Genome Sequence and QTL Analyses Using Backcross Recombinant Inbred Lines (BILs) and BILF1 Lines Uncover Multiple Heterosis-related Loci

Abstract

: Heterosis is an interesting topic for both breeders and biologists due to its practical importance and scientific significance. Cultivated rice (Oryza sativa L.) consists of two subspecies, indica and japonica, and hybrid rice is the predominant form of indica rice in China. However, the molecular mechanism underlying heterosis in japonica remains unclear. The present study determined the genome sequence and conducted quantitative trait locus (QTL) analysis using backcross recombinant inbred lines (BILs) and BILF₁ lines to uncover the heterosis-related loci for rice yield increase under a japonica genetic background. The BIL population was derived from an admixture variety Habataki and japonica variety Sasanishiki cross to improve the genetic diversity but maintain the genetic background close to japonica. The results showed that heterosis in F₁ mainly involved grain number per panicle. The BILF₁s showed an increase in grain number per panicle but a decrease in plant height compared with the BILs. Genetic analysis then identified eight QTLs for heterosis in the BILF₁s; four QTLs were detected exclusively in the BILF₁ population only, presenting a mode of dominance or super-dominance in the heterozygotes. An additional four loci overlapped with QTLs detected in the BIL population, and we found that Grains Height Date 7 (Ghd7) was correlated in days to heading in both BILs and BILF₁s. The admixture genetic background of Habataki was also determined by subspecies-specific single nucleotide polymorphisms (SNPs). This investigation highlights the importance of high-throughput sequencing to elucidate the molecular mechanism of heterosis and provides useful germplasms for the application of heterosis in japonica rice production.

Keywords: heterosis; high-throughput sequence; rice; yield components.

Figure 1

Schematic overview of the parent backcross recombinant inbred line (BIL) system construction and the map of genome-wide graphic genotypes. (A) The technology roadmap using genome sequence and quantitative trait locus (QTL) analysis of BILs and BILF₁s to uncover heterosis-related loci for yield increase. (B) Graphic genotypes of 85 BILs were identified by a sliding window approach along each chromosome. Various colors represent different genotypes. (C) The introgression rate of the Habataki pedigree among the BILs. (D) The correlation between the introgression rate of the Habataki pedigree and yield-related traits. The dotted lines indicate significance at the 5% level.

Figure 2

Heterosis in F₁ plants. (A) The plant architecture of F₁ plant and parental lines. Scale bar = 10 cm. (B) The panicle of F₁ plants and parental lines. Scale bar = 1 cm. (C) Grains of F₁ plants and parental lines. Scale bar = 10 cm. (D–I) the yield-related traits of F₁ plants and parental lines.

Figure 3

The distribution of yield-related traits in BILs and BILs. (A–F) The distribution of days to heading, number of panicles, plant height, grain number per panicle, setting rate, and 1000-grain weight in BILs and BILF₁s.

Figure 4

The position of quantitative trait locuses (QTLs) for yield-related traits and heterosis QTLs in BILs and BILF₁s. Different colors represent the QTLs detected in BILs and BILF₁s.

Figure 5

Grain number per panicle of each genotype for the four QTLs detected in BIL and BILF_1s. The number inside the column represents the number of plants for each genotype. All data are given as mean ± s.e.m.,different letters indicate the significant differences at the 5% level.

Figure 6

Overview of the subspecies-specific SNPs and introgression in Sasanishiki and Habataki. Tracks from the outer to inner circles indicate the following. (A) The chromosome length. The loci of grain number per panicle are indicated on the inside of the circle. (B) The distribution of 81,690 subspecies-specific SNPs in the genome. (C) The introgression of japonica-type SNPs into the genome of Habataki. (D) The introgression of indica-type SNPs in the genome of Sasnishiki.