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1.
Plant Genome ; 13(1): e20014, 2020 03.
Artigo em Inglês | MEDLINE | ID: mdl-33016635

RESUMO

Genomic prediction (GP) might be an efficient way to improve haploid induction rate (HIR) and to reduce the laborious and time-consuming task of phenotypic selection for HIR in maize (Zea mays L.). In this study, we evaluated GP accuracies for HIR and other agronomic traits of importance to inducers by independent and cross-validation. We propose the use of GP for cross prediction and parental selection in the development of new inducer breeding populations. A panel of 159 inducers from Iowa State University (ISU set) was genotyped and phenotyped for HIR and several agronomic traits. The data of an independent set of 53 inducers evaluated by the University of Hohenheim (UOH set) was used for independent validation. The HIR ranged from 0.61 to 20.74% and exhibited high heritability (0.90). High cross-validation prediction accuracy was observed for HIR (r = 0.82), whereas for other traits it ranged from 0.36 (self-induction rate) to 0.74 (days to anthesis). Prediction accuracies across different sets were higher when the larger panel (ISU set) was used as a training population (r = 0.54). The average HIR of the 12,561 superior predicted progenies (µSP ) ranged from 1.00-18.36% and was closely related to the corresponding midparent genomic estimated breeding value (GEBV). A predicted genetic variance (VG ) of reduced magnitude was observed in the twenty crosses with highest midparent GEBV or µSP for HIR. Our results indicate that although GP is a useful tool for parental selection, decisions about which cross combinations should be pursued need to be based on optimal trade-offs between maximizing both µSP and VG .


Assuntos
Modelos Genéticos , Zea mays , Genoma , Genômica , Haploidia , Zea mays/genética
2.
Nat Commun ; 11(1): 4954, 2020 10 02.
Artigo em Inglês | MEDLINE | ID: mdl-33009396

RESUMO

Genetic variation is of crucial importance for crop improvement. Landraces are valuable sources of diversity, but for quantitative traits efficient strategies for their targeted utilization are lacking. Here, we map haplotype-trait associations at high resolution in ~1000 doubled-haploid lines derived from three maize landraces to make their native diversity for early development traits accessible for elite germplasm improvement. A comparative genomic analysis of the discovered haplotypes in the landrace-derived lines and a panel of 65 breeding lines, both genotyped with 600k SNPs, points to untapped beneficial variation for target traits in the landraces. The superior phenotypic performance of lines carrying favorable landrace haplotypes as compared to breeding lines with alternative haplotypes confirms these findings. Stability of haplotype effects across populations and environments as well as their limited effects on undesired traits indicate that our strategy has high potential for harnessing beneficial haplotype variation for quantitative traits from genetic resources.


Assuntos
Haplótipos/genética , Característica Quantitativa Herdável , Zea mays/genética , Biblioteca Gênica , Variação Genética , Genoma de Planta , Estudo de Associação Genômica Ampla , Haploidia , Melhoramento Vegetal , Análise de Componente Principal , Zea mays/crescimento & desenvolvimento
3.
PLoS Pathog ; 16(8): e1008772, 2020 08.
Artigo em Inglês | MEDLINE | ID: mdl-32866214

RESUMO

The tick-borne apicomplexan parasite, Babesia bovis, a highly persistent bovine pathogen, expresses VESA1 proteins on the infected erythrocyte surface to mediate cytoadhesion. The cytoadhesion ligand, VESA1, which protects the parasite from splenic passage, is itself protected from a host immune response by rapid antigenic variation. B. bovis relies upon segmental gene conversion (SGC) as a major mechanism to vary VESA1 structure. Gene conversion has been considered a form of homologous recombination (HR), a process for which Rad51 proteins are considered pivotal components. This could make BbRad51 a choice target for development of inhibitors that both interfere with parasite genome integrity and disrupt HR-dependent antigenic variation. Previously, we knocked out the Bbrad51 gene from the B. bovis haploid genome, resulting in a phenotype of sensitivity to methylmethane sulfonate (MMS) and apparent loss of HR-dependent integration of exogenous DNA. In a further characterization of BbRad51, we demonstrate here that ΔBbrad51 parasites are not more sensitive than wild-type to DNA damage induced by γ-irradiation, and repair their genome with similar kinetics. To assess the need for BbRad51 in SGC, RT-PCR was used to observe alterations to a highly variant region of ves1α transcripts over time. Mapping of these amplicons to the genome revealed a significant reduction of in situ transcriptional switching (isTS) among ves loci, but not cessation. By combining existing pipelines for analysis of the amplicons, we demonstrate that SGC continues unabated in ΔBbrad51 parasites, albeit at an overall reduced rate, and a reduction in SGC tract lengths was observed. By contrast, no differences were observed in the lengths of homologous sequences at which recombination occurred. These results indicate that, whereas BbRad51 is not essential to babesial antigenic variation, it influences epigenetic control of ves loci, and its absence significantly reduces successful variation. These results necessitate a reconsideration of the likely enzymatic mechanism(s) underlying SGC and suggest the existence of additional targets for development of small molecule inhibitors.


Assuntos
Antígenos de Protozoários , Babesia bovis , Conversão Gênica/imunologia , Genoma de Protozoário/imunologia , Proteínas de Protozoários , Rad51 Recombinase , Antígenos de Protozoários/genética , Antígenos de Protozoários/imunologia , Babesia bovis/genética , Babesia bovis/imunologia , DNA de Protozoário/genética , DNA de Protozoário/imunologia , Haploidia , Proteínas de Protozoários/genética , Proteínas de Protozoários/imunologia , Rad51 Recombinase/genética , Rad51 Recombinase/imunologia
4.
PLoS One ; 15(9): e0233072, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32911495

RESUMO

In mammals, the fusion of two gametes, an oocyte and a spermatozoon, during fertilization forms a totipotent zygote. There has been no reported case of adult mammal development by natural parthenogenesis, in which embryos develop from unfertilized oocytes. The genome and epigenetic information of haploid gametes are crucial for mammalian development. Haploid embryonic stem cells (haESCs) can be established from uniparental blastocysts and possess only one set of chromosomes. Previous studies have shown that sperm or oocyte genome can be replaced by haESCs with or without manipulation of genomic imprinting for generation of mice. Recently, these remarkable semi-cloning methods have been applied for screening of key factors of mouse embryonic development. While haESCs have been applied as substitutes of gametic genomes, the fundamental mechanism how haESCs contribute to the genome of totipotent embryos is unclear. Here, we show the generation of fertile semi-cloned mice by injection of parthenogenetic haESCs (phaESCs) into oocytes after deletion of two differentially methylated regions (DMRs), the IG-DMR and H19-DMR. For characterizing the genome of semi-cloned embryos further, we establish ESC lines from semi-cloned blastocysts. We report that polyploid karyotypes are observed in semi-cloned ESCs (scESCs). Our results confirm that mitotically arrested phaESCs yield semi-cloned embryos and mice when the IG-DMR and H19-DMR are deleted. In addition, we highlight the occurrence of polyploidy that needs to be considered for further improving the development of semi-cloned embryos derived by haESC injection.


Assuntos
Clonagem de Organismos/métodos , Desenvolvimento Embrionário , Haploidia , Partenogênese , Poliploidia , Animais , Linhagem Celular , Células-Tronco Embrionárias/citologia , Feminino , Masculino , Camundongos , Camundongos Endogâmicos C57BL , Camundongos Endogâmicos DBA
5.
Zhonghua Xue Ye Xue Za Zhi ; 41(7): 557-563, 2020 Jul 14.
Artigo em Chinês | MEDLINE | ID: mdl-32810962

RESUMO

Objective: To compare the clinical efficacy of different doses of rabbit antithymocyte globulin (rATG) in haplo-HSCT in the treatment of hematologic malignancies. Methods: Malignant hematological patients treated at our hospital from March 2013 to December 2018 were retrospectively analyzed. These patients were divided into three groups as per three doses of ATG (6 mg/kg, 7.5 mg/kg, and 9 mg/kg) in the conditioning regimens. The transplant outcomes were compared in terms of the occurrence of acute graft versus host disease (GVHD) , infection, and survival. Results: ①Total 288 patients were enrolled in the study, including 182 men and 106 women, with a median age of 18 (6-62) years. Total 110 patients were diagnosed with acute lymphoblastic leukemia (ALL) , 128 with acute myelogenous leukemia (AML) , 8 with chronic myeloid leukemia (CML) , 28 with myelodysplastic syndrome (MDS) , and 14 with mixed cell leukemia (MAL) . There were 159 patients in the ATG-6 group, 72 in the ATG-7.5 group, and 57 in the ATG-9 group. The median follow-up time of post transplantation was 14 (0.2-74) months. ②The incidence of neutrophil engraftment (96.9% , 97.2% , and 96.5% , respectively) and platelet engraftment (92.5% , 87.5% , and 86% , respectively) did not significantly differ among the ATG-6, ATG-7.5, and ATG-9 groups (P=0.972, P=0.276) . The incidence of grades 2-4 acute GVHD was 14.5% , 11.1% , and 8.8% in the three groups, respectively (P=0.493) , chronic GVHD incidence in the three group was 8.8% , 14.3% and 12.0% , respectively (P=0.493) . The infection rates of CMV and EBV in the ATG-9 group (77.2% and 12.5% ) were significantly higher than those in the ATG-6 (43.3% and 3.5% ) , and ATG -7.5 group (44.4% and 1.5% ) (P<0.001 and P=0.033, respectively) . ③Among the three groups, there were no significant difference in the 3-year overall survival [68.5% (95% CI 60.3% -77.9% ) , 60.1% (95% CI 48.3% -74.8% ) , 64.7% (95% CI 51.9% -80.7% ) ], cumulative incidences of relapse [34.6% (95% CI 34.3% -35.1% ) , 38.0% (95% CI 37.3% -38.7% ) , 20.6% (95% CI 20.0% -21.3% ) ], disease-free survival [53.3% (95% CI 44.9% -63.4% ) , 51.9% (95% CI 41% -65.8% ) , 63.9% (95% CI 51.9% -78.7% ) ] and non-relapse mortality [24.2% (95% CI 23.8% -24.5% ) , 26.0% (95% CI 25.4% -26.6% ) , 23.6% (95% CI 26.3% -28.2% ) ] (P=0.648, P=0.165, and P=0.486 and P=0.955) . Conclusion: Low dose (6 mg/kg) of rATG may increase the risk of grade Ⅱ-Ⅳ aGVHD, and a high dose (9 mg/kg) of ATG could significantly increase the risk of CMV and EBV infection. Median dose (7.5 mg/kg) of ATG is expected to reduce the incidence of moderate to severe aGVHD and viral infections without increasing the mortality.


Assuntos
Doença Enxerto-Hospedeiro , Neoplasias Hematológicas , Transplante de Células-Tronco Hematopoéticas , Adolescente , Adulto , Soro Antilinfocitário , Criança , Feminino , Haploidia , Humanos , Masculino , Pessoa de Meia-Idade , Estudos Retrospectivos , Condicionamento Pré-Transplante , Adulto Jovem
6.
PLoS One ; 15(8): e0237711, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32810182

RESUMO

Alleles at the Glu-1 loci play important roles in the functional properties of wheat flour. The effects of various high-molecular-weight glutenin subunit (HMW-GS) compositions on quality traits and bread-making properties were evaluated using 235 doubled haploid lines (DHs). The experiment was conducted in a split plot design with two water regimes as the main plot treatment, and DH lines as the subplot treatments. Results showed that the presence of subunit pair 5+10 at the Glu-D1 locus, either alone or in combination with others, appears to provide an improvement in quality and bread-making properties. At the Glu-A1 locus, subunit 1 produced a higher Zeleny sedimentation value (Zel) and stretch area (SA) than subunit 2* when subunits 14+15 and 5+10 were expressed at the Glu-B1 and Glu-D1 loci, and 2* had a positive effect on the maximum dough resistance (Rmax) when subunits 14+15 and 5'+12 were expressed at the Glu-B1 and Glu-D1 loci, respectively. Given subunit 1 at the Glu-A1 locus and 5'+12 at the Glu-D1 locus, the effects of Glu-B1 subunits 14+15 on the tractility (Tra), dough stability time (ST), and dough development time (DT) under the well-watered regime were significantly higher than those of Glu-B1 subunits 13+16. However, 13+16 had a positive effect on SA under the rain-fed regime when subunits 2* and 5+10 were expressed at the Glu-A1 and Glu-D1 loci, respectively. Multiple comparisons analysis revealed that the Zel and Rmax of the six subunits and eight HMW-GS compositions were stable under different water regimes. Overall, subunit compositions 1, 13+16 and 5+10 and 1, 14+15 and 5+10 had higher values for quality traits and bread-baking properties under the two water regimes. These results could play a positive guiding role in selecting and popularizing varieties suitable for production and cultivation in local areas.


Assuntos
Qualidade dos Alimentos , Glutens/genética , Melhoramento Vegetal , Subunidades Proteicas/genética , Triticum/química , Irrigação Agrícola/métodos , Pão/normas , China , Farinha/normas , Genes de Plantas/genética , Loci Gênicos , Glutens/metabolismo , Haploidia , Peso Molecular , Subunidades Proteicas/química , Triticum/genética , Triticum/crescimento & desenvolvimento
7.
PLoS Negl Trop Dis ; 14(8): e0008480, 2020 08.
Artigo em Inglês | MEDLINE | ID: mdl-32813714

RESUMO

Clonorchiasis is a neglected tropical disease caused by the Chinese liver fluke, Clonorchis sinensis, and is often associated with a malignant form of bile duct cancer (cholangiocarcinoma). Although some aspects of the epidemiology of clonorchiasis are understood, little is known about the genetics of C. sinensis populations. Here, we conducted a comprehensive genetic exploration of C. sinensis from endemic geographic regions using complete mitochondrial protein gene sets. Genomic DNA samples from C. sinensis individuals (n = 183) collected from cats and dogs in China (provinces of Guangdong, Guangxi, Hunan, Heilongjiang and Jilin) as well as from rats infected with metacercariae from cyprinid fish from the Russian Far East (Primorsky Krai region) were deep sequenced using the BGISEQ-500 platform. Informatic analyses of mitochondrial protein gene data sets revealed marked genetic variation within C. sinensis; significant variation was identified within and among individual worms from distinct geographical locations. No clear affiliation with a particular location or host species was evident, suggesting a high rate of dispersal of the parasite across endemic regions. The present work provides a foundation for future biological, epidemiological and ecological studies using mitochondrial protein gene data sets, which could aid in elucidating associations between particular C. sinensis genotypes/haplotypes and the pathogenesis or severity of clonorchiasis and its complications (including cholangiocarcinoma) in humans.


Assuntos
Clonorquíase/parasitologia , Clonorchis sinensis/genética , DNA Mitocondrial/genética , Variação Genética , Animais , China/epidemiologia , Clonorquíase/epidemiologia , Haploidia , Interações Hospedeiro-Parasita , Humanos , Filogenia , Federação Russa/epidemiologia
8.
Nat Biotechnol ; 38(9): 1044-1053, 2020 09.
Artigo em Inglês | MEDLINE | ID: mdl-32686750

RESUMO

De novo assembly of a human genome using nanopore long-read sequences has been reported, but it used more than 150,000 CPU hours and weeks of wall-clock time. To enable rapid human genome assembly, we present Shasta, a de novo long-read assembler, and polishing algorithms named MarginPolish and HELEN. Using a single PromethION nanopore sequencer and our toolkit, we assembled 11 highly contiguous human genomes de novo in 9 d. We achieved roughly 63× coverage, 42-kb read N50 values and 6.5× coverage in reads >100 kb using three flow cells per sample. Shasta produced a complete haploid human genome assembly in under 6 h on a single commercial compute node. MarginPolish and HELEN polished haploid assemblies to more than 99.9% identity (Phred quality score QV = 30) with nanopore reads alone. Addition of proximity-ligation sequencing enabled near chromosome-level scaffolds for all 11 genomes. We compare our assembly performance to existing methods for diploid, haploid and trio-binned human samples and report superior accuracy and speed.


Assuntos
Genoma Humano/genética , Sequenciamento de Nucleotídeos em Larga Escala/métodos , Sequenciamento por Nanoporos , Análise de Sequência de DNA/métodos , Algoritmos , Benchmarking , Cromossomos Humanos/genética , Aprendizado Profundo , Genômica , Antígenos HLA/genética , Haploidia , Sequenciamento de Nucleotídeos em Larga Escala/normas , Humanos , Análise de Sequência de DNA/normas
9.
Nat Protoc ; 15(8): 2705-2727, 2020 08.
Artigo em Inglês | MEDLINE | ID: mdl-32681154

RESUMO

Invasive fungal infections caused by Candida species are life threatening with high mortality, posing a severe public health threat. New technologies for rapid, genome-wide identification of virulence genes and therapeutic targets are urgently needed. Our recent engineering of a piggyBac (PB) transposon-mediated mutagenesis system in haploid Candida albicans provides a powerful discovery tool, which we anticipate should be adaptable to other haploid Candida species. In this protocol, we use haploid C. albicans as an example to present an improved version of the mutagenesis system and provide a detailed description of the protocol for constructing high-quality mutant libraries. We also describe a method for quantitative PB insertion site sequencing, PBISeq. The PBISeq library preparation procedure exploits tagmentation to quickly and efficiently construct sequencing libraries. Finally, we present a pipeline to analyze PB insertion sites in a de novo assembled genome of our engineered haploid C. albicans strain. The entire protocol takes ~7 d from transposition induction to having a final library ready for sequencing. This protocol is highly efficient and less labor intensive than alternative approaches and significantly accelerates genetic studies of Candida.


Assuntos
Candida/genética , Elementos de DNA Transponíveis/genética , Genoma Fúngico/genética , Haploidia , Mutagênese Insercional/métodos
10.
Nature ; 582(7810): 78-83, 2020 06.
Artigo em Inglês | MEDLINE | ID: mdl-32494067

RESUMO

Human evolutionary history is rich with the interbreeding of divergent populations. Most humans outside of Africa trace about 2% of their genomes to admixture from Neanderthals, which occurred 50-60 thousand years ago1. Here we examine the effect of this event using 14.4 million putative archaic chromosome fragments that were detected in fully phased whole-genome sequences from 27,566 Icelanders, corresponding to a range of 56,388-112,709 unique archaic fragments that cover 38.0-48.2% of the callable genome. On the basis of the similarity with known archaic genomes, we assign 84.5% of fragments to an Altai or Vindija Neanderthal origin and 3.3% to Denisovan origin; 12.2% of fragments are of unknown origin. We find that Icelanders have more Denisovan-like fragments than expected through incomplete lineage sorting. This is best explained by Denisovan gene flow, either into ancestors of the introgressing Neanderthals or directly into humans. A within-individual, paired comparison of archaic fragments with syntenic non-archaic fragments revealed that, although the overall rate of mutation was similar in humans and Neanderthals during the 500 thousand years that their lineages were separate, there were differences in the relative frequencies of mutation types-perhaps due to different generation intervals for males and females. Finally, we assessed 271 phenotypes, report 5 associations driven by variants in archaic fragments and show that the majority of previously reported associations are better explained by non-archaic variants.


Assuntos
Introgressão Genética/genética , Genoma Humano/genética , Genômica , Mutação , Homem de Neandertal/genética , Animais , Feminino , Estudos de Associação Genética , Haploidia , Humanos , Islândia , Masculino , Fenótipo , Filogenia
11.
Yi Chuan ; 42(5): 466-482, 2020 May 20.
Artigo em Inglês | MEDLINE | ID: mdl-32431298

RESUMO

Haploid induction is one of the main techniques for breeding new varieties of major crops, and its key steps are improving the haploid induction rate and simplifying the induction procedure. With the development and innovation of plant haploid induction technologies, haploid breeding has been widely used in varietal improvement of important crops, showing the advantages of rapid homozygosity of heterozygous genes, shortening breeding period, and improving breeding efficiency. The combination of haploid breeding with crossing breeding, mutation breeding, reverse breeding, and molecular marker-assisted selection will greatly improve the effectiveness of crop breeding. Haploids and doubled haploids have demonstrated their usefulness in production of genetic populations, characterization of gene functions, and transgenic and cytological studies in plants. In this review, we summarize the progress of haploid induction technologies in view of various haploid induction techniques and applications of haploids and double haploids. In particular, the advances on the haploid induction in several major crops by genome editing were briefly described. Finally, we discuss current issues and future perspectives in this field, so as to promote the application of the haploid induction techniques, especially the techniques of creating haploid inducer lines by genome editing in crop breeding.


Assuntos
Produtos Agrícolas/genética , Haploidia , Melhoramento Vegetal/métodos , Edição de Genes
13.
Ann Hematol ; 99(6): 1389-1400, 2020 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-32291495

RESUMO

Two anti-thymocyte globulin (ATG) forms are used in graft-versus-host disease (GVHD) prophylaxis during haploidentical hematopoietic stem cell transplantations (haplo-HSCTs): ATG-thymoglobulin (ATG-T) and ATG-fresenious (ATG-F). However, comparable dosages for haplo-HSCT remain unclear. We compared and evaluated the effects of ATG-T (7.5 mg/kg) or ATG-F (20 mg/kg) dosages in a relatively homogenous population in haplotype HSCT settings. Patients administered ATG-T 7.5 mg/kg (n = 81) or ATG-F 20 mg/kg (n = 35) as part of GVHD prophylaxis during haplo-HSCT were enrolled. Incidence and severity of GVHD, Epstein-Barr virus (EBV) infection, and immune cell recovery were compared using the Mann-Whitney U rank test and chi-square test. Cumulative incidences of GVHD, EBV infection and its subgroups, and relapse mortality were computed; overall survival (OS) was analyzed using the Kaplan-Meier method, with the log-rank test used for univariate comparison. Risk factors for OS were analyzed by the Cox proportional hazards model. Incidence and cumulative incidence of all grades of acute GVHD and subgroups were comparable in both groups (all p > 0.05); however, cumulative incidence of any grade and limited chronic GVHD was significantly higher in the ATG-T group (p = 0.002, p = 0.007, respectively). Cumulative incidences of EBV infections, EBV-DNAemia, and EBV-related diseases were similar; relapse mortality and OS rates were comparable between both groups (all p > 0.05). ATG-T dosage (7.5 mg/kg) appeared comparable to ATG-F dosage (20 mg/kg) for haplo-HSCT. Currently approved ATG-T and ATG-F doses appear efficient to balance the risk-benefit ratio of GVHD, OS, relapse mortality, and EBV infection in haplo-HSCT.


Assuntos
Soro Antilinfocitário/administração & dosagem , Infecções por Vírus Epstein-Barr/tratamento farmacológico , Doença Enxerto-Hospedeiro/tratamento farmacológico , Neoplasias Hematológicas/tratamento farmacológico , Transplante de Células-Tronco Hematopoéticas/tendências , Adolescente , Adulto , Criança , Pré-Escolar , Infecções por Vírus Epstein-Barr/epidemiologia , Feminino , Seguimentos , Doença Enxerto-Hospedeiro/epidemiologia , Haploidia , Neoplasias Hematológicas/epidemiologia , Transplante de Células-Tronco Hematopoéticas/efeitos adversos , Humanos , Imunossupressores/administração & dosagem , Masculino , Pessoa de Meia-Idade , Estudos Retrospectivos , Adulto Jovem
14.
PLoS One ; 15(4): e0221603, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32343696

RESUMO

Increased genetic gain for complex traits in plant breeding programs can be achieved through different selection strategies. The objective of this study was to compare potential gains for grain yield in a winter wheat breeding program through estimating response to selection R values across several selection approaches including phenotypic (PS), marker-based (MS), genomic (GS), and a combination of PS and GS (PS+GS). Ten populations of Washington State University (WSU) winter wheat breeding lines including a diversity panel and F5 and double haploid lines evaluated from 2015 to 2019 growing seasons for grain yield in Lind and Pullman, WA, USA were used in the study. Selection was conducted by selecting the top 20% of lines based on observed yield (PS strategy), genomic estimated breeding values (GS), presence of yield "enhancing" alleles of the most significant single nucleotide polymorphism (SNP) markers identified from genome-wide association mapping (MS), and high observed yield and estimated breeding values (PS+GS). Overall, PS compared to other individual selection strategies (MS and GS) showed the highest mean response (R = 0.61) within the same environment. When combined with GS, a 23% improvement in R for yield was observed, indicating that gains could be improved by complementing traditional PS with GS within the same environment. Validating selection strategies in different environments resulted in low to negative R values indicating the effects of genotype-by-environment interactions for grain yield. MS was not successful in terms of R relative to the other selection approaches; using this strategy resulted in a significant (P < 0.05) decrease in response to selection compared with the other approaches. An integrated PS+GS approach could result in optimal genetic gain within the same environment, whereas a PS strategy might be a viable option for grain yield validated in different environments. Altogether, we demonstrated that gains through increased response to selection for yield could be achieved in the WSU winter wheat breeding program by implementing different selection strategies either exclusively or in combination.


Assuntos
Melhoramento Vegetal/métodos , Triticum/crescimento & desenvolvimento , Grão Comestível/genética , Grão Comestível/crescimento & desenvolvimento , Genoma de Planta , Genômica , Haploidia , Polimorfismo de Nucleotídeo Único , Estações do Ano , Seleção Genética , Triticum/genética
15.
PLoS One ; 15(4): e0230820, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32298285

RESUMO

The high toxicity of cadmium (Cd) and its ready uptake by plants has become a major agricultural problem. To investigate the genetic architecture and genetic regulation of Cd tolerance in barley, we conducted quantitative trait loci (QTL) analysis in the phenotypically polymorphic Oregon Wolfe Barley (OWB) mapping population, derived from a cross between Rec and Dom parental genotypes. Through evaluating the Cd tolerance of 87 available doubled haploid lines of the OWB mapping population at the seedling stage, one minor and one major QTL were detected on chromosomes 2H and 6H, respectively. For chlorosis and necrosis traits, the major QTL explained 47.24% and 38.59% of the phenotypic variance, respectively. RNA-Seq analysis of the parental seedlings under Cd treatment revealed 542 differentially expressed genes between Cd-tolerant Rec and Cd-susceptible Dom genotypes. By analyzing sequence variations in transcribed sequences of the parental genotypes, 155,654 SNPs and 1,525 InDels were identified between the two contrasting genotypes and may contribute to Cd tolerance. Finally, by integrating the data from the identified QTLs and RNA-Seq analysis, 16 Cd tolerance-related candidate genes were detected, nine of which were metal ion transporters. These results provide promising candidate genes for further gene cloning and improving Cd tolerance in barley.


Assuntos
Cádmio/toxicidade , Tolerância a Medicamentos/genética , Hordeum/efeitos dos fármacos , Hordeum/genética , Locos de Características Quantitativas/genética , Mapeamento Cromossômico/métodos , Cromossomos de Plantas/efeitos dos fármacos , Cromossomos de Plantas/genética , Haploidia , Oregon , Fenótipo , Polimorfismo de Nucleotídeo Único/genética , RNA-Seq/métodos , Plântula/efeitos dos fármacos , Plântula/genética , Estresse Fisiológico/genética , Sequenciamento Completo do Exoma/métodos
16.
PLoS One ; 15(3): e0230326, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32160264

RESUMO

Milling properties and flour color are essential selection criteria in soft wheat breeding. However, high phenotypic screening costs restrict selection to relatively few breeding lines in late generations. To achieve marker-based selection of these traits in early generations, we performed genetic dissection of quality traits using three doubled haploid populations that shared the high-quality soft wheat variety Kitahonami as the paternal parent. An amplicon sequencing approach allowed effective construction of well-saturated linkage maps of the populations. Marker-based heritability estimates revealed that target quality traits had relatively high values, indicating the possibility of selection in early generations. Taking advantage of Chinese Spring reference sequences, joint linkage maps of the three populations were generated. Based on the maps, multifamily quantitative trait locus (QTL) analysis revealed a total of 86 QTLs for ten traits investigated. In terms of target quality traits, 12 QTLs were detected for flour yield, and 12 were detected for flour redness (a* value). Among these QTLs, six for flour yield and nine for flour a* were segregating in more than two populations. Some relationships among traits were explained by QTL collocations on chromosomes, especially group 7 chromosomes. Ten different ideotypes with various combinations of favorable alleles for the flour yield and flour a* QTLs were generated. Phenotypes of derivatives from these ideotypes were predicted to design ideal genotypes for high-quality wheat. Simulations revealed the possibility of breeding varieties with better quality than Kitahonami.


Assuntos
Farinha , Melhoramento Vegetal/métodos , Locos de Características Quantitativas , Triticum/genética , Alelos , Mapeamento Cromossômico , Cruzamentos Genéticos , Ligação Genética , Haploidia , Fenótipo
17.
Nat Commun ; 11(1): 1128, 2020 02 28.
Artigo em Inglês | MEDLINE | ID: mdl-32111832

RESUMO

The sterol-regulatory element binding proteins (SREBP) are central transcriptional regulators of lipid metabolism. Using haploid genetic screens we identify the SREBP Regulating Gene (SPRING/C12ORF49) as a determinant of the SREBP pathway. SPRING is a glycosylated Golgi-resident membrane protein and its ablation in Hap1 cells, Hepa1-6 hepatoma cells, and primary murine hepatocytes reduces SREBP signaling. In mice, Spring deletion is embryonic lethal yet silencing of hepatic Spring expression also attenuates the SREBP response. Mechanistically, attenuated SREBP signaling in SPRINGKO cells results from reduced SREBP cleavage-activating protein (SCAP) and its mislocalization to the Golgi irrespective of the cellular sterol status. Consistent with limited functional SCAP in SPRINGKO cells, reintroducing SCAP restores SREBP-dependent signaling and function. Moreover, in line with the role of SREBP in tumor growth, a wide range of tumor cell lines display dependency on SPRING expression. In conclusion, we identify SPRING as a previously unrecognized modulator of SREBP signaling.


Assuntos
Colesterol/metabolismo , Glicoproteínas de Membrana/metabolismo , Proteínas de Membrana/metabolismo , Transdução de Sinais , Proteínas de Ligação a Elemento Regulador de Esterol/metabolismo , Animais , Linhagem Celular , Desenvolvimento Embrionário/genética , Retículo Endoplasmático/metabolismo , Expressão Gênica , Complexo de Golgi/metabolismo , Haploidia , Hepatócitos/metabolismo , Humanos , Peptídeos e Proteínas de Sinalização Intracelular/genética , Peptídeos e Proteínas de Sinalização Intracelular/metabolismo , Metabolismo dos Lipídeos/genética , Fígado/metabolismo , Glicoproteínas de Membrana/genética , Proteínas de Membrana/genética , Camundongos , Camundongos Endogâmicos C57BL , Proteínas de Ligação a Elemento Regulador de Esterol/genética
18.
PLoS One ; 15(2): e0228411, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32023320

RESUMO

Kernel abortion is common phenomenon in vivo haploid induction and closely linked with haploid induction rate, but little information of kernel abortion is available and its genetic basis still unclear. We used two mapping populations including 186 and 263 F2.3 family lines to analyze the different degree of kernel abortion and identify quantitative trait loci (QTL) responsible for kernel abortion during haploid induction. In total 62 putative QTL, accounting for 3.27-14.70% of the phenotypic variation in kernel abortion traits, were detected across all 10 chromosomes. Ten QTL with over 10% contribution to phenotypic variation were affecting the fifth level of endosperm abortion (EnA5th), endosperm abortion (EnA) and total abortion (TA). Co-localization among kernel abortion traits QTL was observed in both populations and among different kernel abortion types. Five overlaps were indentified in the QTL for kernel abortion traits and HIR traits. Maize chromosome bins 3.01-3.02, 3.04-3.06, 4.05-4.06, 5.03-5.04, 8.06 were QTL hotspots for three or four traits related to the kernel abortion during haploid induction. Total kernel abortion rate (TAR) and HIR showed highly significant positive correlation. These findings may help to reveal haploid induction mechanisms and improve haploid production efficiency.


Assuntos
Cromossomos de Plantas/genética , Haploidia , Locos de Características Quantitativas , Sementes/crescimento & desenvolvimento , Zea mays/crescimento & desenvolvimento , Zea mays/genética , Mapeamento Cromossômico , Cruzamentos Genéticos , Endosperma , Epistasia Genética , Ligação Genética , Fenótipo , Sementes/genética
19.
Plant Sci ; 293: 110337, 2020 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-32081276

RESUMO

In vivo doubled haploid (DH) technology is widely used in commercial maize (Zea mays L.) breeding. Haploid genome doubling is a critical step in DH breeding. In this study, inbred lines GF1 (0.65), GF3(0.29), and GF5 (0) with high, moderate, and poor spontaneous haploid genome doubling (SHGD), respectively, were selected to develop mapping populations for SHGD. Three QTL, qshgd1, qshgd2, and qshgd3, related to SHGD were identified by selective genotyping. With the exception of qshgd3, the source of haploid genome doubling alleles were derived from GF1. Furthermore, RNA-Seq was conducted to identify putative candidate genes between GF1 and GF5 within the qshgd1 region. A differentially expressed formin-like protein 5 transcript was identified within the qshgd1 region.


Assuntos
Genes de Plantas/genética , Haploidia , Locos de Características Quantitativas/genética , Zea mays/genética , Alelos , Sequência de Bases , Cruzamento , Mapeamento Cromossômico , Regulação para Baixo , Forminas/genética , Genoma de Planta , Genótipo , Fenótipo , Polimorfismo de Nucleotídeo Único , Análise de Sequência de RNA
20.
J Biosci Bioeng ; 129(6): 706-714, 2020 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-32085973

RESUMO

Among sake yeast strains, Kyokai no. 7 (K7) and its closely related strains (K7 group) are predominantly used because of their excellent brewing properties. In the sake industrial sector, the need for various types of yeast strains is high. Although crossbreeding is an effective method for generating genetic diversity that should result in diverse characteristics, most K7 group strains lack normal sporulation ability, including the ability to undergo meiotic chromosomal recombination, which leads to difficulties in crossbreeding. Accordingly, the improvement of sake yeast strains primarily depends on mutagenesis and suitable selection in a stepwise manner. Our recent study revealed that the long-preserved sake yeast strain Hiroshima no. 6 (H6) does not belong to the K7 group despite genetically being extremely similar. In addition, H6 exhibited normal sporulation. Thus, we isolated haploid cells from H6 and mated them with previously isolated haploid cells of K7 group strains. The crossbred diploid strains had normal sporulation ability; hence, we performed tetrad analysis. The brewing characteristics of the obtained haploid set were extremely diverse. Principal component analysis based on the volatile and organic acid components measured using small-scale sake brewing tests revealed that the haploid strains derived from each diploid strain displayed a characteristic distribution. Thus, we demonstrated the availability of genetic crossbreeding using H6 with sporulation ability to facilitate both the development of novel sake yeast strains with many desirable characteristics and analyses of the function of sake yeast.


Assuntos
Bebidas Alcoólicas/análise , Haploidia , Proteínas de Saccharomyces cerevisiae/genética , Saccharomyces cerevisiae/genética , Diploide , Fermentação , Genótipo , Proteínas de Saccharomyces cerevisiae/metabolismo
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