scholarly journals Identification and Validation of Candidate Genes Conferring Resistance to Downy Mildew in Maize (Zea mays L.)

Genes ◽  
2020 ◽  
Vol 11 (2) ◽  
pp. 191
Author(s):  
Hyo Chul Kim ◽  
Kyung-Hee Kim ◽  
Kitae Song ◽  
Jae Yoon Kim ◽  
Byung-Moo Lee
Keyword(s):  
Candidate Genes ◽  
Downy Mildew ◽  
Rflp Markers ◽  
Chromosome 2 ◽  
Tropical Regions ◽  
Peronosclerospora Sorghi ◽  
Relative Expression Level ◽  
Significant Yield ◽  
Polymerase Chain ◽  
Variation Explained

Downy mildew (DM) is a major disease of maize that causes significant yield loss in subtropical and tropical regions around the world. A variety of DM strains have been reported, and the resistance to them is polygenically controlled. In this study, we analyzed the quantitative trait loci (QTLs) involved in resistance to Peronosclerospora sorghi (sorghum DM), P. maydis (Java DM), and Sclerophthora macrospora (crazy top DM) using a recombinant inbred line (RIL) from a cross between B73 (susceptible) and Ki11 (resistant), and the candidate genes for P. sorghi, P. maydis, and S. macrospora resistance were discovered. The linkage map was constructed with 234 simple sequence repeat (SSR) and restriction fragment length polymorphism (RFLP) markers, which was identified seven QTLs (chromosomes 2, 3, 6, and 9) for three DM strains. The major QTL, located on chromosome 2, consists of 12.95% of phenotypic variation explained (PVE) and a logarithm of odds (LOD) score of 14.12. Sixty-two candidate genes for P. sorghi, P. maydis, and S. macrospora resistance were obtained between the flanked markers in the QTL regions. The relative expression level of candidate genes was evaluated by quantitative real-time polymerase chain reaction (qRT-PCR) using resistant (CML228, Ki3, and Ki11) and susceptible (B73 and CML270) genotypes. For the 62 candidate genes, 15 genes were upregulated in resistant genotypes. Among these, three (GRMZM2G028643, GRMZM2G128315, and GRMZM2G330907) and AC210003.2_FG004 were annotated as leucine-rich repeat (LRR) and peroxidase (POX) genes, respectively. These candidate genes in the QTL regions provide valuable information for further studies related to P. sorghi, P. maydis, and S. macrospora resistance.

Identification of RFLP markers linked to a gene for downy mildew resistance (Sdm) in sorghum

1996 ◽  
Vol 74 (2) ◽  
pp. 315-317 ◽  
Author(s):  
Boung-Jun Oh ◽  
Richard A. Frederiksen ◽  
Clint W. Magill
Keyword(s):  
Disease Resistance ◽  
Linkage Group ◽  
Downy Mildew ◽  
Fragment Length Polymorphism ◽  
Hybrid Breeding ◽  
Rflp Markers ◽  
Downy Mildew Resistance ◽  
Peronosclerospora Sorghi ◽  
Sorghum Accession ◽  
Restriction Fragment Length

The Sdm locus in sorghum accession SC325 confers resistance to downy mildew caused by pathotypes 1 and 3 of Peronosclerospora sorghi. Restriction fragment length polymorphism linkage analysis placed the Sdm locus near loci detected by probes pSbTXS552 and pSbTXS361 at 5.0 and 7.9 cM, respectively. Fragment patterns for the cross segregating for disease resistance differed from those for the original mapping cross, preventing assignment of Sdm to a linkage group. Keywords: Peronosclerospora sorghi, resistance, RFLP, linkage, hybrid breeding.

scholarly journals High resolution mapping and candidate gene identification of downy mildew race 16 resistance in spinach

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Gehendra Bhattarai ◽  
Wei Yang ◽  
Ainong Shi ◽  
Chunda Feng ◽  
Braham Dhillon ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Downy Mildew ◽  
Association Analysis ◽  
Spinacia Oleracea ◽  
Genotyping By Sequencing ◽  
Significant Snps ◽  
Snp Markers ◽  
Resistance Locus ◽  
Downy Mildew Resistance ◽  
Mildew Resistance

Abstract Background Downy mildew, the most devastating disease of spinach (Spinacia oleracea L.), is caused by the oomycete Peronospora effusa [=P. farinosa f. sp. spinaciae]. The P. effusa shows race specificities to the resistant host and comprises 19 reported races and many novel isolates. Sixteen new P. effusa races were identified during the past three decades, and the new pathogen races are continually overcoming the genetic resistances used in commercial cultivars. A spinach breeding population derived from the cross between cultivars Whale and Lazio was inoculated with P. effusa race 16 in an environment-controlled facility; disease response was recorded and genotyped using genotyping by sequencing (GBS). The main objective of this study was to identify resistance-associated single nucleotide polymorphism (SNP) markers from the cultivar Whale against the P. effusa race 16. Results Association analysis conducted using GBS markers identified six significant SNPs (S3_658,306, S3_692697, S3_1050601, S3_1227787, S3_1227802, S3_1231197). The downy mildew resistance locus from cultivar Whale was mapped to a 0.57 Mb region on chromosome 3, including four disease resistance candidate genes (Spo12736, Spo12784, Spo12908, and Spo12821) within 2.69–11.28 Kb of the peak SNP. Conclusions Genomewide association analysis approach was used to map the P. effusa race 16 resistance loci and identify associated SNP markers and the candidate genes. The results from this study could be valuable in understanding the genetic basis of downy mildew resistance, and the SNP marker will be useful in spinach breeding to select resistant lines.

scholarly journals Gene Expression in First Trimester Preeclampsia Placenta

2010 ◽  
Vol 13 (2) ◽  
pp. 134-139 ◽  
Author(s):  
Sandra A. Founds ◽  
Lauren A. Terhorst ◽  
Kirk P. Conrad ◽  
W. Allen Hogge ◽  
Arun Jeyabalan ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Chorionic Villus ◽  
First Trimester ◽  
Chorionic Villus Sampling ◽  
Qrt Pcr ◽  
Individualized Care ◽  
Additional Control ◽  
Polymerase Chain ◽  
The Difference

Background. The goal of this study was to further validate eight candidate genes identified in a microarray analysis of first trimester placentas in preeclampsia. Material and method. Surplus chorionic villus sampling (CVS) specimens of 4 women subsequently diagnosed with preeclampsia (PE) and 8 control women (C) without preeclampsia analyzed previously by microarray and 24 independent additional control samples (AS) were submitted for confirmatory studies by quantitative real-time polymerase chain reaction (qRT-PCR). Results. Downregulation was significant in FSTL3 in PE as compared to C and AS (p = .04). PAEP was downregulated, but the difference was only significant between C and AS (p = .002) rather than between PE and either of the control groups. Expression levels for CFH, EPAS1, IGFBP1, MMP12, and SEMA3C were not statistically different among groups, but trends were consistent with microarray results; there was no anti-correlation. S100A8 was not measurable in all samples, probably because different probes and primers were needed. Conclusions. This study corroborates reduced FSTL3 expression in the first trimester of preeclampsia. Nonsignificant trends in the other genes may require follow-up in studies powered for medium or medium/large effect sizes. qRT-PCR verification of the prior microarray of CVS may support the placental origins of preeclampsia hypothesis. Replication is needed for the candidate genes as potential biomarkers of susceptibility, early detection, and/or individualized care of maternal—infant preeclampsia.

Investigation of LDHA and COPB1 as candidate genes for muscle development in the MYOD1 region of pig chromosome 2

2009 ◽  
Vol 37 (1) ◽  
pp. 629-636 ◽  
Author(s):  
Haifang Qiu ◽  
Xuewen Xu ◽  
Bing Fan ◽  
Max F. Rothschild ◽  
Yerle Martin ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Muscle Development ◽  
Chromosome 2

Comparative mapping of a QTL controlling black point formation in barley

2008 ◽  
Vol 35 (5) ◽  
pp. 427 ◽  
Author(s):  
Timothy J. March ◽  
Jason A. Able ◽  
Kerrie Willsmore ◽  
Carolyn J. Schultz ◽  
Amanda J. Able
Keyword(s):  
Candidate Genes ◽  
Sequence Similarity ◽  
Rice Genome ◽  
In Silico Analysis ◽  
Barley Grain ◽  
Future Research ◽  
Rflp Markers ◽  
Physiological Disorder ◽  
High Sequence Similarity ◽  
Black Point

The dark discoloration of the embryo end of barley grain (known as black point) is a physiological disorder and the discovery of a quantitative trait locus (QTL) on 2H confirms this trait is controlled genetically. The mechanisms underlying black point tolerance can now be dissected through identification of candidate genes. Comparisons between the QTL identified on chromosomes 2H of barley and 2B of wheat suggest that they are in similar positions near the centromere. In silico analysis, using rice, identified genes residing on two comparative chromosomes (4 and 7) of the rice genome. Analysis of the 12.6 Mb region revealed 1928 unique annotations classified into 11 functional categories. Expressed sequence tags (ESTs) with high sequence similarity to enzymes proposed to be involved in black point formation were used to develop restriction fragment length polymorphisms (RFLPs). To ensure an even coverage of markers across the QTL, RFLP markers were also developed from other ESTs. Mapping of these markers has reduced the QTL region from 28 to 18 cM. This study has identified candidate genes for the control of black point formation and paves the way for future research to develop black point resistant barley cultivars.

scholarly journals Characterization, Tissue Expression, and Imprinting Analysis of the Porcine CDKN1C and NAP1L4 Genes

2012 ◽  
Vol 2012 ◽  
pp. 1-7 ◽  
Author(s):  
Shun Li ◽  
Juan Li ◽  
Jiawei Tian ◽  
Ranran Dong ◽  
Jin Wei ◽  
...  
Keyword(s):  
Skeletal Muscle ◽  
Small Intestine ◽  
Candidate Genes ◽  
Tissue Specificity ◽  
Mammalian Species ◽  
Tissue Expression ◽  
Chromosome 2 ◽  
Porcine Chromosome ◽  
Rt Pcr ◽  
Lung And Kidney

CDKN1C and NAP1L4 in human CDKN1C/KCNQ1OT1 imprinted domain are two key candidate genes responsible for BWS (Beckwith-Wiedemann syndrome) and cancer. In order to increase understanding of these genes in pigs, their cDNAs are characterized in this paper. By the IMpRH panel, porcine CDKN1C and NAP1L4 genes were assigned to porcine chromosome 2, closely linked with IMpRH06175 and with LOD of 15.78 and 17.94, respectively. By real-time quantitative RT-PCR and polymorphism-based method, tissue and allelic expression of both genes were determined using F1 pigs of Rongchang and Landrace reciprocal crosses. The transcription levels of porcine CDKN1C and NAP1L4 were significantly higher in placenta than in other neonatal tissues (P<0.01) although both genes showed the highest expression levels in the lung and kidney of one-month pigs (P<0.01). Imprinting analysis demonstrated that in pigs, CDKN1C was maternally expressed in neonatal heart, tongue, bladder, ovary, spleen, liver, skeletal muscle, stomach, small intestine, and placenta and biallelically expressed in lung and kidney, while NAP1L4 was biallelically expressed in the 12 neonatal tissues examined. It is concluded that imprinting of CDKN1C is conservative in mammals but has tissue specificity in pigs, and imprinting of NAP1L4 is controversial in mammalian species.

Abstract 414: Ath28 Congenic Mice Confirm Atherosclerosis Modifying Gene on the Distal End of Chromosome 2

2017 ◽  
Vol 37 (suppl_1) ◽  
Author(s):  
Juying Han ◽  
Jonathan D Smith
Keyword(s):  
Body Weight ◽  
Total Cholesterol ◽  
Candidate Genes ◽  
Aortic Root ◽  
The Body ◽  
Chow Diet ◽  
Chromosome 2 ◽  
Congenic Mice ◽  
Cholesterol Levels ◽  
Dd Mice

Objective: Strain intercrosses between apoE-deficient mice on the AKR (athero-resistant) and DBA/2 (athero-sensitive) strains identified the Ath28 quantitative trait locus (QTL) on the distal end of chromosome 2 (chr 2). We bred congenic mice on the DBA/2 background containing AKR alleles on chr 2 from 172.5 to 180 Mb in order to confirm the presence of atherosclerosis modifying genes in this region. Methods and Results: We used marker assisted backcrossing to generate DBA/2.AKR (chr 2) apoE-deficient congenic mice. High density genotyping using the MegaMuga array revealed that the AKR strain donated DNA on chr 2 from 171.5 Mb to the end of the chromosome, with the most distal marker tested at 180 Mb, while DBA/2 markers were found elsewhere in the genome. Mice heterozygote for the congenic interval were intercrossed to generate progeny homozygous for the AKR allele (AA) or the DBA/2 allele (DD). Female and male mice were fed a chow diet and sacrificed at 16 weeks of age. In the females, there was no effect on body weight; the total cholesterol levels trended 13% lower for the DD vs. AA mice (p=0.07); and, the HDL-C levels were 55% higher for the DD vs. AA mice (p=0.05). Despite having lower total cholesterol levels, the DD mice had 68% larger aortic root lesion areas (p=0.05, N=10 and 14 for AA and DD mice, respectively). In the males, the body weight was 12% higher in the DD vs. AA mice (p<0.01); the total cholesterol levels were similar in the DD and AA mice; and, the HDL-C levels were 73% higher for the DD vs. AA mice (p<0.05). The male DD mice had 27% larger aortic root lesion areas (NS), but we are adding more mice to this study to determine if this is significant (N=6 and 11 for AA and DD mice, respectively). Conclusions: Ath28 congenic mice confirm the presence of an atherosclerosis modifying gene on the distal end of chr 2 in chow-fed females. This interval in chr 2 contains over 100 genes. Our prior identification of missense variants between these strains, as well as transcriptomic and eQTL analyses have identified some candidate genes in this interval including Cstf1, Ctcfl, Zbp1, Ankrd60, Gnas, Cdh4, Ctsz, and Rae1 . Further functional genomic studies and creating mice with smaller congenic intervals will be needed in order to narrow the list of candidate genes for in vivo testing.

Development of a polymerase chain reaction diagnostic test for the detection of the biotrophic pathogen Plasmopara halstedii in sunflower

1999 ◽  
Vol 45 (9) ◽  
pp. 797-803 ◽  
Author(s):  
Patricia Roeckel-Drevet ◽  
Jeanne Tourvieille ◽  
Joël R Drevet ◽  
Véronique Says-Lesage ◽  
Paul Nicolas ◽  
...  
Keyword(s):  
Polymerase Chain Reaction ◽  
Helianthus Annuus ◽  
Downy Mildew ◽  
Random Amplified Polymorphic Dna ◽  
Parasitic Fungus ◽  
Sequence Information ◽  
Chain Reaction ◽  
Plasmopara Halstedii ◽  
Polymerase Chain

The obligate parasitic fungus-like organism Plasmopara halstedii (Farl.) Berl. et De Toni, is the causal agent of downy mildew disease in sunflower (Helianthus annuus). New races of this economically important parasite are regularly detected throughout the world. In addition, fungicide-resistant isolates have been reported in Europe and North America. These observations of parasite evolution, as well as the risk of propagation of the disease by infected seeds, means that it is necessary to guarantee the absence of Plasmopara halstedii in seed shipments. We report here the development of a rapid assay that can be used to detect infection by Plasmopara halstedii in plant tissues. Based on the nucleotide sequence information obtained from one cloned random amplified polymorphic DNA fragment, specific oligonucleotides were designed and used as primers for in vitro DNA amplification by polymerase chain reaction. An amplification product was detected on agarose gel stained with ethidium bromide when DNA from various Plasmopara halstedii races was tested, whereas no amplified DNA was detected when DNA from other origins was tested, including DNA from the host plant. The sensitivity of the technique was evaluated. The assay successfully reveals the presence of Plasmopara halstedii in infected sunflower plants prior to sporulation.Key words : diagnosis, polymerase chain reaction, SCAR, downy mildew, Helianthus annuus.

138. GENOME-WIDE LINKAGE SCAN FOR FAMILIAL DIZYGOTIC TWINNING

2010 ◽  
Vol 22 (9) ◽  
pp. 56
Author(s):  
J. N. Painter ◽  
G. Willemsen ◽  
D. R. Nyholt ◽  
C. Hoekstra ◽  
D. Duffy ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Complex Trait ◽  
Potential Candidate ◽  
Chromosome 2 ◽  
Family Work ◽  
Linkage Analyses ◽  
Genome Wide ◽  
A Genome ◽  
The Usa ◽  
Genetic And Environmental Factors

The tendency to conceive dizygotic (DZ) twins is a complex trait influenced by genetic and environmental factors. To search for new candidate loci for twinning we have conducted a genome-wide linkage scan in 525 families using microsatellite and single nucleotide polymorphism (SNP) marker panels. Non-parametric linkage analyses including 523 families containing a total of 1115 mothers of DZ twins (MODZT) from Australia and New Zealand (ANZ) and The Netherlands (NL) produced four linkage peaks above the threshold for suggestive linkage, including a highly suggestive peak at the extreme telomeric end of chromosome 6 with an exponential (exp)LOD score of 2.813 (P = 0.0002). Since the DZ twinning rate increases steeply with maternal age independent of genetic effects, we also investigated linkage including only families where at least one MODZT gave birth to her first set of twins before the age of 30. These analyses produced a maximum expLOD score of 2.718 (p = 0.0002), largely due to linkage signal from the ANZ cohort, however, ordered subset analyses indicated this result is most likely a chance finding in the combined dataset. Linkage analyses were also performed for two large DZ twinning families from the USA, one of which produced a peak on chromosome 2 in the region of two potential candidate genes. Sequencing of FSHR and FIGLA, along with INHBB in MODZTs from two large NL families with family-specific linkage peaks directly over this gene, revealed a potentially functional variant in the 5’ untranslated region of FSHR that segregated with the DZ twinning phenotype in the UT family. Work is continuing screening candidate genes. Our data provide further evidence for complex inheritance of familial DZ twinning.

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