Minor Loci Research Articles

Genome-wide association mapping of phenotypic traits subject to a range of intensities of natural selection in Timema cristinae.

The genetic architecture of adaptive traits can reflect the evolutionary history of populations and also shape divergence among populations. Despite this central role in evolution, relatively little is known regarding the genetic architecture of adaptive traits in nature, particularly for traits subject to known selection intensities. Here we quantitatively describe the genetic architecture of traits that are subject to known intensities of differential selection between host plant species in Timema cristinae stick insects. Specifically, we used phenotypic measurements of 10 traits and 211,004 single-nucleotide polymorphisms (SNPs) to conduct multilocus genome-wide association mapping. We identified a modest number of SNPs that were associated with traits and sometimes explained a large proportion of trait variation. These SNPs varied in their strength of association with traits, and both major and minor effect loci were discovered. However, we found no relationship between variation in levels of divergence among traits in nature and variation in parameters describing the genetic architecture of those same traits. Our results provide a first step toward identifying loci underlying adaptation in T. cristinae. Future studies will examine the genomic location, population differentiation, and response to selection of the trait-associated SNPs described here.

Quantitative Trait Loci Underlying Partial Resistance to Cercospora sojina Race 2 Detected in Soybean Seedlings in Greenhouse Assays

Cercospora sojina (Hara), an air-borne pathogen, infects soybean [Glycine max (L.) Merr.] leaves causing frog-eye leaf spot (FLS). Three major genes (Rcs1-3) underlie resistance to the major races of FLS but two were not yet mapped. In addition quantitative trait loci provide partial resistance to many strains. FLS race 2 was an isolate first collected in the 1950’s when damaging FLS first arose. ‘Essex’ was partially resistant while ‘Forrest’ was partially susceptible to mixed races of FLS. The objective here was to identify quantitative trait loci underlying resistance to FLS race 2 in the greenhouse using recombinant inbred lines (RILs) derived from the cross of Essex by Forrest. C. sojina race 2 (ATCC 44531) was used to induce leaf symptoms on one hundred F5:14 RILs derived from the cross of Essex by Forrest. The leaf symptoms were measured at 21 days after manual infestation by wounding (dai) and again at 42 dai to show resistance to reinfestation of new leaves from the primary lesions without wounding. Bags over leaves were not used to better simulate field conditions. However, there was no significant correlation between FLS severity at 21 and 42 dai (r =0.08 and P= 0.005). At 21 dai there was a strongly significant QTL near Satt319 on LG C2 (chromosome 7; LOD 3.8; R2 52%) where the Essex allele reduced leaf symptoms by 0.7 units. At 42 dai there was a strongly significant QTL near Satt632 on LG A2 (chromosome 8; R2 was 15%; LOD was 3.6) where the Essex allele reduced leaf symptoms by 0.4 units. Neither locus mapped to the location of Rcs3. By ANOVA thirteen additional minor loci were detected on LGs A1, B1, F, G, H, I, J, K, L, M and O. At two loci (LG B1 and O) the Forrest allele appeared to reduce FLS at both 21 and 42 dai. Eight loci may have reduced FLS at 21 dai (0.006 < P < 0.049; 4% < R2 > 9%) of which 5 had beneficial alleles from Forrest. Seven loci may have reduced FLS at 42 dai (0.001 < P < 0.04; 4% < R2 < 15%) of which 4 had beneficial alleles from Forrest. Therefore, quantitative resistance to race 2 of FLS was inferred to have major loci contributions from Essex and minor loci contributions from both Forrest and Essex. Resistance was dependent on plant age. Breeding and selection for FLS will be complex and may be more efficient with the markers, germplasm and models of inheritance reported here.

Syngeneic and Allogeneic Hematopoietic Stem Cell Transplantation In Mice With Myelodysplastic Syndrome

The myelodysplastic syndromes (MDS) are clonal hematopoietic malignancies characterized by dysplasia, ineffective hematopoiesis and a propensity for progression to acute myeloid leukemia (AML). Allogeneic hematopoietic stem cell transplantation (HSCT) remains the only curative therapy for the majority of patients. However, overall survival (OS) of patients with MDS following allogeneic HSCT is only about 40%, due to both relapse and non-relapse mortality (NRM) including graft versus host disease (GVHD). Available data suggests that long-term survival following HSCT for MDS is due both to myeloablative therapy and a graft versus tumor (GVT) effect. Mice that express a NUP98-HOXD13 (NHD13) transgene develop MDS with virtually 100% penetrance. In order to develop a pre-clinical model for the study of MDS HSCT, we transplanted NHD13 mice, which are bred on a C57 Bl6 background, with bone marrow harvested from syngeneic C57Bl6 donors. Sub lethally irradiated (650 rad) recipient NHD13 mice transplanted with syngeneic donor cells relapsed early, with no therapeutic benefit in terms of hematologic parameters in peripheral blood or survival. However, lethally irradiated (1000 rad) recipient mice that were transplanted with syngeneic donor bone marrow (BM) showed complete normalization of peripheral blood counts significantly enhanced survival (median survival of 15 months) compared with non-transplanted NHD13 mice (median survival 10 months). Although there were no detectable MDS cells for up to 38 weeks post-transplant, all mice eventually relapsed and died. In order to determine if a GVT effect could enhance survival, we performed 3 types of allogeneic HSCT with donor BM that was mismatched at minor histocompatibility antigen loci (C3H.SW x C57Bl6 donors); donor BM only, donor BM with donor splenocytes (6 x 10E06 CD3+ T cells), and donor BM with donor regulatory T cells (Treg). None of these forms of allogeneic HSCT let to enhanced survival compared to that achieved with syngeneic HSCT. The early relapse rate for allogeneic HSCT with donor BM only was decreased compared to the syngeneic HSCT group (8.3% vs 28% at post-transplantation week 6 and 17% vs 43% at post-transplantation week 16); however, the relapse rate at 38 weeks was similar between the two groups (83.3% vs 85.7%). Adding donor splenocytes, containing reactive T-cells, dramatically decreased the relapse rate, such that the relapse rate was only 20% at post-transplantation week 38, suggesting a GVT effect. This GVT effect was accompanied by a severe GVH effect, and OS was not different between the allogeneic BM + splenocyte and the syngeneic HSCT groups. In an attempt to induce a GVT effect without a severe GVHD, we transplanted allogeneic Treg cells along with allogeneic BM, however, survival and relapse rates were similar to those with allogeneic BM only. Taken together, these findings suggest that a lethal dose of ionizing radiation (1000 rads) is insufficient to eradicate the MDS initiating cell, and that transplantation of donor CD3+ splenocytes leads to decreased relapse rates, but at the cost of severe GVHD. We suggest that the NHD13 mice are a feasible pre-clinical model for the study of HSCT for MDS. Disclosures:No relevant conflicts of interest to declare.

Close To Clinics: Acute Gvhd In a Novel Chemotherapy Based Minor Mismatch Transplantation Model

GVHD (graft-vs-host disease) is one of the major complications after allogeneic hematopoietic stem cell transplantation leading to substantial morbidity and mortality. Several murine models are used to investigate this systemic inflammatory disease in vivo and to identify possible targets for clinical treatment. However, current well-established murine GVHD models have their clinical limitations as they are based on major histocompatibility mismatches and only lethal irradiation as conditioning. Development of new treatment options would be forwarded by the availability of a more clinically relevant murine model.To reflect the clinical situation of transplantation and GVHD, we established a new murine GVHD model which is based on Chemotherapy conditioning and MHC-matched bone marrow transplantation (BMT). In LP/J -> C57BL/6 mouse model, our chemotherapy transplantation protocol resulted in stable full donor chimerism and development of acute GVHD.C57BL/6 recipients were conditioned with a 7-day busulfan-cyclophosphamide Chemotherapy protocol. Mice received for 5 days 20 mg/kg/day busulfan intraperitoneally (i.p.) and the last three days additionally 100 mg/kg/day cyclophosphamide. After a two-day resting phase, recipients were transplanted with 1.5 x 107 bone marrow and 2 x 106 splenic T cells from LP/J donors. Recipients showed good engraftment with already 80 % engraftment in peripheral blood at day 15 after BMT. 90 % donor chimerism in peripheral blood and bone marrow could be shown already at day 30 after BMT.LP/J and C75BL/6 mice share the same haplotype (H2b) with only mismatches at different minor histocompatibility loci. As in clinical BMT, GVHD still arises after MHC-matched transplantation because of multiple minor mismatches. We could show in our LP -> C57BL/6 model typical features of acute GVHD. Allogeneic transplanted animals showed significant decreased survival compared to syngeneic transplanted animals (Figure 1A). GVHD animals exhibited GVHD-typical weight loss (Figure 1B) and a significant increased clinical GVHD index consisting of five clinical parameters: weight loss, posture, activity, fur and skin (Figure 1C). Our model showed a strong skin phenotype, especially between day 15 and 25 after BMT extensive scurf spread over the whole body combined with fur loss. Pronounced weight loss and highest clinical GVHD index were monitored between day 15 and 25, implicating this period as acute phase of GVHD. Histopathologic analysis of GVHD organs (large bowel, liver and skin) confirmed acute GVHD symptoms in our model as histopathological scores after Lerner (1974,Transplant Proc 6:367-371) were significantly increased in GVHD animals compared to BMT recipients without GVHD (Figure 1D). [Display omitted] We next characterized systemic inflammation in our model by determining the number of circulating inflammatory cells in peripheral blood at different time points by flow cytometry. CD8+ T cells were significantly increased in GVHD animals in acute phase (day 15 after BMT), whereas CD4+ T cells were elevated in late phase (day 50-60 after BMT). These data suggests, that in our model two inflammatory phases occur, an early acute CD8-driven and a late CD4-driven phase.Finally, we could demonstrate GVHD-typical T cell infiltration in GHVD target organs in acute phase (Figure 2). In large and small bowel, liver and skin CD4 and CD8 infiltration was significantly elevated in GVHD animals, however, CD8 infiltration was more prominent. We conclude that CD8 T cells play a prominent role in acute phase of GVHD in our model. [Display omitted] In summary, we could establish a novel chemotherapy based minor mismatch GVHD model which shows good engraftment, typical features of acute GVHD and systemic and target organ specific inflammation. Our murine GVHD model closely resembles the clinical situation of MHC-matched stem cell transplantation and may help to better understand pathogenic mechanisms in GVHD and develop new treatment options. Disclosures:No relevant conflicts of interest to declare.

Trends of karyotypical evolution in the pearl cichlid, Geophagus brasiliensis, from southern Brazil

Chromosomal rearrangements such as inversions can facilitate speciation even in the presence of gene flow. The present study aims to analyze the karyotypic variation in six populations of Geophagus brasiliensis from southern Brazil. All specimens showed 2n=48 chromosomes, but three karyotypes were found to have one, two or three pairs of submetacentric chromosomes. Although G. brasiliensis did not exhibit variation in the diploid number, it presented a wide interpopulational variation mainly regarding the karyotype formula and specific chromosomal markers. Differences in the location of the major and minor rDNA loci were observed among the populations. Moreover, different patterns were observed in the distribution of the constitutive heterochromatin, presenting intra- and interpopulational variation. This supports the hypothesis that this taxon represents a complex species or that cryptic species are included in this group, indicating a possibleprocess of sympatric speciation. By potentially restricting gene flow between heterokaryotypes, the segregating chromosome rearrangements we describe for G. brasiliensis may play a role in diversification in this species complex.

Identification of multiple interacting alleles conferring low glycerol and high ethanol yield in Saccharomyces cerevisiae ethanolic fermentation

BackgroundGenetic engineering of industrial microorganisms often suffers from undesirable side effects on essential functions. Reverse engineering is an alternative strategy to improve multifactorial traits like low glycerol/high ethanol yield in yeast fermentation. Previous rational engineering of this trait always affected essential functions like growth and stress tolerance. We have screened Saccharomyces cerevisiae biodiversity for specific alleles causing lower glycerol/higher ethanol yield, assuming higher compatibility with normal cellular functionality. Previous work identified ssk1E330N…K356N as causative allele in strain CBS6412, which displayed the lowest glycerol/ethanol ratio.ResultsWe have now identified a unique segregant, 26B, that shows similar low glycerol/high ethanol production as the superior parent, but lacks the ssk1E330N…K356N allele. Using segregants from the backcross of 26B with the inferior parent strain, we applied pooled-segregant whole-genome sequence analysis and identified three minor quantitative trait loci (QTLs) linked to low glycerol/high ethanol production. Within these QTLs, we identified three novel alleles of known regulatory and structural genes of glycerol metabolism, smp1R110Q,P269Q, hot1P107S,H274Y and gpd1L164P as causative genes. All three genes separately caused a significant drop in the glycerol/ethanol production ratio, while gpd1L164P appeared to be epistatically suppressed by other alleles in the superior parent. The order of potency in reducing the glycerol/ethanol ratio of the three alleles was: gpd1L164P > hot1P107S,H274Y ≥ smp1R110Q,P269Q.ConclusionsOur results show that natural yeast strains harbor multiple specific alleles of genes controlling essential functions, that are apparently compatible with survival in the natural environment. These newly identified alleles can be used as gene tools for engineering industrial yeast strains with multiple subtle changes, minimizing the risk of negatively affecting other essential functions. The gene tools act at the transcriptional, regulatory or structural gene level, distributing the impact over multiple targets and thus further minimizing possible side-effects. In addition, the results suggest polygenic analysis of complex traits as a promising new avenue to identify novel components involved in cellular functions, including those important in industrial applications.

Quantitative trait locus mapping reveals conservation of major and minor loci for powdery mildew resistance in four sources of resistance in mungbean [Vigna radiata (L.) Wilczek

Powdery mildew (PM) is a common and serious disease of mungbean [Vigna radiata (L.) Wilczek]. A few quantitative trait loci (QTL) for PM resistance in mungbean have been reported. The objective of this study was to locate QTL for PM resistance in two resistant accessions V4718 and RUM5. Simple sequence repeat markers were analyzed in an F2 population from a cross between Kamphaeng Saen 1 (KPS1; susceptible to PM) and V4718 (resistant to PM), and in F2 and BC1F1 populations from a cross between Chai Nat 60 (CN60; susceptible to PM) and RUM5 (resistant to PM). Progenies of 134 F2:3 and F2:4 lines derived from KPS1 × V4718, and 190 F2:3 and 74 BC1F1:2 lines derived from CN60 × RUM5 and CN60 × (CN60 × RUM5), respectively, were evaluated for response to PM under field conditions. Multiple interval mapping identified a major QTL on linkage group (LG) 9 and two minor QTL on LG4 for the resistance in V4718, and detected two major QTL on LG6 and LG9 and one minor QTL on LG4 for the resistance in RUM5. Comparative linkage analysis of the QTL for PM resistance in this study and in previous reports suggests that the resistance QTL on LG9 in V4718, RUM5, ATF3640 and VC6468-11-1A are the same locus or linked. One QTL on LG4 is the same in three sources (V4718, RUM5 and VC1210A). Another QTL on LG6 is the same in two sources (RUM5 and VC6468-11-1A). In addition, one QTL in V4718 on LG4 appears to be a new resistance locus. These different resistance loci will be useful for breeding durably PM-resistant mungbean cultivars.

Identification of genomic loci associated with crown rust resistance in perennial ryegrass (Lolium perenne L.) divergently selected populations

The inheritance of crown rust resistance in perennial ryegrass is complex with both major and minor quantitative trait loci (QTL) being detected on all seven linkage groups. However, QTL mapping populations have only few segregating alleles, limiting the transferability of results to other materials. In this study, a synthetic population was developed from four crown rust resistant and susceptible parents as starting material for a divergent selection experiment of crown rust resistance to be closer to practice in plant breeding programs, and to identify genome regions relevant across a broader range of genotypes. Following three cycles of directional selection, perennial ryegrass populations were produced with a two-fold difference in average rust resistance. Divergently selected populations were genotyped at 7 resistance gene analog-derived expressed sequence tag (RGA-derived EST) as well as 15 simple sequence repeat (SSR) loci. A test for selective neutrality (Waples test), which tests the hypothesis of genetic drift versus selection, identified significant differences in allele frequencies for 7 loci (32%). The selection effect was bidirectional with the same loci showing significant response in both positively and negatively selected populations. A region under selection represented by markers LpSSR006 and EST13 on linkage group (LG) 4 was further confirmed by colocation with two separate QTL for crown rust resistance in a VrnA, a two-way pseudo-testcross mapping population. This suggests suitability of alleles identified for introgression into perennial ryegrass germplasm, where quantitative resistance to crown rust is desired.

Quantitative trait analysis of yeast biodiversity yields novel gene tools for metabolic engineering

Engineering of metabolic pathways by genetic modification has been restricted largely to enzyme-encoding structural genes. The product yield of such pathways is a quantitative genetic trait. Out of 52 Saccharomyces cerevisiae strains phenotyped in small-scale fermentations, we identified strain CBS6412 as having unusually low glycerol production and higher ethanol yield as compared to an industrial reference strain. We mapped the QTLs underlying this quantitative trait with pooled-segregant whole-genome sequencing using 20 superior segregants selected from a total of 257. Plots of SNP variant frequency against SNP chromosomal position revealed one major and one minor locus. Downscaling of the major locus and reciprocal hemizygosity analysis identified an allele of SSK1, ssk1E330N…K356N, expressing a truncated and partially mistranslated protein, as causative gene. The diploid CBS6412 parent was homozygous for ssk1E330N…K356N. This allele affected growth and volumetric productivity less than the gene deletion. Introduction of the ssk1E330N…K356N allele in the industrial reference strain resulted in stronger reduction of the glycerol/ethanol ratio compared to SSK1 deletion and also compromised volumetric productivity and osmotolerance less. Our results show that polygenic analysis of yeast biodiversity can provide superior novel gene tools for metabolic engineering.

FISH of 5S rDNA and telomeric (TTAGGG) n repeats in normal and translocated populations of the frog Quasipaa boulengeri (Anura, Ranidae)

Quasipaa boulengeri, a spiny frog, is widely distributed in the low mountain regions, around Sichuan Basin. Our previous study revealed five karyotypes, caused by a translocation, that are randomly distributed throughout different populations. 5S rDNA and telomere sequence (TTAGGG)n are potential good markers for chromosome identification and karyological evolution. In this study, we examined the sequences of 14 populations using fluorescence in situ hybridization (FISH) to detect if there is any variation between karyologically normal and translocated populations. 5S rDNA loci were located at the same position on chromosomes 1 in 7 translocated populations. In two of the seven normal populations, 5S rDNA also occurred on chromosome 5 in addition to chromosome 1. Our findings further indicate that the 5S rDNA on No. 1 most likely represents the ancestral condition, while the minor loci represent the derived state. Signal density variations of the 5S rDNA were observed beteween homologous chromosomes or sister chromatids of pair 1 in both normal and translocated populations. Telomere sequences were identically located on all ends of the 26 chromosomes in seven rearranged populations, however, no ITSs were observed on the translocated chromosomes 1 and 6. Two of the six normal populations were found to contain ITSs which indicates that populations with translocation events diverged prior to those with ITSs rearrangements. In the KKS and BF populations, the ITSs of chromosome 3 are not always found on both homologues. Inter-chromosomal signal strength of telomeric sequences commonly differs within all populations.

A Critical Role of MyD88 Signaling in Donor T Cells for Graft-Versus-Host Disease (GVHD) and Graft-Versus-Leukemia Effect (GVL) After Experimental Allogeneic Hematopoietic Stem Cell Transplantation (allo-HSCT)

AbstractAbstract 1893The therapeutic potential of allogeneic hematopoietic stem cell transplantation (allo-HSCT) relies on the graft-versus-leukemia effect (GVL) to eradicate residual tumor cells by immunologic mechanisms. However, graft-versus-host disease (GVHD) remains the major toxicity of allo-HSCT. Alloreactive donor T cells are important effector cells in the development of GVHD, and proinflammatory cytokines enhance the generation of donor antihost cytotoxic function. Myeloid differentiation factor (MyD88) is a cytoplasmic adaptor molecule essential for integrating and transducing the signals generated by the Toll-like receptor (TLR) family. TLR engagement on professional antigen-presenting cells induces their maturation, resulting in optimal T-cell activation. However, recent advances indicate that the adjuvant effects of certain TLR agonists may also be attributed to the activation of TLRs and MyD88 directly in T cells. Both CD4 and CD8 T cells express functional TLRs. It remains to be defined whether direct TLR signaling on donor T cells is critical for GVHD or GVL activity.We used C57BL/6 (H-2b) → B6D2F1 (H-2b/d) experimental allo-HSCT model, which differs at major and minor histocompatibility loci, to address the role of donor T cell MyD88 signaling on GVHD and GVL. Lethally irradiated recipient mice were transplanted TCD-BM (5 × 106) together with either wild-type (WT) or MyD88 knock out (KO) mice spleen T cells (1 × 106) on day 0 and then host-type P815 mastocytoma or L1210 leukemia (H-2d) cells were injected either intravenously (3 × 103) or subcutaneously (1 × 106) on day 1 to generate a GVHD/GVL model. First of all, clinical GVHD scores were comparable between recipients of WT T cells and MyD88 KO T cells. At 70 days post-allo-HSCT, 50 % of allogeneic recipients of WT T cells died due to severe GVHD, but necropsy showed no evidence of tumor. In contrast, 83.5% of those of MyD88 KO T cells died with gross evidence of tumors (P<.05). Moreover, subcutaneous tumors in the allogeneic recipients receiving MyD88 KO T cells exhibited markedly increased growth in vivo compared to those receiving WT T cells (tumor volume on day 41, 15205.6 vs. 373.9 mm3, P<.01). GVHD mortality is critically dependent on donor CD4 T cells in this donor/recipient strain combination (B6 → B6D2F1) and CD8 T cells that mediate cytotoxicity are more potent effectors of GVL. The percentages of donor T cells to undergo proliferation or apoptosis in response to alloantigens in vivo between the two T cell types was examined; apoptosis of CD8 T cells in recipients of MyD88 KO T cells was significantly enhanced compared to those of WT T cell recipients (P<.01) whereas apoptosis of CD4 T cells was comparable between two groups. Resultingly, the percentages of CD8 T cells in recipients of MyD88 KO T cells were significantly lower (P<.01). We next examined the effects of MyD88 signaling in donor T cells on cytolytic activity to host antigens. Splenocytes harvested from WT mice showed stronger cytolytic activity against P815 targets compared to those from MyD88 KO mice (P<.01). After allogeneic mixed leukocyte reaction, responder T cells from MyD88 KO mice showed markedly reduced IFN-γ, MCP-1 and IL-17A production with a significant augmentation in IL-10 secretion. We further evaluated the effect of T-cell MyD88 deficiency on GVL mediated by the intensity of total body irradiation (TBI) conditioning (1300 vs. 900 cGy, Exp Hematol 2011; 39: 1018–29). Enhanced GVL in the allogeneic recipients receiving 1300 cGy TBI was not shown in the recipients of MyD88 KO T cells.In summary, these results highlight a critical role for MyD88 signaling in T-cell activation and cytotoxicity, offering the opportunity for improving GVL activity by targeting TLR-MyD88 signaling within donor T cells. Furthermore, these data demonstrated that MyD88 deficiency in T cells can impair cytolytic function or subsequent GVL activity of CD8 T cells without significant change in the severity of CD4-dependent GVHD. This difference is attributed to the fact that MyD88 deficiency in T cells causes an enhanced apoptosis of donor CD8 T cells but not donor CD4 T cells in vivo after HSCT. Disclosures:No relevant conflicts of interest to declare.

Marker-assisted development and characterization of a set of Triticum aestivum lines carrying different introgressions from the T. timopheevii genome

A set of common wheat introgression lines carrying one or two introgressions from Triticum timopheevii was produced by means of marker-assisted backcross selection. The starting material consisted of two BC1F20 (T. aestivum*2/T. timopheevii) lines with resistance to leaf rust, stem rust, powdery mildew, spot blotch, and loose smut and containing multiple 1At, 2At, 2G, 3AtL, 3GL, 4GL, 5AtL, 5GL, and 6G T. timopheevii chromosome fragments. The two lines were crossed with, and backcrossed three times to common wheat cultivar Saratovskaya 29. In total, 275 BC2F1 and BC3F2 plants were characterized by microsatellite markers and in situ hybridization. Molecular and cytological analyses revealed 38 plants with a single introgression from chromosomes 2G, 5GL, or 6G of T. timopheevii and 72 plants, each with two introgressions, among them three plants carrying a T. timopheevii translocation involving the D genome (2DS.2GL). It was observed that the lengths of fragments introgressed from the At genome were more than halved in the BC2 generation, while the lengths of 2G and 5GL introgressed fragments were only slightly reduced after the third backcross. The introgression lines were tested for resistance to the native Puccinia triticina population of the Western Siberian region of Russia. Lines with a single introgressed 5GL region carrying the major leaf rust resistance locus, QLr.icg-5B, were completely resistant. The presence of two minor resistance loci, QLr.icg-2A and QLr.icg-1A, suppressed disease development and reduced the number of urediniospores by up to 25 % but did not lead to a hypersensitive response. The introgression lines therefore constitute promising sources of new resistance to Puccinia triticina.

Association of Freezing Tolerance to LpCBFIIIb and LpCBFIIIc Gene Polymorphism in Perennial Ryegrass Accessions

ABSTRACTPerennial ryegrass (Lolium perenne L.) is considered a premier turfgrass and forage grass worldwide yet susceptibility to freezing damage limits its use. C‐repeat binding factor (CBF) dehydration‐responsive element‐binding protein (DREB) related genes are considered important for the regulation of abiotic stress in plants. In this study, CBF DREB‐related genes in perennial ryegrass, also known as LpCBF genes, were resequenced from cultivated and landrace plants from a worldwide collection. A total of 109 plants survived clonal propagation and were tested for freezing tolerance. The resulting data was subjected to mixed model analysis to determine whether the freezing tolerance is related to single nucleotide polymorphism (SNP) and indel markers within two genes, LpCBFIIIb and LpCBFIIIc. One major quantitative trait locus (QTL) was discovered in LpCBFIIIc for freezing tolerance, with the majority of the plants possessing the superior allele. Several minor loci were also discovered in this gene, but no significant loci were discovered in LpCBFIIIb.

Donor–Recipient Sex Mismatch in Kidney Transplantation

The lack of reliable human proxies for minor (ie, non-HLA) histocompatibility loci hampers the ability to leverage these factors toward improving transplant outcomes. Despite conflicting reports of the effect of donor-recipient sex mismatch on renal allografts, the association between acute rejection of renal allografts and the development of human alloantibodies to the male H-Y antigen suggested to us that donor-recipient sex mismatch deserved re-evaluation. To evaluate whether the relationships between donor sex and allograft failure differed by recipient sex. We studied recipients of deceased-donor (n = 125,369) and living-donor (n = 63,139) transplants in the United States Renal Data System. Using Cox proportional hazards models stratified by donor type, we estimated the association between donor-recipient sex mismatch and death-censored allograft failure with adjustment for known risk factors, with and without the use of multiple imputation methods to account for potential bias and/or loss of efficiency due to missing data. The advantage afforded by male donor kidneys was more pronounced among male than among female recipients (8% vs 2% relative risk reduction; interaction P < 0.01). This difference is of the order of magnitude of several other risk factors affecting donor selection decisions. Donor-recipient sex mismatch affects renal allograft survival in a direction consistent with immune responses to sexually determined minor histocompatibility antigens. Our study provides a paradigm for clinical detection of markers for minor histocompatibility loci.

Genetic mapping of two QTL from the wild tomato Solanum pimpinellifolium L. controlling resistance against two-spotted spider mite (Tetranychus urticae Koch)

A novel source of resistance to two-spotted spider mite (Tetranychus urticae Koch) was found in Solanum pimpinellifolium L. accession TO-937 and thereby a potential source of desirable traits that could be introduced into new tomato varieties. This resistance was found to be controlled by a major locus modulated by minor loci of unknown location in the genome of this wild tomato. We first applied a bulked segregant analysis (BSA) approach in an F(4) population as a method for rapidly identifying a genomic region of 17 cM on chromosome 2, flanked by two simple sequence repeat markers, harboring Rtu2.1, one of the major QTL involved in the spider mite resistance. A population of 169 recombinant inbred lines was also evaluated for spider mite infestation and a highly saturated genetic map was developed from this population. QTL mapping corroborated that chromosome 2 harbored the Rtu2.1 QTL in the same region that our previous BSA findings pointed out, but an even more robust QTL was found in the telomeric region of this chromosome. This QTL, we termed Rtu2.2, had a LOD score of 15.43 and accounted for more than 30% of the variance of two-spotted spider mite resistance. Several candidate genes involved in trichome formation, synthesis of trichomes exudates and plant defense signaling have been sequenced. However, either the lack of polymorphisms between the parental lines or their map position, away from the QTL, led to their rejection as candidate genes responsible for the two-spotted spider mite resistance. The Rtu2 QTL not only serve as a valuable target for marker-assisted selection of new spider mite-resistant tomato varieties, but also as a starting point for a better understanding of the molecular genetic functions underlying the resistance to this pest.

Identification of novel causative genes determining the complex trait of high ethanol tolerance in yeast using pooled-segregant whole-genome sequence analysis.

High ethanol tolerance is an exquisite characteristic of the yeast Saccharomyces cerevisiae, which enables this microorganism to dominate in natural and industrial fermentations. Up to now, ethanol tolerance has only been analyzed in laboratory yeast strains with moderate ethanol tolerance. The genetic basis of the much higher ethanol tolerance in natural and industrial yeast strains is unknown. We have applied pooled-segregant whole-genome sequence analysis to map all quantitative trait loci (QTL) determining high ethanol tolerance. We crossed a highly ethanol-tolerant segregant of a Brazilian bioethanol production strain with a laboratory strain with moderate ethanol tolerance. Out of 5974 segregants, we pooled 136 segregants tolerant to at least 16% ethanol and 31 segregants tolerant to at least 17%. Scoring of SNPs using whole-genome sequence analysis of DNA from the two pools and parents revealed three major loci and additional minor loci. The latter were more pronounced or only present in the 17% pool compared to the 16% pool. In the locus with the strongest linkage, we identified three closely located genes affecting ethanol tolerance: MKT1, SWS2, and APJ1, with SWS2 being a negative allele located in between two positive alleles. SWS2 and APJ1 probably contained significant polymorphisms only outside the ORF, and lower expression of APJ1 may be linked to higher ethanol tolerance. This work has identified the first causative genes involved in high ethanol tolerance of yeast. It also reveals the strong potential of pooled-segregant sequence analysis using relatively small numbers of selected segregants for identifying QTL on a genome-wide scale.

Preliminary study on ‘genomewide selection’ for maize (Zea mays L.) breeding in Japanese public sectors: Estimated selection response in the first selfing cycle of single‐cross progeny

AbstractJapanese public sectors are now expected to breed high‐yielding silage maize varieties highly adapted to the Japanese climates in order to support the governmental policy to raise the feed self‐sufficiency ratio from 26% (in 2008) to 38% by 2020. ‘Genomewide selection (GwS)’ is a technique to substitute a part of phenotyping with molecular marker genotyping, and is thought to be suitable to accumulate favorable genes in many minor quantitative trait loci (QTLs) whereby yield is thought to be controlled. The purpose of this study was to use computer simulations to evaluate the potential of GwS from the viewpoint of maize breeding sections of Japanese public sectors interested in rapider yield improvement through selection at early breeding stages. It was assumed in each repeat of the simulation experiments that eight S1 (first selfing generation) candidates were selected from 1000 solely on their molecular marker information obtained from testcross investigation with GwS. The experiments indicated that (i) shorter intervals of molecular marker loci led to moderately larger selection response (SR) when the intervals were more than 20 cM, but not when they were less than 20 cM, (ii) higher heritability unexceptionally led to larger SR, and (iii) larger training population size led to slightly larger SR in most cases. The results suggest that it is important for the success of GwS to obtain high heritability in the field for testcross investigation, and that GwS will be a powerful tool for maize breeding sections of Japanese public sectors targeting rapider yield improvement.

Mapping QTL for Fusarium wilt Race 2 partial resistance in pea (Pisum sativum)

With 3 figures and 4 tablesAbstractFusarium oxysporum f.sp. pisi (Fop) exists in pea production regions worldwide and causes a vascular wilt resulting in significant crop losses. Four races of Fop have been identified, and resistance to each was reportedly conferred by an individual single dominant gene. Fnw confers resistance to Fop race 2, which can be a serious pathogen for both green and dry pea production in the Pacific Northwest region of the United States. The objectives of this research were to (i) place Fnw on the Pisum genetic map, (ii) detect additional genetic factors associated with resistance to race 2 and (iii) identify closely linked markers for use in pea breeding A recombinant inbred line (RIL) population of 187 F7‐derived lines from the cross ‘Shawnee’/‘Bohatyr’ was developed by single‐seed decent. All 187 RILs, the parents and one set of race 2 pea differential entries were inoculated with Fop race 2 under controlled conditions in three experiments, each with two or three replications per entry. Disease reactions were recorded as percentage diseased plants 10–14 days postinoculation or at regular intervals through flowering or early pod fill. Data for progressive wilting over time, typical of Fop race 2, were used to calculate area under disease progress curve (AUDPC) values. Data for percentage diseased plants placed the putative single gene Fnw on Pisum sativum linkage group IV, with LOD scores ranging from 40.0 to 65.6 and minor loci on LG III (LOD 3.97 and 4.60). AUDPC values allowed for the detection of additional QTL on linkage group III with LOD scores of 3.97 and 4.60. The presence of recombinants in the population indicated that complementary genes were contributed by each parent, both of which showed intermediate reaction to Fop race 2. Results of this research provide a basis for marker‐assisted selection of the major Fnw loci in both green and dry pea breeding programmes, but additional research is necessary to fully characterize the complementary gene action governing resistance of the two minor loci identified.

A CCCH-Type Zinc Finger Nucleic Acid-Binding Protein Quantitatively Confers Resistance against Rice Bacterial Blight Disease

Bacterial blight is a devastating disease of rice (Oryza sativa) caused by Xanthomonas oryzae pv oryzae (Xoo). Zinc finger proteins harboring the motif with three conserved cysteine residues and one histidine residue (CCCH) belong to a large family. Although at least 67 CCCH-type zinc finger protein genes have been identified in the rice genome, their functions are poorly understood. Here, we report that one of the rice CCCH-type zinc finger proteins, C3H12, containing five typical CX(8)-CX(5)-CX(3)-H zinc finger motifs, is involved in the rice-Xoo interaction. Activation of C3H12 partially enhanced resistance to Xoo, accompanied by the accumulation of jasmonic acid (JA) and induced expression of JA signaling genes in rice. In contrast, knockout or suppression of C3H12 resulted in partially increased susceptibility to Xoo, accompanied by decreased levels of JA and expression of JA signaling genes in rice. C3H12 colocalized with a minor disease resistance quantitative trait locus to Xoo, and the enhanced resistance of randomly chosen plants in the quantitative trait locus mapping population correlated with an increased expression level of C3H12. The C3H12 protein localized in the nucleus and possessed nucleic acid-binding activity in vitro. These results suggest that C3H12, as a nucleic acid-binding protein, positively and quantitatively regulates rice resistance to Xoo and that its function is likely associated with the JA-dependent pathway.

Genetic analysis of Soil-Borne Cereal Mosaic Virus response in durum wheat: evidence for the role of the major quantitative trait locus QSbm.ubo-2BS and of minor quantitative trait loci

Genetic analysis of Soil-Borne Cereal Mosaic Virus (SBCMV) resistance in durum wheat was carried out using a population of 180 recombinant inbred lines (RILs) obtained from Simeto (susceptible) × Levante (resistant). The RILs were characterized for SBCMV response in the field under severe and uniform SBCMV infection in two growing seasons and genotyped with simple sequence repeat (SSR) and Diversity Arrays Technology® markers. Transgressive segregation was observed for disease reaction as estimated by symptom severity scores and virus concentration in leaves. Heritability of the disease response was high, with h2 values consistently above 80%. A major quantitative trait locus (QTL) (QSbm.ubo-2BS) in the distal telomeric region of chromosome 2BS accounted for 60–70% of the phenotypic variation for symptom severity, 40–55% for virus concentration and 15–30% for grain yield. The favorable allele was contributed by Levante. Seven additional QTL influenced SBCMV resistance, with the low-susceptibility allele contributed by Levante at five QTL and by Simeto at the remaining two. The meta-QTL analysis carried out using the data from two mapping populations (Simeto × Levante and Meridiano × Claudio) suggests that in both populations SBCMV resistance is likely controlled by QSbm.ubo-2BS. Our results confine QSbm.ubo-2BS to a c. 2-cM-wide interval flanked by SSR markers that are already being used for marker-assisted selection.