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Rice grain yield is determined by three major “visible” morphological traits: grain weight, grain number per panicle, and effective tiller number, which are affected by a series of “invisible” physiological factors including nutrient use efficiency and photosynthetic efficiency. In the past few decades, substantial progress has been made on elucidating the molecular mechanisms underlying grain yield formation, laying a solid foundation for improving rice yield by molecular breeding. This review outlines our current understanding of the three morphological yield-determining components and summarizes major progress in decoding physiological traits such as nutrient use efficiency and photosynthetic efficiency. It also discusses the integration of current knowledge about yield formation and crop improvement strategies including genome editing with conventional and molecular breeding.

The objective of the study was to understand the genetic basis of eight traits conferring grain appearance and yield in a recombinant inbred line (RIL8) derived from a cross between cultivated Indica rice varieties Dexiang074B and Pujiang6. We conducted whole genome re‐sequencing for the two parental lines and genotyping by sequencing (GBS) for the RIL8 population. Next, we aligned the clean reads to the rice genome Nipponbare IRGSP 1.0, constructed the genetic linkage map (GLM), and performed the quantitative trait loci (QTL) analysis. In total, 2631 high‐quality markers were generated for 315 RIL8 samples. We identified a rice GLM containing 12 linkage groups (total map distance: 1946.71 cM; average map distance: 0.74 cM) and 98 QTLs related to the rice yield, including 31 high credible QTLs. In addition, 39 QTLs were identified to be associated with the G*E interaction. While most of the QTLs were co‐localized with previously reported rice QTLs, some novel QTLs were identified for the first time in this study. These findings provide a genetic basis for developing cultivated rice with good economic characteristics based on molecular breeding technologies.

Obtaining genetic variation information from indica rice hybrid parents and identification of loci associated with heterosis are important for hybrid rice breeding. Here, we resequence 1,143 indica accessions mostly selected from the parents of superior hybrid rice cultivars of China, identify genetic variations, and perform kinship analysis. We find different hybrid rice crossing patterns between 3- and 2-line superior hybrid lines. By calculating frequencies of parental variation differences (FPVDs), a more direct approach for studying rice heterosis, we identify loci that are linked to heterosis, which include 98 in superior 3-line hybrids and 36 in superior 2-line hybrids. As a proof of concept, we find two accessions harboring a deletion in OsNramp5, a previously reported gene functioning in cadmium absorption, which can be used to mitigate rice grain cadmium levels through hybrid breeding. Resource of indica rice genetic variation reported in this study will be valuable to geneticists and breeders., 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).

Sphingomonas carotinifaciens strain L9-754T (DSM 27347) is a gram-negative, chemoheterotrophic, and rod-shaped endophyte isolated from the stem tissues of Jatropha curcas L. This strain has putative in vitro antagonistic ability against the plant pathogenic fungus Magnaporthe grisea. A draft genome of L9-754T was obtained using the PacBio SMRT cell platform. By analyzing the genome of strain L9-754T, a gene cluster (GQR91_18700 - GQR91_18715) related to an antioxidant enzyme was identified in the obtained draft genome. The information obtained from the draft genome is expected to reveal the putative properties helpful in biocontrol applications.

Objectives Achromobacter spanius is a newly described, non-fermenting, Gram-negative, coccoid pathogen isolated from human blood. Whole-genome sequencing of the A. spanius type strain was performed to investigate the mechanism of pathogenesis of this strain at a genomic level. Methods The complete genome of A. spanius type strain DSM 23806T was sequenced using single-molecule real-time (SMRT) DNA sequencing. Results The complete genome of DSM 23806T consists of one circular DNA chromosome of 6 425 783 bp with a G + C content of 64.26%. The entire genome contains 5804 predicted coding sequences (CDS) and 55 tRNAs. Genomic island (GI) analysis showed that this strain encodes several important pathogenesis- and resistance-related genes. Conclusions These results strongly suggest that GIs provide some fitness advantages in A. spanius type strain DSM 23806T. This report provides an extensive understanding of A. spanius at a genomic level as well as an understanding of the evolution of A. spanius.

Premature leaf senescence (PLS), which has a significant impact on yield, is caused by various underlying mechanisms. Glycosyltransferases, which function in glycosyl transfer from activated nucleotides to aglycones, are involved in diverse biological processes, but their roles in rice leaf senescence remain elusive. Here, we isolated and characterized a leaf senescence-related gene from the Premature Leaf Senescent mutant (pls2). The mutant phenotype began with leaf yellowing at tillering and resulted in PLS during the reproductive stage. Leaf senescence was associated with an increase in hydrogen peroxide (H2O2) content accompanied with pronounced decreases in net photosynthetic rate, stomatal conductance, and transpiration rate. Map-based cloning revealed that a mutation in LOC_Os03g15840 (PLS2), a putative glycosyltransferase- encoding gene, was responsible for the defective phenotype. PLS2 expression was detected in all tissues surveyed, but predominantly in leaf mesophyll cells. Subcellular localization of the PLS2 was in the endoplasmic reticulum. The pls2 mutant accumulated higher levels of sucrose together with decreased expression of sucrose metabolizing genes compared with wild type. These data suggested that the PLS2 allele is essential for normal leaf senescence and its mutation resulted in PLS.

Achromobacter insolitus is a newly described, Gram-negative, small (1-2 mm long) and coccoid pathogen that has been isolated from leg wound. Due to its potential threat to human beings, the type strain of this species LMG 6003T was completely sequenced in this study. The genomic analysis revealed that the genome of LMG 6003T consists of one circular DNA chromosome of 6 492 697 bp with a GC content of 65.10%. The entire genome contains 6208 predicted coding genes, 61 tRNAs and 13 rRNA genes. Comparative genome analysis between LMG 6003T and another selected 10 sequenced Achromobacter revealed that 725 genes only exist in LMG 6003T. In particular, these genes include several important pathogenic-related genes such as Type IV prepilin peptidase (TadV/CpaA), Type VI secretion lipoprotein (VasD) and type 1 fimbriae major subunit (FimA). Genomic island (GI) analysis also suggests the existence of GIs in LMG 6003T. All these results strongly suggest the unique genomic features in LMG 6003T against other Achromobacter species. This report will provide us with an extended understanding of A. insolitus at the genomic level and would be helpful for understanding the evolution of the Achromobacter genus.

The genetic distances among 18 cytoplasmic male sterile lines and 11 restorer lines were analyzed with molecular markers derived from yield-related functional genes. The correlation between parental genetic distance and heterosis was investigated by analyzing the performance of 47 combinations. The results showed that the genetic distance was significantly correlated with yield heterosis (r=0.29*), but not significantly correlated with heterosis for other traits, such as number of effective panicles per plant, seed setting rate, 1000-grain weight, number of grains per panicle and theoretical yield. However, the correlation coefficient was so small that the parental genetic distance could not to be used to predict heterosis.

Two recombinant inbred line (RIL) populations, one derived from a cross between Zhongyouzao 8 (indica) and Toyonishiki (japonica) and the other from a cross between Qishanzhan (indica) and Akihikari (japonica), were grown in Liaoning and Sichuan Provinces, China, to study the panicle type index (PTI, the ratio of a number of node position on panicle axis where the secondary branch with the most numerous secondary branch grains is located to the number of primary branches) and its relationships with subspecies characteristics and yield traits. With continuous distribution of PTI and numerous of lines with different PTIs in the progenies, indica-japonica hybridization could be a method for breeding cultivars with ideal panicle type. PTI was significantly influenced by environments, with a significant decrease from Liaoning to Sichuan. A significantly negative correlation was found between PTI and most of subspecies characteristics. PTI varied remarkably with different subspecies types. As a whole, it showed a trend of indica (H)>indicalinous (H')>japonicalinous (K')>japonica (K). However, it is not appropriate to regard PTI as a parameter for subspecies classification in rice because it was recombined in the filial generations of cross between indica and japonica rice. The negative correlations were found between PTI and most of panicle characteristics, as well as yield-related traits. Based on PTI, most of lines from the two populations were middle dominant panicle type (the number of grains on the secondary branch is numerous in middle position of the panicle) and lower dominant panicle type (the number of grains on the secondary branch is numerous in lower position of the panicle and becomes less towards the top of panicle) with significant yield advantages.

Hybrid rice breeding is the combining ability breeding. Screening hybrid rice combinations with high special combining ability (SCA) is able to breed strong superiority combinations with practical values. In this study, the genetic distances (GD) of nine three-line hybrid rice (5 CMS lines and 4 restorer lines) were examined using SSR markers. Based on yield performances of 20 hybrid crosses (5 x 4 NCII), the relationships between SCA, heterosis and GD were studied. The correlations of yield SCA with the control heterosis (r1=0.5609) and the average heterosis (r2=0.541) were significant, but not significant with GD (r=0.2143). Thus, the heterosis can be reflected by SCA; the hybrid parents selected in this study can be used to develop strong superiority combinations; but the SCA cannot be reflected by GD, which needs further study.

Two recombinant inbred lines (RILs) populations, RILSA derived from the cross between “Zhongyouzao8” (indica) and “Toyonihiki” (japonica) rice cultivars, and RILSB derived from the cross between “Qishanzhan” (indica) and “Akihikari” (japonica) rice cultivars, were grown in Liaoning and Sichuan Provinces, China to understand the effects of ecological environments on the subspecies characteristics and economic traits in filial generations of cross between indica and japonica. The results showed that both the subspecies characteristics and economic traits changed significantly. The effects of ecological environments on Cheng’s index and six subspecies characteristics were different on the basis of populations or characteristics. The distribution of Cheng’s index in RILSA was japonicalinous in Liaoning and Sichuan. The distribution of Cheng’s index in RILSB approached to normal distribution in Liaoning, but it was japonicalinous in Sichuan. As a whole, the two populations were more japonicalious in Sichuan than in Liaoning. The panicle number, seed setting rate and per-thousand-grain weight were decreased significantly in Sichuan. The grain number per panicle showed no significant change. A significant positive correlation was found between Cheng’s index and the economic traits, including six subspecies traits. It suggested that the reason that the filial generation of cross between indica and japonica in northern China showed japonicanous subspecies characteristics might be the artificial selection by breeders on the economic traits. In addition, indica-japonica differentiation and the relationship with ecological environments were discussed.

A single dominant gene Gc controls the trait of high chlorophyll (Chl) content in rice (cultivar (cv.) Zhenshan 97B). The contents of Chl b and total Chl increased 100% and 25%, respectively, when Gc was introduced. In addition, photosynthetic rate, biomass and grain yield also increased by 20%, 17% and 16%, respectively. Three simple sequence repeats (SSR) markers (rm462, rm6340 and rm6464) that are linked to Gc were identified by amplification of DNA samples from near-isogenic lines using two hundred pairs of primers. The genetic distances on the short arm of rice chromosome 1 between Gc and rm6464, rm6340 and rm462 were 0, 0.588 and 1.18 cM, respectively.

The recombinant inbred lines (RILs) population derived from the cross between “Zhongyouzao8” (hsien or indica) and “Fengjin” (keng or japonica) was grown in Liaoning and Sichuan Provinces to compare the subspecies characteristics under different environments. The results showed that the distribution of Cheng’s index was japonicalinous. The population was more japonicalinous in Sichuan than that in Liaoning as a whole. Further analysis indicated that indica and indica-cline in Sichuan were more indicalinous than those in Liaoning, japonica and japonica-cline in Sichuan were more japonicalinous than those in Liaoning. The effects of environment on six characteristics of Cheng’s index were different because of different characters, as well as on the correlations between the six characters, the Cheng’s index and the vascular bundle traits. For example, the length of the first and second rachis and leaf pubescence were more japonicalinous in Sichuan than in Liaoning, while the length/width ratio of spikelets and glume color at heading time were more indicalinous in Sichuan than in Liaoning. The vascular bundle characteristics of RILs in different environments changed remarkably. The number of large vascular bundles in panicle neck was less in Sichuan than in Liaoning, while the number of small vascular bundles in panicle neck and second top stem was greater in Sichuan than in Liaoning. The ratio of large to small vascular bundles in panicle neck decreased and the ratio of large vascular bundles between the second top stem and panicle neck increased in Sichuan. Though total trend was the vascular bundle ratio of large to small in indica was greater than that in japonica and the ratio of large vascular bundles in indica was less than that in japonica, it is not appropriate that the vascular bundle ratio of large to small and the ratio of large vascular bundles are regarded as the parameters for subspecies classification in rice. The vascular bundles characteristics from typical indica or japonica were recombined in the population derived from indica and japonica crossing.