Analysis of Shoot Architecture Traits in Edamame Reveals Potential Strategies to Improve Harvest Efficiency

Abstract

Edamame is a type of green, vegetable soybean and improving shoot architecture traits for edamame is important for breeding of high-yield varieties by decreasing potential loss due to harvesting. In this study, we use digital imaging technology and computer vision algorithms to characterize major traits of shoot architecture for edamame. Using a population of edamame PIs, we seek to identify underlying genetic control of different shoot architecture traits. We found significant variations in the shoot architecture of the edamame lines including long-skinny and candle stick-like structures. To quantify the similarity and differences of branching patterns between these edamame varieties, we applied a topological measurement called persistent homology. Persistent homology uses algebraic geometry algorithms to measure the structural similarities between complex shapes. We found intriguing relationships between the topological features of branching networks and pod numbers in our plant population, suggesting combination of multiple topological features contribute to the overall pod numbers on a plant. We also identified potential candidate genes including a lateral organ boundary gene family protein and a MADS-box gene that are associated with the pod numbers. This research provides insight into the genetic regulation of shoot architecture traits and can be used to further develop edamame varieties that are better adapted to mechanical harvesting.

Keywords: breeding; edamame; persistent homology; phenotyping; shoot architecture.

FIGURE 1

Workflow of phenomics analysis of edamame shoot architecture and canopy cover. Step 1. Data from a mini-core collection of edamame varieties were used for this study. Step 2. Individual plant was imaged twice on a black background. Step 3. Unmanned aerial vehicle was used to collect canopy cover data over the growth season. Step 4. Selected varieties were used for detailed characterization of the shoot architecture. Step 5. Phenotypic data analyses were performed. Step 6. Potential genetic control points of shoot architecture were analyzed.

FIGURE 2

Parameter correlations for images of edamame shoot architecture. (A) 12 geometric traits were measured in this study. PH, plant height; MBL, main branch length; PN, pod number; TBL, total branch length; APBL, average primary branch length; FNH, first node height; PPA10, percent of pod above 10 cm from ground; FPH, first pod height; NPB, number of primary branches; FIL, first internode length; SIL, second internode length; TIL, third internode length. Numbers on top of the bars are Pearson Correlation Coefficient (PCC). * indicates statistical significance (p < 0.01). (B) Scatter plot of plant height measurement between technical replications (front and back images of the same plant). (C) Scatter plot of first internode length. Red arrow indicates an outlier data point.

FIGURE 3

Distribution of shoot architecture parameters in edamame plants. (A) Histograms and density plots for main branch length, plant height and average primary branch length. (B) Boxplot shows the distribution of first pod height, first, second and third internode lengths. (C) Density plots compare first node height with first pod height and 5% pod height. (D) Histograms and density plots for number of pods per plant and number of pods above 10 cm from ground. (E) Boxplot of canopy cover changes in the growth season.

FIGURE 4

Correlation analysis of traits characterized in this study. (A) correlation between edamame shoot architecture traits with topological traits (MDS1, 2, and 3). Trait names are described in Figure 2 and main text. PN, pod number; NPB, number of primary branches; SI, short internode; FIL, first internode length; SIL, second internode length; TIL, third internode length; TBL, total branch length; APBL, average primary branch length; CC61DAP, canopy cover 61 days after planting; CC81DAP, canopy cover 81 days after planting; FNH, first node height; MBL, main branch length; PH, plant height; PN10, pod number above 10 cm from ground; P5H, height above ground for 5% pods; P1H, height above ground for 1% pods; FPH, first pod height. (B) Comparison of MDS1 and MDS2 with plant height. (C) Comparison of MDS1 and MDS2 with pod number.