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Grain size is a key constituent of grain weight and appearance in rice. However, insufficient attention has been paid to the small-effect quantitative trait loci (QTLs) on the grain size. In the present study, residual heterozygous populations were developed for mapping two genetically linked small-effect QTLs for grain size. After the genotyping and the phenotyping of five successive generations, qGS7.1 was dissected into three QTLs and two were selected for further analysis. The qTGW7.2a was finally mapped into a 21.10 kb interval containing four annotated candidate genes. Transcript levels assay showed that the expression of the candidates LOC_Os07g39490 and the LOC_Os07g39500 were significantly reduced in the NIL-qTGW7.2aBG1. The cytological observation indicated that qTGW7.2a regulated the grain width through controlling the cell expansion. Using the same strategy, qTGW7.2b was fine-mapped into a 52.71 kb interval containing eight annotated candidate genes, showing a significant effect on the grain length and width with opposite allelic directions, but little on the grain weight. Our study provides new genetic resources for yield improvement and for fine-tuning of grain size in rice.

Grain size is a major determinant of grain weight, which is one of the components of rice yield. The objective o this study was to identify novel, and important quantitative trait loci (QTLs) for grain size and weight in rice. QTLs were mapped using a BC4F4 population including 192 backcross inbred lines (BILs) derived from a backcross between Xiaolijing (XLJ) and recombinant inbred lines (RILs). The mapping population was planted in both Lingshui (Hainan, 2015) and Fuyang (Zhejiang, 2016), with the short- and long-day conditions, respectively. A total of 10 QTLs for grain length, four for grain width, four for the ratio of grain length to width, and 11 for grain weight were detected in at least one environment and were distributed across 11 chromosomes. The phenotypic variance explained ranged from 6.76–25.68%, 14.30–34.03%, 5.28–26.50%, and 3.01–22.87% for grain length, grain width, the ratio of grain length to width, and thousand grain weight, respectively. Using the sequential residual heterozygotes (SeqRHs) method, qGS7.1, a QTL for grain size and weight, was mapped in a 3.2-Mb interval on chromosome 7. No QTLs about grain size and weight were reported in previous studies in this region, providing a good candidate for functional analysis and breeding utilization.

The efficiency of hybrid rice seed production can be improved by increasing the percentage of exserted stigmas. To identify quantitative trait loci (QTLs) for this trait, we conducted QTL mapping using 75 chromosome segment substitution lines (CSSLs) developed from a cross between the donor parent, Xieqingzao B (XQZB), a maintainer line which has high stigma exsertion and the recurrent parent, Zhonghui 9308 (ZH9308), a restorer line which has low stigma exsertion. A total of nine QTLs (qSSE5, qSSE10, qSSE11, qDSE10, qDSE11, qTSE5, qTSE6, qTSE10, and qTSE11) for single stigma exsertion (SSE), dual stigma exsertion (DSE) and total stigma exsertion (TSE) were assessed in two environments (Hainan and Zhejiang). Six of these QTLs (qSSE10, qSSE11, qDSE10, qDSE11, qTSE10, and qTSE11) were found in both environments, while one QTL (qTSE6) was found in only Hainan, and two QTLs (qSSE5 and qTSE5) were found in only Zhejiang. The qSSE10, qSSE11, qDSE10, qDSE11, qTSE6, qTSE10, and qTSE11 alleles, which are derived from the parent XQZB, exhibited a positive additive effect. In contrast, the qSSE5 and qTSE5 alleles, which are derived from the parent ZH9308, exhibited a negative additive effect. The SSE, DSE and TSE traits were significantly correlated with each other in an environmentally dependent manner. These results indicated that the lines showing higher values for SSE were more likely to exhibit increased values for DSE, which would ultimately increase TSE. To evaluate the advantage of exserted stigmas for cross-pollination, single, dual and total stigma exsertion should be considered separately in future attempts at genetic improvement to achieve increased production of rice hybrid seeds. This study also provides information for fine mapping, gene cloning and particularly marker-assisted selection (MAS), on the latter and with an emphasis the phenotypic effects and implications of the QTLs for practical use in hybrid rice breeding.

The role of photoperiod sensitivity (PS) of flowering genes have become well recognized in rice, whereas little attention has been drawn to the non-PS component of these genes, especially to their influence on gene-by-gene interactions. Rice populations in which the photoperiod-sensitive allele at Hd1 has become insensitive to photoperiod but continued to affect heading date (HD) were used in this study to fine-map a quantitative trait locus (QTL) for HD and analyze its genetic relationship to Hd1. The QTL was delimitated to a 96.3-kb region on the distal end of the long arm of chromosome 7. Sequence comparison revealed that this QTL is identical to Hd2. In the near-isogenic line (NIL) populations analyzed, Hd1 and Hd2 were shown to be photoperiod insensitive and have pleiotropic effects for HD, plant height and yield traits. The two genes were found to largely act additively in regulating HD and yield traits. The results indicate that non-PS components of flowering genes involved in photoperiod response play an important role in controlling flowering time and grain yield in rice, which should allow breeders to better manipulate pleiotropic genes for balancing adaptability and high-yielding accumulation.

Pyrimidine nucleotides are important metabolites that are building blocks of nucleic acids, which participate in various aspects of plant development. Only a few genes involved in pyrimidine metabolism have been identified in rice and the majority of their functions remain unclear. In this study, we used a map-based cloning strategy to isolate a UMPK gene in rice, encoding the UMP kinase that phosphorylates UMP to form UDP, from a recessive mutant with pale-green leaves. In the mutant, UDP content always decreased, while UTP content fluctuated with the development of leaves. Mutation of UMPK reduced chlorophyll contents and decreased photosynthetic capacity. In the mutant, transcription of plastid-encoded RNA polymerase-dependent genes, including psaA, psbB, psbC and petB, was significantly reduced, whereas transcription of nuclear-encoded RNA polymerase-dependent genes, including rpoA, rpoB, rpoC1, and rpl23, was elevated. The expression of UMPK was significantly induced by various stresses, including cold, heat, and drought. Increased sensitivity to cold stress was observed in the mutant, based on the survival rate and malondialdehyde content. High accumulation of hydrogen peroxide was found in the mutant, which was enhanced by cold treatment. Our results indicate that the UMP kinase gene plays important roles in regulating chloroplast development and stress response in rice.

We identified the rice floral organ development mutant, termed as open hull and male sterile 1 ( ohms1 ), from the progeny of the indica restorer line Zhonghui 8015 treated with 60Co γ-ray irradiation. The ohms1 mutant exhibited an open hull and lemma- and palea-like structure conversion between the anthers and stigma, which resulted in the ohms1 mutant spikelet showing ‘tridentate lemma’. The ohms1 mutant was entirely sterile but had 60%–70% fertile pollen. Genetic analysis and gene mapping showed that ohms1 was controlled by a single recessive gene, and the mutant gene was fine-mapped to a 42-kb interval on the short arm of chromosome 3 between markers KY2 and KY29. Sequence analysis of the four open reading frames in this region revealed that the mutant carried a single nucleotide transformation (A to G) at the last base of the fifth intron, which was likely corresponded to ohms1 phynotype, in an MIKC type MADS-box gene OsMADS1 (LOC_Os03g11614). Enzyme digestion and cDNA sequencing further indicated that the variable splicing was responsible for the deletion of the sixth exon in ohms1 , but no structural changes in the MADS domain or amino acid frame shifts appeared. Additionally, real-time fluorescent quantitative PCR analysis showed that the OsMADS1 expression level decreased significantly in the ohms1 mutant. The expression levels of rice flowering factors and floral glume development-related genes also changed significantly. These results demonstrate that OsMADS1 may play an important role in rice floral organ development, particularly in floral glume development and floret primordium differentiation. [ABSTRACT FROM AUTHOR]

A recombinant inbred line population derived from a super hybrid rice Xieyou 9308 (Xieqingzao B/Zhonghui 9308) and its genetic linkage map were used to detect quantitative trait loci (QTLs) for rice yield traits under the low and normal nitrogen (N) levels. A total of 52 QTLs for yield traits distributed in 27 regions on 9 chromosomes were detected, with each QTL explaining 4.93%–26.73% of the phenotypic variation. Eleven QTLs were simultaneously detected under the two levels, and 30 different QTLs were detected under the two N levels, thereby suggesting that the genetic bases controlling rice growth under the low and normal N levels were different. QTLs for number of panicles per plant, number of spikelets per panicle, number of filled grains per panicle, and grain density per panicle under the two N levels were detected in the RM135–RM168 interval on chromosome 3. QTLs for number of spikelets per panicle and number of filled grains per panicle under the two N levels, as well as number of panicles per plant and grain density per panicle, under the low N level, were detected in the RM5556–RM310 interval on chromosome 8. The above described QTLs shared similar regions with previously reported QTLs for rice N recycling. [ABSTRACT FROM AUTHOR]

Hybrid rice has contributed greatly to the self-sufficiency of food supply in China. To meet the future demand for rice production, a national program on super rice breeding was established in China in 1996. The corresponding targets, breeding strategies and most significant advances are reviewed in this paper. New plant type models have been modified to adjust to various rice growing regions. In recognition of the importance of applying parents with intermediate subspecies differentiation in increasing F1 yield, medium type parental lines were selected from populations derived from inter-subspecies crosses with the assistance of DNA markers for subspecies differentiation. Results also indicate that a substantial increase of biomass is the basis for further enhancement of the grain yield potential, and amelioration of leaf characteristics is helpful in increasing the photosynthetic rate. Thirty-four super hybrid rice varieties have been released commercially, growing in a total area of 13.5 million hm2 and producing 6.7 thousand million kg more rice in 1998-2005. Although remarkable progress has been made in super hybrid rice breeding in China, selections on the root system and integration of more biotechnological tools remain a great challenge. [ABSTRACT FROM AUTHOR]

Background China has been successful in breeding hybrid rice strains, but is now facing challenges to develop new hybrids with high-yielding potential, better grain quality, and tolerance to biotic and abiotic stresses. This paper reviews the most significant advances in hybrid rice breeding in China, and presents a recent study on fine-mapping quantitative trait loci (QTLs) for yield traits. Scope By exploiting new types of male sterility, hybrid rice production in China has become more diversified. The use of inter-subspecies crosses has made an additional contribution to broadening the genetic diversity of hybrid rice and played an important role in the breeding of super rice hybrids in China. With the development and application of indica-inclined and japonica-inclined parental lines, new rice hybrids with super high-yielding potential have been developed and are being grown on a large scale. DNA markers for subspecies differentiation have been identified and applied, and marker-assisted selection performed for the development of restorer lines carrying disease resistance genes. The genetic basis of heterosis in highly heterotic hybrids has been studied, but data from these studies are insufficient to draw sound conclusions. In a QTL study using stepwise residual heterozygous lines, two linked intervals harbouring QTLs for yield traits were resolved, one of which was delimited to a 125-kb region. Conclusions Advances in rice genomic research have shed new light on the genetic study and germplasm utilization in rice. Molecular marker-assisted selection is a powerful tool to increase breeding efficiency, but much work remains to be done before this technique can be extended from major genes to QTLs. [ABSTRACT FROM AUTHOR]