Genome‐wide expression quantitative trait locus studies facilitate isolation of causal genes controlling panicle structure

The morphology of rice (Oryza sativa L.) panicles is an important determinant of grain yield, and elucidation of the genetic control of panicle structure is very important for fulfilling the demand for high yield in breeding programs. In a quantitative trait locus (QTL) study using 82 backcross inbred lines (BILs) derived from Koshihikari and Habataki, 68 QTLs for 25 panicle morphological traits were identified. Gene expression profiling from inflorescence meristems of BILs was obtained. A combination of phenotypic QTL (pQTL) and expression QTL (eQTL) analysis revealed co‐localization between pQTLs and eQTLs, consistent with significant correlations between phenotypic traits and gene expression levels. By combining pQTL and eQTL data, two genes were identified as controlling panicle structure: OsMADS18 modulates the average length of the primary rachis and OsFTL1 has pleiotropic effects on the total number of secondary rachides, number of grains per panicle, plant height and the length of flag leaves. Phenotypes were confirmed in RNA interference knocked‐down plants and overexpressor lines. The combination of pQTL and eQTL analysis could facilitate identification of genes involved in rice panicle formation.     

Fine Mapping and Candidate Gene Prediction of the Quantitative Trait Locus <i>qPL8</i> for Panicle Length in Rice

Rice panicle is the sink organ where assimilation product accumulates, and its morphology determines the rice yield. Panicle length has been suggested as a yield-related trait, but the genetic factor for its control is still limited. In this study, we carried out fine-mapping of qPL8, a QTL identified for panicle length in our previous work. Near isogenic line (NIL) with qPL8 exhibited elongated panicle without obvious effect on other panicle elements. With five key recombinants from NIL population, the locus was finally narrowed down to a 278-kb region, where 44 genes are annotated. By comparing the genomic sequence of two parents, 17 genes were identified with SNPs or InDels variations in the coding region. Expression analysis showed that eight genes were up-regulated in the NIL with qPL8. Considering both the coding variation and expression status, several candidate genes for the locus were identified, and OsMADS37 was raised as the most possible candidate. Interestingly, an expression QTL (eQTL) also resides in the locus, leading to a cluster of gene expression variation in the region. This study will facilitate the application of qPL8 locus in rice breeding for yield potential.     

水稻突变体des2和des5的研究和定位

小穗发育是决定水稻产量的主要农艺性状,鉴定控制小穗发育的关键基因对研究和分析调控农艺性状的分子机理是至关重要的.本文中,我们鉴定了一组小穗数目明显减少的突变体,命名为decteased spikelets(des),这里详细研究des2和des5两个突变体.结果显示des2是由单基因隐性位点控制,图位克隆将此位点定位到6号染色体的长臂上,并最终克隆了此基因,发现des2是moc1的一个新的等位突变体.定位克隆和序列分析显示在des5中,LAX基因的编码HLH(螺旋一环一螺旋)结构域的区域发生了一个点突变,暗示des5是lax的一个新的等位突变体.我们的结果暗示小穗和水稻叶腋分枝的发育受相同的遗传途径调控.     

A spectrum of genes expressed during early stages of rice panicle and flower development

To unravel gene expression patterns during rice inflorescence development, particularly at early stages of panicle and floral organ specification, we have characterized random cloned cDNAs from developmental-stage-specific libraries. cDNA libraries were constructed from rice panicles at the stage of branching and flower primordia specification or from panicles undergoing floral organogenesis. Partial sequence analysis and expression patterns of some of these random cDNA clones from these two rice panicle libraries are presented. Sequence comparisons with known DNA sequences in databases reveal that approximately sixtyeight per cent of these expressed rice genes show varying degrees of similarity to genes in other species with assigned functions. In contrast, thirtytwo per cent represent uncharacterized genes. cDNAs reported here code for potential rice homologues of housekeeping molecules, regulators of gene expression, and signal transduction molecules. They comprise both single-copy and multicopy genes, and genes expressed differentially, both spatially and temporally, during rice plant development. New rice cDNAs requiring specific mention are those with similarity toCOP1, a regulator of photomorphogenesis inArabidopsis; sequence-specific DNA binding plant proteins like AP2-domain-containing factors; genes that specify positional information in shoot meristems like leucine-rich-repeat-containing receptor kinases; regulators of chromatin structure like Polycomb domain protein; and also proteins induced by abiotic stresses.     

Abscisic acid promotes flowering and enhances LcAP1 expression in Litchi chinensis Sonn.

In order to investigate the role of abscisic acid in litchi flowering, litchi trees were treated with exogenous ABA before or when panicle primordia emerged. The results showed that ABA spraying when panicle primordia emerged reduced the number of leaves per panicle, enhanced the number of axillary panicles per panicle and the ratio of axillary panicles to total nodes per panicle. When trees were treated with ABA before panicle primordia emerged, the number of flowers per panicle in the ABA-treated trees was higher than that of the control. The ABA biosynthesis inhibitor naproxen reduced the percentage of flowering terminal shoots and number of flowers in one panicle, and suppressed the litchi homologue gene (LcAP1). To confirm whether the enhanced AP1 expression depended on H₂O₂, NO and calcium, the effect of ABA was compared with that of ABA plus NO scavenger 2-phenyl-4,4,5,5-tetramethylimidazoline-1-oxyl3-oxide (PTIO), or the H₂O₂ trapper dimethylthiourea (DMTU), the calcium chelator glycol-bis (β-amino ethyl ether)-N,N,N′,N′-tetraacetic acid (EGTA) and calcium channel blocker LaCl₃. The results showed that ABA enhanced AP1 expression, but the inductive effects were suppressed by DMTU, EGTA and LaCl₃ but not PTIO, suggesting that ABA promotion of LcAP1 expression may be H₂O₂ and calcium dependent but not NO dependent.     

粳稻穗部性状遗传分析

从粳稻（Oryzasativassp.japonica）RIL群体中选取每穗颖花数极端少的品系丙堡3201和丙堡3205及每穗颖花数极端多的品系丙堡3145和丙堡3214,配制丙堡3201×丙堡3145和丙堡3214×丙堡3205两个组合的P1、P2、F1、B1、B2和F26个世代,调查每穗颖花数、每穗实粒数、穗长、一次枝梗数和二次枝梗数的表型分布,并运用主基因＋多基因混合遗传模型,对这5个性状进行了遗传分析。结果表明,每穗颖花数性状在2个组合的各分离世代均未出现超亲分离,而其它4个性状均有不同程度的超亲分离。一次枝梗数受1对主基因＋多基因控制;其余4个性状均受2对主基因＋多基因控制。每穗颖花数、每穗实粒数、穗长和二次枝梗数4个性状以主基因遗传为主,一次枝梗数性状以多基因遗传为主。     

Over-expression of the rice LRK1 gene improves quantitative yield components

In rice ( Oryza sativa L.), the number of panicles, spikelets per panicle and grain weight are important components of grain yield. These characteristics are controlled by quantitative trait loci (QTLs) and are derived from variation inherent in crops. As a result of the complex genetic basis of these traits, only a few genes involved in their control have been cloned and characterized. We have previously map-cloned a gene cluster including eight leucine-rich repeat receptor-like kinase ( LRK ) genes in Dongxiang wild rice ( Oryza rufipogon Griff.), which increased the grain yield by 16%. In the present study, we characterized the LRK1 gene, which was contained in the donor parent (Dongxiang wild rice) genome and absent from the recurrent parent genome (Guichao2, Oryza sativa L. ssp. indica ). Our data showed that rice LRK1 is a plasma membrane protein expressed constitutively in leaves, young panicles, roots and culms. The over-expression of rice LRK1 results in increased panicles, spikelets per panicle, weight per grain and enhanced cellular proliferation, leading to a 27.09% increase in total grain yield per plant. The increased number of panicles and spikelets per panicle are associated with increased branch number. Our data suggest that rice LRK1 regulates rice branch number by enhancing cellular proliferation. The functional characterization of rice LRK1 facilitates an understanding of the mechanisms involved in cereal crop yield, and may have utility in improving grain yield in cereal crops.     

Genetic architecture of purple pigmentation and tagging of some loci to SSR markers in pearl millet, Pennisetum glaucum (L.) R. Br

This report describes the construction of integrated genetic maps in pearl millet involving certain purple phenotype and simple sequence repeat (SSR) markers. These maps provide a direct means of implementing DNA marker-assisted selection and of facilitating "map-based cloning" for engineering novel traits. The purple pigmentation of leaf sheath, midrib and leaf margin was inherited together 'en bloc' under the control of a single dominant locus (the 'midrib complex') and was inseparably associated with the locus governing the purple coloration of the internode. The purple panicle was caused by a single dominant locus. Each of the three characters (purple lamina, purple stigma and purple seed) was governed by two complementary loci. One of the two loci governing purple seed was associated with the SSR locus Xpsmp2090 in linkage group 1, with a linkage value of 22 cM, while the other locus was associated with the SSR locus Xpsmp2270 in linkage group 6, with a linkage value of 23 cM. The locus for purple pigmentation of the midrib complex was either responsible for pigmentation of the panicle in a pleiotropic manner or was linked to it very closely and associated with the SSR locus Xpsmp2086 in linkage group 4, with a suggestive linkage value of 21 cM. A dominant allele at this locus seems to be a prerequisite for the development of purple pigmentation in the lamina, stigma and seed. These findings suggest that the locus for pigmentation of the midrib complex might regulate the basic steps in anthocyanin pigment development by acting as a structural gene while other loci regulate the formation of color in specific plant parts.     

Genetics and sequence analysis of the pcnB locus, an Escherichia coli gene involved in plasmid copy number control.

Mutations at the Escherichia coli pcnB locus reduce the copy number of ColE1-like plasmids. We isolated additional mutations in this gene and conducted a preliminary characterization of its product. F-prime elements carrying the pcnB region were constructed and used to show that the mutations were recessive. The wild-type pcnB gene was cloned into a low-copy-number plasmid, and its nucleotide sequence was determined. The sequence analysis indicated that pcnB is probably the first gene in an operon that contains one or more additional genes of unknown function. The pcnB locus should encode a polypeptide of 47,349 daltons (Da). A protein of this size was observed in minicells carrying a pcnB+ plasmid, and transposon insertions and deletions that truncated this protein generally abolished pcnB function. One exceptional transposon insertion at the promoter-distal end of the pcnB gene truncated the 47-kDa protein by about 20% but did not abolish complementation activity, indicating that the C-terminus of the PcnB product is dispensable. The deduced amino acid sequence of PcnB revealed numerous charged residues and, with 10% arginines, an overall basic character, suggesting that PcnB might interact with DNA or RNA in a structural capacity. Disruption of the pcnB gene by insertional mutagenesis caused a reduction in growth rate, indicating that PcnB has an important cellular function.     

粳稻穗部性状遗传分析

从粳稻(Oryza sativa ssp. japonica)RIL群体中选取每穗颖花数极端少的品系丙堡3201和丙堡3205及每穗颖花数极端多的品系丙堡3145和丙堡3214, 配制丙堡3201×丙堡3145和丙堡3214×丙堡3205两个组合的P₁、P₂、F₁、B₁、B₂和F₂ 6个世代, 调查每穗颖花数、每穗实粒数、穗长、一次枝梗数和二次枝梗数的表型分布, 并运用主基因+多基因混合遗传模型,对这5个性状进行了遗传分析。结果表明, 每穗颖花数性状在2个组合的各分离世代均未出现超亲分离, 而其它4个性状均有不同程度的超亲分离。一次枝梗数受1对主基因+多基因控制; 其余4个性状均受2对主基因+多基因控制。每穗颖花数、每穗实粒数、穗长和二次枝梗数4个性状以主基因遗传为主, 一次枝梗数性状以多基因遗传为主。     

The psp locus of Yersinia enterocolitica is required for virulence and for growth in vitro when the Ysc type III secretion system is produced

The phage shock protein locus (pspFpspABCDE) of Escherichia coli has proved to be something of an enigma since its discovery. The physiological functions of the psp locus, including those of the predicted effector protein PspA, are unknown. In a previous genetic screen, we determined that a Yersinia enterocolitica pspC mutant was severely attenuated for virulence. In this study, the psp locus of Y. enterocolitica was characterized further. The pspC gene of Y. enterocolitica was found to be important for normal growth when the Ysc type III secretion system was expressed in the laboratory. This growth defect was specifically caused by production of the secretin protein, YscC. Expression of the psp genes was induced when the type III secretion system was functional or when only the yscC gene was expressed. This induction of psp gene expression required a functional pspC gene. Most significantly, evidence suggests that the expression of at least one gene that is not part of the psp locus is regulated by Psp proteins. This unidentified gene (or genes) may also be important for growth when the type III secretion system is expressed. These conclusions are supported by the effects of various psp mutations on virulence. This is the first indication that Psp proteins might be involved in the regulation of genes besides the psp locus itself.     

Autosomal Dominant Postaxial Polydactyly, Nail Dystrophy, and Dental Abnormalities Map to Chromosome 4p16, in the Region Containing the Ellis–van Creveld Syndrome Locus

We have studied a four-generation family with features of Weyers acrofacial dysostosis, in which the proband has a more severe phenotype, resembling Ellis-van Creveld syndrome. Weyers acrofacial dysostosis is an autosomal dominant condition with dental anomalies, nail dystrophy, postaxial polydactyly, and mild short stature. Ellis-van Creveld syndrome is a similar condition, with autosomal recessive inheritance and the additional features of disproportionate dwarfism, thoracic dysplasia, and congenital heart disease. Linkage and haplotype analysis determined that the disease locus in this pedigree resides on chromosome 4p16, distal to the genetic marker D4S3007 and within a 17-cM region flanking the genetic locus D4S2366. This region includes the Ellis-van Creveld syndrome locus, which previously was reported to map within a 3-cM region between genetic markers D4S2957 and D4S827. Either the genes for the condition in our family and for Ellis-van Creveld syndrome are near one another or these two conditions are allelic with mutations in the same gene. These data also raise the possibility that Weyers acrofacial dysostosis is the heterozygous expression of a mutation that, in homozygous form, causes the autosomal recessive disorder Ellis-van Creveld syndrome.     

Canopy analysis on the relationships between leaf area index and productivity in lowland rice,Oryza sativa,L.

Summary Different densities of populations were created under field conditions at two levels of N and canopy analysis was made with variety Sona on different growth parameters governing productivity. The relationships between leaf area index (LAI) and dry matter, grain yield and grain number were quadratic. LAI vs panicle number and grain number vs grain yield relationships were linear. The panicle number and grains per panicle are found to be compensatory for one another. The intercepting points of the two appear to be around 400 panicles per square metre with a grain range of 90–100 per panicle. re]19750228     

Low temperature-induced leaf senescence and the expression of senescence-related genes in the panicles of <Emphasis Type="Italic">Litchi chinensis</Emphasis>

Litchi is one of the most important subtropical evergreen fruit trees in Southern Asia. Litchi floral buds are a mix of axillary or apical panicle primordia, leaf primordia, and rudimentary leaves. Under usual winter and early spring conditions, the axillary panicle primordia prevail, and the rudimentary leaves abscise when low temperatures reach a certain threshold. The floral buds ultimately develop into pure panicles. Understanding the regulatory mechanism of rudimentary leaf senescence is of great importance for litchi flowering. In this study, litchi potted trees at the floral differentiation stage were treated with low and high temperatures in order to induce senescence or development of leaves. The microstructure of the petiole base of the rudimentary leaves was determined. The results show several layers of flattened cells forming in the abscission zone of the rudimentary leaves that were treated with low temperatures as well as an obvious boundary regarded as the abscission layer zone. We also determined the gene expression in the leaves with different developmental fate. The results show that the LcRboh, LcMC-1-like, and LcPirin genes were significantly induced in the rudimentary leaves treated with low temperatures, and the expression increased with the proceeding of senescence. The expression of the genes encoding class Ι β-1,3-glucanase and β-xylosidase also increased with the senescence, suggesting their possible involvement in the low temperature-induced senescence of the rudimentary leaves.