Mapping QTL for leaf pigment content at dynamic development stage and analyzing Meta-QTL in rice

Abstract

Leaf pigment content is a complicated quantitative trait which results from the cooperation of multiple related genes or quantitative trait loci (QTL) in rice. So far, more than 600 QTL for leaf pigment content has been reported. However, most QTL positions could not be directly compared with each other. In this study, our goal was to analyze consistent QTL regions affecting leaf pigment content by applying a genome wide QTL meta-analysis approach. 20 QTL related to leaf pigment content were detected at 5 different growth periods in 134 recombinant inbred lines (RILs) from a typical Indica-Japonica cross derived from PA64s and 9311 (two parents of super hybrid rice Liangyoupei 9). There was a candidate gene GLTP in the region of 3 QTL (qFS_Chla4, qFS_Chla+b4, and qFS_Car4), which related to component of chloroplast thylakoid membranes. After sequencing and qRT-PCR analysis, the gene showed significant difference in parents of the RILs. Meta-analysis was performed on 618 QTL collected from 38 previous studies. Consequently, a total of 64 MQTL (Meta-QTL) were obtained, of which 58.95% confidence intervals (CI) were smaller than the average Cl of the original QTL. In addition, 64 MQTL covered 6 of 20 QTL detected. Among them, four main QTL were included in 3 MQTL, and phenotypic variation of 21 MQTL was greater than 20%. The traits with higher number of QTL had higher number of MQTL, and candidate genes in overlapping MQTL include multiple effects. 7 candidate genes related to leaf pigment content were found in 4 MQTL spanning physical intervals < 0.5 Mb. These findings are not only anticipated to help molecular marker-assisted selection and pyramiding, but also contribute to determine candidate genes that regulate pigment content.