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

Location: Grain Legume Genetics Physiology Research

2023 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 the final report for project 2090-21220-002-000D, Enhanced Agronomic Performance and Disease Resistance in Edible Legumes, which has been replaced by new project 2090-21220-003-000D, Enhancing Yield, Disease Resistance, and Agronomic Performance in Edible Legumes. For additional information, see the new project report. In support of Objective 1, common bean and pea genetic populations were successfully used to characterize resistances to geminiviruses, luteoviruses, potyviruses, bacterial blights, and foliar and soil borne fungal pathogens. ARS researchers in Pullman, Washington, determined how several genes (bgm-1, BGY 4.1, 7.1, and 8.1) interacted to confer resistance to Bean golden yellow mosaic virus (BGYMV). A genetic marker for resistance to Bean golden yellow mosaic virus was identified that helps breeders develop more disease resistant bean varieties. Markers detecting mutations and candidate genes for bc-1 (RLK - receptor like kinase), and bc-2 and bc-u (Vps4 AAAC ATPase ESCRT proteins) genes, were developed to reveal new adjustments to the host-pathogen interaction for resistance to Bean common mosaic virus. Genetic characterization of resistance to white mold disease in dry bean validated major effect resistance genes. Markers linked with the resistance genes provide a foundation for developing marker-assisted selection for resistance to white mold. The ARS researchers developed two molecular markers that identify variants of the elF4E gene in pea associated with resistance to Pea seedborne mosaic virus (PSbMV) and are 100% accurate in identifying pea lines with resistance to different strains of the virus. A new source of resistance to PSbMV was discovered in the pea line PI 143485. Lines from the Pea and Lentil Single Plant Core Collections were characterized for resistance to Fusarium avenaceum and 11 genes across four chromosomes were associated with resistance to F. avenaceum in lentil, with pea work in progress. Two pea accessions, PI 166159 and 250441, were identified with excellent resistance to F. avenaceum and are being used in breeding populations to improve resistance. Eighteen genetic markers and seventeen candidate genes were identified that confer resistance in pea to the pea aphid that transmits Bean leafroll virus. Other trait-linked markers developed for marker-assisted selection in bean include genes responsible for resistance to anthracnose, common bacterial blight, and bean rust diseases. Other bean traits that were genetically characterized include association of seedling root growth with yield across diverse environments, seed coat color genes, slow darkening seed coat trait in pinto and carioca beans, seed and canning quality, pod morphology in snap bean, and various traits (phenology, biomass, seed quality) including thermal and multi-spectral imaging associated with abiotic stress tolerance. In support of Objective 2, five dry bean cultivars, four pintos USDA Basin, USDA Cody, USDA Diamondback, and USDA Rattler, and one small red USDA Lava, were released with licenses with private seed companies already awarded or pending. Marker-assisted selection for traits developed in Objective 1 was used in the development of these cultivars. The cultivars possess resistance to viruses and bean rust and exhibit high yield potential under both stressed (low soil fertility, drought, soil compaction) and non-stressed production environments. Ground, air, and satellite based high resolution imagery were compared for their ability to evaluate traits rapidly and remotely in bean. All three methods identified remote sensed traits (GNDVI, thermal, plant area) that could be useful in a breeding program. For example, such remote sensing traits were used to identify pinto bean cultivars with higher yield potential across different tillage treatments and drought induced by deficit irrigation. In 2023 there were 65 new crosses conducted between parents with complimentary traits and more than 450 populations or breeding lines were planted in field trials in support of a continued breeding pipeline for dry bean germplasm enhancement and development of improved cultivars. Twenty-three pea accessions originating from 17 countries and four continents were determined to have complete resistance to Bean leafroll virus (BLRV) and are being used to map genes associated with resistance. The cultivar ‘Lifter’ was identified with excellent resistance to BLRV and Pea enation mosaic virus and has the highest level of resistance to pea aphid observed in screened material, which indicates it is an important parent for breeding programs.

Accomplishments
1. Improved breeding strategy for incorporating virus resistance in common bean. Beet curly top virus (BCTV) reduces yield and quality of common bean grown west of the Continental Divide. The best strategy to control the disease is to develop new varieties with improved resistance. Unfortunately, it is especially challenging to breed beans for BCTV resistance because field infections may not be reliable and greenhouse screening methods are cumbersome. ARS researchers in Prosser, Washington, developed a trio of DNA markers for detecting and distinguishing among three origins of the Bct-1 resistance gene, one of which is most desired because it confers a higher level of resistance. This new knowledge is being used by breeders to develop new bean cultivars for growers with improved virus resistance.

2. Improved aphid resistance for virus control in pea. Bean leafroll virus (BLRV) is transmitted by pea aphids and reduces yield and quality of peas produced across the United States. Resistance to aphids is a novel strategy for BLRV control but screening for insect resistance is complex. ARS scientists in Prosser, Washington, identified 17 candidate genes that influenced aphid resistance in a population of 301 pea accessions, and the cultivar ‘Lifter’ was the most resistant line identified. Knowledge gained about genes and sources of resistance are used by breeders to develop new pea varieties which provide growers with improved resistance to both pea aphid and BLRV.

Review Publications
Miklas, P.N., Soler-Garzon, A., Valentini, G., Pastor-Corrales, M.A. 2023. Registration of ‘USDA Rattler’ pinto bean. Journal of Plant Registrations. 17(2):271-279. https://doi.org/10.1002/plr2.20289.
Miklas, P.N., Kelly, J.D., Cichy, K.A. 2022. Dry bean breeding and production technologies. In: Siddiq, M., Uebersax, M.A., editors. Dry Beans and Pulses: Production, processing, and nutrition. 2nd edition. Hoboken, NJ: John Wiley & Sons Ltd. p. 29-56.
Mclean, P.E., Lee, R., Howe, K.J., Osborne, C., Grimwood, J., Levy, S., Haugrud, A.P., Plott, C., Robinson, M., Skiba, R.M., Tanha, T., Zamani, M., Thannhauser, T.W., Glahn, R.P., Schmutz, J., Osorno, J., Miklas, P.N. 2022. The common bean V gene encodes flavonoid 3'5' hydroxylase: A major mutational target for flavonoid diversity in angiosperms. Frontiers in Plant Science. 13:869582. https://doi.org/10.3389/fpls.2022.869582.
Saballos, A., Soler-Garzon, A., Brooks, M.D., Hart, J., Lipka, A., Miklas, P.N., Peachey, R.E., Tranel, P., Williams, M. 2022. Multiple genomic regions govern tolerance to sulfentrazone in snap bean (Phaseolus vulgaris L.). Frontiers in Agronomy. 4. Article 869770. https://doi.org/10.3389/fagro.2022.869770.
Parker, T.A., Gallegos, J.A., Beaver, J., Brick, M., Brown, J.K., Cichy, K.A., Debouck, D., Delgado-Salinas, A., Dohle, S., Ernest, E., Estevez de Jensen, C., Gomez, F., Hellier, B.C., Karasev, A.V., Kelly, J.D., McClean, P., Miklas, P.N., Myers, J.R., Osorno, J., Pasche, J.S., Pastor-Corrales, M.A., Porch, T.G., Steadman, J.R., Urrea, C., Wallace, L.T., Diepenbrock, C.H., Gepts, P. 2022. Genetic resources and breeding priorities in Phaseolus beans: Vulnerability, resilience, and future challenges. Plant Breeding Reviews. Volume 46. Somerset, New Jersey: John Wiley & Sons, Inc. p. 289-420. https://doi.org/10.1002/9781119874157.ch6.
Das, S., Porter, L.D., Ma, Y., Coyne, C.J., Chaves-Cordoba, B., Naidu, R.A. 2022. Resistance in lentil (Lens culinaris) genetic resources to the pea aphid (Acyrthosiphon pisum). Entomologia Experimentalis et Applicata. 170(8):755-769. https://doi.org/10.1111/eea.13202.
Williamson-Benavides, B.A., Sharpe, R., Nelson, G., Bodah, E.T., Porter, L.D., Dhingra, A. 2021. Identification of root rot resistance QTLs in pea using Fusarium solani f. sp. pisi-responsive differentially expressed genes. Frontiers in Genetics. 12. Article 629267. https://doi.org/10.3389/fgene.2021.629267.
Zitnick-Anderson, K., Porter, L.D., Hanson, L.E., Pasche, J.S. 2021. Identification, laboratory, greenhouse and field handling of Aphanomyces euteiches on pea (Pisum sativum). Plant Health Progress. 22(3):392-403. https://doi.org/10.1094/PHP-01-21-0011-FI.
Soler-Garzon, A., McClean, P., Miklas, P.N. 2021. Coding mutations in vacuolar protein-sorting 4 AAA+ ATPase endosomal sorting complexes required for transport protein homologs underlie bc-2 and new bc-4 gene conferring resistance to Bean common mosaic virus in common bean. Frontiers in Plant Science. 12. Article 769247. https://doi.org/10.3389/fpls.2021.769247.
Escobar, E., Oladzad, A., Simons, K., Miklas, P.N., Lee, R., Schroder, S., Bandillo, N., Wunsch, M., McClean, P., Osorno, J. 2022. New genomic regions associated with white mold resistance in dry bean using a MAGIC population. The Plant Genome. 15(1). Article e20190. https://doi.org/10.1002/tpg2.20190.
Rahman, M.M., Porter, L.D., Ma, Y., Coyne, C.J., Zheng, P., Chaves-Cordoba, B., Naidu, R.A. 2023. Resistance in pea (Pisum sativum) genetic resources to the pea aphid, Acyrthosiphon pisum. Entomologia Experimentalis et Applicata. 171(6):435-448. https://doi.org/10.1111/eea.13296.