Performing Department
(N/A)
Non Technical Summary
The continued improvement of alfalfa requires broad genetic variation. Genebanks, such as the USDA ARS National Plant Germplasm System (NPGS), contain thousands of accessions of alfalfa germplasm that could contain desirable alleles not present in commercial breeding programs. Our project is a long-term endeavor to concentrate desirable genetic diversity from the NPGS collection into a small number of regionally-adapted germplasm pools for incorporation into modern alfalfa breeding programs. Our team includes alfalfa breeders, geneticists, and curators from throughout the northern United States (NY, WI, WA, and CA) and has previously developed over 30 germplasm populations as part of this project. The goals of this proposal are to (1) characterize the genetic diversity of 1,000 germplasm accessions and map genes using existing data; (2) phenotypically evaluate unique and previously unused accessions and previously created germplasm populations in multi-location trials under different managements, (3) release at least eight germplasm pool populations, and (4) conduct outreach activities including with private sector breeders regarding the value of this germplasm. We will use genetic alfalfa-specific SNP markers (DArT) developed by the Cornell-based and USDA ARS-supported Breeding Insight program in all our analyses. These pools will provide unique genetic variation for future breeding in the northern US. Results of our project will be extended to seed companies, producers, and crop consultants through field days, extension bulletins, social media, and websites. This project addresses ASAFS program area 1. Increase alfalfa forage and seed yields and forage quality through plant breeding to reduce biotic and abiotic stresses.@font-face{panose-1:2 4 5 3 5 4 6 3 2 4;mso-font-charset:0;mso-generic-mso-font-pitch:variable;mso-font-signature:-536870145 1107305727 0 0 415 0;}p.MsoNormal, li.MsoNormal, div.MsoNormal{mso-style-unhide:no;mso-style-qformat:yes;mso-style-parent:"";margin:0in;mso-pagination:widow-orphan;;mso-fareast-mso-fareast-language:EN-US;}p.Default, li.Default, div.Default{mso-style-name:Default;mso-style-unhide:no;mso-style-parent:"";margin:0in;mso-pagination:none;mso-layout-grid-align:none;text-autospace:none;;mso-fareast-mso-fareast-language:EN-US;}.MsoChpDefault{mso-style-type:export-only;mso-default-props:yes;;mso-ansi-;mso-bidi-;mso-font-kerning:0pt;mso-ligatures:none;}div.WordSection1{page:WordSection1;}
Animal Health Component
50%
Research Effort Categories
Basic
25%
Applied
50%
Developmental
25%
Goals / Objectives
Our long-term goal is to develop new breeding pools from untapped genetic resources to improve biomass yield, forage nutritive value, and other traits to maintain and increase productivity in climates of the future. In previous iterations of this project, we have developed initial populations of both northern- and southern-adapted pools. For this proposal, we intend to characterize these populations both phenotypically and genetically, identify genetic loci contributing to agronomic and morphological traits, and release the initial populations through the official channels of our respective institutions, making them available through the NPGS for distribution to interested researchers and seed companies. In addition, we will continue to make selections within these pools in our on-going base broadening effort to make these populations relevant to commercial breeding programs.The specific objectives of this project are as follows:Assess genetic diversity among NPGS accessions and map important traits.Create and evaluate germplasm pools under multiple management systems.Release new pre-bred improved germplasm pools for community use.Extend information regarding germplasm pools and their performance.
Project Methods
Objective 1. Assess genetic diversity among NPGS accessions and map important traitsObjective 1.1. Genotyping the progenitor accessions to current germplasm pre-breeding pools and additional germplasm incorporated into these poolsFor this objective, we will genotype ~1,000 accessions, including the 250 accessions initially evaluated and adding another 750 accessions from the collection to be selected for diversity of geographic origin, improvement status (landrace and wild germplasm), and the availability of characterization data in GRIN-Global for multiple traits. Accessions in the core collection (~200) will be included and 10-15 cultivars from the North American cultivated gene pool will be included for comparison. We will determine accession genotypes using the Breeding Insights 3K DArTag capture set (Zhao et al., 2023). We will estimate allele frequencies within each accession and use the frequencies for subsequent analyses. Accessions will be clustered using principal components analysis based on allele frequencies.Objective 1.2. Mining NPGS GRIN-Global data to assess the genetic basis of key traitsWe will conduct a genome-wide association study (GWAS) to identify genetic markers linked to key traits, especially disease and insect resistances, which have been previously been obtained using standard tests and included in the NPGS GRIN system database. The accessions we analyze in Obj. 1.1. will have been selected to maximize our ability to conduct meaningful GWAS. We will conduct GWAS and also develop genomic prediction models using GAPIT in TASSEL 5.0 (Bradbury et al., 2007).Objective 2. Create and evaluate germplasm pools under multiple managementsObj. 2.1. Continue current evaluation trials of the Round 1 Cycle 2 populationsThe R1C2 populations are growing in space-planted nurseries in NY, WI, and CA and Canadian collaborators (AB, QC). Plants have been evaluated for biomass, growth habit, plant height, maturity, fall growth, and persistence and additional data will be collected throught 2025. In 2025, plants will be selected at each location and intercrossed to form Round 1 Cycle 3 (R1C3). From each spaced plant trial at each location, we will select the "best" plants within geographic pools from among all the location-specific populations. Between 5 to 10% will be selected at each test location to generate the next cycle for each pool. Plants will be selected among the survivors for vigor, freedom from root and shoot diseases or insect pests, and autumn regrowth. Plants will be dug from the field and moved to the greenhouse for intercrossing either by hand or using bee pollinators in isolation cages. Seed will be harvested individually from each plant and an equal quantity bulked from each plant. Syn2 seed production in WA in 2027 using populations combined across locations.Obj. 2.2. Evaluate unique germplasm identified in Obj. 1.1 for new enhanced populationsThe evaluation will include at least 100 new accessions and will also include R2C1 and R1C2 germplasm for comparative purposes. We will have 3000 plants in each nursery at each location (20 plants per entry, 10 in each replication). The evaluation will be planted in 2025 as a multi-location (CA, NY, WI) trial, evaluated for biomass, growth habit, plant height, maturity, fall growth, and persistence traits through 2027. After the period of the proposal, plants will be selected and recombined in 2028 to form the subsequent cycle (R3C1). Syn1 seed will be produced at each location by hand intercrossing in the greenhouse in 2029, and Syn2 seed will be produced in WA in bee cage isolation in 2030.Obj. 2.3. Evaluation of germplasm pool populations in multiple environmentsEight populations are available in hand from earlier iterations of this project, representing the four germplasm origins (SIBR, CASIA, EURO, OTTM) and two rounds of germplasm evaluations. Trials will be conducted on research stations and on-farm in each participating state (CA, WI, and NY). The on-station trials will include three management treatments: monoculture, grass overseeding, and a regionally relevant abiotic stress treatment (e.g., deficit irrigation (CA), low fertility (NY, WI)). Planting will take place during the 2025 growing season. At each location (CA, WI, and NY) the experiment will be planted as a split block design with six blocks (two replicates × three treatments) with each entry replicated two times within each of the six blocks. Plots will be planted as single or paired rows between 15 and 25 feet long depending on planting equipment and seed availability. Grass overseeding block treatments will be broadcast overseeded with perennial forage grasses prior to drilling alfalfa plots. In the establishment year, we will evaluate seedling establishment and vigor. In subsequent years we will evaluate persistence, vigor, and damage from regionally relevant disease and insect pests. We will also take tissue samples for genotyping at establishment and twice annually thereafter to explore genetic shifts in populations due to stand thinning over time. Where possible, we will use the Field Book app (Rife and Poland, 2014) and standardized trait ontologies to facilitate cross-location analyses. The on-farm trials will be conducted using a single management treatment and planted within a larger production field, using the management practices the farmer would typically use on their farm.DNA marker profiles using the DArTag system will be obtained on DNA from pooled field collected tissue and data will be evaluated to determine if shifts in population allele frequencies have occurred over time and among different locations by determining if populations have differentiated according to Fst using a smoothing-spline technique (Beissinger et al. 2015).Obj. 2.4. Evaluate germplasm pools in hybrids or strain crosses with commercial cultivars.We will work directly with commercial breeding companies to generate germplasm pool × advanced elite breeding population hybrids or strain crosses. These will be created by each company using the germplasm pool or pools they are most interested in evaluating. Because this objective will necessarily involve proprietary germplasm and intellectual property constraints, the exact way that evaluation trials will be pursued subsequently will be determined at our advisory board meeting, with all companies at the table. We will evaluate variety trial data of yield and other traits (fall height, vigor, persistence) using standard mixed models and mean separations. The value of populations containing germplasm pool parentage will be determined by comparison to elite check cultivars and breeding lines in the trials.Objective 3. Release new germplasm poolsThe project team has selected and produced seed of eight pre-breeding populations (four populations each from R1C2 and R2C1). Seed of all eight populations will be in hand by Fall 2024. These populations will be submitted as joint germplasm releases through all three institutions (UC-Davis, USDA-ARS, Cornell) and contributed to NPGS as new accessions. Data from previous trials together with disease and insect resistance information obtained from our commercial partners (see letters of support) will be used as justification for release. The release process will be initiated in Fall 2024 and will go through release committees at all participating locations. Additional populations developed over the course of the project will also be released when sufficient seed is available, likely after the end of this project.