Dynamic QTL mapping revealed primarily the genetic structure of photosynthetic traits in castor (Ricinus communis L.)

High photosynthetic efficiency is the basis of high biomass and high harvest index in castor (Ricinus communis L.). Understanding the genetic law of photosynthetic traits will facilitate the breeding for high photosynthetic efficiency. In this study, the dynamic QTL mapping was performed with the populations F2 and BC1 derived from 2 parents with significant difference in net photosynthetic rate (Pn) at 3 stages, in order to reveal the genetic structure of photosynthetic traits. In F2 population, 26 single-locus QTLs were identified, including 3/3/1 (the QTL number at stage I/II/III, the same below), 1/2/0, 1/2/2, 1/3/1, 0/1/1, and 1/1/2 QTLs conferring Pn, water use efficiency (Wue), transpiration rate (Tr), stomatal conductance (Gs), intercellular CO2 concentration (Ci) and chlorophyll content (Cc), with a phenotypic variation explained (PVE) of 8.40%/8.91%/6.17%, 5.36%/31.74%/0, 7.31%/12.80%/15.15%, 1.60%/6.44%/0.02%, 0/1.10%/0.70% and 2.77%/3.96%/6.50% respectively. And 53 epistatic QTLs (31 pairs) were identified, including 2/2/5, 5/6/3, 4/4/2, 6/3/2, 3/2/0 and 4/0/0 ones conferring the above 6 traits, with a PVE of 6.52%/6.47%/19.04%, 16.72%/15.67%/14.12%, 18.57%/15.58%/7.34%, 21.72%/8.52%/7.13%, 13.33%/4.94%/0 and 7.84%/0/0 respectively. The QTL mapping results in BC1 population were consistent with those in F2 population, except fewer QTLs detected. Most QTLs identified were minor-effect ones, only a few were main-effect ones (PVE > 10%), focused on 2 traits, Wue and Tr, such as qWue1.1, qWue1.2, FqTr1.1, FqTr6, BqWue1.1 and BqTr3; The epistatic effects, especially those related to the dominance effects were the main genetic component of photosynthetic traits, and all the epistatic QTLs had no single-locus effects except qPn1.2, FqGs1.2, FqCi1.2 and qCc3.2; The detected QTLs underlying each trait varied at different stages except stable QTLs qGs1.1, detected at 3 stages, qWue2, qTr1.2 and qCc3.2, detected at 2 stages; 6 co-located QTLs were identified, each of which conferring 2–5 different traits, demonstrated the gene pleiotropy between photosynthetic traits; 2 QTL clusters, located within the marker intervals RCM1842-RCM1335 and RCM523-RCM83, contained 15/5 (F2/BC1) and 4/4 (F2/BC1) QTLs conferring multiple traits, including co-located QTLs and main-effect QTLs. The above results provided new insights into the genetic structure of photosynthetic traits and important references for the high photosynthetic efficiency breeding in castor plant.