Research Project: Enhanced Agronomic Performance and Disease Resistance in Edible Legumes

Location: Grain Legume Genetics Physiology Research

2019 Annual Report

Objectives
Development and release of novel edible legume germplasm lines and cultivars with enhanced traits that benefit breeders, growers, consumers, and the environment, represent the long-term goals for this project. Given favorable outcomes, breeders will benefit from germplasm releases, growers from increased yield potential and nitrogen fixation, consumers from healthy low cost food with improved quality, and the environment from reduced pesticide use. Germplasm lines which incorporate novel traits from exotic sources into near-commercial seed market types will provide public and private breeders with useful traits for cultivar development. Moving traits from exotic sources into adapted commercial cultivars is an otherwise arduous task for most breeding programs. Thus, these germplasm releases will facilitate adoption of new traits by breeders and increase genetic diversity in their programs which is crucial for advancing yield potential and for sustainability in the long term. It is expected that some breeding lines with exceptional performance generated by this project will be released as cultivars. Another long-term goal is to better understand the genetics underpinning complex traits and leverage this knowledge to improve breeding strategies. High-throughput next generation sequencing combined with optical mapping and updated reference genomes will significantly facilitate genetic studies geared toward advancing our breeding efforts. We will seek better markers for indirect selection of economically important traits in pea and common bean and examine new marker-assisted breeding strategies. Populations generated for genetic analyses will be used for breeding and vice versa. Such dual purpose populations facilitate simultaneous advancement toward our long-term goals (germplasm development and genetic knowledge from genomic analyses). For the next five years this project will focus on the following objectives. Objective 1: Develop genomic analysis populations, and use them to improve genetic understanding of complex traits as well as to accelerate breeding for improved agronomic traits, including biological nitrogen fixation, drought tolerance, tolerance to low soil fertility, and resistance to problematic bacterial, fungal, and viral diseases. Objective 2: Develop, evaluate, and release fresh green pea and dry bean (kidney, pinto, black) germplasm with improved agronomic performance combined with durable disease resistance.

Approach
1. Research Goal: Genetic factors which condition complex stress resistance traits will be positioned on physical maps, with associated genomic sequences leveraged for marker-assisted breeding. Select populations will be evaluated for response to abiotic stresses (drought, low fertility) and diseases (Bean Common Mosaic Virus [BCMV], common bacterial blight [CBB], Fusarium root rot, Pea Seed-borne Mosaic Virus [PSbMV] and white mold) and genotyped with genomic markers (single-nucleotide polymorphisms [SNPs]). Linkage maps will be developed and quantitative trait loci (QTL) detected. SNPs with potential marker-assisted selection applications will be detected by melting temperature Tm-shift analysis. Reference genome data bases will be used for physical mapping, validating genetic map positions, and candidate gene discovery. If the BARCBean6K_3 BeadChip SNP array we intend to use for bean studies provides inadequate marker coverage then it may be necessary to generate additional SNPs through genotyping-by sequencing (GBS). 2. Research Goal: Combining independent QTL and major resistant genes will improve genetic resistance to abiotic stresses and contribute to durable disease resistance in pea and dry bean, and be combinable with quality attributes and enhanced agronomic performance. Bean improvement efforts will be based on the use of F4 bulk breeding populations. These populations derive from Andean Diversity Panel accessions selected to combine resistance to both biotic and abiotic stresses. All materials in the F4 generation and later must perform well under multiple stresses in the white mold nursery, terminal drought trial, low nitrogen (N)trial, purgatory plot (drought, soil compaction, low fertility, and root rots), and in the non-stress trial used to determine maximum yield potential, in order to be advanced for subsequent testing. Measured traits recorded for each plot in each trial will include grain yield, seed weight, early plant vigor, plant height, growth habit, flowering date and maturity, days to seed fill, biomass, pod wall ratio, Normalized Difference Vegetation Index (NDVI), and canopy temperature. Individual populations will be chosen for use in the Genome Wide Association Study (GWAS) to detect genomic regions under selection in different stress environments. Resistance to halo blight in beans will be improved by combining HB4.2 and HB5.1 QTL with major genes Pse-2 and Pse-3, which can produce lines that have durable resistance to all nine differential races of the pathogen Pseudomonas syringae. Seed quality and yield potential will be improved in pinto beans by developing lines through crosses between the new pinto germplasm releases USPT-WM-12 and PRP 153 and commercial pinto varieties. If no useful QTLs for abiotic stress resistance in beans are detected then these traits will be improved by phenotypic selection. Pea germplasm from the NPGS Pea Core Collection, commercial pea cultivars and advanced breeding lines will be screened for resistance to Bean Leaf Roll Virus (BLRV). Germplasm with resistance to BLRV will be identified that can be used in breeding programs to develop resistant cultivars.

Progress Report
In support of Objective 1, there were 30 dry bean populations initiated and advanced in the field to facilitate genetic studies of economically important traits including tolerance to drought and heat stress, and durable resistance to bacterial and viral diseases. Two inbred populations with 150 inbred lines in each population were generated for genomic analyses of drought tolerance and resistance to white mold disease, respectively. These 300 lines were grown in the field to generate enough seed for replicated field trials in subsequent years. Genomic analyses of five previously developed genetic populations led to the discovery and validation of two new genes that confer resistance to Bean golden yellow mosaic virus (BGYMV), which is a devastating disease of dry beans in Central America. These new genes will help breeders develop dry bean varieties for Central America with resistance to this major virus. Ten other populations were evaluated with hundreds of thousands of genetic markers to characterize genes conferring resistance to Bean common mosaic virus, which is a major problem in the U.S. and worldwide. Pea accessions (444 lines) from the Pisum Collection and commercial cultivars (28 lines) commonly grown in the U.S. were evaluated for resistance to Fusarium root rot using a greenhouse screening method. Of the pea lines evaluated, 34 lines demonstrated partial resistance to root rot in repeated greenhouse tests. The two most resistant lines were selected for developing segregating populations for genetic mapping and study of the resistance trait. Forty-two commercial pea varieties and 328 pea lines from the Pisum Core Collection were evaluated for resistance to Pea seedborne mosaic virus (PSbMV) in greenhouse tests. Five commercial lines and 22 lines from the Pisum core collection were resistant. Molecular markers for resistance to PSbMV were developed. The markers linked to PSbMV resistance and resistant lines provide breeders with new tools and germplasm to develop varieties with improved resistance. Dry bean breeding nurseries, drought and disease trials, and preliminary and advanced yield trials, comprising 900 lines and 2700 research plots, were planted in 2019 in support of Objective 2. Thirteen superior advanced lines including nine pinto, two pink, and two red beans, were increased and distributed to collaborators for examination of their potential release as new varieties. A new ‘environmentally friendly’ pinto bean variety PT11-13, which has tolerance to drought and low fertility stresses that enables production with less water and fertilizer, was approved for release by the Office of Technology Transfer. Twelve commercial pea varieties were identified with resistance to Bean leaf roll virus (BLRV). This information was shared with commercial breeders and is being used to identify, maintain, and deploy BLRV resistance in new pea cultivars.

Accomplishments
1. New genes and genetic markers for developing virus resistance in dry beans. Bean golden yellow mosaic virus devastates dry bean production in the tropics (Central America and the Caribbean). Total crop loss will result during severe epidemics. Researchers in Prosser, Washington, along with collaborators from Fargo, North Dakota, Columbia, Honduras, and Puerto Rico worked together to identify new genes for resistance to bean golden yellow mosaic virus. The same team developed genetic markers that breeders are using to easily detect these resistance genes. These new genes and markers enable breeders to more rapidly develop improved bean varieties with resistance to this major virus problem and enhance global food security.

Review Publications
Mendoza, F., Wiesinger, J., Lu, R., Nchimbi, S., Miklas, P.N., Kelly, J.D., Cichy, K.A. 2018. Prediction of cooking time for soaked and unsoaked dry beans (Phaseolus vulgaris L.) using hyperspectral imaging technology. The Plant Phenome Journal. https://doi.org/10.2135/tppj2018.01.0001.
Boydston, R.A., Porter, L.D., Chaves-Cordoba, B., Khot, L., Miklas, P.N. 2018. The impact of tillage on pinto bean cultivar response to drought induced by deficit irrigation. Soil and Tillage Research. 180:63-72. https://doi.org/10.1016/j.still.2018.02.011.
Strock, C., Burridge, J., Massas, A., Beaver, J., Camilo, S., Fourie, D., Jochua, C., Miguel, M., Miklas, P.N., Mndolwa, E., Nchimbi-Msolla, S., Porch, T.G., Rosas, J., Trapp, J., Beebe, S., Lynch, J. 2019. Seedling root architecture and its relationship with seed yield across diverse environments in Phaseolus vulgaris. Field Crops Research. 237:53-64. https://doi.org/10.1016/j.fcr.2019.04.012.
Oladzad, A., Porch, T.G., Rosas, J.C., Moghaddam, S., Beaver, J., Beebe, S.E., Burridge, J., Jochua, C.N., Magalhaes, A.M., Miklas, P.N., Ratz, B., White, J.W., Lynch, J., McClean, P.E. 2019. Single and multi-trait GWAS identify genetic factors associated with production traits in common bean under abiotic stress environments. G3, Genes/Genomes/Genetics. 9(6):1881-1892. https://doi.org/10.1534/g3.119.400072.
Ranjan, R., Chandel, A., Khot, L., Bahlol, H., Zhou, J., Boydston, R.A., Miklas, P.N. 2019. Irrigated pinto bean crop stress and yield assessment using ground based low altitude remote sensing technology. Information Processing in Agriculture. https://doi.org/10.1016/j.inpa.2019.01.005.
Alvares, R., Stonehouse, R., Souza, T., Melo, P., Miklas, P.N., Bett, K., Melo, L., Rodrigues, L., Souza, L., Pereira, H. 2019. Generation and validation of genetic markers for the selection of carioca dry bean genotypes with the slow darkening seed coat trait. Euphytica. 215:141. https://doi.org/10.1007/s10681-019-2461-y.
Rashed, A., Feng, X., Prager, S., Porter, L.D., Knodel, J., Karasev, A., Eigenbrode, S.D. 2018. Vector-borne viruses of pulse crops, with a particular emphasis on North American cropping systems. Annals of the Entomological Society of America. 11(4):205-227. https://doi.org/10.1093/aesa/say014.
Chang, H., Sang, H., Wang, J., McPhee, K.E., Zhuang, X., Porter, L.D., Chilvers, M.I. 2018. Exploring the genetics of lesion and nodal resistance in pea (Pisum sativum L.) to Sclerotinia sclerotiorum using genome-wide association studies and RNA-Seq. Plant Direct. 2(6):e00064. https://doi.org/10.1002/pld3.64.
Mgbechi-Ezeri, J., Johnson, K.B., Porter, L.D., Nnadozie, O. 2018. Development of a protocol to phenotype sweet cherry (Prunus avium L.) for resistance to bacterial canker. Crop Protection. 112:246-251. https://doi.org/10.1016/j.cropro.2018.06.009.