The liner electrons transport rate (ETR) of non-foliar green organs, such as siliques, can comparable to that of green leaves, however, their net photosynthetic rate (A) are considerably different. Does the distribution of electrons to photorespiration or nitrogen metabolism could be the primary cause? Literatures also showed that the non-foliar organs can use respiratory released CO2 to maintain carbon balance. For instance, CO2 in silique cavity can be as high as 2000 μmol mol-1. During gas exchange measurements, the LI-6400 could not take the CO2 change in silique cavity into account. Does this mean that we underestimate the real A of siliques by ignoring the use of respiratory CO2, and this is the reason why the detected A is different between two organs but their ETR are same. If this is the case, how to measure the real A of siliques?
Most green organs got their chloroplasts in tissue layers that play a regulatory role in seed development. but ETR should be mainly of respiratory origin or by mitochondria, you may see the refs in a nice forum about by stoicsmile https://www.reddit.com/r/askscience/comments/k0p5y/what_gas_would_be_in_a_pumpkin/
This is a difficult question to answer because there can be many reasons for the discrepancy between ETR and Anet. It is unlikely to be photorespiration if the CO2 concentration in the silique is very high. You can measure photorespiration by measuring the A/Ci response.
Literature also suggests that siliques contain much less chlorophyll compared to leaves, which may reduce light absorption and reduce Anet.
Many non-leaf photosynthetic organs refix CO2 released from mitochondrial respiration, therefore, simple gas exchange measurements can not count for that, to my understanding.
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