Identification and Fine Mapping of qCTH4, a Quantitative Trait Loci Controlling the Chlorophyll Content from Tillering to Heading in Rice(Oryza sativa L.)

Abstract

The chlorophyll content is one of the most important traits selected by breeders, and it is controlled by quantitative trait loci (QTLs) derived from natural variations in rice. We analyzed the QTL controlling chlorophyll content by using 94 RILs derived from a cross between 2 japonica rice cultivars, Lijiangxintuanheigu (LTH) and Shennong265 (SN265). Twenty-two QTLs controlling chlorophyll content at tillering stage, heading stage, and maturity stage were detected, respectively. Among them, Rice cv. LTH had a positive allele only at 1 locus (qCTH4) on chromosome 4. Further analysis indicated that the genetic effect of qCTH4 was the net effects within the period from tillering to heading. The QTL qCTH4 controlling chlorophyll content from tillering to heading locates between RM255 and RM349 on chromosome 4 with a LOD score 19.41, and the QTL qCTH4 explains 61.42% of phenotypic variation. In order to eliminate the influence of other QTLs, 1 single residual heterozygous plant, RH-qCTH4, was selected based on the genotypes of 114 Simple Sequence Repeat (SSR) markers. Using the segregating population derived from RH-qCTH4 by self-crossing, this region was narrowed down to an interval between RM3276 and RM17494 in an approximately 771kb target region. These results are useful for map-based cloning of qCTH4 and for marker-assisted selection of high photosynthetic efficiency variety.

Genetic Architecture of Natural Variation in Rice Chlorophyll Content Revealed by a Genome-Wide Association Study

“…382 In this article, NAL1 was also shown to be a major gene for natural variation of 383 chlorophyll content. The chromosomal region around NAL1 has been consistently 384 detected with large effects for SPAD value and flag leaf area in different genetic 385 crosses (Yueet al, 2006;Takai et al, 2010;Jiang et al, 2012;Zhang et al, 2014).386Natural variation of NAL1 has been reported in terms of amino acid substitutions, 387 difference of expression levels, and the presence of multiple transcripts. Here we 388 characterized the nucleotide diversity and effects of the major haplotypes of NAL1.389 We detected high-degree polymorphism in 5' UTR and four non-synonymous SNPs 390 in the coding region, and observed diverse effects of the major haplotypes.…”

Fine mapping a major QTL qFCC7 L for chlorophyll content in rice (Oryza sativa L.) cv. PA64s

“…Some QTLs detected in this study were in or near the regions which have been reported previously. The QTLs between SNP1-10 and SNP1-27 are near to the region of qCHM1 (RM490-RM580) reported by Jiang et al (2012) and HSPAD-1b (RM6902-RM8111) identified the qFCC7 L region with 93-11 genetic background showed a higher SPAD value than 93-11 (Fig. 3a).…”

“…The QTLs between SNP4-246 and SNP4-271 are corresponding to qCH4, qCM4b and qCTH4 (RM255-RM559) found by Jiang et al (2012) and qLSCHL4 (STS4-5-RM349) detected by Zhang et al (2014). We also detected some new loci, the qSCC5 H between SNP5-203 and SNP5-226 controlling the Chl content of second leaf in high N level at heading stage, the qFCC8 L between SNP8-139 and SNP8-164 explaining 9.4 % of phenotypic variations of the FL Chl content at initial heading stage.…”

“…Some studies have demonstrated a positive relationship between leaf photosynthesis and leaf Chl content (Kura-Hotta et al 1987;Xu et al 1997;Hu et al 2009). Using different populations, many QTLs related to Chl content have been reported (Wang et al 2003;Teng et al 2004;Jiang et al 2012). In this study, a mapping population developed from two parental lines, one with high Chl content but low yield potential (PA64s) and another with low Chl content but high yield (93-11), provided a unique opportunity to identify QTLs for the Chl content which contributed to the high heterosis of the pioneer hybrid rice LYP9 developed by crossing these two parents and would benefit the molecular breeding of new hybrid rice genotypes.…”

“…Hu et al (2009) detected 13 main QTLs controlling Chl content under well-watered and water stressed conditions on chromosomes 1, 2, 3, 4, 5, 6, and 10. Jiang et al (2012) identified 22 QTLs related to Chl content using 94 recombinant inbred lines (RILs) derived from a cross between two japonica cultivars, Lijiangxintuanheigu (LTH) and Shennong 265 (SN265), and these QTLs distributed over all chromosomes except chromosome 5. Zhang et al (2014) discovered five QTLs controlling Chl content on chromosomes 1, 4, 7, 12 and two QTLs on chromosomes 4 and 12 at heading and maturity stages, respectively.…”