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Hybrid rice cultivars are widely planted around the world. Here, the authors resequence 1,143 indica accessions, focusing on the parents of superior hybrid rice lines in China, and reveal genetic loci that are associated with heterosis via measuring frequency of parental variation difference (FPVD).

Remobilization of pre-anthesis NSCs (non-structural carbohydrates) is significant for effective grain filling in rice (Oryza sativa L.). However, abundant starch particles as an important component of NSCs are still present in the leaf sheath and stem at the late stage of grain filling. There are no studies on how bioengineering techniques can be used to improve the efficiency of NSC remobilization. In this study, RAmy1A was expressed under the senescence-specific promoter of SAG12, which was designed to degrade starch in the leaf sheath and stem during grain filling. RAmy1A mRNA successfully accumulated in the leaf, stem, and sheath of transgenic plants after anthesis. At the same time, the starch and total soluble sugar content in the leaf, stem, and leaf sheath were obviously decreased during the grain-filling period. The photosynthetic rate of transgenic lines was higher than that of the wild types by an average of 4.0 and 9.9%, at 5 and 10 days after flowering, respectively. In addition, the grain-filling rate of transgenic lines was faster than that of the wild types by an average of 26.09%. These results indicate an enhanced transport efficiency of NSCs from source tissues in transgenic rice. Transgenic rice also displayed accelerated leaf senescence, which was hypothesized to contribute to decreased grain weight.

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.

“Easy-to-shatter” trait is a major cause of rice crop yield losses, emphasizing the economic value of developing elite rice cultivars with reduced seed shattering capable of achieving higher yields. In the present study, we describe the development of new indica rice lines that exhibit lower rates of seed shattering following the targeted CRISPR/Cas9-mediated editing of the qSH1 gene. We were able to identify qSH1 mutant T0 transgenic plants, with transgene-free homozygous mutants being obtained via segregation in the T1 generation. We then utilized two T2 transgene-free homozygous lines in order to assess the degree of seed shattering and major agronomic traits of these mutant lines and of wild-type rice plants (HR1128-WT). This approach revealed that qsh1 homozygous mutant lines exhibited significantly reduced seed shattering relative to HR1128-WT without any significant changes in other analyzed agronomic traits. We then used these mutant lines to develop new promising hybrid rice lines with intermediate seed shattering. Overall our results reveal that combining targeted gene editing via CRISPR/Cas9 with heterosis utilization approach can allow for the efficient development of novel promising hybrid rice cultivars that exhibit a intermediate of seed shattering, thereby ensuring better stability and improved rice yields.

Panicle traits are among the most important agronomic characters which directly relate to yield in rice. Grain number (GN), panicle length (PL), primary branch number (PBN), and secondary branch number (SBN) are the major components of rice panicle structure, and are all controlled by quantitative trait loci (QTLs). In our research, four advanced backcross overlapping populations (BIL152, BIL196a, BIL196b, and BIL196b-156) carrying introgressed segments from chromosome 6 were derived from an indica/japonica cross that used the super-hybrid rice restorer line HR1128 and the international sequenced japonica cultivar 'Nipponbare' as the donor and recurrent parents, respectively. The four panicle traits, GN, PL, PBN, and SBN, were evaluated for QTL effects using the inclusive composite interval mapping (ICIM) method in populations over two years at two sites. Results showed that a total of twelve QTLs for GN, PL, PBN, and SBN were detected on chromosome 6. Based on marker loci physical positions, the QTLs were found to be tightly linked to three important chromosomal intervals described as RM7213 to RM19962, RM20000 to RM20210, and RM412 to RM20595. Three QTLs identified in this study, PL6-5, PBN6-1, and PBN6-2, were found to be novel compared with previous studies. A major QTL (PL6-5) for panicle length was detected in all four populations at two locations, and its position was narrowed down to a 1.3Mb region on chromosome 6. Near isogenic lines (NILs) carrying PL6-5 will be developed for fine mapping of the QTL, and our results will provide referable information for gene excavation of panicle components in rice.

Microbial exopolysaccharide (EPS) is an important biological resource, and EPS production from endophytes has attracted much attention in recent years. To explore more EPS-producing strain resources as well as soybean endophytic resources, in this study, the strain with the highest EPS yield was screened from soybean seeds, and its morphological and molecular identification, biological characteristics (temperature, pH, rotation speed, sucrose tolerance, NaCl tolerance) and physiological and biochemical studies were carried out. The results showed that the maximum EPS yield of strain SE01 was 0.63 g/L after 48 h fermentation. Colony of strain SE01 was round, with smooth edge, milky white, and glossy and sticky surface. Under microscope, the bacterium after Gram staining was short, pink and rod-shaped, which identified to Gram-negative bacterium. The results of physiological and biochemical experiments and 16S rDNA identification showed that strain SE01 was Enterobacter cloacae, and named Enterobacter cloacae SE01. The optimum growth conditions of Enterobacter cloacae SE01 were temperature 30 ℃, pH5, and rotational speed 120 r/min. The strain SE01 had high tolerance to sucrose, but low tolerance to NaCl. Increasing the concentration of NaCl could inhibit its growth. This study provides data support for the development and application of soybean endophytic EPS.

Conventional production of hybrid rice seeds is based on sowing and transplanting parental lines separately ('separate seeding and transplanting', SST). To decrease the labour inputs of field management, a labour-saving model was implemented under a strategy of directly seeding the two parents as a mixture ('mixed direct seeding', MDS) to produce hybrid seeds. The strategy utilized a 'yellow-hull/red-hull' pair, ensuring that the female parent could be easily separated from the male parent after mixed harvesting. To assess the effects of MDS on seed production, two pairs, P88S/G-4 and Y58S/G-15, were tested and compared with those under SST at the same female/male seed ratio of 5:1 in 2015 and 2016. The parental lines for two pairs flowered synchronously, and the male sterile lines presented a high total stigma exertion rate in SST that ranged from 75.82% to 93.27%. At maturity, the hybrid seeds generated on seed parents were harvested together with those from pollen parents, and later, the hybrids were successfully colour sorted at a correctness rate of more than 99.90% on a machine. In MDS, the heading date of tested lines was advanced by 2~6 days. The outcrossing rate was improved by 8.59% and 7.61%, and the total panicle number increased by 4.78% and 5.80%, respectively. Ultimately, the actual yield in MDS significantly exceeded that in SST by 12.56% for P88S/G-4 and 8.95% for Y58S/G-15. This model succeeded in recycling hybrid seeds via color sorting and seems promising for decreasing labour inputs in hybrid seed production. [ABSTRACT FROM AUTHOR]