De novo assembly of two chromosome-level rice genomes and bin-based QTL mapping reveal genetic diversity of grain weight trait in rice

Abstract

Following the "green revolution," indica and japonica hybrid breeding has been recognized as a new breakthrough in further improving rice yields. However, heterosis-related grain weight QTLs and the basis of yield advantage among subspecies has not been well elucidated. We herein de novo assembled the chromosome level genomes of an indica/xian rice (Luohui 9) and a japonica/geng rice (RPY geng) and found that gene number differences and structural variations between these two genomes contribute to the differences in agronomic traits and also provide two different favorable allele pools to produce better derived recombinant inbred lines (RILs). In addition, we generated a high-generation (> F₁₅) population of 272 RILs from the cross between Luohui 9 and RPY geng and two testcross hybrid populations derived from the crosses of RILs and two cytoplasmic male sterile lines (YTA, indica and Z7A, japonica). Based on three derived populations, we totally identified eight 1,000-grain weight (KGW) QTLs and eight KGW heterosis loci. Of QTLs, qKGW-6.1 and qKGW-8.1 were accepted as novel KGW QTLs that have not been reported previously. Interestingly, allele genotyping results revealed that heading date related gene (Ghd8) in qKGW-8.1 and qLH-KGW-8.1, can affect grain weight in RILs and rice core accessions and may also play an important role in grain weight heterosis. Our results provided two high-quality genomes and novel gene editing targets for grain weight for future rice yield improvement project.

Keywords: 1,000-grain weight; genome sequencing; heterosis loci; rice; yield improvement.

FIGURE 1

Whole plant phenotype (A), genomic characteristics (B), and large structural variations (C) between RPY geng and Luohui 9. The tracks from outside to inside are the chromosome, gene density, repeat sequence density, and GC content and the different color links represent orthologous gene pairs among chromosomes in (B).

FIGURE 2

Thousand-grain weight in 2019HN, 2019LS, 2018EZ and 2017EZ.

FIGURE 3

The positions of QTLs, MetaQTLs, and known KGW-related genes.

FIGURE 4

1000-grain weight of different allele combinations of qKGW-6.1 and qKGW-8.1. In (A), (C–F): qKGW-6.1 AA + qKGW-8.1 AA, (B): qKGW-6.1 AA + qKGW-8.1 BB; (C): qKGW-6.1 BB + qKGW-8.1 AA; (D): qKGW-6.1 BB + qKGW-8.1 AA.

FIGURE 5

The candidate gene prediction of qKGW-8.1. (A). Protein sequence alignment results of Nipponbare, RPYgeng (FaGhd8), Luohui 9 (MoGhd8). (B) The 1,000-grain weight of RPY geng (AA) and Luohui 9 (BB) allele recombinant inbred lines (RILs). (C) The 1,000-grain weight of different allele rice core accessions.

FIGURE 6

Grain weight heterosis loci in two testcross populations. Black represents QTL loci in recombinant inbred lines (RILs). Red and blue loci represent heterosis-related QTLs of YTA and Z7A testcross population, respectively.