scholarly journals Identification and Fine Mapping of qPBR10-1, A Novel Locus Controlling Panicle Blast Resistance in Pigm-Containing P/TGMS Line

2021 ◽  
Author(s):  
Yunyu Wu ◽  
Ning Xiao ◽  
Yuhong Li ◽  
Qiang Gao ◽  
Yuese Ning ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Blast Resistance ◽  
Expression Patterns ◽  
Genotyping By Sequencing ◽  
Hypothetical Protein ◽  
Phenotypic Variance ◽  
Advanced Backcross ◽  
Family Protein ◽  
Panicle Blast ◽  
Genes Encoding

Abstract Rice blast is one of the most widespread and devastating diseases in rice production. Tremendous success has been achieved in identification and characterization of genes and quantitative trait loci (QTLs) conferring seedling blast resistance, however, genetic studies on panicle blast resistance have lagged far behind. In this study, two advanced backcross inbred sister lines (MSJ13 and MSJ18) were obtained in the process of introducing Pigm into C134S, and showed significant differences in the panicle blast resistance. One F2 population derived from the crossing MSJ13/MSJ18 was used to QTL mapping for panicle blast resistance using Genotyping by Sequencing (GBS) method. A total of 7 QTLs were identified, including a major QTL qPBR10-1 on chromosome 10 that explaining 24.21% of phenotypic variance with LOD scores of 6.62. Furthermore, qPBR10-1 was verified via the BC1F2 and BC1F3 population and narrowed to a 60.6-kb region with six candidate genes predicted, including two genes encoding exonuclease family protein, two genes encoding hypothetical protein, and two genes encoding transposon protein. The nucleotide variations and the expression patterns of the candidate genes were identified and analyzed between MSJ13 and MSJ18 through sequence comparison and RT-PCR approach, and results indicated that ORF1 and ORF2 encoding exonuclease family protein might be the causal candidate genes for panicle blast resistance in the qPBR10-1 locus.

scholarly journals Identification and fine mapping of qPBR10-1, a novel locus controlling panicle blast resistance in Pigm-containing P/TGMS line

2021 ◽  
Author(s):  
Yunyu Wu ◽  
Ning Xiao ◽  
Yuhong Li ◽  
Qiang Gao ◽  
Yuese Ning ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Sequence Comparison ◽  
Blast Resistance ◽  
Rt Pcr ◽  
Advanced Backcross ◽  
Family Protein ◽  
Panicle Blast ◽  
Genes Encoding ◽  
Causal Candidate ◽  
Major Qtl

Abstract Background Rice blast is one of the most widespread and devastating diseases in rice production. Tremendous success has been achieved in identification and characterization of genes and quantitative trait loci (QTLs) conferring seedling blast resistance, however, genetic studies on panicle blast resistance have lagged far behind. Results In this study, two advanced backcross inbred sister lines (MSJ13 and MSJ18) were obtained in the process of introducing Pigm into C134S, and showed significant differences in the panicle blast resistance. One F2 population derived from the crossing MSJ13/MSJ18 was used to QTL mapping for panicle blast resistance using Genotyping by Sequencing (GBS) method. A total of 7 QTLs were identified, including a major QTL qPBR10-1 on chromosome 10 that explaining 24.21% of phenotypic variance with LOD scores of 6.62. Furthermore, qPBR10-1 was verified via the BC1F2 and BC1F3 population and narrowed to a 60.6-kb region with six candidate genes predicted, including two genes encoding exonuclease family protein, two genes encoding hypothetical protein, and two genes encoding transposon protein. The nucleotide variations and the expression patterns of the candidate genes were identified and analyzed between MSJ13 and MSJ18 through sequence comparison and RT-PCR approach, and results indicated that ORF1 and ORF2 encoding exonuclease family protein might be the causal candidate genes for panicle blast resistance in the qPBR10-1 locus. Conclusions A total of 7 QTLs conferring panicle blast resistance was identified from one F2 population derived from the crossing between two advanced backcross inbred sister lines MSJ13 and MSJ18, which harbored the broad-spectrum resistance gene Pigm. A major QTL qPBR10-1 was fine mapped in a 60.6-kb region with six candidate genes predicted, and ORF1 and ORF2 encoding exonuclease family protein might be the causal candidate genes for panicle blast resistance in the qPBR10-1 locus through sequence comparison and RT-PCR approach.

Insights into the heat-responsive transcriptional network of tomato contrasting genotypes

2021 ◽  
Vol 19 (1) ◽  
pp. 44-57
Author(s):  
Sirine Werghi ◽  
Charfeddine Gharsallah ◽  
Nishi Kant Bhardwaj ◽  
Hatem Fakhfakh ◽  
Faten Gorsane
Keyword(s):  
Heat Stress ◽  
Heat Shock ◽  
Candidate Genes ◽  
Expression Patterns ◽  
Response Strategies ◽  
Transcriptional Reprogramming ◽  
Genes Encoding ◽  
Breeding Programmes ◽  
Gene Transcripts ◽  
Resource Data

AbstractDuring recent decades, global warming has intensified, altering crop growth, development and survival. To overcome changes in their environment, plants undergo transcriptional reprogramming to activate stress response strategies/pathways. To evaluate the genetic bases of the response to heat stress, Conserved DNA-derived Polymorphism (CDDP) markers were applied across tomato genome of eight cultivars. Despite scattered genotypes, cluster analysis allowed two neighbouring panels to be discriminate. Tomato CDDP-genotypic and visual phenotypic assortment permitted the selection of two contrasting heat-tolerant and heat-sensitive cultivars. Further analysis explored differential expression in transcript levels of genes, encoding heat shock transcription factors (HSFs, HsfA1, HsfA2, HsfB1), members of the heat shock protein (HSP) family (HSP101, HSP17, HSP90) and ascorbate peroxidase (APX) enzymes (APX1, APX2). Based on discriminating CDDP-markers, a protein functional network was built allowing prediction of candidate genes and their regulating miRNA. Expression patterns analysis revealed that miR156d and miR397 were heat-responsive showing a typical inverse relation with the abundance of their target gene transcripts. Heat stress is inducing a set of candidate genes, whose expression seems to be modulated through a complex regulatory network. Integrating genetic resource data is required for identifying valuable tomato genotypes that can be considered in marker-assisted breeding programmes to improve tomato heat tolerance.

scholarly journals Novel Organ-Specific Genetic Factors for Quantitative Resistance to Late Blight in Potato

2019 ◽  
Author(s):  
Deissy Katherine Juyo Rojas ◽  
Johana Carolina Soto Sedano ◽  
Agim Ballvora ◽  
Jens Léon ◽  
Teresa Mosquera Vásquez
Keyword(s):  
Late Blight ◽  
Candidate Genes ◽  
Genome Wide Association Study ◽  
Quantitative Resistance ◽  
Genotyping By Sequencing ◽  
Phenotypic Variance ◽  
Resistance Response ◽  
Genome Wide ◽  
A Genome ◽  
Organ Specific

AbstractPotato, Solanum tuberosum, is one of the highest consumed food in the world, being the basis of the diet of millions of people. The main limiting and destructive disease of potato is late blight, caused by Phytophtora infestans. Here, we present a multi-environmental analysis of the response to P. infestans using an association panel of 150 accessions of S. tuberosum Group Phureja, evaluated in two localities in Colombia. Disease resistance data were merged with a genotyping matrix of 83,862 SNPs obtained by 2b-restriction site–associated DNA and Genotyping by sequencing approaches into a Genome-wide association study. We are reporting 16 organ-specific QTL conferring resistance to late blight. These QTL explain from 13.7% to 50.9% of the phenotypic variance. Six and ten QTL were detected for resistance response in leaves and stem, respectively. In silico analysis revealed 15 candidate genes for resistance to late blight. Four of them have no functional genome annotation, while eleven candidate genes code for diverse proteins, including one leucine-rich repeat kinase.

scholarly journals Identification of Soybean Genes Whose Expression is Affected by the Ensifer fredii HH103 Effector Protein NopP

2018 ◽  
Vol 19 (11) ◽  
pp. 3438 ◽  
Author(s):  
Jinhui Wang ◽  
Jieqi Wang ◽  
Chunyan Liu ◽  
Chao Ma ◽  
Changyu Li ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Recombinant Inbred Lines ◽  
Expression Patterns ◽  
Dry Weight ◽  
Genomic Region ◽  
Wild Type ◽  
Host Proteins ◽  
Pcr Assay ◽  
Qrt Pcr ◽  
Genes Encoding

In some legume–rhizobium symbioses, host specificity is influenced by rhizobial nodulation outer proteins (Nops). However, the genes encoding host proteins that interact with Nops remain unknown. We generated an Ensifer fredii HH103 NopP mutant (HH103ΩNopP), and analyzed the nodule number (NN) and nodule dry weight (NDW) of 10 soybean germplasms inoculated with the wild-type E. fredii HH103 or the mutant strain. An analysis of recombinant inbred lines (RILs) revealed the quantitative trait loci (QTLs) associated with NopP interactions. A soybean genomic region containing two overlapping QTLs was analyzed in greater detail. A transcriptome analysis and qRT-PCR assay were used to identify candidate genes encoding proteins that interact with NopP. In some germplasms, NopP positively and negatively affected the NN and NDW, while NopP had different effects on NN and NDW in other germplasms. The QTL region in chromosome 12 was further analyzed. The expression patterns of candidate genes Glyma.12g031200 and Glyma.12g073000 were determined by qRT-PCR, and were confirmed to be influenced by NopP.

scholarly journals Genotyping-by-Sequencing Based Genetic Mapping Identified Major and Consistent Genomic Regions for Productivity and Quality Traits in Peanut

2021 ◽  
Vol 12 ◽  
Author(s):  
Mangesh P. Jadhav ◽  
Sunil S. Gangurde ◽  
Anil A. Hake ◽  
Arati Yadawad ◽  
Supriya S. Mahadevaiah ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Oil Quality ◽  
Genotyping By Sequencing ◽  
Phenotypic Variance ◽  
Potential Candidate ◽  
Quality Traits ◽  
Single Marker Analysis ◽  
Main Effect ◽  
Genomic Regions ◽  
Main Effect Qtls

With an objective of identifying the genomic regions for productivity and quality traits in peanut, a recombinant inbred line (RIL) population developed from an elite variety, TMV 2 and its ethyl methane sulfonate (EMS)-derived mutant was phenotyped over six seasons and genotyped with genotyping-by-sequencing (GBS), Arachis hypogaea transposable element (AhTE) and simple sequence repeats (SSR) markers. The genetic map with 700 markers spanning 2,438.1 cM was employed for quantitative trait loci (QTL) analysis which identified a total of 47 main-effect QTLs for the productivity and oil quality traits with the phenotypic variance explained (PVE) of 10–52% over the seasons. A common QTL region (46.7–50.1 cM) on Ah02 was identified for the multiple traits, such as a number of pods per plant (NPPP), pod weight per plant (PWPP), shelling percentage (SP), and test weight (TW). Similarly, a QTL (7.1–18.0 cM) on Ah16 was identified for both SP and protein content (PC). Epistatic QTL (epiQTL) analysis revealed intra- and inter-chromosomal interactions for the main-effect QTLs and other genomic regions governing these productivity traits. The markers identified by a single marker analysis (SMA) mapped to the QTL regions for most of the traits. Among the five potential candidate genes identified for PC, SP and oil quality, two genes (Arahy.7A57YA and Arahy.CH9B83) were affected by AhMITE1 transposition, and three genes (Arahy.J5SZ1I, Arahy.MZJT69, and Arahy.X7PJ8H) involved functional single nucleotide polymorphisms (SNPs). With major and consistent effects, the genomic regions, candidate genes, and the associated markers identified in this study would provide an opportunity for gene cloning and genomics-assisted breeding for increasing the productivity and enhancing the quality of peanut.

scholarly journals Candidate Defense Genes as Predictors of Quantitative Blast Resistance in Rice

2004 ◽  
Vol 17 (10) ◽  
pp. 1146-1152 ◽  
Author(s):  
Bin Liu ◽  
Shaohong Zhang ◽  
Xiaoyuan Zhu ◽  
Qiyun Yang ◽  
Shangzhong Wu ◽  
...  
Keyword(s):  
Complex Traits ◽  
Agronomic Traits ◽  
Blast Resistance ◽  
Quantitative Resistance ◽  
Field Tests ◽  
Interval Mapping ◽  
Oxalate Oxidase ◽  
Advanced Backcross ◽  
Genes Encoding ◽  
Disease Pressure

Although quantitative trait loci (QTL) underpin many desirable agronomic traits, their incorporation into crop plants through marker-assisted selection is limited by the low predictive value of markers on phenotypic performance. Here we used candidate defense response (DR) genes to dissect quantitative resistance in rice using recombinant inbred (RI) and advanced backcross (BC) populations derived from a blast-resistant cultivar, Sanhuangzhan 2 (SHZ-2). Based on DNA profiles of DR genes, RI lines were clustered into two groups corresponding to level of resistance. Five DR genes, encoding putative oxalate oxidase, dehydrin, PR-1, chitinase, and 14-3-3 protein, accounted for 30.0, 23.0, 15.8, 6.7, and 5.5% of diseased leaf area (DLA) variation, respectively. Together, they accounted for 60.3% of the DLA variation and co-localized with resistance QTL identified by interval mapping. Average phenotypic contributions of oxalate oxidase, dehydrin, PR-1, chitinase, and 14-3-3 protein in BC lines were 26.1, 19.0, 18.0, 11.5, and 10.6%, respectively, across environments. Advanced BC lines with four to five effective DR genes showed enhanced resistance under high disease pressure in field tests. Our results demonstrate that the use of natural variation in a few candidate genes can solve a long-standing problem in rice production and has the potential to address other problems involving complex traits.

scholarly journals Lens orientalis Contributes Quantitative Trait Loci and Candidate Genes Associated With Ascochyta Blight Resistance in Lentil

2021 ◽  
Vol 12 ◽  
Author(s):  
Rama Harinath Reddy Dadu ◽  
Ido Bar ◽  
Rebecca Ford ◽  
Prabhakaran Sambasivam ◽  
Janine Croser ◽  
...  
Keyword(s):  
Quantitative Trait Loci ◽  
Candidate Genes ◽  
Quantitative Trait ◽  
Mapping Population ◽  
Ascochyta Blight ◽  
Genotyping By Sequencing ◽  
Defense Responses ◽  
Phenotypic Variance ◽  
Genetic Dissection ◽  
Trait Loci

Australian lentil production is affected by several major biotic constraints including Ascochyta blight (AB), caused by Ascochyta lentis, a devastating fungal disease. Cultivation of AB resistant cultivars, alongside agronomic management including fungicide application, is the current most economically viable control strategy. However, the breakdown of AB resistance in cultivars, such as Northfield and Nipper, suggests the need for introgression of new and diverse resistance genes. Successful introgression entails an understanding of the genetic basis of resistance. In this context, a biparental mapping population derived from a cross between a recently identified AB resistant accession ILWL 180 (Lens orientalis) and a susceptible cultivar ILL 6002 was produced. A genetic linkage map was constructed from single-nucleotide polymorphism markers generated using a genotyping-by-sequencing transcript approach. Genetic dissection of the mapping population revealed a major quantitative trait loci (QTL) region nested with three QTLs on linkage group 5 and explained 9.5–11.5 percent (%) of phenotypic variance for AB resistance. Another QTL was identified on LG2 with phenotypic variance of 9.6%. The identified QTL regions harbored putative candidate genes potentially associated with defense responses to A. lentis infection. The QTL analysis and the candidate gene information are expected to contribute to the development of diagnostic markers and enable marker-assisted resistance selection in lentil breeding programmes.

scholarly journals Two Auxinic Herbicides Affect Brassica napus Plant Hormone Levels and Induce Molecular Changes in Transcription

Biomolecules ◽  
2021 ◽  
Vol 11 (8) ◽  
pp. 1153
Author(s):  
Jutta Ludwig-Müller ◽  
Roman Rattunde ◽  
Sabine Rößler ◽  
Katja Liedel ◽  
Freia Benade ◽  
...  
Keyword(s):  
Brassica Napus ◽  
Expression Patterns ◽  
Growth Conditions ◽  
Growth Stages ◽  
Auxin Response ◽  
Time Points ◽  
Genes Encoding ◽  
Different Temperatures ◽  
Indigenous Plant ◽  
Over Time

With the introduction of the new auxinic herbicide halauxifen-methyl into the oilseed rape (Brassica napus) market, there is a need to understand how this new molecule interacts with indigenous plant hormones (e.g., IAA) in terms of crop response. The aim of this study was to investigate the molecular background by using different growth conditions under which three different auxinic herbicides were administered. These were halauxifen-methyl (Hal), alone and together with aminopyralid (AP) as well as picloram (Pic). Three different hormone classes were determined, free and conjugated indole-3-acetic acid (IAA), aminocyclopropane carboxylic acid (ACC) as a precursor for ethylene, and abscisic acid (ABA) at two different temperatures and growth stages as well as over time (2–168 h after treatment). At 15 °C growth temperature, the effect was more pronounced than at 9 °C, and generally, the younger leaves independent of the developmental stage showed a larger effect on the alterations of hormones. IAA and ACC showed reproducible alterations after auxinic herbicide treatments over time, while ABA did not. Finally, a transcriptome analysis after treatment with two auxinic herbicides, Hal and Pic, showed different expression patterns. Hal treatment leads to the upregulation of auxin and hormone responses at 48 h and 96 h. Pic treatment induced the hormone/auxin response already after 2 h, and this continued for the other time points. The more detailed analysis of the auxin response in the datasets indicate a role for GH3 genes and genes encoding auxin efflux proteins. The upregulation of the GH3 genes correlates with the increase in conjugated IAA at the same time points and treatments. Also, genes for were found that confirm the upregulation of the ethylene pathway.

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 Profiles Associated with Radio-Responsiveness in Locally Advanced Rectal Cancer

Biology ◽  
2021 ◽  
Vol 10 (6) ◽  
pp. 500
Author(s):  
Jeeyong Lee ◽  
Junhye Kwon ◽  
DaYeon Kim ◽  
Misun Park ◽  
KwangSeok Kim ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Expression Profiles ◽  
Cell Cycle Control ◽  
Methylation Status ◽  
Locally Advanced ◽  
Gene Expression Profiles ◽  
Advanced Rectal Cancer ◽  
Bioinformatic Analysis ◽  
Locally Advanced Rectal Cancer ◽  
Genes Encoding

LARC patients were sorted according to their radio-responsiveness and patient-derived organoids were established from the respective cancer tissues. Expression profiles for each group were obtained using RNA-seq. Biological and bioinformatic analysis approaches were used in deciphering genes and pathways that participate in the radio-resistance of LARC. Thirty candidate genes encoding proteins involved in radio-responsiveness–related pathways, including the immune system, DNA repair and cell-cycle control, were identified. Interestingly, one of the candidate genes, cathepsin E (CTSE), exhibited differential methylation at the promoter region that was inversely correlated with the radio-resistance of patient-derived organoids, suggesting that methylation status could contribute to radio-responsiveness. On the basis of these results, we plan to pursue development of a gene chip for diagnosing the radio-responsiveness of LARC patients, with the hope that our efforts will ultimately improve the prognosis of LARC patients.

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