Development of New Selection Tools and Crop Varieties for Sustainable Agriculture

Three main populations have been evaluated in this project. One population, the BeanCAP Middle American Diversity Panel (MDP), includes 280 highly diverse common bean varieties that are all descended from one of the domestication events in common bean. These were genotyped by Illumina BARCBean6K_3 Beadchip and Genotyping by Sequencing (GBS). These were grown to identify the genetic basis of canopy height, growth rate, and other canopy characteristics. A second population was developed specifically to study early season growth rate. It consists of 240 recombinant inbred lines descended from crosses between Black Nightfall and Orca. Black Nightfall is a fast growing variety that competes effectively against weeds. Orca is very slow growing, and is not competitive against weeds. This population segregates for early season growth rate. DNA from each RIL was extracted through a modified CTAB procedure, and genotyped with the BARCBean6K_3 BeadChip. A genetic map was constructed based on this data using the ASMap package in R, and QTL mapping was conducted using R/qtl. The third population is a diverse assemblage of breeding materials and the heirloom varieties and university-developed types they are descended from. Hundreds of heirloom varieties were grown between 2013 and 2016 to identify promising candidates. No heirloom lines combined rapid early season growth rate, bean common mosaic virus (BCMV) resistance, and consistently high yields. Donors for these characteristics were carefully chosen, and cross-pollinations were conducted between heirloom types and breeding lines developed by universities. The breeding program has progressed by a) the pedigree method, selecting for the above-mentioned characteristics and ideal seed coat color, and b) recurrent backcrossing for BCMV resistance. In the latter case, naturally occurring resistance alleles are "diluted" into the genetic background of the heirloom by a series of selections and cross-pollinations with the heirloom parent (recurrent backcrossing).

During the growing season, flights were conducted weekly from 3 weeks after planting (WAP) to 6 WAP for all populations. Until 3 WAP, the plants are small and the aerial imagery is not sufficiently detailed to generate meaningful data. Starting around 6 WAP, the plants transition into reproductive growth and begin to lodge, so increased canopy area after this point is not necessarily beneficial. Later flights were conducted throughout the season to continue the evaluation of canopy health throughout the growing season. This series of flights was conducted using a Phantom 3 Pro over the MDP and breeding population in 2016. In 2017, Phantom 3s were used to collect true color red/green/blue (RGB) and multispectral data over the MDP and Black Nightfall/Orca populations. The RGB and multispectral data were collected using a stock camera and Parrot Sequoia, respectively. Flights were typically planned in DJI Ground Station Pro. Imagery was processed into orthomosaics and digital surface models using Pix4Dmapper Pro. QGIS was used to extract data from each plot in the field, and advanced data extraction and statistical analyses and were done in R.

RGB, multispectral, and thermal data were collected for all populations in 2018. The 2018 breeding populations had been narrowed down to 10 breeding lines, five heirloom varieties, and three varieties released by universities as controls. These breeding lines were grown in three replicates in each of three organic field locations, along with a single replicate in one conventional field. In 2017 and 2018, the MDP was grown as two independent augmented designs, while the Black Nightfall/Orca population was grown in a single augmented design. The 2018 breeding trials were located on certified organic farms in San Diego, Monterey, and Yolo counties in California. In 2016, the MDP was grown in a single augmented design. In 2019, the Black Nightfall/Orca population is being grown in two augmented designs for a third and final season. The 2019 breeding trials include three replicates of eight breeding lines, five heirloom parents, and three university-developed controls. This trial is being conducted in Yolo, San Mateo, San Luis Obispo, and San Diego counties in California, and at Fedco seeds (two replicates) in Maine. Tests of some of these lines is also occurring in Shasta county and a second location in Yolo county. Row 7 seeds is conducting a taste test of the varieties. 

Raw imagery from drones was compiled into orthomosaics and digital surface models using Pix4Dmapper. Using QGIS, a grid of shapefiles was laid over each field using the vector grid function. Normalized Difference Vegetation Index (NDVI) orthomosaics were then used to separate canopy from soil based on an NDVI threshold of 0.5. This layer was used to calculate canopy area and eliminate soil values as needed. Digital surface models were used to extract the heights of plants and soil in each plot. The median elevation of the soil was subtracted from the mean canopy elevation to determine the average height of plants in a plot. Maximum plant heights were determined based on the median soil elevation subtracted from the maximum canopy elevation. This process requires only a few minutes to accomplish per field once the models are loaded into QGIS, regardless of the number of plots, making it scale efficiently for large trials. UAV-determined canopy heights were then compared to hand-measured heights. Genome wide association studies (GWAS) were carried out for changes in canopy area, height, and other characteristics in the MDP. This was done by GLM in TASSEL through the SNiPlay web interface. A minor allele frequency threshold of 0.1 was used for all tests, with a correction for population structure using the first five principal components of the genetic data. Significance was determined based on a Bonferroni correction based on an alpha of 0.05.