Analysis of Physiological Variations and Genetic Architecture for Photosynthetic Capacity of Japanese Soybean Germplasm

Abstract

The culmination of conventional yield improving parameters has widened the margin between food demand and crop yield, leaving the potential yield productivity to be bridged by the manipulation of photosynthetic processes in plants. Efficient strategies to assess photosynthetic capacity in crops need to be developed to identify suitable targets that have the potential to improve photosynthetic efficiencies. Here, we assessed the photosynthetic capacity of the Japanese soybean mini core collection (GmJMC) using a newly developed high-throughput photosynthesis measurement system “MIC-100” to analyze physiological mechanisms and genetic architecture underpinning photosynthesis. K-means clustering of light-saturated photosynthesis (Asat) classified GmJMC accessions into four distinct clusters with Cluster2 comprised of highly photosynthesizing accessions. Genome-wide association analysis based on the variation of Asat revealed a significant association with a single nucleotide polymorphism (SNP) on chromosome 17. Among the candidate genes related to photosynthesis in the genomic region, variation in expression of a gene encoding G protein alpha subunit 1 (GPA1) showed a strong correlation (r = 0.72, p < 0.01) with that of Asat. Among GmJMC accessions, GmJMC47 was characterized by the highest Asat, stomatal conductance (gs), stomatal density (SDensity), electron transfer rate (ETR), and light use efficiency of photosystem II (Fv’/Fm′) and the lowest non-photochemical quenching [NPQ(t)], indicating that GmJMC47 has greater CO2 supply and efficient light-harvesting systems. These results provide strong evidence that exploration of plant germplasm is a useful strategy to unlock the potential of resource use efficiencies for photosynthesis.

Implementation of theoretical non-photochemical quenching (NPQ(T)) to investigate NPQ of chickpea under drought stress with High-throughput Phenotyping

“…The following applications under fully light adapted conditions of NPQ (T) and ФPSII for the method-implementation during drought stress and recovery were comparable in terms of repeatability with previous studies on chickpea on ФPSII 8 . Furthermore, the values of NPQ (T) were similar to experiments with maize under drought stress and soybean under cold stress 28 , 29 , 33 . In addition, NPQ (T) was able to detect more variation within the plant genetic resources than other chlorophyll fluorescence measurements.…”

Genome-wide association study of leaf photosynthesis using a high-throughput gas exchange system in rice

“…MIC-100 exploits a closed-gas exchange system and thus requires 15-20 seconds for each measurement, which corresponds to less than ~ 90% of the conventional open-gas exchange systems (See Tanaka et al (2021) for the details of the system). MIC-100 enables to measure A of several hundred leaves per day in the eld (Honda et al 2021;Shamim et al 2022). Furthermore, the measured values of A in MIC-100 highly correlated with those of LI-6400XT and LI-6800 (LI-COR Biosciences, Lincoln, NE, USA), the standard open-gas exchange systems, under high light conditions (Tanaka et al 2021; Takaragawa and Matsuda 2023).…”

“…The low measurement e ciency is also problematic in doing genome-wide association study (GWAS), a method analyzing associations between phenotypic values and nucleotide polymorphisms in diverse sets of varieties, because GWAS usually requires a greater number of phenotypic data than the conventional QTL analysis (Verdeprado et al 2018). There are only a few examples of GWAS applying for gas exchange analysis (Ortiz et al 2017;Qu et al 2017;Shamim et al 2022). The development of high-throughput measurement systems for leaf gas exchange is essential for further advancement of crop breeding.…”

Applicability of a Closed and Rapid Gas-exchange System to Leaf Photosynthetic Measurements in Tropical Fruit Trees

“…Newly developed closed and rapid systems have been used to measure individual leaf photosynthesis in herbaceous crops, such as rice (Honda et al, 2021), soybean (Shamim et al, 2022), sugarcane, Erianthus (Takaragawa and Matsuda, 2023), and passion fruit (Kondo and Morizono, 2022), but their accuracy and usefulness in measuring individual leaf photosynthesis in tree crops, such as fruit trees, have not been investigated.…”