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

Location: Grain Legume Genetics Physiology Research

2018 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
This is a new project which continues and expands research from project 2090-21220-001-00D “Enhanced Disease and Abiotic Stress Resistance in Edible Legumes”, which ended April 24, 2018. Please see the annual report for the previous project for additional information. Objective 1: Twenty genetic dry bean populations were initiated and have been planted in the field for increase and selection of genomic analysis populations. Objective 2: Dry bean breeding nurseries, preliminary and advanced yield trials comprising 1800 lines in 4200 research plots have been planted in the field. Forty-two commercial pea cultivars and 328 pea lines from the Pisum Core Collection located in Pullman, Washington, were evaluated for resistance to Pea Seedborne Mosaic virus in greenhouse tests in Prosser, Washington. Both objectives fall under NP301 Plant Genetic Resources, Genomics, and Genetic Improvement; Component 1: Crop Genetic Improvement, Problem Statements 1A, Trait discovery, analysis, and superior breeding methods and 1B, New crops, new varieties; and enhanced germplasm with superior traits.

Accomplishments

Review Publications
Sankaran, S., Zhou, J., Khot, L., Trapp, J., Mndolwa, E., Miklas, P.N. 2018. High-throughput field phenotyping in dry bean using small unmanned aerial vehicle based multispectral imagery. Computers and Electronics in Agriculture. 151:84-92. https://doi.org/10.1016/j.compag.2018.05.034.
Kelly, J., Varner, G., Miklas, P.N., Cichy, K.A., Wright, E. 2018. Registration of 'Cayenne' small red bean cultivar. Journal of Plant Registrations. 12:194-198. https://doi.org/10.3198/jpr2017.05.0033crc.
McClean, P., Bett, K., Stonehouse, R., Lee, R., Pflieger, S., Moghaddam, S., Geffroy, V., Miklas, P.N., Mamidi, S. 2018. White seed color in common bean (Phaseolus vulgaris L.) results from convergent evolution in the P (pigment) gene. New Phytologist. https://doi.org/10.1111/nph.15259.