Performing Department
(N/A)
Non Technical Summary
Upland cotton is the main source of textile fibers worldwide, with a focus on improving the quality of these fibers for years. Despite advancements, progress in enhancing fiber quality has been slow due to complex factors influencing these traits. The use of high-tech tools like the High-Volume Instrument (HVI) has made fiber quality assessment more reliable, yet these methods can overlook specific fiber attributes and suffer from sampling biases. To address these challenges, our project aims to refine fiber analysis techniques, aiming for greater accuracy and efficiency. We plan to develop better methods for evaluating cotton fibers directly, bypassing current limitations and improving the precision of fiber quality measurements. Our goals include enhancing microscopy-based techniques, creating fair sampling protocols, and conducting genetic studies to pinpoint quality traits, alongside providing interdisciplinary training for a Ph.D. student. Ultimately, our work seeks to produce high-quality Upland cotton germplasm, benefiting breeders, growers, and researchers across various sectors. This initiative responds to the cotton industry's need for higher crop value, aiming to make farming more profitable, resilient, and sustainable.
Animal Health Component
0%
Research Effort Categories
Basic
50%
Applied
25%
Developmental
25%
Goals / Objectives
Our overarching goals are to: develop a scalable, microscopy-based individual cotton fiber phenotyping platform that minimizes bias and reduces type II errors associated with current techniques. The ultimate vision is to quantitatively capture a wide range of essential fiber measurements, enabling a thorough understanding of the genetic basis of key cotton fiber quality traits with high precision. We will leverage unique genomic/genetic/population resources already collected in a currently active USDA-AFRI (2021-11395) project aimed to genetically dissect cottonseed oil and fusarium wilt traits to genetically map a multitude of fiber quality traits high resolution. We aim to identify functional alleles and biomarkers diagnostic of key fiber quality traits. The research outcomes will directly benefit breeders, growers, and allied scientists across public, private, and non-profit industries. In the short term, we aim to apply these outcomes to enable precise and larger genetic gains in fiber quality with a vision of developing cotton lines with the yield potential of Uplands and the fiber quality of Pimas enhancing the profitability, resilience, and sustainability of farming operations. This project will lay the foundation for producing high-yielding designer cottons with improved functional properties, making them more competitive with synthetic alternatives and reducing environmental impacts. Through our efforts, we anticipate significant progress in the cotton farming and processing industries, offering valuable advantages to stakeholders and contributing to a more sustainable and competitive future for natural fibers.
Project Methods
The phenotyping method proposed to be developed in this project will capture a multitude of fiber quality traits in a quantitative manner, that is currently impossible with HVI and AFIS. This project builds upon significant development in resources that include: 1) foundational and simplified protocol for cross-sectional cotton fiber histology and light microscopy; 2) first-generation image analysis platform integrated with machine-learning; 3) Segregating RIL population that includes reference-grade genome assemblies for each parent and whole-genome sequences of the segregants. The project is organized into 2 primary objectives:Objective 1. Improve and scale our current fiber histology, image acquisition, and analysis techniques for throughput, resolution, and accuracy.We will also develop an appropriate unbiased phenotyping/sampling protocol for the field. This objective aims to achieve a comprehensive understanding of the phenotypic variance in fiber quality across diverse environments over a span of 2 years. This endeavor will enable us to develop insights into the environmental influences (G x E interactions) on this trait. The enhanced embedding method ensures consistency, thereby maintaining a uniform fiber embedding process across samples and significantly contributing to the reliability and accuracy of our results. Furthermore, our approach involves analyzing a broader fiber area, utilizing three different fiber embeddings, and measuring 60 individual fiber cross-sections per boll, with four bolls examined per plant.Objective 2. Conduct a genetic study on a RIL population that segregates for fiber quality traits to generate diagnostic biomarkers for key fiber quality traits and new knowledge of their genetic underpinnings. We expect to comprehensively understand QTL(s), biochemical pathways, candidate genes, and functional alleles involved in various cotton fiber quality traits through genetic map construction combined with multi-year and quantitative phenotypes. We will deliver validated biomarkers for predicting these traits in breeding pipelines.The project will be evaluated and/or quantified for its impact on the intended audience based on a mixed-methods approach, combining quantitative and qualitative data collection techniques, including surveys, interviews, and analysis of attendance records at workshops and extension activities. Pre- and post-project assessments will be conducted to measure changes in knowledge and practices among the target audience.