Analysis of quantitative trait loci affecting chlorophyll content of rice leaves in a double haploid population and two backcross populations

Abstract

Chlorophyll content, one of the most important physiological parameters related to plant photosynthesis, is usually used to predict yield potential. To map the quantitative trait loci (QTLs) underlying the chlorophyll content of rice leaves, a double haploid (DH) population was developed from an indica/japonica (Zhenshan 97/Wuyujing 2) crossing and two backcross populations were established subsequently by backcrossing DH lines with each of their parents. The contents of chlorophyll a and chlorophyll b were determined by using a spectrophotometer to directly measure the leaf chlorophyll extracts. To determine the leaf chlorophyll retention along with maturation, all measurements were performed on the day of heading and were repeated 30 days later. A total of 60 QTLs were resolved for all the traits using these three populations. These QTLs were distributed on 10 rice chromosomes, except chromosomes 5 and 10; the closer the traits, the more clustering of the QTLs residing on common rice chromosomal regions. In general, the majority of QTLs that specify chlorophyll a content also play a role in determining chlorophyll b content. Strangely, chlorophyll content in this study was found mostly to be lacking or to have a negative correlation with yield. In both backcross F1 populations, overdominant (or underdominant) loci were more important than complete or partially dominant loci for main-effect QTLs and epistatic QTLs, thereby supporting previous findings that overdominant effects are the primary genetic basis for depression in inbreeding and heterosis in rice.

Keywords: BC; BCF(1); DH; DH×WY; DH×ZS; E-QTLs; GF; Gene action; HMP; ICa; ICb; II/ICa; II/ICb; II/ISF; II/ISS; IICa; IICb; IISF; IISS; ISF; ISS; KGW; LOD; LR; M-QTLs; Molecular mapping; Oryza sativa L; PL; Permanent BC population; Pigment content; QTLs; R(2); RIL; SDEN; SP; SPAD readings of the flag leaves measured on the day of heading; SPAD readings of the second leaves measured on the day of heading; SPAD values of the flag leaves measured at 30days after heading; SPAD values of the second leaves measured at 30days after heading; SS; SSR; TC; TP; WY; WYF1; WYHMP; Wuyujing; YD; ZS; ZSF1; ZSHMP; Zhenshan; a; additive effect; backcross; backcross F1; d; dominance; double haploid; epistatic quantitative trait loci; grain weight per 1000 grains; grain yield per plant; grain-filling degree; leaf chlorophyll a content at developmental stage I; leaf chlorophyll a content at developmental stage II; leaf chlorophyll b content at developmental stage I; leaf chlorophyll b content at developmental stage II; likelihood ratio; log likelihood value; main-effect quantitative trait loci; mid-parental heterosis; mid-parental heterosis in WYF1; mid-parental heterosis in ZSF1 population; number of tillers per plant; panicle length; quantitative trait loci; ratio of IICa to ICa; ratio of IICb to ICb; recombinant inbred line; relative contribution of a genetic component; seed-setting rate; setting grain density per panicle; simple sequence repeat; spikelet per panicle; testcross; the ratio of IISF to ISF; the ratio of IISS to ISS.