencing effort will quantitatively validate the methodology as well as provide an initial estimate of mutation frequency.The exome capture and sequencing will then be carried out on an additional 2,000 M2 families, with the exact number being determined by the mutagenesis rate calculated from the pilot study of 24 M2 families. We aim to sequence enough M2 families to identify 5 - 10 mutant alleles for each of the predicted quinoa genes in the genome. This extensive sequencing effort will ensure that these mutant lines can be made publicly available as an extensive mutant collection from which researchers and plant breeders can request lines containing mutations in their particular gene(s) of interest.As a first step in demonstrating the utility of the EMS mutant population, we will identify the genes and mutations that underlie the accumulation of bitter saponins in the seeds. First, we will target genes known to regulate saponin biosynthesis (Figure 5), including a candidate bHLH transcription factor (CqTSARL1) that we previously identified as putatively regulating the presence/absence of saponins in two independent segregating populations. The availability of complete exome sequences will enable us to identify all mutant lines that contain mutations in these saponin pathway genes. We will determine whether seeds of these lines contain saponins by subjecting M3 seed from each line to the well-established foam test. If the seeds contain saponins (as the wild-type PI 614886 accession does), the seed will produce foam when agitated in water. In addition, we will perform the foam test with M3 seed of all sequenced mutant families, in order to potentially identify saponin-free lines resulting from mutations in genes not previously known to regulate saponin accumulation.We will substantially expand the features of our existing genomic database, ChenopodiumDB (http://www.cbrc.kaust.edu.sa/chenopodiumdb/). Specifically, we will add or expand the following functionalities:Expansion of existing genomic resources to include all variants identified in the set of 200 C. berlandieri accessions.Addition of a phenotypic data resource feature that will house phenotypic data generated from the interspecific crosses, as well as future phenotypic data from quinoa and related species which individual researchers will be able to upload.Addition of a mutant resource feature, to include phenotypic and genotypic data for the EMS mutant population, as well as the ability to request seed from this population.The ChenopodiumDB is currently administered from a server in Saudi Arabia; we proposed to transfer administration of the database to Brigham Young University.We will host a genomics-enabled breeding workshop for participants who agree to evaluate our materials. We envision that the workshop will include hands-on instruction of common genomics methods, including genome assembly, read mapping, variant calling, and QTL and GWAS mapping approaches.

Progress 05/01/23 to 04/30/24

Outputs
Target Audience:1. Students, who were targeted in order to provide training in genetics and plant biology. 2. Other quinoa researchers and non-commercial growers, who were targeted in order to share knowledge and genetic resources. Changes/Problems:As part of our third goal, we had planned to host a training program during the summer of 2024; however, decided not to hold the meeting this summer because of the International Quinoa Symposium that was organized for July 2024. We will plan to host the training program in early 2025. What opportunities for training and professional development has the project provided?We hosted a visiting student, John Ithiru, from the lab of Dr. Sadanand Dhekney from the HBCU University of Maryland Eastern Shore. We also sent three BYU undergraduate students, Lesley Warner, Kayla Stephenson, and Preston Mayer, on a trip to Bolivia as part of joint trip with BYU Engineering (GEO) students. On this trip, students built and demonstrated how to operate affordable quinoa washers to remove saponins from the seed coats. We sent another BYU student, Ashlyn Anderson, on an internship to Malawi to participate in quinoa production. How have the results been disseminated to communities of interest?Presentations, journal article, and book chapters have been authored by all three project directors/co-PDs at conferences, including the Plant and Animal Genome 31 Conference. We have also continued distributing seeds from our interspecific crosses to quinoa researchers and growers, as described above. What do you plan to do during the next reporting period to accomplish the goals?During the next reporting period, we will accomplish the following, related to the three main objectives: 1. Introduce new genetic variation into quinoa by performing crosses with wild relatives. We will continue to develop new populations and advance all populations toward the F5 generation. We will finish our analysis of the sequencing of advanced selection lines from quinoa x C. berlandieri crosses to identify introgressed regions. We will analyze annotated genes in the introgressed regions to identify candidate genes underlying traits coming from the wild parents, including heat tolerance. 2. Introduce new variation into quinoa through random mutagenesis. We will finalize the manuscript and publish the results of the mutant population and sequencing analysis. We will continue to perform phenotypic screens to identify mutant traits in these lines. 3. Promote use of the new quinoa variation introduced in Objectives 1 and 2. We will update the quinoadb.org database to include the EMS mutagenesis sequencing data and the sequencing data from C. berlandieri. We will continue distributing interspecific population seeds to quinoa researchers and growers. We will organize a training program at BYU for quinoa researchers from North and South America to teach them how to utilize these genetic and genomic resources. 4. Host the three-month Fulbright visit in upcoming December-January-February of Dr. Sabrina Costa-Tartara of the Universidad Nacional de Lujan. She will be learning DNA sequence assembly methods and diversity evaluation methodologies on selected quinoa and wild (C. hircinum and C. berlandieri) lines. 5. Resequence extracted DNA from accessions of C. berlandieri from Manitoba, North Dakota, Iowa, and Ohio that represent the var. bushianum ecotype and integrate these data into our phylogenetic analysis from Maughan et al. (2024) to verify that this represents a unique ecotype/botanical variety or subspecies. The paper included only a single accession resembling this ecotype (BYU 1312 from Missouri), which is especially interesting germplasm due to its large seed size, daylength/flowering response gradient (longer from Canada southwards), enormous leaves, and sympatry with an extinct North American domesticated cultigen (C. berlandieri subsp. jonesianum).

Impacts
What was accomplished under these goals? Increased demand for quinoa has prompted a need for expanding domestic and global quinoa production, but quinoa is not well-adapted to growth conditions outside regions where it has traditionally been grown in South America. To increase the genetic variation needed in order to improve quinoa production in new areas, we have accomplished the following during this period of the project, in relation to the three main objectives: 1. Introduce new genetic variation into quinoa by performing crosses with wild relatives. We previously produced a reference genome assembly of C. berlandieri, performed shallow whole-genome sequencing of 75 additional accessions of C. berlandieri, and generated several interspecific crosses between accessions of C. berlandieri and quinoa. This year, we submitted a manuscript reporting the C. berlandieri reference genome and resequencing. We also performed whole-genome resequencing of 15 advanced selection lines produced through previous crosses between quinoa and C. berlandieri and are currently analyzing the sequencing data to identify genomic regions that were introgressed into the quinoa genome from the wild parents. These advanced lines are being field-tested in Kenya, Malawi, Peru, Argentina, France, and in Guyana in a collaboration between BYU and the University of Maryland-Eastern Shore (UMES), the latter receiving funding from an 1890 Land Grant consortium on the UMES side. 2. Introduce new variation into quinoa through random mutagenesis. We previously generated approximately 5,000 EMS mutant quinoa families and sequenced approximately 600 families using whole-genome or whole-exome sequencing. This year, we finished analysis of all sequencing data and are preparing a manuscript for publication. We are also working to upload all the sequencing data to our quinoadb.org database. Several new mutant phenotypes have been identified, including putative mutations underlying the phenotypes. 3. Promote use of the new quinoa variation introduced in Objectives 1 and 2. To make the genome sequencing data produced throughout this project, we continue the process of creating a genomic database for quinoa and its relatives. The database is now publicly available, and we are continuing to upload new data. We have also continued to distribute seed from our populations to interested scientists, including sending seed this year to Dr. Alejandro Bonifacio from the PROINPA institute in Bolivia.

Publications

  • Type: Journal Articles Status: Published Year Published: 2023 Citation: Rey E, Maughan PJ, Maumus F, Lewis D, Wilson L, Fuller J, Schm�ckel SM, Jellen EN, Tester M, Jarvis DE. A chromosome-scale assembly of the quinoa genome provides insights into the structure and dynamics of its subgenomes. Communications Biology 6:1263 (2023)
  • Type: Journal Articles Status: Published Year Published: 2024 Citation: Cueva Flores L, Gutierrez-Rosales R, Zeballos O, Condori-Apfata J, Lipa-Mamani L, Macedo-Valdivia D, Gomez-Pando L, Zhang C, Jellen EN, Mayta Anco ME. Effects of salt stress on tolerant accessions of quinoa at the morphological and metabolic levels. Chilean Journal of Agricultural Research 84:56-69
  • Type: Journal Articles Status: Accepted Year Published: 2024 Citation: Alania-Choque J, Vasquez-Espinoza L, Anculle-Arenas A, Bustamante-Mu�oz JL, Jellen EN, Gutierrez-Rosales RO, Mayta-Anco ME. Morphological characterization and agronomic evaluation of 25 accessions of Chenopodium quinoa in the Peruvian Coastal Desert, Agronomy (accepted pending revisions, 2024)
  • Type: Book Chapters Status: Published Year Published: 2023 Citation: Curti RN, Ortega-Baes P, Sajam J, Jarvis DE, Jellen EN, Tester M, Bertero D. Exploration and collection of quinoas wild ancestor in Argentina. In Biosaline Agriculture as a Climate Change Adaptation for Food Security. 167-178 (2023)
  • Type: Conference Papers and Presentations Status: Published Year Published: 2024 Citation: Kalt TK, Hopkins B, Jarvis DE, Ioannou V, Jellen EN. Analysis of nitrogen accumulation and gene expression in seven cultivated and wild quinoas. Plant and Animal Genome 31, San Diego, CA (2024)
  • Type: Conference Papers and Presentations Status: Published Year Published: 2024 Citation: Free A, Maughan PJ, Jellen EN, Jarvis DE. Genomic characterization of EMS-induced mutants in Chenopodium quinoa. Plant and Animal Genome 31, San Diego, CA (2024)
  • Type: Conference Papers and Presentations Status: Published Year Published: 2024 Citation: Marcheschi AK, Maughan PJ, Jarvis DE, Jellen EN. The genome of huauzontle (Chenopodium berlandieri), a North American relative of quinoa. Plant and Animal Genome 31, San Diego, CA (2024)
  • Type: Conference Papers and Presentations Status: Published Year Published: 2024 Citation: Jaggi K, Jellen EN, Jarvis DE, Krak K, Mandak B, Maughan PJ. A pangenome for Chenopodium. Plant and Animal Genome 31, San Diego, CA (2024)
  • Type: Conference Papers and Presentations Status: Published Year Published: 2024 Citation: Jellen EN, Roser RL, Brady RC, Maughan PJ, Jarvis DE, Jaggi K. Development of quinoa x pitseed goosefoot populations: genomics and breeding compatibility. Plant and Animal Genome 31, San Diego, CA (2024)
  • Type: Conference Papers and Presentations Status: Published Year Published: 2024 Citation: Torres K, Bratsman S, Gottfredson S, Borgmeier A, Cox B, Evans RP, Frandsen PB, Hadfield R, Jarvis DE, Jellen EN, Kokkonen A, Linde J, Lin YF, Maughan PF, Mulford T, Parker A, Smith SM, Young LA. Genome assembly of Dysphania ambrosioides. Plant and Animal Genome 31, San Diego, CA (2024)
  • Type: Conference Papers and Presentations Status: Published Year Published: 2024 Citation: Jellen EN, Maughan PJ, Jarvis DE, Genomic considerations in quinoa breeding via wide crossing with pitseed goosefoot (Chenopodium berlandieri). Plant and Animal Genome 31, San Diego, CA (2024)
  • Type: Theses/Dissertations Status: Submitted Year Published: 2024 Citation: Jaggi, K. Chromosome-scale assemblies and a pangenome reveal LTR repeat dynamics as a major driver of genome evolution in Chenopodium. Masters thesis. Brigham Young University (2024)
  • Type: Journal Articles Status: Published Year Published: 2024 Citation: Maughan PJ, Jarvis DE, de la Cruz-Torres E, Jaggi KE, Warner HC, Marcheschi AK, Bertero HD, Gomez-Pando L, Fuentes F, Mayta-Anco ME, Curti R, Rey E, Tester M, Jellen EN. North American pitseed goosefoot (Chenopodium berlandieri) is a genetic resource to improve Andean quinoa (C. quinoa). Scientific Reports 14:12345 (2024)


Progress 05/01/22 to 04/30/23

Outputs
Target Audience:1. Students, who were targeted in order to provide training in genetics and plant biology. 2. Other quinoa researchers and non-commercial growers, who were targeted in order to share knowledge and genetic resources. Changes/Problems:We previously proposed sequencing approximately 800-1,000 EMS mutant families; however, given the observed mutation rate, we calculate that we should reach our goal of an average of 10 mutant alleles per family by analyzing our existing sequencing results from approximately 600 families. We will use money saved from this part of the project to perform genotyping of the Real x BYU 937 F5 population to enable QTL mapping. What opportunities for training and professional development has the project provided?One undergraduate students participated in an internship at 25:2 Solutions; this is a private company with whom we are collaborating on quinoa breeding research. We also resubmitted a proposal to establish a formal collaboration with Dr. Helena Storchova from the Institute of Experimental Botany at the Czech Academy of Sciences to use our EMS mutant lines to study genes that regulate flowering time in quinoa and its relative, which will involve sending an undergraduate to Prague for a summer internship. We have continued a collaboration with Dr. Anand Dhekney from the plant breeding program at the 1890 Land Grant University of Maryland Eastern Shore. Our idea is to utilize the hot, humid Atlantic Tidewater environment and sandy soils for breeding quinoa that will be adapted to production under similar climatic and soil conditions in coastal Guyana. This will also provide opportunities for students from both institutions to collaborate on diverse teams of student-researchers. We also took several graduate and undergraduate students to Morocco to participate in quinoa field trials. How have the results been disseminated to communities of interest?Presentations, journal article, and book chapters have been authored by all three project directors/co-PDs at conferences, including the Plant and Animal Genome 30 Conference. We have also continued distributing seeds from our interspecific crosses to quinoa researchers and growers, as described above. What do you plan to do during the next reporting period to accomplish the goals?During the next reporting period, we will accomplish the following, related to the three main objectives: 1. Introduce new genetic variation into quinoa by performing crosses with wild relatives. We will continue to develop new populations and advance all populations toward the F5 generation. We will to perform QTL mapping in the Real x BYU 937 F5 population. As part of a collaboration with King Abdullah University, we will generate chromosome-scale assemblies of 3 more accessions of C. berlandieri. We will also perform resequencing of 10 additional accessions. 2. Introduce new variation into quinoa through random mutagenesis. We will finish analysis of all sequencing data and publish the results. We will continue to perform phenotypic screens to identify mutant traits in these lines. 3. Promote use of the new quinoa variation introduced in Objectives 1 and 2. We will update the quinoadb.org database to include the EMS mutagenesis sequencing data and the sequencing data from C. berlandieri. We will continue distributing interspecific population seeds to quinoa researchers and growers. We will organize a training program at BYU for quinoa researchers from North and South America to teach them how to utilize these genetic and genomic resources.

Impacts
What was accomplished under these goals? Increased demand for quinoa has prompted a need for expanding domestic and global quinoa production, but quinoa is not well-adapted to growth conditions outside regions where it has traditionally been grown in South America. To increase the genetic variation needed in order to improve quinoa production in new areas, we have accomplished the following during this period of the project, in relation to the three main objectives: 1. Introduce new genetic variation into quinoa by performing crosses with wild relatives. We previously produced a reference genome assembly of C. berlandieri, performed shallow whole-genome sequencing of 75 additional accessions of C. berlandieri, and generated three interspecific crosses between accessions of C. berlandieri and quinoa. This year, we advanced the Real-1 x BYU 937 population to the F5 generation and are preparing to perform QTL mapping for various traits in this population; performed several additional cross-combinations; and performed resequencing of 10 additional Chenopodium diploid species. We also produced draft or complete reference-quality genome assemblies of three additional Chenopodium species that, together with assemblies that we previously produced, represent all known sub-genomes of the genus. We have also performed field trials and seed increases of some interspecific populations at the University of Maryland Eastern Shore, in collaboration with Sadanand Dhekney. 2. Introduce new variation into quinoa through random mutagenesis. We previously generated approximately 5,000 EMS mutant quinoa families and sequenced approximately 600 families using whole-genome or whole-exome sequencing. This year, we are finishing the analysis of all this sequencing data and are compiling the identified mutations into a searchable database based on gene or mutation type. We also continue screening the mutations to identify those likely to result in mutant phenotypes. 3. Promote use of the new quinoa variation introduced in Objectives 1 and 2. To make the genome sequencing data produced throughout this project, we continue the process of creating a genomic database for quinoa and its relatives. We previously purchased a new computer server housed at BYU and are continuing to transfer and modify the existing ChenopodiumDB to this server. To make the database easier to find, we have purchased the domain quinoadb.org to host the database. In addition, this domain also links to a database of plant traits. Thus, the database will include both genetic and phenotypic data for quinoa and its relatives, facilitating the adoption of these resources domestically and around the world. We also continue the process of distributing seed from the crosses described in Objective 1 and from the EMS mutants described in Objective 2 to quinoa growers and researchers around the world. Specifically, we have sent or are preparing to send seed to the following: Dr. Christian Jung, Christian-Albrechts University of Kiel, Germany Dr. Nguyen Long, Vietnam National Agricultural University, Hanoi, Vietnam Dr. Mark Tester, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia Dr. Hassan Munir, Faisalabad Agricultural University, Pakistan Dr. Moses Maliro, Lilongwe University of Agriculture and Natural Resources, Bunda, Malawi Dr. Peter Bulli, Jaramogi Oginga Odinga University of Science and Technology, Bondo, Kenya Dr. Ouafae Benlhabib, Institut Agronomique et Veterinaire-Hassan II, Rabat, Morocco Dr. Didier Bazile, CIRAD, Montpelier, France Dr. Eulogio de la Cruz, Instituto Nacional de Investigaciones Nucleares, Ocoyoacac, Mexico Premdat Beecham, National Agricultural Research and Extension Institute, Mon Repos, Guyana Ana Eguiluz Universidad Nacional de Agricultura La Molina, Lima, Peru Dr. Mayela Mayta, Universidad Nacional de San Agustín, Arequipa, Peru Dr. Jorge Rojas, Universidad Mayor de San Simón, Cochabamba, Bolivia Dr. Marín Condori, Universidad Autónoma de Gabriel Rene Moreno, Santa Cruz, Bolivia Dr. Francisco Fuentes, Universidad Pontificia Católica, Santiago, Chile Dr. Daniel Bertero, Universidad de Buenos Aires, Buenos Aires, Argentina Dr. Ramiro Curti, Universidad Nacional de Salta, Salta, Argentina Dr. Cedric Habiyaremye, Global Participatory Quinoa Research Program, Rwanda

Publications

  • Type: Conference Papers and Presentations Status: Published Year Published: 2022 Citation: Jarvis DE, Maughan PJ, Hameed A, Jellen EN. Genetic and genomic resources for studying abiotic stress tolerance in quinoa. Gordon Research Conference (Salt and Water Stress in Plants), Les Diablerets, Switzerland (2022)
  • Type: Theses/Dissertations Status: Published Year Published: 2022 Citation: Parker AA. Implementation of a genome-wide survey of induced mutations to identify agronomically valuable variants in Chenopodium quinoa. Masters thesis, BYU, 2022
  • Type: Conference Papers and Presentations Status: Published Year Published: 2023 Citation: Jaggi K, Jarvis DE, Jellen EN, Krak K, Mandak B, Maughan PJ. Subgenome assembly and comparison of six Chenopodium subgenomes. Plant and Animal Genome 30, San Diego, CA (2023)
  • Type: Conference Papers and Presentations Status: Published Year Published: 2023 Citation: Wilson LB, Maughan PJ, Jellen EN, Jarvis DE. Mutation detection on EMS treated Chenopodium quinoa population. Plant and Animal Genome 30, San Diego, CA (2023)
  • Type: Conference Papers and Presentations Status: Published Year Published: 2023 Citation: Morris A, Rey E, Melino V, Xu J, Jellen EN, Jarvis DE, Maughan PJ, Bertero D, Tester MA. Heat stress effects on in vitro pollen germination and pollen tube elongation in Chenopodium quinoa and wild relatives. Plant & Animal Genome 30, San Diego, CA, (2023)
  • Type: Conference Papers and Presentations Status: Published Year Published: 2023 Citation: Maughan PJ, Young L, Jarvis DE, Hunt SP, Warner HC, Durrant KK, Kohlert T, Curti RN, Bertero D, Filippi GA, Pospisilikova T, Krak K, Mandak B, Jellen EN. A chromosome-scale reference of Chenopodium watsonii helps elucidate relationships within North American A-genome Chenopodium species. Plant & Animal Genome 30, San Diego, CA (2023)
  • Type: Conference Papers and Presentations Status: Published Year Published: 2023 Citation: Warner HC, Jaggi K, Maughan PJ, Jarvis DE, Jellen EN. Evaluation of recombination and identification of hybrids in quinoa x pitseed goosefoot and quinoa x avian goosefoot F2 populations. Plant & Animal Genome 30, San Diego, CA (2023)
  • Type: Conference Papers and Presentations Status: Published Year Published: 2023 Citation: Jarvis DE, Maughan PJ, Jellen EN. Genetic resources for gene discovery and agronomic improvement of quinoa. 8th World Quinoa Congress, Potos�, Bolivia (2023)
  • Type: Book Chapters Status: Published Year Published: 2022 Citation: Rojas-Beltran JA, Rojas-Vargas EL, Mujica A, Jellen EN (2022) Chapter 7: El genoma de la quinua. In: La Quinua, El Grano Sagrado de los Incas, pp 193-246. Beltran JA, Ren G, Mujica A, eds.
  • Type: Book Chapters Status: Published Year Published: 2022 Citation: Rojas-Beltran JA, Gandarillas C, Mujica A, Herbas J, Jellen E, Maughan J, Alanoca C, Rojas-Vargas EL (2022) Chapter 14: Variedades tropicales de quinua en Bolivia. In: La Quinua, El Grano Sagrado de los Incas, pp 385-402. Beltran JA, Ren G, Mujica A, eds.
  • Type: Journal Articles Status: Published Year Published: 2023 Citation: A chromosome-scale reference of Chenopodium watsonii helps elucidate relationships within the North American A-genome Chenopodium species and with quinoa
  • Type: Journal Articles Status: Published Year Published: 2022 Citation: Jarvis DE, Sproul JS, Navarro-Dom�nguez B, Krak K, Jaggi K, Huang Y-F, Huang T-Y, Lin TC, Jellen EN, Maughan PJ. Chromosome-scale genome assembly of the hexaploid Taiwanese goosefoot djulis (Chenopodium formosanum). Genome Biology and Evolution 14:evac120 (2022)


Progress 05/01/21 to 04/30/22

Outputs
Target Audience:The target audiences reached by our efforts during this reporting period include the following: 1. Students, who were targeted in order to provide training in genetics and plant biology. 2. Other quinoa researchers and non-commercial growers, who were targeted in order to share knowledge and genetic resources. Changes/Problems:Because genetic similarity among the first ~75 sequenced accessions of C. berlandieri indicated a high degree of similarity among the major ecotypes, sequencing of additional accessions to reach the targeted number of 200 will be unlikely to uncover new genetic variation. Thus, we previously decided to devote resources to sequencing individuals of the interspecific populations at the F5 generation, rather than sequencing additional accessions. This sequencing will facilitate genetic mapping in order to identify genes underlying desirable traits in these populations. Likewise, we also will divert some of the sequencing resources to better understand diversity within the Chenopodium genus by sequencing species that collectively represent all known sub-genomes in the genus. What opportunities for training and professional development has the project provided?Two undergraduate students participated in an internship at 25:2 Solutions; this is a private company with whom we are collaborating on quinoa breeding research. Another undergraduate is currently in an internship at King Abdullah University of Science and Technology. We are also in the process of entering into a formal collaboration with Dr. Helena Storchova from the Institute of Experimental Botany at the Czech Academy of Sciences to use our EMS mutant lines to study genes that regulate flowering time in quinoa and its relative, which will involve sending an undergraduate to Prague for a summer internship. Finally, we have begun a collaboration with Dr. Anand Dhekney from the plant breeding program at the 1890 Land Grant University of Maryland Eastern Shore. Our idea is to utilize the hot, humid Atlantic Tidewater environment and sandy soils for breeding quinoa that will be adapted to production under similar climatic and soil conditions in coastal Guyana. This will also provide opportunities for students from both institutions to collaborate on diverse teams of student-researchers. How have the results been disseminated to communities of interest?Presentations have been given by all three project directors/co-PDs at the 2nd International Quinoa Research Symposium. We have also begun distributing seeds from our interspecific crosses to quinoa researchers and growers, as described above. What do you plan to do during the next reporting period to accomplish the goals?During the next reporting period, we will accomplish the following, related to the three main objectives: 1. Introduce new genetic variation into quinoa by performing crosses with wild relatives. We will continue to develop new populations and advance all populations toward the F5 generation. We will prepare to perform QTL mapping in these advanced populations. 2. Introduce new variation into quinoa through random mutagenesis. We will finish analysis of all sequencing data and publish the results. We will continue to perform phenotypic screens to identify mutant traits in these lines. 3. Promote use of the new quinoa variation introduced in Objectives 1 and 2. We will update the quinoadb.org database to include the EMS mutagenesis sequencing data and the sequencing data from C. berlandieri. We will continue distributing interspecific population seeds to quinoa researchers and growers.

Impacts
What was accomplished under these goals? Increased demand for quinoa has prompted a need for expanding domestic and global quinoa production, but quinoa is not well-adapted to growth conditions outside regions where it has traditionally been grown in South America. To increase the genetic variation needed in order to improve quinoa production in new areas, we have accomplished the following during this period of the project, in relation to the three main objectives: 1. Introduce new genetic variation into quinoa by performing crosses with wild relatives. We previously produced a reference genome assembly of C. berlandieri and performed shallow, whole-genome sequencing of 75 additional accessions of C. berlandieri. We also previously generated three interspecific crosses between accessions of C. berlandieri and quinoa. This year, we advanced existing crosses of Real-1 x BYU 937 and Real-1 x BYU 1101 to the F4 generation; confirmed five additional cross-combinations; developed SSR markers to identify hybrids from putative F1 hybrids from additional crosses to BYU 14118 (Mojave Desert), BYU 1494 (Sonoran Desert), BYU 1840 (California Coastal C. berlandieri var. sinuatum), and BYU 1866 (Florida ecotype). We performed a whole-genome assembly of the Colorado Plateau AA diploid species C. watsonii and used that to call SNPs in a large panel of >30 AA resequenced diploids to pinpoint the closest A-genome relative of quinoa and berlandieri, which turned out to be the very rare Great Plains psammophyte C. subglabrum. We also sequenced the Eurasian Chenopodium relatives C. formosanum (BBCCDD), C. strictum (CCDD), and C. acuminatum (DD). As part of Objective #1, we had a team of two students take the lead in producing two intertaxa F2 population-based genetic maps - for Real-1 x BYU 937 (population R9) and Real-1 x BYU 1101 (population R11) - from parental SNPs called against the QQ74 quinoa whole-genome assembly using JoinMap. Recombination distance was then linearly plotted against physical distance along each of the 18 pseudochromosomes, with the goal of confirming that the chromosomes were recombining in these wide crosses. Our initial hypothesis was that quinoa would show greater recombination fidelity in cross-combination with its South American ancestor C. hircinum (BYU 1101) and somewhat less fidelity in hybrids with the Texas boscianum genotype (BYU 937). Indeed, we identified fewer SNPs (~1700 in R11 versus ~2500 in R9) in the R11 population due to less DNA sequence divergence; however, the map distances were comparable at 2755 cM and 2600 cM in R11 and R9, respectively. Aside from a large pericentric inversion on chromosome 3B in the QQ74 reference genome and a 4A telomeric inversion of unknown origin in both mapping populations, the only other structural anomaly was a large 6A terminal inversion present only in the R11 map. Our conclusion was that the boscianum Gulf Coast ecotype of pitseed goosefoot is a very acceptable genetic resource for adaptive breeding of Andean-origin quinoa. 2. Introduce new variation into quinoa through random mutagenesis. We previously generated approximately 5,000 EMS mutant quinoa families and sequenced approximately 50 families using either whole-genome or whole-exome sequencing. This year, we sequenced approximately 600 additional families using whole-genome sequencing and are currently in the process of identifying mutations in these families from the sequencing data and compiling the mutations into a searchable database based on gene or mutation type. We have also begun screening the mutations to identify those likely to result in mutant phenotypes. As an example, we have identified several mutants that display a reduced-height phenotype. 3. Promote use of the new quinoa variation introduced in Objectives 1 and 2. To make the genome sequencing data produced throughout this project, we continue the process of creating a genomic database for quinoa and its relatives. We previously purchased a new computer server housed at BYU and are continuing to transfer and modify the existing ChenopodiumDB to this server. To make the database easier to find, we have purchased the domain quinoadb.org to host the database. In addition, this domain also links to a database of plant traits. Thus, the database will include both genetic and phenotypic data for quinoa and its relatives, facilitating the adoption of these resources domestically and around the world. We also continue the process of distributing seed from the crosses described in Objective 1 and from the EMS mutants described in Objective 2 to quinoa growers and researchers around the world. Specifically, we have sent or are preparing to send seed to the following: Dr. Christian Jung, Christian-Albrechts University of Kiel, Germany Dr. Nguyen Long, Vietnam National Agricultural University, Hanoi, Vietnam Dr. Mark Tester, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia Dr. Hassan Munir, Faisalabad Agricultural University, Pakistan Dr. Moses Maliro, Lilongwe University of Agriculture and Natural Resources, Bunda, Malawi Dr. Peter Bulli, Jaramogi Oginga Odinga University of Science and Technology, Bondo, Kenya Dr. Ouafae Benlhabib, Institut Agronomique et Veterinaire-Hassan II, Rabat, Morocco Dr. Didier Bazile, CIRAD, Montpelier, France Dr. Eulogio de la Cruz, Instituto Nacional de Investigaciones Nucleares, Ocoyoacac, Mexico Brian Sears, National Agricultural Research and Extension Institute, Mon Repos, Guyana Dr. Luz Gomez, Universidad Nacional de Agricultura La Molina, Lima, Peru Dr. Mayela Mayta, Universidad Nacional de San Agustín, Arequipa, Peru Dr. Jorge Rojas, Universidad Mayor de San Simón, Cochabamba, Bolivia Dr. Marín Condori, Universidad Autónoma de Gabriel Rene Moreno, Santa Cruz, Bolivia Dr. Francisco Fuentes, Universidad Pontificia Católica, Santiago, Chile Dr. Daniel Bertero, Universidad de Buenos Aires, Buenos Aires, Argentina

Publications

  • Type: Conference Papers and Presentations Status: Published Year Published: 2022 Citation: Jaggi K, Warner H, Jellen EN, Jarvis DE, Young L, Adams A, Brady R, Jellen S, Bertero D, Maughan PJ. Exploitation of wild Chenopodium species for quinoa agronomic improvement. Utah Conference on Undergraduate Research, St. George, UT (2022)
  • Type: Conference Papers and Presentations Status: Published Year Published: 2022 Citation: Young LA, Maughan PJ, Jaggi K, Warner HC, Jarvis DE, Bertero D, Tester MA, Benet-Pierce N, Jellen EN. Identification of the closest extant species to the A-genome diploid ancestors of AABB Chenopodium berlandieri and C. quinoa. Plant and Animal Genome XXIX, San Diego, CA (2022)
  • Type: Conference Papers and Presentations Status: Published Year Published: 2022 Citation: Warner HC, Jaggi K, Maughan PJ, Jarvis DE, Young LA, Adams AB, Brady RC, Jellen SG, Bertero D, Jellen EN. Evaluation of segregation and recombination in quinoa x pitseed goosefoot and quinoa x avian goosefoot F2 populations. Plant and Animal Genome XXIX, San Diego, CA (2022)
  • Type: Conference Papers and Presentations Status: Published Year Published: 2022 Citation: Parker A, Maughan PJ, Jellen EN, Jarvis DE. Implementation of a genome-wide survey of induced mutations to identify agronomically valuable variants in Chenopodium quinoa. Plant and Animal Genome XXIX, San Diego, CA (2022)
  • Type: Conference Papers and Presentations Status: Published Year Published: 2022 Citation: Jarvis DE, Maughan PJ, Jellen EN, Sproul J, Krak K, Dominguez BN, Huang Y. Additional genomic resources in the Amaranthaceae. Plant and Animal Genome XXIX, San Diego, CA (2022)
  • Type: Theses/Dissertations Status: Published Year Published: 2020 Citation: Cox BJ. EMS mutagenesis in quinoa: Developing a genetic resource. Masters thesis, BYU, 2020
  • Type: Book Chapters Status: Published Year Published: 2022 Citation: Rojas-Beltran JA, Rojas-Vargas EL, Mujica A, Jellen EN (2022) Chapter 7: El genoma de la quinua. In: La Quinua, El grano Sagrado de los Incas. Beltran JA, Ren G, Mujica A, eds. Pp 193-246.


Progress 05/01/20 to 04/30/21

Outputs
Target Audience:The target audiences reached by our efforts during this reporting period include the following: 1. Students, who were targeted in order to provide training in genetics and plant biology. 2. Other quinoa researchers and non-commercial growers, who were targeted in order to share knowledge and genetic resources. Changes/Problems:Restrictions imposed due to the coronavirus pandemic limited the number of hours students were able to work on this project; thus, the sequencing the EMS mutant lines has proceeded more slowly than planned. Genetic similarity among the first ~75 sequenced accessions of C. berlandieri indicates a high degree of similarity among the major ecotypes. Thus, sequencing of additional accessions to reach the targeted number of 200 will be unlikely to uncover new genetic variation. We anticipate instead devoting resources to sequencing individuals of the interspecific populations at the F5 generation, rather than sequencing additional accessions. This sequencing will facilitate genetic mapping in order to identify genes underlying desirable traits in these populations. What opportunities for training and professional development has the project provided?Two undergraduate students have been given an internship opportunity at 25:2 Solutions for the summer of 2021. In addition, we have started a collaboration with Dr. Shawn Christensen from the USDA to learn metabolomics. We have also started a collaboration with Dr. Malia Gehan from the Danforth Center to gain expertise in conducting heat stress experiments. How have the results been disseminated to communities of interest?Presentations have been given by all three project directors/co-PDsat the 2nd International Quinoa Research Symposium. We have also begun distributing seeds from our interspecific crosses to quinoa researchers and growers, as described above. What do you plan to do during the next reporting period to accomplish the goals?During the next reporting period, we will accomplish the following, related to the three main objectives: 1. Introduce new genetic variation into quinoa by performing crosses with wild relatives.In the F2 generation, we will perform genetic mapping for seed related traits, including seed color, seed coat thickness, and the presence of trimethyl amines in the seeds. We will advance each population to the F5 generation. We will also perform trial experiments to establish experimental conditions to assess salt and heat tolerance in these populations. 2. Introduce new variation into quinoa through random mutagenesis.We will perform genome sequencing of another approximately 800 mutant lines. We will continue to perform phenotypic screens to identify mutant traits in these lines. 3. Promote use of the new quinoa variation introduced in Objectives 1 and 2.We will finish transferring the ChenopodiumDB database to BYU servers and host it at quinoadb.org. We will finish distributing F2 seeds to quinoa researchers and growers.

Impacts
What was accomplished under these goals? Increased demand for quinoa has prompted a need for expanding domestic and global quinoa production, but quinoa is not well-adapted to growth conditions outside regions where it has traditionally been grown in South America. To increase the genetic variation needed in order to improve quinoa production in new areas, we have accomplished the following during this period of the project, in relation to the three main objectives: 1. Introduce new genetic variation into quinoa by performing crosses with wild relatives. As a first step to using C. berlandieri as a source of novel variation to introduce into quinoa, we have performed genome sequencing of approximately 75 accessions of C. berlandieri and assessed their relatedness. The accessions cluster together mainly according to known groupings of C. berlandieri varieties, indicating that selecting from each of the main groupings for future work will help to represent all the variation present in the species. In related work not part of this grant, we produced a reference-quality genome sequence of a cultivated C. berlandieri known as huauzontle. This reference genome was vital for the comparisons of the 75 other berlandieri accessions. Based on this preliminary genome sequencing analysis of C. berlandieri as well as other preliminary work, we selected a representative accession to cross with quinoa. Specifically, we crossed C. berlandieri var. boscianum (BYU 937), a variety collected from the Texas gulf coast with two quinoa varieties: Real and Surimi. We also crossed a variety of the wild quinoa species C. hircinum (BYU 1101 from Argentina) with quinoa Real and Surimi. The genomes of plants from the first generation (F1) resulting from each of these crosses were sequencing to confirm that they represented true hybrids. This is the first confirmed occurrence of hybrids produced manually between quinoa and the wild species C. berlandieri and C. hircinum. We advanced this first generation to the second generation (F2) and performed partial sequencing of approximately 100 individuals each from the Real x BYU 937 and Real x BYU 1101 crosses. This sequencing data was used to show that the genomes of the two parental species are recombining in the offspring, an important requirement for being able to use these crosses to introduce desirable variation from the wild relatives into quinoa. We have also shown in preliminary assessments that the progeny of these crosses are segregating for traits from both parents. This important work demonstrates that these crosses can indeed be used to map the genes that underlie important traits that can be improved in quinoa, such as heat tolerance. 2. Introduce new variation into quinoa through random mutagenesis. We have introduced new genetic variation into quinoa by treating it with a chemical mutagen, EMS. The EMS treatment has been completed, and seeds have been harvested from approximately5,000 mutant plants. DNA has been sequenced from approximately 50 mutant plants so far, confirming the existence of novel mutations. The identification of a mutation in a gene responsible for producing color in the stem of newly germinated plants served as validation that we can introduce new mutations into quinoa that results in new traits. We are now preparing almost 800 additional plants for sequencing in order to identify the mutations in these plants. DNA has been extracted from almost all plants, and the first 96 samples are almost ready for DNA sequencing. We are also growing these mutant plants to observe any new traits that have resulted because of the mutations, and have already identified putatively useful mutants, including potential dwarf mutants. The identification of these genetic mutations and the new traits resulting from them is an important validation that random mutagenesis can be used to introduce new variation in quinoa in order to improve its growth and production. 3. Promote use of the new quinoa variation introduced in Objectives 1 and 2. To make the genome sequencing data produced throughout this project, we are in the process of creating a genomic database for quinoa and its relatives. To expedite the process, we are modifying the existing ChenopodiumDB, that we previously started as part of another project. We have purchased a new computer server to be housed at BYU and are currently transferring the existing ChenopodiumDB to this server. In addition, to make the database easier to find, we have purchased the domain quinoadb.org to host the database. In addition, we are collaborating with Dr. Mark Tester from King Abdullah University of Science and Technology to host a database of plant traits on quinoadb.org. Thus, the database will include both genetic and phenotypic data for quinoa and its relatives, facilitating the adoption of these resources domestically and around the world. We are also in the process of distributing F2 seed from the crosses described in Objective 1 to quinoa growers and researchers around the world. Specifically, we have sent or are preparing to send seed to the following: Dr. Ouafae Benlhabib, IAV-Hassan II, Rabat, Morocco Dr. Nguyen Long, VNAU, Hanoi, Vietnam Dr. Moses Maliro, LUANAR, Bunda, Malawi Dr. Hassan Munir, UAF, Faisalabad, Pakistan Dr. Francisco Fuentes, PUC, Santiago, Chile Dr. Eulogio de la Cruz, ININ, Ocoyoacac, Mexico Ing. Marin Condori, UAGRM, Santa Cruz de la Sierra, Bolivia Dr. Jorge Rojas, UMSS, Cochabamba, Bolivia Dr. Luz Gomez, UNALM, La Molina, Peru Mr. Jagnarine Singh, NAREI, Demerara, Guyana Dr. Ramiro (El Cocalero) Curti, UNS, CONICET, Salta, Argentina Dr. Mark Tester, KAUST, Thuwal, Saudi Arabia

Publications

  • Type: Conference Papers and Presentations Status: Published Year Published: 2020 Citation: David Jarvis. EMS mutagenesis in quinoa: Demonstrating the utility of genomic resources. 2nd International Quinoa Research Symposium. Aug 17-19, 2020.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2020 Citation: Jeff Maughan. Amaranthaceae genomic resources  BYU. 2nd International Quinoa Research Symposium. Aug 17-19, 2020.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2020 Citation: Rick Jellen. Genetic resources and breeding goosefoots (including quinoa). 2nd International Quinoa Research Symposium. Aug 17-19, 2020.