Identification of QTLs associated with the anaerobic germination potential using a set of Oryza nivara introgression lines.

BACKGROUND: Rice (Oryza sativa L.) is an important crop and a staple food for half of the population around the world. The recent water and labor shortages are encouraging farmers to shift from traditional transplanting to direct-seeding. However, poor germination and slow elongation of the coleoptile constrains large-scale application of direct-seeding. OBJECTIVE: This study was aimed to investigate the genetic basis of the anaerobic germination (AG) potential using a set of Oryza nivara (O. nivara) introgression lines (ILs). METHODS: In this study, a total of 131 ILs were developed by introducing O. nivara chromosome segments into the elite indica rice variety 93-11 through advanced backcrossing and repeated selfing. A high-density genetic map has been previously constructed with 1,070 bin-markers. The seeds of ILs were germinated and used to measure coleoptile length under normal and anaerobic conditions. QTLs associated with AG potential were determined in rice. RESULTS: Based on the high-density genetic map of the IL population, two QTLs, qAGP1 and qAGP3 associated with AG tolerance were characterized and located on chromosomes 1 and 3, respectively. Each QTL explained 15% of the phenotypic variance. Specifically, the O. nivara-derived chromosome segments of the two QTLs were positively tolerance to anaerobic condition by increasing coleoptile length. In a further analysis of public transcriptome data, a total of 26 and 36 genes within qAGP1 and qAGP3 were transcriptionally induced by anaerobic stress, respectively. CONCLUSIONS: Utilization of O. nivara-derived alleles at qAGP1 and qAGP3 can potentially enhance tolerance to anaerobic stress at the germination stage in rice, thereby accelerating breeding of rice varieties to be more adaptative for direct-seeding.

Mass spectrometry-based metabolomics investigation on two different indica rice grains (Oryza sativa L.) under cadmium stress.

Cadmium is a toxic environmental pollutant that is readily absorbed by rice grains and poses serious threats to human health. The selection and breeding of rice varieties with low cadmium accumulation is one of the most economical and ecological methods to reduce cadmium exposure. In this study, two different indica rice grains under cadmium stress were subjected to mass spectrometry-based metabolomics analysis for the first time. When the cadmium concentration increased in rice grains, most carbohydrates and amino acids were down-regulated, except myoinositol that can prevent cadmium toxicity, which was up-regulated. d-Mannitol and l-cysteine were up-regulated with the increase of cadmium concentration in low-cadmium-accumulating rice. Also, organic acids were activated especially 13-(S)-hydroperoxy-9(Z),11(E),15(Z)-octadecatrienoicacid that is related to the alpha-linolenic acid metabolism and jasmonic acid production. The determination of biomarkers and characterization of metabolic pathways might be helpful for the selection of rice varieties with low cadmium accumulation.

The Cds.71 on TMS5 May Act as a Mutation Hotspot to Originate a TGMS Trait in Indica Rice Cultivars.

The gene tms5, which controls thermo-sensitive genic male sterility (TGMS), has been widely used in two-line hybrid rice breeding in China. The tms5 lines have two sources, namely, AnnongS-1 (AnS) and Zhu1S (ZhS) and, interestingly, are commonly subject to an alteration at cds.71. However, whether cds.71 acts as a mutation hotspot is unknown. Herein, another tms5 mutant named T98S (induced from T98B by irradiation) was used to explore this. First, the gene of tms(t) responsible for T98S was fine-mapped on chromosome 2 based on an F2 group of T98S/R893. In T98S, the candidate gene TMS5 (LOC_Os02g12290.1) mutated at cds.71 with a transversion from cytosine (C) to adenine (A), as also observed in AnS and ZhS. Moreover, the entire coding sequence of TMS5 from T98B converted T98S from sterile to fertile by Agrobacterium tumefaciens-mediated transformation, confirming that T98S is controlled by tms5. Next, detection on nearly 40,000 single nucleotide polymorphisms (SNPs) on Rice 56K SNP Array revealed T98S was 99.99% similar to T98B but only 72.84% and 77.47% similar to AnS and ZhS, respectively, demonstrating that T98S originated from T98B rather than from existing tms5 lines. Furthermore, the cds.70 was found to exist as a T/G haplotype, and it was T rather than G that helped to induce a TGMS trait. The T frequency was 67.52% in indica rice but decreased to 1.75% in japonica rice in 2,644 cultivars tested, which partly explains why tms5 mutants were mostly found in indica lines. Our findings provide evidence that cds.71 may act as a mutation hotspot and clues for breeding TGMS lines in a more efficient way.

Genome-wide analysis of the rice J-protein family: identification, genomic organization, and expression profiles under multiple stresses.

J-proteins which function as molecular chaperone played critical roles in plant growth, development, and response to various environment stresses, but little was reported on this gene family in rice. Here, we identified 115 putative rice J-proteins and classified them into nine major clades (I-IX) according to their phylogenetic relationships. Gene-structure analysis revealed that each member of the same clade has same or similar exon-intron structure, and most rice J-protein genes of clade VII were intronless. Chromosomes mapping suggested that tandem duplication was occurred in evolution. Expression profile showed that the 61 rice J-protein genes were expressed in at least one tissue. The result implied that they could be involved in the process of rice growth and development. The RNA-sequencing data identified 96 differentially expressed genes, 59.38% (57/96), 67.71% (65/96), and 62.50% (60/96) genes were induced by heat stress, drought stress, and salt stress, respectively. The results indicated that J-protein genes could participated in rice response to different stresses. The findings in this study would provide a foundation for further analyzing the function of J-proteins in rice.

Potential for high yield with increased seedling density and decreased N fertilizer application under seedling-throwing rice cultivation.

Fertilizer application for rice production has increased significantly in southern China to raise yields, but has led to problems with lodging, quality decline and environmental pollution. Therefore, research on fertilizer-saving cultivation technologies for high-yielding rice is necessary. A two-factor experiment was conducted to evaluate the effects of seedling-addition treatment (SAT) and nitrogen-saving treatment (NST) on yield formation and nitrogen absorption of individual plants and plant groups under the seedling-throwing cultivation system. Numbers of spikelets per panicle and filled grains per panicle of individual plants declined under decreased nitrogen application, but was compensated by substantially increased effective panicles number and total number of glumous flowers under SAT. Under the optimal SAT-NST treatments of 18% less N fertilizer and 32% additional seedlings, yield increased 1.79% and 4.29% compared with that of conventional practice (CK) in 2015 and 2016, respectively. The mature-stage individual-plant biomass under SAT-NST treatments decreased by 27.46% and 20.49% compared with CK in 2015 and 2016, but plant-group biomass did not differ significantly (all >16 t ha-1). Under SAT-NST treatments, effective number of panicles was positively correlated with maximum number of seedlings (r = 0.643) and N absorption amount in the tillering stage (r = 0.901).

Conversion of a rice CMS maintainer into a photo- or thermo-sensitive genetic male sterile line.

A maintainer line of 3-line hybrid rice commonly presents a certain genetic distance to a 2-line restorer line, but in many cases, 2-line restorer lines present defects upon recovery of the object cytoplasmic male sterile (CMS) line of the maintainer line, which impedes the utilization of their heterosis. Here, we report a strategy and an example of converting a maintainer into a photoperiod/temperature-sensitive genic male sterile (P/TGMS) line with an almost identical genetic background, thus maximizing the heterosis. Firstly, through treatment of maintainer line T98B with 60CO-γ irradiation, we identified the TGMS line T98S, which is sterile at higher temperatures and fertile at lower temperatures. Secondly, the T98S line was proven to be identical to T98B with regard to genetic background via an examination of 48 parental polymorphous SSR markers and exhibited excellent blossom traits similar to those of T98B, with an extensive forenoon flowering rate of 75.92% and a high exertion rate of 64.59%. Thirdly, in a combination test, three out of six hybrids from T98S crossed with 2-line restorer lines showed a yield increase of 6.70-15.69% for 2 consecutive years. These results demonstrated that the strategy can generate a new P/TGMS line with strong general combining ability (converted from a maintainer line), thus helping to increase the genetic diversity of male sterile heterotic groups.