[Expressions and clinical significance of GAS1, IL-1RAP and PRF1 in patients with ALK positive anaplastic large cell lymphoma].

Objective: To investigate the expressions of growth arrest-specific protein (GAS1), IL-1 receptor accessory protein (IL-1RAP) and perforin (PRF1) in patients with anaplastic lymphoma kinase positive, anaplastic large cell lymphoma (ALK+ ALCL) and their relationships with clinical significances and the prognoses of ALK+ ALCL. Methods: Twenty-six formalin-fixed paraffin-embedded (FFPE) samples of ALK+ ALCL patients who were diagnosed from January 2011 to September 2016 were collected. Twelve FFPE samples of patients with ALK+ALCL, 13 FFPE samples of patients with peripheral T cell lymphoma (not otherwise specified) (PTCL-NOS) and 8 FFPE samples of patients with angioimmunoblastic T-cell lymphoma (AITL) were used as control groups. RQ-PCR and immunohisto-chemical staining were used to detect the mRNA and protein expressions of GAS1, IL-1RAP and PRF1. The clinical data were analyzed. Results: ①The expression levels of GAS1, IL-1RAP and PRF1 gene and protein in ALK+ ALCL group were higher than those of the control groups (P<0.05), but the expression levels had no statistically significant differences between the control groups (P>0.05). ②Patients with elevated lactate dehydrogenase (LDH) (0.77 vs 1.38, z=-3.292, P=0.001) or International prognostic index (IPI)≥3(0.62 vs 1.29, z=-2.495, P=0.013) had lower expression level of GAS1. Patients with stage Ⅲ/Ⅳ disease (0.89 vs 1.18, z=-2.212, P=0.027) or IPI≥3 (0.48 vs 1.13, z=-2.008, P=0.045) had lower expression level of PRF1. IL-1RAP expression level was not associated with clinical features. ③ALK+ ALCL patients in complete remission (CR) group had higher expression levels of GAS1 and PRF1 than patients in non-remission (NR) group (P values were 0.016 and 0.009). ④Kaplan-Meier survival analysis showed that patients with high expression levels of GAS1 and PRF1 had longer median overall survival and progression-free survival than patients with low expression levels of GAS1 and PRF1. Conclusion: GAS1, IL-1RAP and PRF1 could be molecular markers for ALK+ ALCL patients. They have potential diagnostic value and can be used for differential diagnosis in some difficult cases. ALK+ ALCL patients with high expression levels of GAS1 or PRF1 have better curative effects and prognoses.

[Effects of 13-cis-retinoic acid combined with interferon-α2b in mantle cell lymphoma cell lines (Jeko-1) in vitro].

Objectives: To explore the effects of 13-cis-retinoic acid (13cRA) alone or combined with interferonα-2b (IFNα-2b) for the inhibition of cell growth and apoptosis induction of mantle cell lymphoma cell lines Jeko-1 cells. Methods: Jeko-1 cells were treated by different concentrations of 13cRA alone or combined with IFN-α2b. CCK-8 was used to measure the inhibition effects by different treatments. Cell cycles were analyzed by flow cytometry. Effects on apoptosis were assessed by staining of Annexin Ⅴ/PI. And the levels of Cyclin D1, caspase-9 and Rb proteins were measured by Western blot method. Results: 13cRA alone at different doses and its combination with IFNα-2b inhibited Jeko-1 cells growth and induced apoptosis, but the combination had higher inhibition potential and significant apoptosis rate (P<0.05) . The growth inhibition and apoptosis induction in Jeko-1 cells increased significantly with the elevation of drugs concentration and treating duration (P<0.05) . As well as the percentage of Jeko-1 cells at G(1)/G(2) phases increased (P<0.05) and cells at S phase decreased (P<0.05) , the levels of Cyclin D1 and Rb decreased with elimination caspase-9. Conclusion: 13cRA, IFN-α2b and their combined administration inhibited cells growth and induced apoptosis, decreased the cell populations at S phase and blocked the cells at G(1)/G(2) phase. Combination of the drugs may have a cooperated action. The therapeutic synergistic effects of 13cRA and IFN-α2b were assumed to lower the expression of Cyclin D1 and Rb proteins, and induce apoptosis by activating caspase-9 pathway.

Exosomes mediated transfer of lncRNA UCA1 results in increased tamoxifen resistance in breast cancer cells.

OBJECTIVE: In this study, we firstly compared the loading of urothelial carcinoma-associated 1 (UCA1) in exosomes between tamoxifen sensitive and tamoxifen resistant breast cancer cells and further investigated the role of exosomal transfer of UCA1 in the development of tamoxifen resistance in estrogen receptor (ER) positive breast cancer cells. MATERIALS AND METHODS: Exosomes were isolated from the culture medium of tamoxifen sensitive MCF-7 cells and tamoxifen resistant LCC2 cells. QRT-PCR was performed to analyze UCA1 expression in cells and exosomes. CCK-8 assay, immunofluorescence staining of cleaved caspase-3 and flow cytometric analysis of annexin V/PI staining were used to assess tamoxifen sensitivity. RESULTS: UCA1 is significantly increased not only in LCC2 cells, but also in exosomes released from LCC2 cells. The increase in exosomes is more evident than in cells. MCF-7 cells pretreated with exos/LCC2 had a significantly increased cell viability, a decreased expression of cleaved caspase-3 and a lower ratio of apoptosis after tamoxifen treatment. The exos/LCC2 with impaired UCA1 loading had significantly suppressed capability to promote tamoxifen resistance in MCF-7 cells. CONCLUSIONS: UCA1 is significantly loaded in exosomes from tamoxifen resistant LCC2 cells. Exosomes mediated transfer of UCA1 can significantly increase tamoxifen resistance in ER-positive MCF-7 cells.

[Anti-tumor effects of 13-cis-retinoic acid combined with interferon α-2b in animal model of mantle cell lymphoma].

Objective: To determine the anti-tumor effects of 13-cis-retinoic acid (13cRA) combined with interferonα-2b (IFNα-2b) in mantle cell lymphoma (MCL) animal model. Methods: The animal model of MCL was established by introducing Jeko-1 cell line into severe combined immunodeficiency disease mice. The successfully tumor-developed mice were assigned to different groups treated with negative control group (solvents), 13cRA (high dose: 200mg/kg; middle dose: 100mg/kg; low dose: 50 mg/kg) alone, IFNα-2b alone or combination of different dose of 13cRA with IFNα-2b, and positive control group (bortezomib, rituximab, cyclophosphamide), respectively. Variations of tumor volume were observed regularly. The relative tumor proliferation rate and tumor inhibition rate were calculated. Immunohistochemistry stain was used to detect the Ki-67 expression and TUNEL was applied to measure the apoptosis of tumor cells. Furthermore, the levels of Cyclin D1, caspase 9 and Rb protein were measured by Western-blot method. Results: ① The relative tumor proliferation rates (T/C%)were 30%, 37%, 32% and 33% in middle dose, high dose groups of 13cRA as well as their combination with IFN α-2b, respectively. ② Comparing with the negative control, both 13cRA at different doses and its combination with IFNα-2b remarkably inhibited the tumor growth (P<0.05), while no statistic significance existed in different dose group of 13cRA. IFN-α 2b alone didn't demonstrate the tumor-inhibition effects (P>0.05). Middle dose of 13cRA and its combination with IFN-α-2b demonstrated relatively high tumor-inhibition effects (59.2% and 62.6% respectively), which were similar to the effects in positive control (69.4%). ③ There was no statistic difference of Ki-67 in each experimental group. ④ Comparing with negative control group, all doses of 13cRA and their combinations with IFNα-2b remarkably increased the apoptosis (P<0.05), similar to the positive control group (P>0.05). However, IFNα-2b alone didn' t promote the apoptosis of tumor tissue (P=0.098). ⑤ Comparing with negative control group, IFNα-2b combined with each dose of 13cRA significantly decreased the levels of cycling D1 and procaspase-9, while increased the level of cleaved caspase-9 (P<0.05), which were similar to the positive control group (P>0.05). Nevertheless, 13cRA alone didn't demonstrate such effects. Conclusion: In the MCL animal model, IFNα-2b alone showed no effects, but combined with IFNα-2b, 13cRA displayed anti-tumor effects at different doses. The anti-tumor mechanism of 13cRA combined with IFNα-2b was probably down-regulation of the cyclin D1 expression, inhibition of cell proliferation and induction of apoptosis by activating caspase-9.

MiR-30a and miR-205 are downregulated in hypoxia and modulate radiosensitivity of prostate cancer cells by inhibiting autophagy via TP53INP1.

OBJECTIVE: MiR-30a and miR-205 are two miRNAs downregulated in prostate cancer and are involved in autophagy regulation. However, how they are downregulated in prostate cancer is still not clear. In this study, we firstly investigated the association between miR-30a and miR-205 downregulation and hypoxia in prostate cancer. Then, we further investigated the regulative effect of miR-30a on TP53INP1 and autophagy-related radiosensitivity of process cancer cells. MATERIALS AND METHODS: The expression change of miR-30a, miR-205 and Dicer after hypoxic treatment were measured in DU145 and LNCaP cells. The effect of miR-30a and miR-205 on irradiation-induced autophagy and radiosensitivity of the cancer cells were also explored. The regulative effect of miR-30a on TP53INP1 expression and the effect of miR-30a/miR-205/TP53INP1 axis on autophagy and radiosensitivity regulation were further studied. RESULTS: MiR-30a and miR-205 were downregulated under hypoxia as a result of impaired Dicer expression in DU145 and LNCaP cells. Enforced miR-30a and miR-205 expression attenuated irradiation-induced autophagy and also sensitized the cells to irradiation. Dual luciferase assay and following Western blot analysis showed that miR-30a directly targets 3'UTR of TP53INP1 and decreases its expression at protein level. Both miR-30a and miR-205 modulate radiosensitivity of prostate cancer cells at least via TP53INP1. CONCLUSIONS: This study revealed that miR-30a and miR-205 are two hypoxia responsive miRNAs, which simultaneously target TP53INP1 and suppress its expression. The miR-30a/miR-205/TP53INP1 axis is involved in autophagy and radiosensitivity regulation, which represents a potential therapeutic target for the treatment of prostate cancer.

MiR-365 participates in coronary atherosclerosis through regulating IL-6.

OBJECTIVE: This study aims to investigate the role and mechanism of miR-365 in the coronary atherosclerosis (AS). PATIENTS AND METHODS: Blood were collected from AS patients and healthy people, coronary plaque and adjacent arterial tissue were collected from AS patients. QRT-PCR method was used to detect expressions of miR-365 and IL-6 in coronary plaque, blood monocytes, and serum. Western blot was applied to detect IL-6 protein expression in coronary plaque and blood monocytes, and ELISA was used to detect IL-6 protein expression in serum. RESULTS: Compared with the normal group, IL-6 expression was significantly increased in coronary plaque, blood monocytes, and serum both in mRNA level and in protein level, while miR-365 expression was significantly decreased (p < 0.05). CONCLUSIONS: IL-6 expression was significantly up-regulated in coronary plaque, blood monocytes, and serum, whereas miR-365 expression was down-regulated. MiR-365 may regulate the pathogenesis and immune response in AS through targeting IL-6.

Roles of adrenomedullin and hypoxia-inducible factor 1 alpha in patients with varicocele.

This study aimed to assess any changes in the plasma concentrations of adrenomedullin (ADM) and hypoxia-inducible factor 1 alpha (HIF 1a) in patients with varicocele (VC). Plasma concentrations of ADM and HIF 1a were measured in brachial vein (BV) and internal spermatic vein (ISV) of 30 fertile VC subjects and 35 untreated infertile VC patients. The results demonstrated that plasma levels of ADM and HIF 1a were significantly higher in ISV than those in BV in the fertile or infertile group respectively. The values of ADM and HIF 1a in BV or ISV of the infertile group were significantly higher than in BV or ISV of the fertile group respectively. Similar changes in values of reactive oxygen metabolites (ROM) were observed. Plasma HIF 1a concentration positively correlated with ROM levels. Plasma ADM concentration positively correlated with ROM values and HIF 1a levels in the two groups. Moreover, remarkable improvement in clinical sperm parameters was observed 3 months after surgery for the infertile patients. It is concluded that ADM may participate, along with HIF 1a, in mechanisms that aid spermatogenic cells in adapting to hypoxia. These predictors may have potential in infertility development in VC patients. Furthermore, early surgical repair is extremely important for infertile VC patients with poor semen quality.

Molecular cloning and immune response analysis of putative variable lipoproteins from Mycoplasma mycoides subsp capri.

Mycoplasma mycoides subsp capri is the cause of goat "MAKePS" (Mastitis, Arthritis, Keratoconjunctivitis, Pneumonia, Septicemia) syndrome. We identified three genes (GL_ 000459; 000461; 000462) as variable lipoprotein genes in the M. mycoides subsp capri str. PG3 genome by genomic information and comparative genomic analyses. To study the role of variable lipoproteins in M. mycoides subsp capri pathogenesis and evaluate the immunogenic and protective potentials of those proteins, we constructed the expression systems and expressed the mature peptide portion of the three proteins in E. coli. We also determined the titers and opsonophagocytosis activity of total IgG antibodies and the levels of Th1 and Th2 cytokines in sera, and we ran a lymphocyte proliferation assay in mice immunized with recombinant proteins His-tag-GL000459, His-tag-GL000461, and His-tag-GL000462. These three lipoproteins induced humoral and cellular immune responses in the immunized mice. Additionally, the whole blood opsonophagocitic in vitro assay demonstrated that the antibodies produced by the immunized groups can neutralize strain PG3; consequently, these three variable lipoproteins could be the major surface antigens in M. mycoides subsp capri str. PG3.

Elevated expression of CX3C chemokine receptor 1 mediates recruitment of T cells into bone marrow of patients with acquired aplastic anaemia.

OBJECTIVE: Acquired aplastic anaemia (AA) is a T-cell-mediated, organ-specific autoimmune disease characterized by haematopoietic stem cell destruction in the bone marrow. The exact molecular mechanism of T-cell trafficking into the bone marrow is unclear in AA. Very late activation antigen-4 (VLA-4) and CX3C chemokine receptor 1 (CX3CR1) play active roles in many autoimmune diseases. Therefore, we investigated whether VLA-4 and CX3CR1 also contribute to T-cell migration into the bone marrow in acquired AA. DESIGN, SETTING AND SUBJECTS: Expression levels of CX3CR1 and VLA-4 and their ligands [fractalkine (CX3CL1) and vascular cell adhesion molecule-1 (VCAM-1)] were examined in 63 patients with AA and 21 healthy control subjects. T-cell chemotaxis and adhesion were analysed in 17 patients with severe AA. We also prospectively evaluated the expression pattern of CX3CR1 during treatment with antithymocyte globulin plus cyclosporine in 11 patients with severe AA. RESULTS: The proportion of peripheral and bone marrow CD4(+) and CD8(+) T cells expressing CX3CR1 and the level of CX3CL1 was increased in patients with AA. However, there was no significant difference in VLA-4 expression or VCAM-1 levels. Functional studies demonstrated that chemotaxis towards autologous bone marrow plasma or soluble CX3CL1 was significantly higher in T cells from AA patients and could be blocked by CX3CR1 inhibitors. CX3CR1-mediated T-cell adhesion was also upregulated in these patients. The expression of CX3CR1 was associated with the efficacy of immunosuppressive therapy. CONCLUSION: The present findings demonstrate that CX3CR1 plays a pivotal role in recruitment of T cells into the bone marrow in acquired AA and is a potential therapeutic target for treatment of this disorder.

Natural IgG antibodies in normal rabbit serum are involved in killing of the ompP2 mutant of Haemophilus parasuis SC096 strain via the classical complement pathway.

Serum resistance in Haemophilus parasuis strain SC096 has been shown to be dependent on expression of the outer membrane protein P2 (OmpP2) and loss of the ompP2 gene results in significantly greater sensitivity to both porcine and rabbit sera. However, the mechanism of complement activation by the serum sensitive ΔompP2 strain is unknown. In this study, the classical complement pathway is demonstrated to be the main pathway for killing the H. parasuis ΔompP2 strain, and not the mannan-binding lectin (MBL) or alternative pathway. In addition, absorption of antibodies against ΔompP2 strain or depletion of IgGs from serum inhibited serum killing activity, which could be restored by addition of heat-inactivated serum or purified IgGs. Western blot analysis indicated that the OmpP2 mutant could bind significantly more IgGs than the wild type strain SC096 when incubated with serum. Finally, IgGs in normal rabbit serum targeted to the OMPs, but not lipooligosaccharide (LOS) in the OmpP2 mutant strain were found to be involved in bacterial killing indicating that the bactericidal epitope(s) is in the outer membrane proteins.

Fine mapping of a major quantitative trait loci, qSSP7, controlling the number of spikelets per panicle as a single Mendelian factor in rice.

In our previous studies, one putative QTL affecting number of spikelets per panicle (SPP) was identified in the pericentromeric region of rice chromosome 7 using a recombinant inbred population. In order to define the QTL (qSPP7), RI50, a recombinant inbred line with 70% of genetic background same as the female parent of Zhenshan 97, was selected to produce near-isogenic lines for the target region in the present study. In a BC(2)F(2) population consisting of 190 plants, the frequency distribution of SPP was shown to be discontinuous and followed the expected Mendelian ratios (1:2:1 by progeny test) for single locus segregation. qSPP7 was mapped to a 0.4 cM region between SSR marker RM3859 and RFLP marker C39 based on tests of the BC(2)F(2) population and its progeny. Its additive and dominant effects on SPP were 51.1 and 24.9 spikelets, respectively. Of great interest, the QTL region also had effects on grain yield per plant (YD), 1,000 grain weight (GW), tillers per plant (TPP) and seed setting ratio (SR). Significant correlations were observed between SPP and YD (r = 0.66) and between SPP and SR (r = -0.29) in the progeny test. 1082 extremely small panicle plants of a BC(3)F(2) population containing 8,400 individuals were further used to fine map the QTL. It turns out that qSPP7 co-segregated with two markers, RM5436 and RM5499 spanning a physical distance of 912.4 kb. Overall results suggested that recombination suppression occurred in the region and positional cloning strategy is infeasible for qSPP7 isolation. The higher grain yield of Minghui 63 homozygote as compared to the heterozygote suggested that Minghui 63 homozygote at qSPP7 in hybrid rice could further improve its yield.

Genetic basis of 17 traits and viscosity parameters characterizing the eating and cooking quality of rice grain.

A recombinant inbred line population derived from a cross between Zhenshan 97 and Delong 208 was used to analyze the genetic basis of the cooking and eating quality of rice as reflected by 17 traits (or parameters). These traits include amylose content (AC), gel consistency (GC), alkali spreading value (ASV), cooked rice elongation (CRE), and 13 parameters from the viscosity profile. All the traits, except peak paste viscosity (PKV), time needed from gelatinization to peak (BAtime), and CRE, can be divided into two classes according to their interrelationship. The first class consists of AC, GC, and most of the paste viscosity parameters that form a major determinant of eating quality. The second class includes ASV, pasting temperature (Atemp) and pasting time (Atime), which characterize cooking process. We identified 26 QTL (quantitative trait locus or loci) in 2 years; nine QTL clusters emerged. The two major clusters, which correspond to the Wx and Alk loci, control the traits in the first and second classes, respectively. Some QTL are co-located for the traits belonging to the same class and also for the traits to a different class. The Wx locus also affects on ASV while the Alk locus also makes minor contributions to GC and some paste viscosity parameters. The QTL clusters on other chromosomes are similar to the Wx locus or Alk locus, although the variations they explained are relatively minor. QTL for CRE and PKV are dispersed and independent of the Wx locus. Low paste viscosity corresponds to low AC and soft gel, which represents good eating quality for most Chinese consumers; high ASV and low Atemp, together with reduced time to gelatinization and PKV, indicate preferred cooking quality. The genetic basis of Atemp, Atime, BAtime, peak temperature, peak time, paste viscosity at 95 degrees C, and final paste viscosity is newly examined to reveal a complete and dynamic viscosity profile.

Fine mapping of f5-Du, a gene conferring wide-compatibility for pollen fertility in inter-subspecific hybrids of rice (Oryza sativa L.).

Wide-compatibility varieties (WCVs), comprising a special class of rice germplasm, are able to produce fertile hybrids when crossed with both indica and japonica varieties. Dular, a landrace variety from India, has both a wide spectrum and high level of wide-compatibility when crossed with a range of indica and japonica varieties. In previous studies, an allele at the f5 locus from Dular (f5-Du) was identified as a neutral allele conferring wide-compatibility with a large effect on both pollen and spikelet fertility. Using a population of 1993 hybrid plants derived from a cross between ZS(f5-Du/f5-ZS) (F1 of near isogenic line of Zhenshan 97 containing f5-Du) and Balilla (a japonica tester), f5-Du was genetically mapped to an interval of about 1.6 cM, with 0.8 cM from both SSR markers WFPM3 and WFPR1. Combined with bioinformatic analysis, a contig map was constructed for the f5 region, consisting of five bacterial artificial chromosome (BAC) or P1 artificial chromosome (PAC) clones and spanning approximately 437 kb in length. By assaying the recombinant events in the region with markers developed using the sequence information, the f5 locus was further narrowed down to a 70 kb fragment containing nine predicted genes. The result will be very useful for cloning this gene and marker-assisted transferring of the neutral allele in rice breeding programs.

Delimitation of the rice wide compatibility gene S5 ( n ) to a 40-kb DNA fragment.

Wide compatibility varieties (WCVs) are a special class of rice (Oryza sativa L.) germplasm that produces hybrids with normal pollen and spikelet fertility when crossed with both indica and japonica subspecies. The wide compatibility gene S5 ( n ) has been used extensively in inter-subspecific hybrid breeding programs. We previously mapped the S5 locus to a 2.2-cM genomic region between RM253 and R2349 on chromosome 6, using a population of 356 F(1) plants derived from the three-way cross 02428/Nanjing11//Balilla. In this study, a chromosome walking strategy was employed to construct a physical map covering this genomic region using these two closest markers as the starting points. A physical map consisting of six overlapping BAC clones was formed, spanning a genomic region of 540-kb in length. By analyzing recombination events from a population of 8,000 F(1) plants derived from a three-way cross based on near isogenic lines of the S5 locus, the S5 locus was localized to a DNA fragment of 40-kb in length, flanked by two shotgun subclones, 7B1 and 15D2. Sequence analysis of this fragment predicted five open reading frames, encoding xyloglucan fucosyltransferases, dnak-type molecular chaperone BiP, a putative eukaryotic aspartyl protease, and a hypothetical protein. This result will be very useful in molecular cloning of the S5 ( n ) allele and marker-assisted transferring of the wide compatibility gene in rice breeding programs.

Identification and confirmation of three neutral alleles conferring wide compatibility in inter-subspecific hybrids of rice (Oryza sativa L.) using near-isogenic lines.

Wide-compatibility varieties (WCVs) are a special class of rice germplasm that is able to produce fertile hybrids when crossed to both indica and japonica subspecies. Previous studies determined 'Dular' and 02428 as two WCVs and identified a number of QTLs as having large effects on fertility of inter-subspecific hybrids. In this study, we developed five near-isogenic lines (NILs) for three of the QTLs, f5, f6 and S5, by backcrossing and marker-assisted selection, using "Dular" and 02428 as the donors and "Zhenshan 97" as the recipient. Three of the NILs each carried one introgressed allele, and two NILs each carried two introgressed alleles in combinations. The NILs were testcrossed to an indica tester "Nanjing 11" and a japonica tester "Balilla". The results showed that the f5 allele from "Dular"(f5-Du) is a neutral allele conferring wide compatibility, with a large effect on both pollen and spikelet fertility, and the f6 allele from "Dular" (f6-Du) is a neutral allele for spikelet fertility with smaller effect. The S5 allele from 02428 (S5-08) was confirmed to be a neutral allele for spikelet fertility. It is likely that f6 and S5 are the same locus as deduced by their genomic locations and effects. The results also showed that even in combination, two neutral alleles of different loci were not able to produce normal fertility hybrids in typical indica-japonica crosses. The implications of the findings in rice breeding programs are discussed.

Localization of pms3, a gene for photoperiod-sensitive genic male sterility, to a 28.4-kb DNA fragment.

Photoperiod-sensitive genic male-sterile (PSGMS) rice, in which pollen fertility is regulated by day-length, originally arose as a natural mutant in the rice cultivar Nongken 58 (Oryza sativa ssp. japonica). Previous studies identified pms3 on chromosome 12 as the locus of the original PSGMS mutation. In this study we have assigned the pms3 locus to a 28.4-kb DNA fragment by genetic and physical mapping. A cross between Nongken 58S (PSGMS line) and DH80 was used to produce an F2 population of about 7000 plants, from which 892 highly sterile individuals were obtained for recombination analysis. By analyzing recombination events in the sterile individuals using a total of 157 RFLP probes from a BAC contig covering the pms3 region, the pms3 locus was localized to a sub-region of less than 1.7 cM. Further analysis of recombination events using 49 additional probes isolated from this sub-region identified markers flanking the pms3 region on each side; these markers are only 28.4-kb apart. Sequence analysis of this fragment predicted the presence of five ORFs, found high homology with two ESTs in public databases, and detected three SNPs between the mutant and the wild-type parents, which may be helpful for identifying a candidate gene for pms3.

The main effects, epistatic effects and environmental interactions of QTLs on the cooking and eating quality of rice in a doubled-haploid line population.

Amylose content (AC), gel consistency (GC) and gelatinazation temperature (GT) are three important traits that influence the cooking and eating quality of rice. The objective of this study was to characterize the genetic components, including main-effect quantitative trait loci (QTLs), epistatic QTLs and QTL-by-environment interactions (QEs), that are involved in the control of these three traits. A population of doubled haploid (DH) lines derived from a cross between two indica varieties Zhenshan 97 and H94 was used, and data were collected from a field experiment conducted in two different environments. A genetic linkage map consisting of 218 simple sequence repeat (SSR) loci was constructed, and QTL analysis performed using QTLMAPPER 1.6: resolved the genetic components into main-effect QTLs, epistatic QTLs and QEs. The analysis detected a total of 12 main-effect QTLs for the three traits, with a QTL corresponding to the Wx locus showing a major effect on AC and GC, and a QTL corresponding to the Alk locus having a major effect on GT. Ten digenic interactions involving 19 loci were detected for the three traits, and six main-effect QTLs and two pairs of epistatic QTLs were involved in QEs. While the main-effect QTLs, especially the ones corresponding to known major loci, apparently played predominant roles in the genetic basis of the traits, under certain conditions epistatic effects and QEs also played important roles in controlling the traits. The implications of the findings for rice quality improvement are discussed.

Genetic dissection of embryo sac fertility, pollen fertility, and their contributions to spikelet fertility of intersubspecific hybrids in rice.

The partial sterility of hybrids has been a major barrier for utilization of the strong heterosis expressed in hybrids between Oryza sativa ssp. indica and O. sativa ssp. japonica. Wide-compatibility varieties, comprising a special class of germplasm, are able to produce fertile hybrids when crossed to both indica and japonica varieties. However, all the work on wide compatibility and majority of studies on indica/japonica hybrid sterility reported so far were based only on spikelet fertility; thus, it is not known to what extent male and female gamete abortions influence hybrid sterility. In this study, we investigated pollen fertility, embryo sac fertility, and spikelet fertility in an F1 population of 202 true hybrid plants derived from a three-way cross ('02428'/'Nanjing 11'//'Balilla'). A partial regression analysis showed that the pollen and embryo sac fertility contributed almost equally to spikelet fertility. QTL analysis based on a linkage map of 191 polymorphic marker loci identified two QTLs for pollen fertility, one QTL for embryo sac fertility, and three QTLs for spikelet fertility. The S5 locus, previously identified as a locus for wide compatibility by spikelet fertility analysis, is a major locus for embryo sac fertility, and a QTL on chromosome 5 had a major effect on pollen fertility. These two loci coincided with the two major QTLs for spikelet fertility. The study also detected a QTL on chromosome 8, showing a large effect on spikelet fertility but no effect on either pollen or embryo sac fertility. Very little interaction among the QTLs was detected. The implications of the findings in rice breeding programs are discussed.

Comparison of quantitative trait loci controlling seedling characteristics at two seedling stages using rice recombinant inbred lines.

A better understanding of the genetics of seedling characteristics in rice could be helpful in improving rice varieties. Zhenshan 97 and Minghui 63, the parents of Shanyou 63, an elite hybrid developed during the last decade in China, vary greatly with respect to their physiological and morphological traits at the seedling growth stage. In this study, we used a population of 240 recombinant inbred lines derived from a cross between Zhenshan 97 and Minghui 63 to identify quantitative trait loci (QTL) for seedling characteristics. All plant material was grown in hydroponic culture. Data for the following characters were collected at 30 days and 40 days post-sowing: plant height, shoot dry matter weight (SDW), maximum root length, root dry weight (RDW), total dry weight, and root-shoot ratio (the ratio of SDW to RDW). Analysis using composite interval mapping detected 16 QTL for the six traits in 30-day-old seedlings. Of these 16 QTL, Minghui 63 alleles increased trait values at only two of them. The QTL in the vicinity of R3166 on chromosome 5 simultaneously influenced PH, SDW, MRL, RDW, and TDW in the same direction. Twenty QTL were detected for the same traits in the 40-day-old seedlings. However, at this stage Minghui 63 alleles increased trait values at eight QTL. The QTL linked to R3166 also affected PH, SDW, MRL, RDW, and TDW. Only four QTL were common to the two stages. These results clearly indicate that different genes (QTL) control the same traits during different time intervals. Zhenshan 97 alleles had positive effects during the first 30 days of seedling growth, but thereafter the positive effects of Minghui 63 alleles on seedling growth gradually became more pronounced.