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Summary: Amylose content is a crucial physicochemical property responsible for the eating and cooking quality of rice (Oryza sativa L.) grain and is mainly controlled by the Waxy (Wx) gene. Previous studies have identified several Dull genes that modulate the expression of the Wxb allele in japonica rice by affecting the splicing efficiency of the Wxb pre‐mRNA. Here, we uncover dual roles for a novel Dull gene in pre‐mRNA splicing and microRNA processing. We isolated the dull mutant, du13, with a dull endosperm and low amylose content. Map‐based cloning showed that Du13 encodes a C2H2 zinc‐finger protein. Du13 coordinates with the nuclear cap‐binding complex to regulate the splicing of Wxb transcripts in rice endosperm. Moreover, Du13 also regulates alternative splicing of other protein‐coding transcripts and affects the biogenesis of a subset of microRNAs. Our results reveal an evolutionarily conserved link between pre‐mRNA splicing and microRNA biogenesis in rice endosperm. Our findings also provide new insights into the functions of Dull genes in rice and expand our knowledge of microRNA biogenesis in monocots. [ABSTRACT FROM AUTHOR]

Summary: Starch accounts for over 80% of the total dry weight in cereal endosperm and determines the kernel texture and nutritional quality. Amyloplasts, terminally differentiated plastids, are responsible for starch biosynthesis and storage. We screened a series of rice mutants with floury endosperm to clarify the mechanism underlying amyloplast development and starch synthesis. We identified the floury endosperm19 (flo19) mutant which shows opaque of the interior endosperm. Abnormal compound starch grains (SGs) were present in the endosperm cells of the mutant. Molecular cloning revealed that the FLO19 allele encodes a plastid‐localized pyruvate dehydrogenase complex E1 component subunit α1 (ptPDC‐E1‐α1) that is expressed in all rice tissues. In vivo enzyme assays demonstrated that the flo19 mutant showed decreased activity of the plastidic pyruvate dehydrogenase complex. In addition, the amounts of monogalactosyldiacylglycerol (MGDG) and digalactosyldiacylglycerol (DGDG) were much lower in the developing flo19 mutant endosperm, suggesting that FLO19 participates in fatty acid supply for galactolipid biosynthesis in amyloplasts. FLO19 overexpression significantly increased seed size and weight, but did not affect other important agronomic traits, such as panicle length, tiller number and seed setting rate. An analysis of single nucleotide polymorphism data from a panel of rice accessions identified that the pFLO19L haplotype was positively associated with grain length, implying a potential application in rice breeding. In summary, our study demonstrates that FLO19 is involved in galactolipid biosynthesis which is essential for amyloplast development and starch biosynthesis in rice. [ABSTRACT FROM AUTHOR]

Summary: Spikelet is the primary reproductive structure and a critical determinant of grain yield in rice. The molecular mechanisms regulating rice spikelet development still remain largely unclear.Here, we report that mutations in OsPEX5, which encodes a peroxisomal targeting sequence 1 (PTS1) receptor protein, cause abnormal spikelet morphology.We show that OsPEX5 can physically interact with OsOPR7, an enzyme involved in jasmonic acid (JA) biosynthesis and is required for its import into peroxisome. Similar to Ospex5 mutant, the knockout mutant of OsOPR7 generated via CRISPR‐Cas9 technology has reduced levels of endogenous JA and also displays an abnormal spikelet phenotype. Application of exogenous JA can partially rescue the abnormal spikelet phenotype of Ospex5 and Osopr7. Furthermore, we show that OsMYC2 directly binds to the promoters of OsMADS1, OsMADS7 and OsMADS14 to activate their expression, and subsequently regulate spikelet development.Our results suggest that OsPEX5 plays a critical role in regulating spikelet development through mediating peroxisomal import of OsOPR7, therefore providing new insights into regulation of JA biosynthesis in plants and expanding our understanding of the biological role of JA in regulating rice reproduction. [ABSTRACT FROM AUTHOR]

Key message: FLO15encodes a plastidic glyoxalase I protein, OsGLYI7, which affects compound starch granule formation and starch synthesis in rice endosperm.Abstract: Starch synthesis in rice (Oryza sativa) endosperm is a sophisticated process, and its underlying molecular machinery still remains to be elucidated. Here, we identified and characterized two allelic rice floury endosperm 15 (flo15) mutants, both with a white-core endosperm. The flo15 grains were characterized by defects in compound starch granule development, along with decreased starch content. Map-based cloning of the flo15 mutants identified mutations in OsGLYI7, which encodes a glyoxalase I (GLYI) involved in methylglyoxal (MG) detoxification. The mutations of FLO15/OsGLYI7 resulted in increased MG content in flo15 developing endosperms. FLO15/OsGLYI7 localizes to the plastids, and the in vitro GLYI activity derived from flo15 was significantly decreased relative to the wild type. Moreover, the expression of starch synthesis-related genes was obviously altered in the flo15 mutants. These findings suggest that FLO15 plays an important role in compound starch granule formation and starch synthesis in rice endosperm. [ABSTRACT FROM AUTHOR]

Pyruvate kinase (PK) is a key enzyme in glycolysis and carbon metabolism. Here, we isolated a rice (Oryza sativa) mutant, w59, with a white‐core floury endosperm. Map‐based cloning of w59 identified a mutation in OsPKpα1, which encodes a plastidic isoform of PK (PKp). OsPKpα1 localizes to the amyloplast stroma in the developing endosperm, and the mutation of OsPKpα1 in w59 decreases the plastidic PK activity, resulting in dramatic changes to the lipid biosynthesis in seeds. The w59 grains were also characterized by a marked decrease in starch content. Consistent with a decrease in number and size of the w59 amyloplasts, large empty spaces were observed in the central region of the w59 endosperm, at the early grain‐filling stage. Moreover, a phylogenetic analysis revealed four potential rice isoforms of OsPKp. We validated the in vitro PK activity of these OsPKps through reconstituting active PKp complexes derived from inactive individual OsPKps, revealing the heteromeric structure of rice PKps, which was further confirmed using a protein–protein interaction analysis. These findings suggest a functional connection between lipid and starch synthesis in rice endosperm amyloplasts. Pyruvate kinase (PK) functions in glycolysis. Mutation in plastidic OsPKpα1 resulted in dramatic changes to lipid and starch biosynthesis in rice endosperm. As plastidic PK plays a fundamental role in generating the precursors for fatty acid biosynthesis, our findings suggest a functional connection between lipid and starch synthesis in amyloplasts. [ABSTRACT FROM AUTHOR]

Heterosis is a phenomenon whereby hybrids of inbred lines produce favourable phenotypes that exceed those of their parents. Traits of interest are higher yield and stronger stress tolerance. The two-line super-hybrid rice 'Liangyoupei9' ( LYP9) shows superiority to both its elite inbred line '93-11' and 'Pei'ai64s' (' PA64s') parents and conventional hybrids. However, the genetic basis of its hybrid vigour, especially yield determination, remains elusive. In the present study, a set of 156 chromosome segment substitution lines ( CSSLs) carrying overlapping segments from ' PA64s' in a genetic background of '93-11' were constructed and planted in six environments. Three major agronomic traits, viz. panicle length ( PL), heading date ( HD) and plant height ( PH), and five yield-related traits, viz. grain weight per panicle ( GWP), number of grains per panicle ( GPP), 1000-grain weight ( TGW), seed set ( SS) and number of panicles of per plant ( PPP), were evaluated over 3 years. Quantitative trait loci ( QTL) analysis was conducted using a likelihood ratio test based on stepwise regression. Forty-six putative QTL distributed on 11 chromosomes were detected in more than one year. Remarkably, GWP of four CSSLs carrying positive yield QTL outperformed the recurrent parent '93-11' by more than 15%, in at least two environments. These results indicate that CSSLs are effective in identifying yield-associated traits, and lines harbouring such QTL will be rich in resources for future molecular breeding programmes. [ABSTRACT FROM AUTHOR]

Abstract: A backcross inbred line population derived from a cross between Koshihikari and Kasalath was used to dissect the genetic relationship among chalkiness, protein content, and paste viscosity properties in rice in three environments. A total of 11 traits (or parameters) were analyzed, including percentage of grains with chalkiness (PGWC), protein content (PC) and protein index (PI), and eight parameters from the viscosity profile. PGWC, PC and PI were significantly correlated with the paste viscosity parameters. We identified 39 QTLs in three environments; ten QTL clusters emerged. Eight QTLs were consistently detected across the three environments and further confirmed using a set of chromosome segment substitution lines (CSSLs) where Kasalath was used as the donor parent and Koshihikari as the recurrent parent. One and two major clusters on chromosome 6 corresponded to the Wx and Alk loci, respectively. The former was responsible for PGWC and most of the viscosity parameters, and the latter for PI and some viscosity parameters. Particularly, QTL qPI-6.1 was linked with both the Wx and Alk loci. The co-locations of QTLs for PGWC and viscosity parameters and the linkage of qPI-6.1 and qBDV-6 at the Wx locus could be largely responsible for the phenotypic correlations between these traits. [Copyright &y& Elsevier]

With 2 figures and 5 tables To discover new resistance genes to rice stripe virus disease (RSVD), quantitative trait loci (QTL) analysis was conducted by using 162 recombinant inbred lines, derived from a cross between 'Guichao 2' and 'Koshihikari', RSVD resistances were evaluated using both artificial inoculation and natural infection methods by scoring the ratio of the disease rating index. Three QTL‐controlling RSVD resistance were detected by the above two methods, which located on chromosomes 4(qStv4), 9(qStv9) and 12(qStv12), respectively. The qStv9 and qStv12 was repeatedly detected in artificial inoculation test in 2006 and 2008. In natural inoculation test, the qStv4 and qStv9 was detected in 2006, and the qStv12 was detected in 2008. As qStv9 and qStv12 explained 11.3–32.1% of the resistance effect from 'Guichao 2' across two environments, they should be a useful genetic resource in rice MAS breeding programme against RSVD. Further analysis revealed that the lines harbouring the alleles of qStv9 and qStv12 exhibited significantly increased resistance to RSVD, implying the possibility of breeding new resistant varieties by pyramiding resistant QTL through marker‐assisted selection. [ABSTRACT FROM AUTHOR]

Chalkiness of rice grain is an important quality component of rice, as it has a profound influence on eating and milling qualities. We has determined the inheritance of percentage of grain with chalkiness (PGWC) using a set of chromosome segment substitution lines, made from a cross between cv. PA64s and cv. 9311. Two loci controlling PGWC, designated as qPGWC-6 and qPGWC-7, were located on, respectively, chromosomes 6 and 7. Comparisons were made between C-51 (a CSSL harbouring qPGWC-7 and having a chalky endosperm) and the recurrent parent 9311 (translucent endosperm) to characterize the physical and chemical differences between translucent and chalky endosperm. Unlike the translucent endosperm, the chalky endosperm contains loosely packed starch granules, and there were significant difference between C-51 and 9311 for amylopectin structure and degree of crystallinity, but not for either amylose content or starch viscosity. Segregation analysis of the F2 population from the cross between C-51 and 9311 showed PGWC is a semi-dominant trait, controlled by single nuclear gene. A large F2 population was constructed from the cross C51 × 9311, and used for the fine mapping of qPGWC-7, which was located to a 44-kb DNA fragment, containing thirteen predicted genes. This result provides a springboard for the map-based cloning of qPGWC-7 and allowed for marker-assisted selection for endosperm texture. [ABSTRACT FROM AUTHOR]

Abstract: Resistant starch (RS) content was determined in 10 indica and japonica milled rices with different levels of amylose. The effect of microbial growth during starch digestion on the measurement of RS, and the correlation between physico-chemical characteristics and RS contents of milled rice were analysed. Results indicated a significant decrease (P <0.01) in assay values of RS after antibiotics addition, and the markedly decreased sample pH due to fermentation might be the main reason for errors in RS determination. Correlation analyses showed that RS contents of milled rice were closely related to amylose content (r =0.75, P <0.05) and protein content (r =0.78, P <0.01). No significant correlation existed between RS content and some relatively simple physical properties, such as width, shape and elongation ratio of rice grain, which were reported to be good indictors of rate of rice starch digestion, while a significant positive correlation was found between elongation ratio and digestible starch in cooked milled rice (r =0.67, P <0.05). [Copyright &y& Elsevier]

Abstract: Northeast regions of China (38–55°N latitude) play an important role in Japonica rice planting. Heading dates of 10 Japonica rice cultivars native to the Northeast of China were investigated and their sensitivities to photoperiod and temperature were analyzed. The results showed that these Japonica rice cultivars were insensitive to photoperiod but strongly sensitive to temperature, i.e. a high temperature can markedly shorten the heading date. Genetic analyses were conducted on these 10 cultivars using a set of heading date tester lines. All these Japonica cultivars carried a dominant early heading gene Ef-1, and most of these cultivars carried the photoperiod insensitivity allele e 1 , and two types of alleles were presented at the Se-1 locus, including recessive photoperiod insensitivity gene Se-1 e and dominant strong photoperiod-sensitivity (PS) gene Se-1 n . The PS of these cultivars carrying E 1 or Se-1 n can be repressed or weakened by Ef-1 and the recessive allele hd2 they carried. These results provided a reasonable explanation to the adaptability of Japonica rice to the high latitude environment of the Northeast China, and could be useful for breeding new cultivars well adapted to the high latitude regions and expanding the rice cultivation range. [Copyright &y& Elsevier]