Source: UNIVERSITY OF CALIFORNIA, DAVIS submitted to
PARTNERSHIP: A SYSTEMS APPROACH TO MECHANICAL HARVESTING IN PEPPER
Sponsoring Institution
National Institute of Food and Agriculture
Project Status
NEW
Funding Source
AFRI COMPETITIVE GRANT
Reporting Frequency
Annual
Accession No.
1030326
Grant No.
2023-67013-39623
Project No.
CA-D-PLS-2769-CG
Proposal No.
2022-10294
Multistate No.
(N/A)
Program Code
A1141
Project Start Date
Mar 1, 2023
Project End Date
Feb 28, 2026
Grant Year
2023
Project Director
Van Deynze, A.
Recipient Organization
UNIVERSITY OF CALIFORNIA, DAVIS
410 MRAK HALL
DAVIS,CA 95616-8671
Performing Department
(N/A)
Non Technical Summary
The long-term goal of this project is to develop competitive green chile pepper varieties amenable to mechanical harvesting. The critical need is to reduce labor costs associated with harvesting of processed peppers, essential for sustainability of the US industry and a growing market worldwide. Our objectives formulate a systems approach combining genomics, physiology, plant breeding, horticulture, and mechanization. They include: 1) Develop breeding lines of green jalapeno and New Mexico chile pepper that combine destemming, plant architecture and uniformity 2) Characterize genotype x environment x management interactions on plant architecture and yield 3) Determine the inheritance of plant architecture and determinacy in pepper 4) Fine-map key loci for destemming in pepper. This project addresses Plant Breeding for Agricultural Production, Priority Code A1141. It addresses Pre-breeding, Germplasm enhancement, Applied quantitative genetics and Cultivar development by breeding and evaluating the performance of improved green chile and jalapeño lines for their efficiency and quality in mechanical harvesting. The outcomes of this work include improved germplasm, genomic tools, understanding of GxExM effects on plant architecture, yield and fruit quality and an understanding of inheritance of traits for mechanically harvested green chiles. The results may extend to other pepper germplasm and vegetables. We have strong K-12 and undergraduate student outreach including addressing minorities and small to medium farms. Research associates, undergraduate and high school students will be trained through experiential learning in this project. We are working with stakeholders, state commodity boards, growers, processors and seed companies that identified this project as a critical need.
Animal Health Component
0%
Research Effort Categories
Basic
(N/A)
Applied
100%
Developmental
(N/A)
Classification

Knowledge Area (KA)Subject of Investigation (SOI)Field of Science (FOS)Percent
20114691081100%
Knowledge Area
201 - Plant Genome, Genetics, and Genetic Mechanisms;

Subject Of Investigation
1469 - Solanaceous and related crops, general/other;

Field Of Science
1081 - Breeding;
Goals / Objectives
The long-term goal of this project is to develop pepper varieties that are amenable to mechanical harvesting. The critical need is to ensure the long-term sustainability of the US chile pepper industry by reducing dependence on the increasingly inadequate supply of manual labor for harvest, as well as mitigating labor's high costs compared to other producing countries. Our supporting objectives formulate a systems approach combining genomics, plant breeding, physiology, horticulture, and mechanization. They include:Develop breeding lines of green jalapeno and New Mexico chile pepper that combine destemming, plant architecture and uniformity.Characterize genotype x environment x management (GxExM) interactions of plant architecture on yield with mechanical harvesting.Determine the genetic basis of plant architecture and determinacy (uniformity of ripening) in pepper.Fine-map key loci and determine physiological interactions of destemming in pepper.This proposal leverages and complements, (but does not duplicate) resources being developed by PDs for a USDA grant# 2021-67013-33942 ending 01/2024 and several other non-USDA sources of funding that combine essential traits for pepper production.
Project Methods
Our methods are integrated with our objectives. The below figure outlines the breeding strategy.Obj. 1. Develop breeding lines of green jalapeno and New Mexico chile pepper that combine destemming, plant architecture and uniformity. Hypothesis: A systems approach that combines multiple traits is required for successful mechanical harvesting of pepper. Methodology: The goal of producing jalapeño and New Mexico type chiles for mechanical harvesting for CA and NM,Obj. 1, we will select and self the best F1s based on marker genotypes for destem and determinacy These will selfed and selected in the field over 3 years. To combine plant architecture into jalapenos, we will test destem/NM F3s for architecture and destem in the field (yr1) to select best lines to cross to destem/det jalapenos. We will also begin backcrossing architecture into elite jalapeños. For NM- types, we have verified that destem can be transferred with QTL on chrm. 3, 4 and 10, but fruit quality is not adequate. As we already selected NM-green chiles (and variety released) for architecture, we will focus on incorporating destemming with green fruit yield and quality for mechanical harvesting using marker assisted backcrossing.Data analyses: Phenotypic data will be adjusted for spatial variation using a mixed linear model with the lmer function in the R-package:lme4, to calculate Best Linear Unbiased Predictions (BLUPs) and Best Linear Unbiased Estimates (BLUEs) to make selections. Predictions of new progeny will be compared to controls based on adjusted means across backgrounds. Heritability will be calculated based on variance components extracted from the mixed linear model. Phenotypic and genetic correlations will be calculated in R to understand any negative trait correlations that may affect selections. Segregation ratios will be verified using c2 analyses.Obj. 2. Characterize genotype x environment x management (GxExM) interactions of plant architecture on yield with mechanical harvesting.Hypothesis: Plant management and architecture are critical components of yield and quality for mechanical harvesting of pepper.Methodology:To study GxExM we will conduct replicated trials (4 reps, RCBD x 2 locations x 2 years) with 12 advanced lines including NM lines selected for mechanical harvesting (but not destemming) selected from previous trials with differing plant architecture and determinacy traits at two seeding rates, 6 and 12 inches (standard) within a row with 30 inches between rows/beds, required for mechanical harvesting with a stripper header.Data Analysis: Phenotypic data will be analyzed as for Obj 1. Effects and variances for G, E, and M and interactions will be calculated across environments to determine the optimum plant architecture and plant spacings for mechanical harvesting yield.Obj. 3. Determine the genetic basis of plant architecture and determinacy (uniformity of ripening) in pepper Hypothesis: Traits for mechanical harvesting are heritable and trackable using DNA markers.Methodology:We are creating 3 populations (200 F2 plants ea.) derived from New Mexico peppers, Odyssey, Iliad and Joe E Parker selected for mechanical harvesting based on plant architecture with UCD14-advanced destem lines. The F2:3 families will be evaluated in NM and CA in replicated (2 reps) augmented designs with 12 plants/plot. They will be genotyped using targeted sequencing array array (384 makers), and evaluated as in Obj 2 except for mechanical harvesting. Similarly, we will evaluate the same traits in a Destem x determinate (Fasciculate) population as well as fruit/node.Data Analysis: We will analyze data as in Obj. 1. Heritability will be calculated based on variance components extracted from the mixed linear model. Phenotypic and genetic correlations will be calculated in R to understand any negative trait correlations that may affect selections. QTL analyses will be with R/qtl using genotypes directly from the array.Obj. 4. Fine map key loci and determine physiological interactions of destemming in pepper.Hypothesis: Destemming of pepper is controlled by major genes that interact with fruit traitsMethodology:We now have studied destemming in pepper in over a dozen jalapeno and New Mexico type populations and environments, detecting QTL on 7 chromosomes, of which we have identified 7 candidate genes on 4 chromosomes involved in the organ abscission pathway. Although there are population-specific QTL, the QTL on Chr.10 for destem force is the major QTL in all populations explaining 30-61% of variance with confidence intervals spanning 1.0-2.9 cM and 38Mb. It also overlaps with a broader QTL for destem rate (Table 3). Based on annotation of pepper genomes [6, 7] there are no obvious candidate genes for abscission in this region. Due its importance, we focus on fine-mapping and understanding the physiological, genetic and genomic basis of this region on destemming in pepper.We have chosen 4 BC1S1 populations (50 plants each) to genotype and map heterozygous crossovers. The 4 populations represent 2 UCD-14-based donor lines and 4 diverse genetic backgrounds backcrossed to a common UC elite jalapeño line. This combination maximizes polymorphism and recombination while normalizing backgrounds to express the trait. Selected lines will then be selfed to create 1000 recombinants (2000 meioses) and fine-mapped with markers across the dstem10.1 QTL to narrow candidate genes using KASP® assays. Recombinant lines homozygous for the two alleles in the region will be phenotyped (15 fruit/line) for destem force and rate in replicated trials 2 locations with parental controls to verify co-segregation. Stain fruit at 19 and 25 days after pollination to detect abscission zones. Furthermore, to study the physiological interactions of destemming we will measure with calipers, the shoulder width and stem scar size of 15 fruit/line that are segregating in these populations.Data analysis: Crossover lines will be identified directly on marker genotypes at interface of heterozygous and homozygous regions for the UCD-14 allele. Regression and correlation analyses will be performed in R for shoulder width, stem scar and destem traits.

Progress 03/01/23 to 02/29/24

Outputs
Target Audience:The target audience for this research project is chile farmers and processors and recruitment of K-12 students. The shift towards mechanical harvesting is crucial for sustaining chile production in US, concentrated in New Mexico and California. However, two significant challenges arise: effectively removing stems during mechanical harvesting and cultivating transplants with growth patterns conducive to mechanical harvesting. The research pursued 3 primary goals: facilitating easy destemming in green chile, breeding for desired plant architecture, and discovering transplant techniques that promote deep root growth and upright plant habits, thereby enhancing the efficiency of mechanical harvesting green chile. Access to destemming germplasm and advanced transplant techniques will allow growers to transition from manual to mechanical harvesting methods, leading to reduced production costs and increased revenue. This shift will contribute to the sustainability of production. Secondly, K-12 children and teachers in Northern California went thru experiential learning modules developed by the UC Davis Student program that trains and employs undergraduates to both create and implement learning modules using pepper diversity as a base. Changes/Problems:We had anticipated the completion of our publications by now, yet the revision phase is proving to be more time-consuming than initially projected. Our aim is to have all publications finalized by July 2024. Despite the delay, we are dedicated to ensuring that our work meets the highest standards of quality and accuracy. In addition, due to high disease pressure in our southern NM research plots in 2023, we have moved our research to the Los Lunas Agricultural Science Center for 2024. No major changes for Davis program. What opportunities for training and professional development has the project provided?There has been significant training opportunities in this grant. In NM, this project is the basis for a Masters student thesis and research associate was trained. IN CA, 2 interns were trained in plant breeding and molecular biology as well as a senior research associate in mechanical harvesting. Over 600 K-6 students were enticed in plant sciences by completing hands on modules learning about pepper diversity and plant breeding (every student took a plant home), as well as undergraduate students were trained in plant breeding and pedogy to implement the K-12 modules. How have the results been disseminated to communities of interest?At a basic level, we have communicated the results and goals to K-12 and teachers and consumers through the New Mexico Pepper Institute. Results were communicated the International Pepper and Solanaceae Genomincs meetings, as well as Seed industry conferences and field days; reaching growers , seed industry and academic audiences. These are our targeted audiences. What do you plan to do during the next reporting period to accomplish the goals?In 2024 we plant to evaluate segregating populations for Fruit quality, plant architecture, determinacy and destemming in both New Mexico and jalapeno types. These will lay the foundation for Obj 3 and 4. We also will run advanced breeding lines and commercial checks in a mechanical trial in Davis focusing on same traits. We will also continue outreach as described for K-12, growers and processors.

Impacts
What was accomplished under these goals? The long-term goal of this project is to develop pepper varieties that are amenable to mechanical harvesting. The critical need is to ensure the long-term sustainability of the US chile pepper industry by reducing dependence on the increasingly inadequate supply of manual labor for harvest, as well as mitigating labor's high costs compared to other producing countries. Our supporting objectives formulate a systems approach combining genomics, plant breeding, physiology, horticulture, and mechanization. They include: 1. Develop breeding lines of green jalapeno and New Mexico chile pepper that combine destemming, plant architecture and uniformity. 2. Characterize genotype x environment x management (GxExM) interactions of plant architecture on yield with mechanical harvesting. 3. Determine the genetic basis of plant architecture and determinacy (uniformity of ripening) in pepper. 4. Fine-map key loci and determine physiological interactions of destemming in pepper. This proposal leverages and complements, (but does not duplicate) resources being developed by PDs for a USDA grant# 2021-67013-33942 ending 01/2024 and several other non-USDA sources of funding that combine essential traits for pepper production. For Objective 1. We have created several populations in both jalapeno and New Mexico pod-type chiles. These were evalaued in nurseries and selections made on plant architecture, destemming force and fruit quality. F3 to F6 and BC2S2 advanced lines were then evaluated with controls in replicated trials over 3 years in NM an d CA. Our findings are detailed in an extensive publication (Hill et al 2023), Joukhadar et al. 2024,and Ortega et al. 2024. For New Mexico type peppers we have successfully conducted backcrossing on the top three breeding lines (385W21, 398W21, and 345W21) which were identified for their larger fruit size while preserving the easy destemming trait. The parentage of 385W21 includes MUC14 and NuMex Joe E. Parker, while 398W21 and 345W21 originate from MUC14 and Odyssey. Consequently, 385W21 underwent backcrossing with NuMex Joe E. Parker, while 398W21 and 345W21 were backcrossed with Odyssey. BC1F1 seeds will be harvested from these crosses and subsequently multiplied in the greenhouse for planting in the 2025 season. Similarly, we have multiple populations segregating for Plant architecture, detsemming and determinacy in jalapenos with BC2S2s or F3s between BC2s and crossed for different combination of traits. We evaluated and selected these in the field at Davis in 2023in 2 reps on single row plots. Each family was rated for each traits with destemming measured with a torque meter for both frequency and force as per Hill et al. (2023). Our analysis of the correlations between fruit morphology characteristics and destemming force suggests a significant relationship between the fruit length and pericarp thickness and their impact on destemming force. Typically, thicker walled and longer fruit tend to have higher destemming forces, although we have observed variations in this correlation in specific crosses. This discovery inspires optimism that intensified future breeding efforts could ultimately result in the development of cultivars that not only meet the demands of the processing industry, but also reduce labor costs and address labor shortages effectively. These populations serve as teh basis for obj. 2-4. Objective 2. We have made signifcant advancements to understand , G x E x M, specifically for transplants specifically with transplants in Jalapeno types. We tested initiating plants with Q-plugs, paperpots and transplanting at 4 weeks vs 6-8 weeks as traditionally in replicated trials.Q-plugs transplanted at 4 weeks dramatcially changed architecture to a plant with with a primary stem followed by bifercation into several secondary branches. Importantly, this also resulted in a deeper more apical dominant tap root system giving strong support to the plant for mechanical harvesting using a "stripper" header type harvester that we are breeding for, i.e. the Etgar series 1000. Mechanical harvest of our best selections resulted in 90% of fruit being harvested with 50% of that fruit being destemmed directly from harvest. These are 2 year averages. Obje 3 and 4 will be addressed in Year 2.

Publications

  • Type: Conference Papers and Presentations Status: Published Year Published: 2024 Citation: Joukhadar, I. (2024) New Mexico Green Chile Mechanization: Current Developments and Innovations. New Mexico Chile Pepper Conference Presentation. Las Cruces, NM.
  • Type: Journal Articles Status: Accepted Year Published: 2024 Citation: Joukhadar, I., Ortega, F., Velasco-Cruz, C., Barchenger, D., Hill, T., Van Deynze, A., Walker, S. (2024) Correlations among New Mexico pod-type green chile (Capsicum annuum) fruit morphology characteristics with destemming force. Submitted for publishing in Crop Science.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2023 Citation: Genetics of destemming in pepper: A step towards mechanical harvesting. 2023. Theresa Hill , Vincenzo Cassibba , Israel Joukhadar , Charles Havlik, Franchesca Ortega , Armando Garcia-Llanos, Stephanie Walker, Allen Van Deynze. Solanaceae Genomics Conference, Montreal, Canada. 14-18, 2023
  • Type: Conference Papers and Presentations Status: Published Year Published: 2023 Citation: Franchesca Ortega , Armando Garcia-Llanos, Stephanie Walker, Allen Van Deynze. UC Davis Plant Breeding Retreat. Bodega Bat, CA, Dec 15, 2023
  • Type: Conference Papers and Presentations Status: Published Year Published: 2023 Citation: Seed Biotechnology Center Update. 2023. Van Deynze, A. California Seed Association. Monterey, CA. September 28, 2023.
  • Type: Journal Articles Status: Accepted Year Published: 2024 Citation: Identification of QTLs involved in easy destemming for New Mexico pod-type green chile. 2024.Franchesca Ortega, Theresa Hill, Allen Van Deynze, Armando Garcia-Llanos, Stephanie Walker. Frontiers in Plant Sciences. In Review