Climate change is an existential threat to global food security. The increases in the frequency and intensity of biotic and abiotic stresses is projected to exacerbate in the future. To expedite the development of improved stress tolerant varieties in crop plants, ,  researchers in the Crop Plants Genetics Laboratory are applying novel genetics, genomics and biotechnology tools to elucidate the molecular basis of various biotic and abiotic stress tolerance attributes essential for adaptation, survival, increased productivity in major field crops such as rice, corn, soybean.

Pyramiding Genes from Multiple Donors to Enhance Salt Tolerance in Rice

Salinity is a major climate-related risk for sustainable rice production. The major obstacle to design salt tolerant varieties is the narrow genetic base of US rice germplasm. Although we have successfully developed salt tolerant breeding lines, the level of salt tolerance in these lines needs further enhancement. Since multiple mechanisms contribute to salt tolerance and favorable alleles are distributed among various donors, pyramiding of genes from multiple donors is needed. The overall goal of this proposal is to exploit the natural genetic variation to develop rice cultivars with enhanced salt tolerance. Our specific objectives are: (a) pyramiding of favorable salt tolerance genes from multiple donors, and (b) identification of superior salt tolerant alleles from multiple donors for rice improvement. Introgression lines developed from multiple donors will be utilized for developing superior salt tolerant lines through pyramiding. Evaluation of these lines for salt tolerance and agronomic performance in greenhouse and field experiments will be done to identify high yielding breeding lines with enhanced salt tolerance. Whole genome and transcriptome sequencing of pyramided lines and parents will be done to identify potential salt tolerant genes and their superior allelic variants. The project will generate advanced breeding lines with enhanced salt tolerance and genomic resources for the public sector breeding program to accelerate development of climate resilient rice varieties and elucidation of the molecular basis of complex salt tolerance mechanisms operating in rice.

Soybean Improvement through Identification and Introgression of Salt Tolerance Genes

Soybean is a major row crop in the state of Louisiana with 860,000 acres planted in 2019. It is largely produced in irrigated areas in Northern Louisiana. These areas are experiencing high levels of salt or chloride from well or surface water. Salinity stress is gradually becoming a major climate-related risk for soybean production in Louisiana and other southern states of the United States. With the drawdown of the aquifers in Northeast Louisiana, salinity will likely become more of a problem in the near future. The area of salt-affected agricultural land is rapidly increasing and is predicted to double in the next 35 years. However, there is no current breeding effort in Louisiana to minimize the impact of salinity stresses on soybean production. Identifying crop traits or genes that improve adaptation of soybean under saline condition will continue to be both priority and challenge for soybean researchers. Therefore, identification of soybean germplasm for salt tolerance genes/traits, genetic dissection of soybean performance under this stress and application of such knowledge in breeding programs are crucial to improve soybean productivity with irrigation from salty wells.

Since the genetic base of North American soybean cultivars is narrow, identification and introgression of novel genes for improved yield and tolerance to salt stress from diverse germplasm is needed to widen the genetic base of the breeding materials to accelerate development of new soybean cultivars. Only one major gene for salt tolerance has been reported by multiple research groups. There are two species of soybean: the cultivated soybean (Glycine max) andthe wild annual soybean (Glycine soja). Abundant soybean germplasm stored in the National Genetic Resources Program (NGRP) of USDA provides unique opportunity to exploit natural genetic variation for genetic improvement.

The long-term goal of this project is to develop soybean varieties with enhanced salinity tolerance. This will be achieved through identification and introduction of salt tolerance genes from selected donors through backcross breeding coupled with marker-assisted selection. The discovery of genes responsible for salinity tolerance as well as introgression lines will provide excellent resources for the soybean breeding program to transfer salinity to advanced breeding lines.

Enhancing Breeding using Corn Genome Data and Corn QTL Near Isogenic Lines for Aflatoxin Reduction

Aflatoxin contamination in corn is a major problem in Southeastern United States. Among various aflatoxin management strategies, the genetic improvement for enhanced host plant resistance is an ideal means to reduce aflatoxin in corn. Over the years of intensive research efforts, it has been confirmed that multiple chromosome positions (genes) in corn collectively convey aflatoxin-reduction. However, each position shows low to moderate effects on the resistant trait. In order to improve the host plant resistance to aflatoxin accumulation, identification of resistance related genes or QTLs and generation of biomarkers are essential for pyramiding these factors to enhance resistance. From previous and current studies, next generation whole genome sequencing was performed on multiple corn breeding lines, including three parental corn inbred lines, Mp313E, MP715, and Va35, as well as multiple QTL-NILs in collaboration with researchers from the Mississippi State University. In this research project, we investigate the major resistance QTLs using genome sequencing and corn QTL near isogenic lines (QTL-NILs) to further our understanding of molecular genetic basis for aflatoxin-reduction in corn and to expedite multiple corn breeding projects using molecular markers generated from this study. The precise breeding of corn aflatoxin resistance relies on sufficient molecular markers, especially gene-based markers, and precise genetic linkage and QTL mapping. This research project will conduct sequence comparison among the QTL-NILs and their parental lines and advances the QTL-NILs through field Aspergillus flavus inoculation evaluations. Our research goal is to expedite the breeding of aflatoxin resistant corn inbred lines by developing precision breeding techniques.

Molecular Genetics of Weediness in Red Rice

Limited knowledge of the origins and evolution of weedy characteristics of monocots limits the formulation of novel genetic strategies to improve crop productivity. Given the high degree of seed dormancy, seed shattering, and many other weedy characteristics in wild grasses, red rice (a noxious weed in rice growing areas of Southern United States), as a model, provides a simple genome structure and availability of enormous genomic resources (e.g. integrated high density genetic and physical map, expressed sequence tags, and whole genome sequences) for molecular dissection of these complex adaptive physiological traits. Compared with the standard mapping population strategies commonly used to determine quantitative trait loci (QTL), introgression line (IL) populations represent a better alternative because of their increased efficiency, immortality and the added advantage of fast-tracking the genome-wide gene discovery process. Our research has determined that red rice ecotypes exhibit a high degree of DNA polymorphism and striking differences in several key domestication-related traits, compared with cultivated rice. Therefore, the primary goal of this proposal is to elucidate the molecular genetic basis of weediness in red rice, with special emphasis on seed dormancy, seed shattering, and flowering, which are key traits for survival and persistence of the majority of weed species. To this end, an introgression library has been developed for precision mapping and discovery of the genetic factors for these key weedy traits and other agronomic traits to improve rice productivity in the United States.