Genetic variation analysis and discovery of major effect genes for photosynthetic traits in apricot

Abstract: 【Objective】Photosynthesis is a crucial physiological process for plant growth and yield formation, and also is an important trait to improve in fruit trees. Elucidating the genetic variation patterns of photosynthetic traits in the F1 generation of apricot populations can provide a theoretical basis for genetic improvement of fruit trees.【Methods】The F1 population of apricot was constructed by a crossing between Chuanshizhong with high photosynthetic rate, and Luotuohuang with low photosynthetic rate. The measurements of photosynthetic rate, stomatal conductance, intercellular CO2 concentration, and transpiration rate were conducted on the two parents and the individuals of the F1 population using Li-6400XT. 【Results】The photosynthetic rate exhibited a range of variation from 67.60 to 109.10 μmol·m^{- 2} ·s^{- 1} in 2015 and 19.50 to 92.60 μmol·m^-2 ·s^-1 in 2016. The directional trends in photosynthetic rates of the hybrid progeny differed between the two years. In 2016, a trend toward higher photosynthetic rates was observed, while in 2017, the trend shifted toward lower photosynthetic rate regions. The photosyntheticrelated traits exhibited a normal distribution, indicating that it would be a typical quantitative genetic characteristic. The broad-sense heritability (H²) of the photosynthetic rate, transpiration rate, and inter-cellular CO2 concentration in the apricot hybrid population were all approximately 0.80, suggesting that the variation in these traits is predominantly attributed to genetic effects, with minimal influence from the environment, indicating substantial genetic potential. The progeny mean values of the photosynthetic traits exceeded the parental mid-values, demonstrating a pattern of overdominant inheritance. Notably, extreme overdominance was observed in hybrid individuals for the photosynthetic rate and stomatal conductance. This implied the possibility of selecting varieties with high photosynthetic rates and stomatal conductance in the offspring. The broad-sense heritability analysis suggested that the photosynthetic rate, transpiration rate, and intercellular CO2 concentration were mainly influenced by genetic effects. A high-density indel genetic map for apricot was constructed, with a total of 1356 co-located markers and an average marker interval of 0.44 cM. The high-density indel genetic map for apricot revealed seven quantitative trait loci (QTLs) related to photosynthetic traits, distributed on linkage groups 1, 4, and 6. Notably, both QTL sites controlling photosynthetic rate were situated on linkage group 1, with positioning intervals consistent in different years (2016: 62.25- 69.00 cM, LOD values ranging from 2.54 to 2.79; 2017: 63.28-69.00 cM, LOD values ranging from 3.96 to 4.14). In 2016, two QTL sites associated with stomatal conductance were detected (61.00-62.25 cM, LOD values 1.68-1.83; 104.42-106.45 cM, LOD values ranging from 1.54 to 1.89), both were located on linkage group 1. In 2017, one QTL site controlling intercellular CO2 concentration was identified (65.40-68.68 cM, LOD values ranging from 3.03 to 3.25). Additionally, one QTL site governing transpiration rate was detected in 2016 and 2017, with positions at 13.50-14.85 cM and 52.60-53.95 cM, and LOD values ranging from 2.01 to 2.17 and 2.20 to 2.21, respectively. Using the Bulked Segregant Analysis (BSA) method, one QTL related to photosynthetic rate was located on Chr7. Gene extraction from QTL intervals using apricot genome and annotation information identified 217, 186, 111, and 114 genes related to photosynthetic rate, stomatal conductance, intercellular CO2 concentration, and transpiration rate, respectively. The enrichment analysis revealed an association between the photosynthetic rate and the carbon fixation pathway, with the involvement of gene PA01G03444 observed in QTLs for transpiration rate and stomatal conductance. Therefore, the PA01G03444 gene would emerge as a potential key regulator of photosynthesis. These findings present valuable gene resources for further investigations on the molecular mechanisms underlying photosynthesis in apricot trees.【Conclusion】The gene PA01G03444 might be the major regulatory gene for photosynthesis, laying the groundwork for screening candidate genes controlling photosynthesis.