Fine mapping of a major quantitative trait locus, qgnp7(t), controlling grain number per panicle in African rice (Oryza glaberrima S.)

Abstract

Grain number per panicle is a major component of rice yield that is typically controlled by many quantitative trait loci (QTLs). The identification of genes controlling grain number per panicle in rice would be valuable for the breeding of high-yielding rice. The Oryza glaberrima chromosome segment substitution line 9IL188 had significantly smaller panicles compared with the recurrent parent 9311. QTL analysis in an F₂ population derived from a cross between 9IL188 and 9311 revealed that qgnp7(t), a major QTL located on the short arm of chromosome 7, was responsible for this phenotypic variation. Fine mapping was conducted using a large F₃ population containing 2250 individuals that were derived from the F₂ heterozygous plants. Additionally, plant height, panicle length, and grain number per panicle of the key F₄ recombinant families were examined. Through two-step substitution mapping, qgnp7(t) was finally localized to a 41 kb interval in which eight annotated genes were identified according to available sequence annotation databases. Phenotypic evaluation of near isogenic lines (NIL-qgnp7 and NIL-qGNP7) indicated that qgnp7(t) has pleiotropic effects on rice plant architecture and panicle structure. In addition, yield estimation of NILs indicated that qGNP7(t) derived from 9311 is the favorable allele. Our results provide a foundation for isolating qgnp7(t). Markers flanking this QTL will be a useful tool for the marker-assisted selection of favorable alleles in O. glaberrima improvement programs.

Keywords: African rice (Oryza glaberrima S.); chromosome segment substituted lines; fine mapping; grain number per panicle.

Fig. 1

Phenotypic performance of 9311 and 9IL188 at Taicang experimental station. A. 9311 and 9IL188 plants at the mature stage. Scale bar = 10 cm, B. Panicle phenotypes of 9311 and 9IL188 at the mature stage, Scale bar = 3 cm. Comparison of plant height (C), grains per panicle (D), panicle length (E), tillers per plant (F), seed setting rate (G), and grain weight (H). Data presented are means with SD (n = 10 plants). ***, P = 0.001; NS, not significant at P = 0.05.

Fig. 2

The graphic genotype of the 9IL188 plant. The black and white chromosome segments were the O. glaberrima homozygote and 9311 homozygote, respectively. Only four chromosomes contained segments of donor parent, O. glaberrima. The other eight chromosomes were fixed with 9311.

Fig. 3

Frequency distribution of grains per panicle in the F₂ population. The three genotypes of homozygous 9311 (9), heterozygote (H), and homozygous O. glaberrima (g) at qgnp7(t) were identified by progeny testing.

Fig. 4

Substitution mapping of qgnp7(t). A. Genetic linkage map of the qgnp7(t) region on chromosome 7 constructed using 152 F₂ plants. qgnp7(t) was mapped to the interval between markers RM298 and RM82. Numbers above the line indicate the genetic distance between adjacent markers, B. High-resolution linkage map of the qgnp7(t) region (AP005632) constructed using 2,258 F₃ plants. The number of recombinants between adjacent markers is indicated above the linkage map, C. Progeny testing of homozygous recombinants localized the qgnp7(t) locus to the region between markers 7Sui21 and 7Sui24. On the right, the phenotypic value (mean ± SD; n = 30 plants) of each F₄ families and two parents were indicated. PH plant height, PL panicle length, GPP grains per panicle.

Fig. 5

Relative expression of the qgnp7(t) candidate genes in two parents (9311 and 9IL188). Panicle materials were collected at Booting Stage. Data presented are means with SE (n = 3 plants). *, P = 0.05; ***, P = 0.001; NS, not significant at P = 0.05.

Fig. 6

The proportion of each internode to stem in NIL-qGNP7 and NIL-qgnp7. Data presented are means with SD (n = 10 plants). IN1–6 internode 1–6.

Fig. 7

The proportion of primary and secondary branches per panicle to total branches per panicle in NIL-qGNP7 and NIL-qgnp7. Data presented are means with SD (n = 10 plants). PB primary branches per panicle, SB secondary branches per panicle.

Fig. 8

Stem cell morphology of NIL-qGNP7 and NIL-qgnp7. A–B. Transverse sections of stems in the heading stage. Sampling site was in the middle of the uppermost internode of the main culm of the plant. Scale bar = 1000 μm and 100 μm; C–D. Longitudinal sections of stems in the heading stage. Sampling site was in the middle of the uppermost internode of the main culm of the plant. Scale bar = 1000 μm and 100 μm.