Unmanned aerial system and satellite-based high resolution imagery for high-throughput phenotyping in dry bean

Dry bean breeding programs are crucial to improve the productivity and resistance to biotic and abiotic stress. Phenotyping is a key process in breeding that refers to crop trait evaluation. In recent years, high-throughput plant phenotyping methods are being developed to increase the accuracy and efficiency for crop trait evaluations. In this study, aerial imagery at different resolutions were evaluated to phenotype crop performance and phenological traits using genotypes from two breeding panels, Durango Diversity Panel (DDP) and Andean Diversity Panel (ADP). The unmanned aerial system (UAS) based multispectral and thermal data were collected for two seasons at multiple time points (about 50, 60 and 75 days after planting/DAP in 2015; about 60 and 75 DAP in 2017). Four image-based features were extracted from multispectral images. Among different features, normalized difference vegetation index (NDVI) data were found to be consistently highly correlated with performance traits (above ground biomass, seed yield), especially during imaging at about 60–75 DAP (early pod development). Overall, correlations were higher using NDVI in ADP than DDP with biomass (r=−0.67 to −0.91 in ADP; r=−0.55 to −0.72 in DDP) and seed yield (r=0.51 to 0.73 in ADP; r=0.42 to 0.58 in DDP) at about 60 and 75 DAP. For thermal data, a temperature data normalization (utilizing common breeding plots in multiple thermal images) was implemented and the MEAN plot temperatures generally correlated significantly with biomass (r=0.28–0.88). Finally, lower resolution satellite images (0.05–5 m/pixel) using UAS data was simulated and image resolution beyond 50 cm was found to reduce the relationship between image features (NDVI) and performance variables (biomass, seed yield). Four different high resolution satellite images: Pleiades-1A (0.5 m), SPOT 6 (1.5 m), Planet Scope (3.0 m), and Rapid Eye (5.0 m) were acquired to validate the findings from the UAS data. The results indicated sub-meter resolution satellite multispectral imagery showed promising application in field phenotyping, especially when the genotypic responses to stress is prominent. The correlation between NDVI extracted from Pleiades-1A images with seed yield (r=0.52) and biomass (r=−0.55) were stronger in ADP; where the strength in relationship reduced with decreasing satellite image resolution. In future, we anticipate higher spatial and temporal resolution data achieved with low-orbiting satellites will increase applications for high-throughput crop phenotyping

Inheritance of Resistance to Common Bacterial Blight in Four Tepary Bean Lines

High levels of resistance to common bacterial blight caused by Xanthomonas campestris pv. phaseoli (Smith) Dye (Xcp) have been observed for tepary bean (Phaseolus acutifolius A. Gray var. latifolius Freeman). However, the inheritance of resistance from this source is unknown for many lines. The inheritance of common bacterial blight resistance was studied in four tepary bean lines crossed with the susceptible tepary bean MEX-114. Progenies were inoculated with a single Xcp strain 484a. Segregation ratios in the F2 generation suggested that resistance in Neb-T-6-s and PI 321637-s was governed by one dominant gene, and Neb T-8a-s had two dominant genes with complementary effects. These hypotheses for inheritance of resistance were supported by various combinations of F1, F3, BC1Pn segregation data in all lines except PI 321637-s where an additional minor-effect gene with recessive inheritance was indicated. Generation means analyses corroborated that multiple resistance genes were present in PI 321638-s. Lack of segregation for susceptibility among testcrosses for allelism between Neb-T-6-s/PI 321637-s, Neb-T-6-s/Neb-T-8a-s, PI 321637-s/Neb-T- 8a-s, and PI 321637-s/PI 321638-s, suggested that one or more loci conditioning resistance to common bacterial blight were in common across the four tepary lines

GGE BIPLOT ANALYSIS OF YIELD STABI LITY FOR ANDEAN DRY BEAN ACCESSIONS GROWN UNDER DIFFERENT ABIOTIC STRESS REGIMES IN TANZANIA

Large seeded Andean dry beans (Phaseolus vulgaris L.) are most preferred in Africa. However, low soil fertility and increasing drought stress conditions due to climate change are among the challenges faced by farmers in this region. The purpose of this study was to identify Andean genotypes with yield stability and to identify the best environments for selection of this trait. GGE-Biplot analysis was used to examine 183 Andean bean genotypes in Tanzania. Results indicated significant environment (E), genotype (G) and genotype x environment (GE) effects for seed yield. The environment explained 46%, genotype 20%, and GE 34% of the total (G + E + GE) variation. Two principal components explained 41.21% (PC1) and 26.35% (PC2) of GGE sum of squares. The Andean genotypes, ADP-102 (Jessica)- purple mottle, large seed, bush plant habit, released by Selian Agriculture Research Institution (ARI) in Tanzania; ADP-220 (G5625)- red, large seed, vine plant habit, from Central America; ADP-276 (G13654) - brown, medium seed, vine, from Mexico; and ADP-648 (‘Red Kloud’) large red kidney, with bush plant habit, were stable across environments and can be recommended for general adaptation across environments. An individual location for selection for yield stability was not identified, thus justifying the continued need for multiple test sites

GGE BIPLOT ANALYSIS OF YIELD STABI LITY FOR ANDEAN DRY BEAN ACCESSIONS GROWN UNDER DIFFERENT ABIOTIC STRESS REGIMES IN TANZANIA

Large seeded Andean dry beans (Phaseolus vulgaris L.) are most preferred in Africa. However, low soil fertility and increasing drought stress conditions due to climate change are among the challenges faced by farmers in this region. The purpose of this study was to identify Andean genotypes with yield stability and to identify the best environments for selection of this trait. GGE-Biplot analysis was used to examine 183 Andean bean genotypes in Tanzania. Results indicated significant environment (E), genotype (G) and genotype x environment (GE) effects for seed yield. The environment explained 46%, genotype 20%, and GE 34% of the total (G + E + GE) variation. Two principal components explained 41.21% (PC1) and 26.35% (PC2) of GGE sum of squares. The Andean genotypes, ADP-102 (Jessica)- purple mottle, large seed, bush plant habit, released by Selian Agriculture Research Institution (ARI) in Tanzania; ADP-220 (G5625)- red, large seed, vine plant habit, from Central America; ADP-276 (G13654) - brown, medium seed, vine, from Mexico; and ADP-648 (‘Red Kloud’) large red kidney, with bush plant habit, were stable across environments and can be recommended for general adaptation across environments. An individual location for selection for yield stability was not identified, thus justifying the continued need for multiple test sites

Agronomic performance and cooking quality characteristics for slow-darkening pinto beans

Slow-darkening (SD) pinto beans (Phaseolus vulgaris L.) possess a desirable new trait, conditioned by the recessive sd gene, that slows seed coat darkening under delayed harvest and under storage. The effect sd may have on performance needs investigation. We examined agronomic performance and cooking quality of SD pinto beans. There were 30 (15 SD and 15 regular darkening [RD]) recombinant inbred lines (RILs) from each of two biparental inbred populations. The 60 RILs were tested across three locations in North Dakota andWashington. In addition, advanced SD and RD pinto breeding lines were tested in trials from 2010 to 2012 and in 2018. Across 2010–2012 trials, the “early generation bred” SD pintos, as a group, had significantly lower emergence, increased lodging, less seed yield, and smaller seed size than the RD group. Conversely, in the 2018 trial, “recently bred” SD pinto breeding lines had competitive agronomic performance to RD lines for seed yield, reduced lodging, and increased emergence. Further research on cooking time is warranted given that SD RILs cooked 20% faster than the RD RILs in one population. Overall, SD pintos exhibited slightly better canning quality than RD pintos. Whether raw or cooked, SD pintos were much lighter in color than RD pintos, emphasizing the need to keep them separated as distinct market classes. Breeders should continue to focus on improving agronomic performance for emergence, lodging, seed yield, seed size, and canning quality of SD pinto beans

Specific Genomic Regions in Common Bean Condition Resistance to Multiple Pathogens

A genetic linkage map of 170 RAPD markers mapped across 79 recombinant inbred lines (Dorado and XAN-176) reveal genomic regions that condition multiple disease resistance to fungal (Ashy Stem Blight—Macrophomina phaseolina), viral (bean golden mosaic virus— BGMV), and bacterial (common bacterial blight—Xanthomonas campestris pv. phaseoli) pathogens of common bean (Phaseolus vulgaris). A genomic site on linkage group US-1 had a major effect, explaining 18%, 34%, and 40% of the variation in phenotypic reaction to ashy stem blight, BGMV, and common bacterial blight disease, respectively. Adjacent to this region was a QTL conditioning 23% of the variation in reaction to another fungal pathogen, web blight (Thanatephorus cucumeris). A second genomic site on linkage group US-1 had minor affect on multiple resistance expression to the same fungal (15%), viral (15%), and bacterial (10%) pathogens. It is unknown whether these specific genomic regions represent a series of linked QTL affecting resistance to each disease separately or an individual locus with pleiotropic effect against all three pathogens

Description of Baetao-Manteiga 41 and ‘Yunguilla’ superior Andean common beans for Tanzanian production environments

An international effort was initiated with the evaluation of a diverse set of largeseeded Andean common beans (Phaseolus vulgaris L.), the Andean Diversity Panel, in sub-Saharan Africa. Several entries in the panel have been selected for extensive characterization on the basis of high performance acrossmultiple location × year trials in Tanzania—conducted both on station and on farm. Baetao- Manteiga 41, tested asADP-190, has a commercialKablanketi (light purple speckled) seed type, and ‘Yunguilla’, tested as ADP-447, has a commercial Calima (red mottled) seed type. Both lines exhibited yield stability, vigorous growth under low fertility conditions, angular leaf spot resistance, andmoderate common bacterial blight resistance; Yunguilla also possessed rust resistance. These two lines were tested, selected, and characterized cooperatively by Sokoine University of Agriculture (SUA), the Tanzanian Agricultural Research Institute (TARI), the USDA-ARS, and the Agricultural Research Council (ARC) of South Africa, and in collaboration with local farmers in Tanzania

Contributions in Puerto Rico to Bean, \u3ci\u3ePhaseolus\u3c/i\u3e spp., Research

Most literature reviews focus on a specific topic. The purpose of this paper, however, is to review the contributions made by a multidisciplinary team of researchers at a specific location (Puerto Rico) over a period of several decades. This paper documents bean research of the University of Puerto Rico and the USDA-ARS Tropical Agriculture Research Station during the past century. The following illustrates the merits of continuity of effort in research and shows that research often follows a logical sequence of actions to solve problems related to genetic improvement as well as to study biotic and abiotic factors that affect common bean production in Central America and the Caribbean. Finally, this narrative demonstrates that the ongoing development of improved bean germplasm lines and cultivars is cyclical and builds upon previous research achievements. The common bean (Phaseolus vulgaris L.) is an important component of the traditional diet in Puerto Rico. The 1900 report of the USDA Puerto Rico Agricultural Experiment Station (USDA-PRAES) noted that rice and beans were staple crops in Puerto Rico and found on the tables of both the rich and poor. Smit et al. (2007) noted that annual per capita consumption of grain legumes, mostly dry beans, in Puerto Rico (6.4 kg) is almost double the per capita consumption in the U.S. (3.4 kg; US Dry Bean Council, 2019). Common and lima beans (Phaseolus lunatus L.) have been produced in the Caribbean for at least 500 years. The grain legume fits well into rotations and is often intercropped with other longer season crops such as plantains and bananas. Small white beans, locally known as ‘Blanca del País’ and striped pink beans known as ‘Colorado del País’ are traditional market classes in Puerto Rico (Koenig, 1953). Consumers in Puerto Rico today consume a wide array of market classes including white, red, pink, pinto, black and kidney beans (Bean Institute, 2018). Although Puerto Ricans represent roughly 1% of the U.S. population, they consume 3.1% of the common and lima beans in the U.S. (Lucier et al., 2000)

Inheritance and QTL Analysis of Field Resistance to Ashy Stem Blight in Common Bean

Ashy stem blight [caused by Macrophomina phaseolina (Tassi) Goid.] can be a serious disease of common bean (Phaseolus vulgaris L.) under drought and high temperature conditions in some regions. The mode of inheritance of valuable sources of resistance is lacking. We studied inheritance of field resistance to ashy stem blight in a recombinant inbred population (’Dorado’ × XAN 176) consisting of 119 F5:7 recombinant inbred lines (RILs) tested in replicated experiments across 2 yr. A score from 1 to 9 (no disease to severe disease) was used to measure disease reaction. Moderate HNs (0.53 and 0.57) and near-normal frequency distribution of RILs for mean disease score each year indicated a lack of discrete segregation classes. The phenotypic variation across a subgroup composed of 79 RILs was further investigated with 165 randomly amplified polymorphic DNA (RAPD) markers by one-way analyses of variance and interval mapping. Five quantitative trait loci (QTL), explaining 19, 15, 15, 13, and 13% of the phenotypic variation for disease score, were detected in 1993. Three of these QTL, explaining 15,12, and 12% of the variation in disease reaction, were detected in 1994. Multiple QTL regression models (P \u3c 0.01) explained up to 47% (four loci) of the phenotypic variation for disease score in 1993 and 28% (three loci) in 1994. The five QTL, all derived from XAN 176, generally showed additive effects. These QTL-linked RAPD markers may prove useful for indirect selection of field resistance to ashy stem blight derived from XAN 176

Genetic Associations in Four Decades of Multienvironment Trials Reveal Agronomic Trait Evolution in Common Bean

Multienvironment trials (METs) are widely used to assess the performance of promising crop germplasm. Though seldom designed to elucidate genetic mechanisms, MET data sets are often much larger than could be duplicated for genetic research and, given proper interpretation, may offer valuable insights into the genetics of adaptation across time and space. The Cooperative Dry Bean Nursery (CDBN) is a MET for common bean (Phaseolus vulgaris) grown for . 70 years in the United States and Canada, consisting of 20–50 entries each year at 10–20 locations. The CDBN provides a rich source of phenotypic data across entries, years, and locations that is amenable to genetic analysis. To study stable genetic effects segregating in this MET, we conducted genome-wide association studies (GWAS) using best linear unbiased predictions derived across years and locations for 21 CDBN phenotypes and genotypic data (1.2 million SNPs) for 327 CDBN genotypes. The value of this approach was confirmed by the discovery of three candidate genes and genomic regions previously identified in balanced GWAS. Multivariate adaptive shrinkage (mash) analysis, which increased our power to detect significant correlated effects, found significant effects for all phenotypes. Mash found two large genomic regions with effects on multiple phenotypes, supporting a hypothesis of pleiotropic or linked effects that were likely selected on in pursuit of a crop ideotype. Overall, our results demonstrate that statistical genomics approaches can be used on MET phenotypic data to discover significant genetic effects and to define genomic regions associated with crop improvement