Flooding for periods lasting as short as two days has been shown to reduce yields by as much as 27% during the early vegetative or early reproductive growth stages. Heavy rain in the early summer could make standing water in the field for several days, which would significantly damage farmers' fields by causing seedling emergence and establishment problems and impair/injure young soybean plants. In recent years, increase of floods from intense precipitation events was observed on a larger scale than in previous decades in the North central areas.
The best strategy to protect farmers from the ravages of flooding is release of new flood-tolerant soybean varieties and their integration into flood-tolerance management systems. PI Nguyen and co-PI Shannon have been actively researching the genetic basis of flood tolerance in soybean. With the proposed partnership among the University of Missouri, the University of Minnesota, and Iowa State University to work on this topic and prior work by members of this team, this NSCRP project is dedicated to solving this problem by taking advantage of the most active and successful breeding pipelines in the world for the release of flood-tolerant varieties.
Drought has become a significant problem that can affect farmers anywhere in the US. Drought stress can not only reduce yield, but also its components, oil, and protein as well as physiological processes such as nitrogen fixation. Drought resiliency in soybean has a short history of research and publication, beginning in the late 1980’s. Slow wilting, which was predicted to improve yield 75-85% under drought stress through a simulation model analysis, is a famous and reliable drought tolerance trait identified so far in soybean research and breeding community. Soybean breeders including Dr. Grover Shannon in this proposal have been developing drought-resilient germplasm and varieties. However, most of the breeding work has been conducted in late maturity groups (MGs) (late IV to VII). These developed drought tolerance traits need to be incorporated into the early MGs (0 to early IV) suitable for the North Central region of the US.
Thus, we propose to characterize soybean germplasm for early season flood tolerance to identify tolerant genetic resources and molecular markers for breeding applications and to develop new soybean varieties with drought and flood tolerance in maturity groups 0 to IV. The expected results will support sustainable soybean production and stabilize farm income in face of the increasing threat of flooding and drought stress in the North Central region.

1. Characterize soybean germplasm for early season flood tolerance at seedling establishment and early vegetative growth stages and identify tolerant genetic resources and molecular markers for breeding applications.
2. Develop flood tolerant germplasm and varieties in early maturity groups (0 to IV) for north central region by introgression of tolerance traits from the already developed genetic resource in later maturity groups (late IV and V).
3. Pyramid drought tolerance with flood tolerance in early maturity groups (0 to IV) soybeans for the north central region.

New genetic resources (lines and genes) for early maturity soybeans (0 to early IV); DNA markers for molecular breeding; Improved high-yielding and germplasm with stable flood and drought tolerance (>15 bu/ac advantage under stresses).

Updated April 7, 2023:
This project aims to (1) characterize soybean germplasm for early season flood tolerance at the seedling establishment and early vegetative growth stages and identify tolerant genetic resources and molecular markers for breeding applications, and (2) develop flood and drought tolerant germplasm and varieties in maturity groups 0 to IV for the north central region by introgression of tolerance traits from the already developed genetic resource in late maturity groups (late IV and early V).
During the first year of the project, we screened a soybean core set (300 diverse lines which were sequenced) for tolerance during seedling emergence and the early vegetative stages (separately) using soil beds in the greenhouse of the University of Missouri.
Significant phenotypic variation in flood tolerance was observed. We selected 60 lines contrasting in flood tolerance level for further confirmation in the greenhouse in April 2023. We will further select the 10 most tolerant and 10 most sensitive lines for field confirmation at 4 locations this summer.
Genome-wide association studies (GWAS) will be performed to identify loci associated with flooding tolerance. DNA makers for the tolerance genes/QTL will be designed and developed for marker-assisted selection. These results are expected to be updated in our next report.
Meanwhile, we validated our DNA markers for gene pyramiding. We are ready to genotype the breeders’ crossing and backcrossing materials starting April 2023.
Soybean breeders at the University of Missouri, Kansas State University, Iowa State University, and the University of Minnesota have successfully developed backcross and forward breeding populations to deliver results for objective 2.

View uploaded report

Updated February 3, 2024:
Obj. 1
• Screen for tolerance during seedling emergence and the early vegetative stages (separately) in a soybean core set (300 diverse lines with WGS data). The experiments will be conducted using soil-beds in the greenhouse of the University of Missouri (Dr. Nguyen) in Yr 1.
At the University of Missouri, 300 diverse lines with whole-genome resequencing data were tested for early season flood tolerance in our flooding channel in the greenhouse for 3 times. Each time, 5 biological replicates were planted for testing. Plants were subjected to flood stress for 8 days and flood injury scores were evaluated for each plant. Significant phenotypic variations in flood tolerance were observed. We selected 60 lines contrasting in flood tolerance level for further confirmation in the greenhouse in fall 2023. We will further select 10 most tolerant and 10 most sensitive lines for field confirmation at 4 locations in 2024 summer.
Genome-wide-association-studies (GWAS) will be performed to identify loci associated with flooding tolerance after phenotypic confirmation of the selected lines in the field test. DNA makers for the tolerance genes/QTL will be designed and developed for marker-assisted selection.
Meanwhile, we validated our DNA markers for gene pyramiding. We genotyped ~500 samples from breeders in this project for marker-assisted backcrossing.
Obj. 2
• Crossing and population development plan to incorporate flood and drought tolerance traits into MG 0-IV soybeans for the North Central region.
At the University of Missouri, four backcross populations were initiated for the flood tolerance genes and four backcross populations were initiated for the slow wilting (drought tolerance) genes in the 2022 winter nursery at Puerto Rico. F1 seeds were made in May 2023 and genotyped to confirm real F1 hybrids. Backcrossing started and is being advanced to BC1F1 generation. BC1F1 plants were genotyped in Nguyen lab to assist crossing design. Forward breed populations are also being advanced to F2 generation in the winter nursery.
During the summer of 2023, we made 2 crosses of elite lines (MG mid to Late IV) conferring drought tolerance (SW) with a FT elite line carrying the two FT alleles from S12-1362. Advancement of the populations is being advanced from the F1 to the F4 generation in the winter nursery.
At the Kansas State University, five slow wilting and five flood tolerant F1 populations were created in the 2023 field season. Two BC1 backcross populations developed in previous generations, one slow wilting and one flood tolerant, were crossed to advance to the BC2 generation. These backcross and F1 populations were planted in the fall greenhouse. Crosses have been made to advance the BC2 generation to the BC3 generation, and the F1 generation crosses to the BC1 generation. Genotyping has been used to track the slow wilting and flood tolerant alleles. In the fall greenhouse, 115 plants were genotyped. Plants possessing the appropriate alleles were found in all populations.
Four elite maturity group 4 parents were used in the forward breeding effort in the summer 2023 growing season. Four populations were created using the slow wilting parent, and four populations were created using the flood tolerant parent. These populations have been advanced to the 2023/2024 winter nursery growing seasons where the F1 and F2 generations will be grown.
At the Iowa State University, two flood tolerant populations were created in winter nursery in Puerto Rico 2022-23 (A22521 – MG2/S12-1362; A22522 – MG3/S12-1362). Thirty F1 seeds were planted in spring 2023 for increase, and the remnant was returned to Ames, IA for planting and backcrossing in the 2023 summer crossing block.
Marker-assisted selection by Nguyen lab was used to identify the F1 plants in two populations (A22521 and A22522) which were segregating for the tolerant gene in summer 2023 crossing block. Prior to the receipt of marker data, pollinations were made with F1 plants within each population using the elite parent as the male (BC1). Only in the later population, MG3/S12-1362, were BC1F1 seeds successfully created using the segregating female parent.
These BC1F1s were bulked for crossing in winter nursery in Costa Rica, and forty seeds (A23522) were planted in ten rows. Plants were tissue-sampled and analyzed with markers; the twenty-eight segregating plants were used as males in crossing with the elite MG3 female.
The estimated harvest date for the BC2F1s is the last week of January. Thirty F1 seeds will be planted the first week of February, and twenty-five single plants will be harvested, threshed, and returned for increase in single rows in the US in May 2024.
Bulk Population Advancement: Of the 30 F1 seeds increased in winter nursery in Puerto Rico in spring 2023, twenty-five plants were harvested and threshed individually; twenty of these were planted in Ames the summer of 2023 in long, single rows for increase. Flower and pubescence colors were observed and recorded. One pod per plant was harvested within each population from plants in the maturity range of 1.9 – 3.3; pods within a population were threshed together, and the F2 seed was sent to winter nursery in Costa Rica for an increase. Two 10-m rows were planted of each population (A22521 and A22522). Our plan was for both rows will be bulk harvested for each population, and F3 seed will be planted in Ames in summer 2024 for increase.
23-B Tests: Three replications of 373 hill plots were grown by the University of Missouri for flood tolerance testing. Of these, four were checks (3 elite checks, one parent), and 369 were entries from six population. Thirty-two entries had better tolerance scores than the most tolerant check, and forty entries had an equivalent score to the most tolerant check.
Three hundred forty-three were also grown in 2023 yield tests in two-row, long-row plots in one replication at three locations in Iowa. Fifty-nine entries from six populations were selected for advancement based on yield, maturity, and flood tolerance.
23-C Tests: Three replications of twenty-six two-row, short-row plots were grown by the University of Missouri for flood tolerance testing. These were composed of seven checks (three elite checks, four parents) and nineteen entries from four populations. Of these, seven entries had equal or better tolerance to the mean of the top three tolerance checks; two entries were more tolerant than the most tolerant check.
~20 entries were grown in two-rep, two-row, long row plots in four to five locations. Nine were selected for advancement based on yield, maturity, and flood tolerance.
At the University of Minnesota, we successfully crossed the flooding and drought tolerant donor parents to two MN lines each. We planted these into our summer crossing block, genotyped them to confirm F1 status, and crossed back to MN current parents to create the BC1F1 seeds. We planted multiple dates of the recurrent parents to help ensure the F1s nick with the RPs. We see this as a success as it was not easy crossing these MG 4 and 5 donor lines with MG 0 and 1 MN parents.
During the summer of 2023, we planted and genotyped all 36 F1 seeds to verify F2 status and heterozygosity for the flooding and drought tolerance alleles. Verified F1 plants were successfully crossed back to their recurrent parents to create 30 BC1 seeds of each type. These seeds are now being stored in our cold storage to build upon of future funding for this project can be secured.

View uploaded report

We characterized soybean germplasm for early season flood tolerance at seedling establishment and early vegetative growth stages and identified 3 genetic loci. Most promising lines have been selected for field confirmation. DNA markers are being developed for marker-assisted selection. Crossings are being made to transfer previously identified flood and drought tolerance genes (4 genes total) from MG 5 soybean lines to MG 0 to early IV soybean varieties for north central region. Forward breeding populations have reached to F2 generation and marker-assisted backcrossing populations have reached to BC1F1 generation.

The technology developed from this project, including germplasm, genes, markers, screen methods, and management strategies will help the research community, private and public breeders, and producers in dealing with flooding and drought stress. We are aiming to improve the yield advantage of 10 to 20 bu/acre under flooding and drought stress in the new lines without compromising yield potential under normal non-stress condition. All those protected bushels will directly transform into the farmers’ profits.