Two recessive genes controlling thermophotoperiod-sensitive male sterility in wheat

Male sterility of wheat-breeding line 337S (Triticum aestivum L.) is sensitive to both short day-length/low temperature and long day-length/high temperature. 337S was crossed with the common wheat variety, Huamai No. 8 and the F₁ was highly fertile. The F₂ population segregated in a 15:1 ratio for fertility/sterility in 243 individuals under long day-length/high-temperature. The two thermophotoperiod-responsive male sterile genes were mapped to chromosomes 5B and 2B using Simple Sequence Repeat (SSR) markers and bulked segregant analysis. Partial linkage maps around the sterility loci of chromosomes 2B and 5B were constructed using the 243 individuals in the F₂ population. One gene (wptms1) for male sterility was flanked by the SSR markers Xgwm335 and Xgwm371 at a genetic distance in chromosome 5B of 4.1 and 24.4 cM, respectively. The second gene (wptms2) was mapped between markers Xgwm374 and Xgwm120 at a genetic distance of 6.6 and 20.9 cM, respectively. The closest linked markers Xgwm335 (wptms1) and Xgwm374 (wptms2) explained 53 and 38% of phenotypic variation for the fertility. The SSR markers provide a useful tool to transfer the male sterile genes into elite wheat germplasm.     

Characterization of fertility alteration and marker validation for male sterility genes in novel PTGMS lines hybrid rice

Photoperiod and thermosensitive genetic male sterile (PTGMS) lines have become one of the main sources of global rice production increasing. This study was conducted to evaluate the fertility alteration and validate the male sterility genes using validation markers in novel Egyptian Indica and Japonica PTGMS lines under natural conditions. The study revealed that the new genetic male sterile lines belong to the type of photo–thermosensitive genetic male sterility (PTGMS). The fertility alteration of these lines has influenced by photoperiod and temperature interaction. The new PTGMS lines have three sensitive periods of fertility alteration; transformation, sterility, and fertility period. Furthermore, the sensitive stage of fertility transformation might be from secondary branch primordial to pollen mother cells (PMC) meiosis. Under the natural Sakha condition, the new PTGMS lines were stable sterile under the condition of day length upper 13,75 h and temperature over 25 °C, while its convert to fertile under day length under 13 h, and temperature lower than 24 °C. The co-dominant markers identified the pms3 and tms5 genes in the new PTGMS lines, indicated that the fertility alteration in these lines controlled by photoperiod and thermosensitive stages.     

Genome-wide analysis of genes targeted by qLTG3-1 controlling low-temperature germinability in rice

The control of seed germination under environmental conditions, where plants will be grown, is important for the adaptability of plants. Low-temperature is one of the most common environmental stress factors that affect plant growth and development and places a major limit on crop productivity in cultivated areas. Previously, qLTG3-1, a major quantitative trait locus controlling low-temperature tolerance at the germination stage in rice (called low-temperature germinability) was identified, which encodes a protein of unknown function. To identify genes targeted by qLTG3-1, a genome-wide expression profiling analysis using the 44 K Rice Oligo microarray was performed. Because the expression of qLTG3-1 was dramatically increased at 1 day after incubation, the expression profiles at this time were compared between Hayamasari, which has a loss-of-function qLTG3-1 allele, and a near isogenic line with a functional allele. A total of 4,587 genes showed significant differences between their expression levels in the two lines. Most of these genes might be involved in the process of seed germination itself, and then a focus was made on qLTG3-1 dependently induced or suppressed genes, defined as ‘qLTG3-1 dependent’ genes. Twenty-nine ‘qLTG3-1 dependent’ genes with diverse functions were categorized, implying that disruption of cellular homeostasis leads to a wide range of metabolic alterations and diverse cross-talk between various signaling pathways. In particular, genes involved in defense responses were up-regulated by qLTG3-1, indicating that qLTG3-1 expression is required for the expression of defense response genes in low-temperature germinability in rice.     

Molecular mapping of two reverse photoperiod-sensitive genic male sterility genes (rpms1 and rpms2) in rice (Oryza sativa L.)

The reverse photoperiod-sensitive genic male sterility (PGMS) and thermo-sensitive genic male sterility (TGMS) lines have an opposite phenotype compared with normal PGMS and TGMS lines widely used by the two-line system in current hybrid rice seed production. Thus, the application of reverse PGMS and TGMS lines can compensate PGMS and TGMS lines in hybrid rice production. YiD1S is a reverse PGMS line, in which pollen fertility is mainly regulated by day-length, but also influenced by temperature. Genetic analysis indicated that male sterility of YiD1S was controlled by two recessive major genes. An F₂ population from a cross between YiD1S and 8528 was developed and used for molecular mapping of the two reverse PGMS genes which were first named rpms1 and rpms2. Both simple sequence repeat (SSR) markers and bulked segregant analysis (BSA) were used in this study. As a result, one reverse PGMS gene (rpms1) was mapped to the interval between SSR markers RM22980 (0.9 cM) and RM23017 (1.8 cM) on chromosome 8. Eight SSR markers, YDS818, RM22984, RM22986, RM22997, YDS816, RM23002, RM339 and YDS810 completely co-segregated with the rpms1 gene. Another reverse PGMS gene (rpms2) was mapped to the interval between SSR markers RM23898 (0.9 cM) and YDS926 (0.9 cM) on chromosome 9. The physical mapping information from publicly available resources shows that the rpms1 and rpms2 loci are located in a region of 998 and 68 kb, respectively. The analysis based on marker genotypes showed that the effect of rpms1 was slightly larger than that of rpms2 and that the two genes interacted in controlling male sterility. H. F. Peng, Z. F. Zhang and B. Wu contributed equally to this work.     

Characterization and mapping of a novel mutant sms1 (senescence and male sterility 1) in rice

Plant senescence plays diverse important roles in development and environmental responses.However,the molecular basis of plant senescence is remained largely unknown.A rice spontaneous mutant with the character of early senescence and male sterility (sms) was found in the breeding line NT10-748.In order to identify the gene SMS1 and the underlying mechanism,we preliminarily analyzed physiological and biochemical phenotypes of the mutant.The mutant contained lower chlorophyll content compared with the wild t...     

Characterization and mapping of a novel mutant sms1 （senescence and male sterility 1） in rice

Plant senescence plays diverse important roles in development and environmental responses.However,the molecular basis of plant senescence is remained largely unknown.A rice spontaneous mutant with the character of early senescence and male sterility (sms) was found in the breeding line NT10-748.In order to identify the gene SMS1 and the underlying mechanism,we preliminarily analyzed physiological and biochemical phenotypes of the mutant.The mutant contained lower chlorophyll content compared with the wild type control and was severe male sterile with lower pollen viability.Genetic analysis showed that the mutant was controlled by a single recessive gene.By the map-based cloning approach,we fine-mapped SMS1 to a 67 kb region between the markers Z3-4 and Z1-1 on chromosome 8 using 1,074 F2 recessive plants derived from the cross between the mutant sms1 (japonica) × Zhenshan 97 (indica),where no known gene involved in senescence or male sterility has been identified.Therefore the SMS1 gene will be a novel gene that regulates the two developmental processes.The further cloning and functional analysis of the SMS1 gene is under way.     

Characterization and detection of epistatic interactions of 3 QTLs, Hd1, Hd2, and Hd3, controlling heading date in rice using nearly isogenic lines

To characterize quantitative trait loci (QTLs), we used marker-assisted selection (MAS) to develop three nearly isogenic lines (NILs) differing only for the presence of a single, specific QTL (QTL-NILs) –Hd1, Hd2, and Hd3 – for heading date in rice. The three lines contained the chromosomal region of the target QTL from donor variety Kasalath(indica) in the genetic background of var. Nipponbare (japonica). To analyze epistatic interactions in pairs of these QTLs, we also used MAS to develop four combined QTL-NILs with 2 of the 3 QTLs or with all 3. Different daylength treatment testing of the QTL-NILs revealed that the three QTLs control photoperiod sensitivity. Genetic analysis of F₂ populations derived from crosses between the three QTL-NILs with a single QTL using molecular markers revealed the existence of epistatic interactions between Hd1 and Hd2, and Hd2 and Hd3. These interactions were also confirmed by the analysis of combined QTL-NILs under different daylength conditions. The existence of an epistatic interaction between Hd1 and Hd3 was also clarified. Based on these results, we suggest that the Kasalath allele of Hd3 does not affect photoperiod sensitivity by itself but that it is involved in enhancement of the expression of the Nipponbare alleles of Hd1 and Hd2. Received: 22 October 1999 / Accepted: 21 March 2000     

Identification of neutral genes at pollen sterility loci Sd and Se of cultivated rice (Oryza sativa) with wild rice (O. rufipogon) origin

Pollen sterility is one of the main hindrances against the utilization of strong intersubspecific (indica-japonica) heterosis in rice. We looked for neutral alleles at known pollen sterility loci Sd and Se that could overcome this pollen sterility characteristic. Taichung 65, a typical japonica cultivar, and its near isogenic lines E7 and E8 for pollen sterility loci Sd and Se were employed as tester lines for crossing with 13 accessions of wild rice (O. rufipogon). Pollen fertility and genotypic segregations of the molecular markers tightly linked with Sd and Se loci were analyzed in the paired F(1)s and F(2) populations. One accession of wild rice (GZW054) had high pollen fertility in the paired F(1)s between Taichung 65 and E7 or E8. Genotypic segregations of the molecular markers tightly linked with Sd and Se loci fit the expected Mendelian ratio (1:2:1), and non-significances were shown among the mean pollen fertilities with the maternal, parental, and heterozygous genotypes of each molecular markers tightly linked with Sd and Se loci. Evidentially, it indicated that the alleles of Sd and Se loci for GZW054 did not interact with those of Taichung 65 and its near isogenic lines, and, thus were identified as neutral alleles Sd(n) and Se(n). These neutral genes could become important germplasm resources for overcoming pollen sterility in indica-japonica hybrids, making utilization of strong heterosis in such hybrids viable.     

RFLP mapping of the genes controlling hybrid breakdown in rice (Oryza sativa L.)

 Complementary recessive genes hwd1 and hwd2 controlling hybrid breakdown (weakness of F₂ and later generations) were mapped in rice using RFLP markers. These genes produce a plant that is shorter and has fewer tillers than normal plants when the two loci have only one or no dominant allele at both loci. A cultivar with two dominant alleles at the hwd1 locus and a cultivar with two dominant alleles at the hwd2 locus were crossed with a double recessive tester line. Linkage analysis was carried out for each gene independently in two F₂ populations derived from these crosses. hwd1 was mapped on the distal region of rice genetic linkage map for chromosome 10, flanked by RFLP markers C701 and R2309 at a distance of 0.9 centiMorgans (cM) and 0.6 cM, respectively. hwd2 was mapped in the central region of rice genetic linkage map for chromosome 7, tightly linked with 4 RFLP markers without detectable recombination. The usefulness of RFLP mapping and map information for the genes controlling reproductive barriers are discussed in the context of breeding using diverse rice germplasm, especially gene introduction by marker-aided selection.     

Analysis of isogenic lines of the soft wheat carrying dominant alleles of Bg, Hg, and Rg1 genes using microsatellite and protein markers

To determine tight linkage between morphological and molecular markers of the first homologous group of chromosomes of common wheat, microsatellite analysis of six near-isogenic lines with marker dominant alleles controlling back color (Bg; 1AS) and hairy glume (Hg; 1AS) and two lines bearing the dominant alleles of the gene for red glume color (Rgl; 1BS) was conducted. The component composition of gliadins in these lines was studied. Tight linkage of Bg, Hg, and Gli-A1 genes with a microsatellite marker Xgwm136 (1AS) and of Rg1 and Gli-B1 genes with markers Xgwm33 and Xgwm550 (1BS) was shown. Based on the results obtained and literature data, the most probable order of morphological and molecular markers on chromosomes of common wheat was determined. On chromosome 1AS, from the centromere to the telomere, the markers are located as follows: Xgwm136-Gli-A1-BgHg; on chromosome 1BS, in the same direction: Xgwm33-Gli-B1-Rg1-Xgwm550.     

Analysis of a dispersed repetitive DNA sequence in isogenic lines of Drosophila

The location of sequences homologous to a cloned D. melanogaster DNA segment, Dm 25, has been examined in polytene chromosomes by hybridization in situ. Dm 25 localizes to multiple sites and shows variation in patterns between different strains and among individuals within wild-type laboratory strains. Analysis of numerous geographically distinct isogenic lines suggests that Dm 25 patterns are determined by germ-line factors and are not the product of strictly somatic events. In general there is wide variation in Dm 25 patterns among different lines, but a significant number of sites are common to two or more distinct lines. Hybridization to restriction digests of genomic DNA suggests that Dm 25 is a moderately repetitive, conserved sequence whose copies are dispersed throughout the genome. Analysis of species other than melanogaster indicates a significant divergence in structure of sequences homologous to Dm 25 as well as a drastic reduction in amount of homology to the melanogaster sequence.     

Differential regulation of host cellular genes by HIV-1 viral protein R (Vpr): cDNA microarray analysis using isogenic virus

HIV-1 Vpr is a protein with multiple functions. It has been suggested that such pleiotropic effects by a viral protein may be mediated by its association with viral and cellular proteins or through modulation of expression of specific cellular genes. To address this, we used cDNA microarray techniques to analyze the regulation of a panel of host cellular genes by HIV-1 Vpr using isogenic HIV-1 either with or without Vpr expression. Results indicate that Vpr downregulated the expression of genes involved in cell cycle/proliferation regulation, DNA repair, tumor antigens, and immune activation factors, and upregulated many ribosomal and structural proteins. These results for the first time reveal the involvement of several potential cellular genes, which may be useful, both for understanding Vpr functions and for the development of therapeutics targeting the Vpr molecule.     

野生稻近等基因系应答低温胁迫的生理生化指标分析

为了解水稻耐冷的生理机制,该文以野生稻近等基因系耐冷水稻品种DC907和其不耐冷受体亲本9311为材料,通过对水稻幼苗低温胁迫处理,检测分析了丙二醛(MDA)、超氧阴离子(O2-)、可溶性糖以及抗氧化酶类[超氧化物歧化酶(SOD)、过氧化物酶(POD)、过氧化氢酶(CAT)和抗坏血酸过氧化物酶(APX)]等生理生化指标...     

Four rice QTL controlling number of spikelets per panicle expressed the characteristics of single Mendelian gene in near isogenic backgrounds

Development of quantitative trait loci (QTL) near isogenic lines is a crucial step to QTL isolation using the strategy of map-based cloning. In this study, a recombinant inbred line (RIL) population derived from two indica rice varieties, Zhenshan 97 and HR5, was employed to map QTL for spikelets per panicle (SPP). One major QTL (qSPP7) and three minor QTL (qSPP1, qSPP2 and qSPP3) were identified on chromosomes 7, 1, 2 and 3, respectively. Four sets of near isogenic lines (NILs) BC₄F₂ targeted for the four QTL were developed by following a standard procedure of consecutive backcross, respectively. These QTL were not only validated in corresponding NILs, but also explained amounts of phenotypic variation with much larger LOD scores compared with those identified in RILs. SPP in the four QTL-NILs expressed bimodal or discontinuous distributions and followed the expected segregation ratio of single Mendelian factor by progeny test. Finally, qSPP1, qSPP2, qSPP3 and qSPP7 were respectively mapped to a locus, 0.5 cM from MRG2746, 0.6 cM from MRG2762, 0.8 cM from RM49 and 0.7 cM from MRG4436, as co-dominant markers on the basis of progeny tests. These results indicate no matter how small effect minor QTL is, QTL may still express the characteristics of single Mendelian factor in NILs and isolation of minor QTL will be possible using high quality NILs. Pyramiding these QTL into a variety will largely enhance rice grain yield.     

Genetic variation of NBS-LRR class resistance genes in rice lines

The use of plant disease resistance (R) genes in breeding programs needs an understanding of their variation patterns. In our current study, we investigated the polymorphisms of 44 NBS-LRR class R-genes among 21 rice cultivars and 14 wild rice populations. Our data suggested that there were four basic types of variations: conserved, diversified, intermediate-diversified, and present/absent patterns. Common characteristics at a locus of conserved R-genes were: copy-number uniformity, clear divergence (long branches) with other paralogs, and highly identical alleles. On the other hand, copy-number variability, a nearly equal and non-zero branch lengths, and high levels of nucleotide diversity were observed at the loci of highly diversified R-genes. Research suggests that the ratio of diverse alleles to the total number of genes at a locus is one of the best criteria to characterize the variation pattern of an R-gene. Our data suggested that a significant genetic reduction was detected only in four present/absent R-genes, compared with the variation observed in wild rice. In general, no difference was detected between wild rice and cultivars, japonica and indica rice, or between lines from different geographic regions. Our results also suggested that R-genes were under strong selection, which shaped R-gene variation patterns. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users. Sihai Yang and Tingting Gu contributed equally to this work.     

Comparison of QTL controlling seedling vigour under different temperature conditions using recombinant inbred lines in rice (Oryza sativa)

BACKGROUND AND AIMS: Seedling vigour is one of the major determinants for stable stand establishment in rice (Oryza sativa), especially in a direct seeding cropping system. The objectives of this study were to identify superior alleles with consistent effects on seedling vigour across different temperature conditions and to investigate genotype x environmental temperature interactions for seedling vigour QTL. METHODS: A set of 282 F13 recombinant inbred lines (RILs) derived from a rice cross were assessed for four seedling vigour traits at three temperatures (25 degrees C, 20 degrees C and 15 degrees C). Using a linkage map with 198 marker loci, the main-effect QTL for the traits were mapped by composite interval mapping. KEY RESULTS: A total of 34 QTL for the four seedling vigour traits were identified. Of these QTL, the majority (82%) were clustered within five genomic regions, designated as QTL qSV-3-1, qSV-3-2, qSV-5, qSV-8-1 and qSV-8-2. All of these five QTL had small individual effects on the traits, explaining 3.1-15.8 % of the phenotypic variation with a mean of 7.3 %. QTL qSV-3-1, qSV-3-2 and qSV-8-1 showed almost consistent effects on the traits across all three temperatures while qSV-5 and qSV-8-2 had effects mainly at the 'normal' temperatures of 20 degrees C and 25 degrees C. Among the five QTL identified, all and four showed additive effects on shoot length and germination rate, respectively. The contributions of these five QTL to shoot length and germination rate were also much larger than those to the other two traits. CONCLUSIONS: A few of genomic regions (or QTL) were identified as showing effects on seedling vigour. For these QTL, significant genotype x environmental temperature interactions were found and these interactions appeared to be QTL-specific. Among the four seedling vigour traits measured, shoot length and germination rate could be used as relatively good indicators to evaluate the level of seedling vigour in rice.