Analysis of QTL for Grain Size in a Rice Chromosome Segment Substitution Line Z1392 with Long Grains and Fine Mapping of qGL-6

Abstract

Background: Grain size affects not only rice yield but is also an important element in quality of appearance. However, the mechanism for inheritance of grain size is unclear.

Results: A rice chromosome segment substitution line Z1392, which harbors three substitution segments and produces grains of increased length, was identified. The three chromosome segments were located on chromosomes 1, 5, and 6, and the average length of the substitution segment was 3.17 Mb. Cytological analysis indicates that the predominant cause of increased grain length in Z1392 could be cell expansion in the glumes. Seven quantitative trait loci (QTLs) for grain size related traits were identified using the secondary F₂ population produced by Nipponbare/Z1392. The inheritance of grain length in Z1392 was mainly controlled by two major QTLs, qGL-5 and qGL-6. qGL-6 was localized on a 1.26 Mb region on chromosome 6, and OsARF19 may be its candidate gene. Based on QTL mapping, three single-segment substitution lines (S1, S2, and S3) and two double-segment substitution lines (D1 and D2) were selected, and the mapping accuracy for qGL-5 and qGL-6 was further verified using three single-segment substitution lines. Analysis of QTL additive and epistatic effects revealed that the additive effect of alleles qGL-5 and qGL-6 from 'Xihui 18' was estimated to increase grain length of Z1392 by 0.22 and 0.15 mm, respectively. In addition, a positive epistatic interaction between qGL-5 and qGL-6 was detected, which indicates that the pyramiding of qGL-5 and qGL-6 for grain length produces a novel genotype with longer grains.

Conclusions: Inheritance of grain length in the triple-segment substitution line Z1392 is mainly controlled by two major QTLs, qGL-5 and qGL-6. qGL-6 was found to be located in a 1.26 Mb region on chromosome 6, and OsARF19 may be its candidate gene. A positive epistatic interaction between qGL-5 and qGL-6 results in longer grains. The present results can be used to facilitate cloning of the qGL-5 and qGL-6 genes and contribute to improvement of grain yield in rice.

Keywords: Chromosome segment substitution line; Epistatic analysis; Grain length; QTL mapping; Rice.

Fig. 1

Substitution segments harbored in the CSSL Z1392 and position of grain size related QTLs. Physical distance (Mb) is specified on the left of each chromosome (based on the Nipponbare reference genome) and markers are specified on the right. The solid black segment is the substitution fragment region from the donor Xihui 18 and the identified QTLs are listed on the left of each chromosome in italics. qGL, QTL for grain length; qGW, QTL for grain width; qRLW, QTL for ratio of length to width; qKWT, QTL for 1000-grain weight

Fig. 2

Phenotype of Nipponbare and Z1392. a, Plant type of Nipponbare (left) and Z1392 (right). b, Main panicle of Nipponbare (left) and Z1392 (right). c, d, Grains of Nipponbare (c) and Z1392 (d). e, f, Brown grains of Nipponbare (e) and Z1392 (f). g-j, Grain length (g), grain width (h), ratia of length to width(i) and 1000-grain weigth(j) of Nipponbare and Z1392. Bars in A and B, 10 cm; C–F, 2 mm

Fig. 3

Scanning electron microscopic observation and analysis of the glume. a–c, Scanning electron micrograph of the lemma (a, d), and inner epidermis (b, e) and outer epidermis (c, f) of the glume of Nipponbare (a-c) and Z1392 (d-f). g-h, Cell length and cell width in the inner epidermis of the lemma of Nipponbare and Z1392. i, Total cell number in the outer epidermis of the lemma along the longitudinal axis of Nipponbare and Z1392. Bars in A and B, 1 mm; B, C, E and F, 100 μm. * and ** indicate a significant difference between the two parents at P < 0.05 and P < 0.01, respectively

Fig. 4

Frequency distributions of grain size related traits in the F₂ population

Fig. 5

Fine mapping of putative qGL-6 and sequence analysis of candidate genes. aqGL-6 was mapped to an interval of 1.26 Mb. b The grain length of the 241 recombinants and 10 Nipponbare. c The DNA sequence of OsARF19 in Z1392 compared with Nipponbare

Fig. 6

Phenotype and genotype analysis of six chromosome segment substitution lines. u is the phenotypic value; a denotes the additive effect; I denotes the epistatic effect. A t-test was used to analyse significant difference