Dataset Information

The additive effects of GS3 and qGL3 on rice grain length regulation revealed by genetic and transcriptome comparisons.

ABSTRACT: Grain length, as a critical trait for rice grain size and shape, has a great effect on grain yield and appearance quality. Although several grain size/shape genes have been cloned, the genetic interaction among these genes and the molecular mechanisms of grain size/shape architecture have not yet to be explored.To investigate the genetic interaction between two major grain length loci of rice, GS3 and qGL3, we developed two near-isogenic lines (NILs), NIL-GS3 (GS3/qGL3) and NIL-qgl3 (gs3/qgl3), in the genetic background of 93-11 (gs3/qGL3) by conventional backcrossing and marker-assisted selection (MAS). Another NIL-GS3/qgl3 (GS3/qgl3) was developed by crossing NIL-GS3 with NIL-qgl3 and using MAS. By comparing the grain lengths of 93-11, NIL-GS3, NIL-qgl3 and NIL-GS3/qgl3, we investigated the effects of GS3, qGL3 and GS3?×?qGL3 interaction on grain length based on two-way ANOVA. We found that GS3 and qGL3 had additive effects on rice grain length regulation. Comparative analysis of primary panicle transcriptomes in the four NILs revealed that the genes affected by GS3 and qGL3 partially overlapped, and both loci might be involved in brassinosteroid signaling.Our data provide new information to better understand the rice grain length regulation mechanism and help rice breeders improve rice yield and appearance quality by molecular design breeding.

SUBMITTER: Gao X

PROVIDER: S-EPMC4479070 | biostudies-literature | 2015

REPOSITORIES: biostudies-literature

ACCESS DATA

Similar Datasets

Project description:Grain length is a prominent determinant for the grain weight and appearance quality of rice. To elucidate the genetic basis of the control of grain length, we conducted quantitative trait locus (QTL) mapping to determine a genomic interval responsible for the a long-grain phenotype observed in a japonica cultivar HD385 by using an F2:3 population and recombinant inbred line (RIL) population, which is are derived from a cross between the long-grain japonica cultivar HD385 and short-grain japonica cultivar Nipponbare (NIP). This led to the identification of a novel QTL, which is located on chromosome 3, for grain length, named qIGL1 (for Increased Grain Length 1); the HD385-derived allele showed enhancement effects on grain length, and such an allele as well as NIP-derived allele are were thus designated qigl1 HD385 and qIGL1NIP, respectively. Genetic analysis revealed that qigl1HD385 displayed semi-dominant effects on grain length. To further narrow down the qIGL1 region, we developed a few advanced backcross populations to determine the precise location of qIGL1. Eventually, qIGL1 was delimited to a 70.8-kb region containing 9 open reading frames (ORFs). A comprehensive analysis indicated that ORF6 and ORF9, separately corresponding to LOC_Os03g30530 and LOC_Os03g30550, are were found to carry base substitutions and/or deletions, which resulted in changes or losses of amino acid residues. However, these alterations in coding sequences does did not significantly change the expression levels of both ORFs. To further elucidate the mechanisms behind the increases of grain length conferred by qigl1HD385, we generated a pair of near-isogenic lines (NILs), termed NIL-qigl1HD385 and NIL-qIGL1NIP, and discovered that introduction of qigl1HD385 into the NIP background significantly lead resulted into the elevations of grain length and 1000-grain weight. Closer inspection of outer epidermal cells of grain surfaces of both lines revealed that the cell length and width in the longitudinal direction are were significantly longer in NIL-qigl1HD385 compared with in NIL-qIGL1NIP, which may might stem partly from the downregulation of several cell cycle-related genes. Hence, our study studies identify identified a new semi-dominant natural allele contributing to the increase of grain length, and further shed light on the regulatory mechanisms of grain length.

Project description:The demand for rice is likely to increase approximately 1.5 times by the year 2050. In contrast, the rice production is stagnant since the past decade as the ongoing rice breeding program is unable to increase the production further, primarily because of the problem in grain filling. Investigations have revealed several reasons for poor filling of the grains in the inferior spikelets of the compact panicle, which are otherwise genetically competent to develop into well-filled grains. Among these, the important reasons are 1) poor activities of the starch biosynthesizing enzymes, 2) high ethylene production leading to inhibition in expressions of the starch biosynthesizing enzymes, 3) insufficient division of the endosperm cells and endoreduplication of their nuclei, 4) low accumulation of cytokinins and indole-3-acetic acid (IAA) that promote grain filling, and 5) altered expressions of the miRNAs unfavorable for grain filling. At the genetic level, several genes/QTLs linked to the yield traits have been identified, but the information so far has not been put into perspective toward increasing the rice production. Keeping in view the genetic competency of the inferior spikelets to develop into well-filled grains and based on the findings from the recent research studies, improving grain filling in these spikelets seems plausible through the following biotechnological interventions: 1) spikelet-specific knockdown of the genes involved in ethylene synthesis and overexpression of β-CAS (β-cyanoalanine) for enhanced scavenging of CN- formed as a byproduct of ethylene biosynthesis; 2) designing molecular means for increased accumulation of cytokinins, abscisic acid (ABA), and IAA in the caryopses; 3) manipulation of expression of the transcription factors like MYC and OsbZIP58 to drive the expression of the starch biosynthesizing enzymes; 4) spikelet-specific overexpression of the cyclins like CycB;1 and CycH;1 for promoting endosperm cell division; and 5) the targeted increase in accumulation of ABA in the straw during the grain filling stage for increased carbon resource remobilization to the grains. Identification of genes determining panicle compactness could also lead to an increase in rice yield through conversion of a compact-panicle into a lax/open one. These efforts have the ability to increase rice production by as much as 30%, which could be more than the set production target by the year 2050.

Dataset Information

The additive effects of GS3 and qGL3 on rice grain length regulation revealed by genetic and transcriptome comparisons.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets