scholarly journals Identification of Novel Loci and Candidate Genes for Cucumber Downy Mildew Resistance Using GWAS

Plants ◽  
2020 ◽  
Vol 9 (12) ◽  
pp. 1659
Author(s):  
Xiaoping Liu ◽  
Hongwei Lu ◽  
Panna Liu ◽  
Han Miao ◽  
Yuling Bai ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Downy Mildew ◽  
Field Trials ◽  
Downy Mildew Resistance ◽  
Allele Mining ◽  
Phenotypic Data ◽  
Homologous Genes ◽  
Genome Wide ◽  
Causal Genes ◽  
Cucumber Downy Mildew

Downy mildew (DM) is one of the most serious diseases in cucumber. Multiple quantitative trait loci (QTLs) for DM resistance have been detected in a limited number of cucumber accessions. In this study we applied genome-wide association analysis (GWAS) to detected genetic loci for DM resistance in a core germplasm (CG) of cucumber lines that represent diverse origins and ecotypes. Phenotypic data on responses to DM infection were collected in four field trials across three years, 2014, 2015, and 2016. With the resequencing data of these CG lines, GWAS for DM resistance was performed and detected 18 loci that were distributed on all the seven cucumber chromosomes. Of these 18 loci, only six (dmG1.4, dmG4.1, dmG4.3, dmG5.2, dmG7.1, and dmG7.2) were detected in two experiments, and were considered as loci with a stable effect on DM resistance. Further, 16 out of the 18 loci colocalized with the QTLs that were reported in previous studies and two loci, dmG2.1 and dmG7.1, were novel ones identified only in this study. Based on the annotation of homologous genes in Arabidopsis and pairwise LD correlation analysis, several candidate genes were identified as potential causal genes underlying the stable and novel loci, including Csa1G575030 for dmG1.4, Csa2G060360 for dmG2.1, Csa4G064680 for dmG4.1, Csa5G606470 for dmG5.2, and Csa7G004020 for dmG7.1. This study shows that the CG germplasm is a very valuable resource carrying known and novel QTLs for DM resistance. The potential of using these CG lines for future allele-mining of candidate genes was discussed in the context of breeding cucumber with resistance to DM.

scholarly journals Identification of novel loci and candidate genes for cucumber downy mildew resistance using GWAS

2020 ◽  
Author(s):  
Xiaoping Liu ◽  
Hongwei Lu ◽  
Panna Liu ◽  
Han Miao ◽  
Zifu Yan ◽  
...  
Keyword(s):  
Candidate Gene ◽  
Candidate Genes ◽  
Downy Mildew ◽  
Theoretical Basis ◽  
Wrky Transcription Factor ◽  
Downy Mildew Resistance ◽  
The Core ◽  
Homologous Genes ◽  
Genome Wide ◽  
Cucumber Downy Mildew

Abstract Background Downy mildew (DM) is one of the most serious diseases in cucumber and brings the loss of yield and profit. Multiple QTLs for DM resistance have been detected, however, no loci related to resistance was reported using genome-wide association analysis (GWAS). In this study, the core germplasm (CG) of cucumber lines that had been constructed and resequenced were used to identify DM resistance Loci using GWAS technology. Results Thirteen loci (dmG1.1, dmG1.2, dmG2.1, dmG2.2, dmG3.1, dmG4.1, dmG4.2, dmG5.1, dmG5.2, dmG6.1, dmG6.2, dmG7.1 and dmG7.2) associated with DM resistance were detected on all the seven chromosomes. Among these loci, dmG2.1 and dmG7.1 were novel loci compared with previous studies. Based on the annotation of homologous genes in Arabidopsis and pairwise LD correlations, Csa1G575030 could be the most likely candidate gene of dmG1.2; Csa2G059820 and Csa2G060360 could be the candidate gene of dmG2.1. A WRKY transcription factor Csa5G606470 could be the candidate gene of dmG5.2. Csa7G004020 could be the candidate gene of dmG7.1. Conclusions These results identify five candidate genes for four loci related to DM resistance in cucumber which provide theoretical basis for gene cloning and genetic breeding of DM resistance in cucumber.

scholarly journals Genome-Wide Association Mapping of Crown and Brown Rust Resistance in Perennial Ryegrass

Genes ◽  
2021 ◽  
Vol 13 (1) ◽  
pp. 20
Author(s):  
Mattia Fois ◽  
Andrea Bellucci ◽  
Marta Malinowska ◽  
Morten Greve ◽  
Anja Karine Ruud ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Perennial Ryegrass ◽  
Rust Resistance ◽  
Genome Wide Association Study ◽  
Complex Trait ◽  
Field Trials ◽  
Brown Rust ◽  
Genome Wide Association ◽  
Phenotypic Data ◽  
Genome Wide

A population of 239 perennial ryegrass (Lolium perenne L.) genotypes was analyzed to identify marker-trait associations for crown rust (Puccinia coronata f. sp. lolii) and brown rust (Puccinia graminis f. sp. loliina) resistance. Phenotypic data from field trials showed a low correlation (r = 0.17) between the two traits. Genotypes were resequenced, and a total of 14,538,978 SNPs were used to analyze population structure, linkage disequilibrium (LD), and for genome-wide association study. The SNP heritability (h2SNP) was 0.4 and 0.8 for crown and brown rust resistance, respectively. The high-density SNP dataset allowed us to estimate LD decay with the highest possible precision to date for perennial ryegrass. Results showed a low LD extension with a rapid decay of r2 value below 0.2 after 520 bp on average. Additionally, QTL regions for both traits were detected, as well as candidate genes by applying Genome Complex Trait Analysis and Multi-marker Analysis of GenoMic Annotation. Moreover, two significant genes, LpPc6 and LpPl6, were identified for crown and brown rust resistance, respectively, when SNPs were aggregated to the gene level. The two candidate genes encode proteins with phosphatase activity, which putatively can be induced by the host to perceive, amplify and transfer signals to downstream components, thus activating a plant defense response.

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 Genome-Wide Association Study of Root Mealiness and Other Texture-Associated Traits in Cassava

2021 ◽  
Vol 12 ◽  
Author(s):  
Kelechi Uchendu ◽  
Damian Ndubuisi Njoku ◽  
Agre Paterne ◽  
Ismail Yusuf Rabbi ◽  
Daniel Dzidzienyo ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Genome Wide Association Study ◽  
Genome Wide Association ◽  
Nucleotide Polymorphisms ◽  
Phenotypic Data ◽  
Genome Wide ◽  
A Genome ◽  
Breeding Programmes ◽  
Vegetables And Fruits ◽  
Genomic Regions

Cassava breeders have made significant progress in developing new genotypes with improved agronomic characteristics such as improved root yield and resistance against biotic and abiotic stresses. However, these new and improved cassava (Manihot esculenta Crantz) varieties in cultivation in Nigeria have undergone little or no improvement in their culinary qualities; hence, there is a paucity of genetic information regarding the texture of boiled cassava, particularly with respect to its mealiness, the principal sensory quality attribute of boiled cassava roots. The current study aimed at identifying genomic regions and polymorphisms associated with natural variation for root mealiness and other texture-related attributes of boiled cassava roots, which includes fibre, adhesiveness (ADH), taste, aroma, colour, and firmness. We performed a genome-wide association (GWAS) analysis using phenotypic data from a panel of 142 accessions obtained from the National Root Crops Research Institute (NRCRI), Umudike, Nigeria, and a set of 59,792 high-quality single nucleotide polymorphisms (SNPs) distributed across the cassava genome. Through genome-wide association mapping, we identified 80 SNPs that were significantly associated with root mealiness, fibre, adhesiveness, taste, aroma, colour and firmness on chromosomes 1, 4, 5, 6, 10, 13, 17 and 18. We also identified relevant candidate genes that are co-located with peak SNPs linked to these traits in M. esculenta. A survey of the cassava reference genome v6.1 positioned the SNPs on chromosome 13 in the vicinity of Manes.13G026900, a gene recognized as being responsible for cell adhesion and for the mealiness or crispness of vegetables and fruits, and also known to play an important role in cooked potato texture. This study provides the first insights into understanding the underlying genetic basis of boiled cassava root texture. After validation, the markers and candidate genes identified in this novel work could provide important genomic resources for use in marker-assisted selection (MAS) and genomic selection (GS) to accelerate genetic improvement of root mealiness and other culinary qualities in cassava breeding programmes in West Africa, especially in Nigeria, where the consumption of boiled and pounded cassava is low.

QTLs and candidate genes for downy mildew resistance conferred by interspecific grape (V. vinifera L. × V. amurensis Rupr.) crossing

2019 ◽  
Vol 244 ◽  
pp. 200-207 ◽  
Author(s):  
Hong Lin ◽  
Huan Leng ◽  
Yinshan Guo ◽  
Satoru Kondo ◽  
Yuhui Zhao ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Downy Mildew ◽  
Downy Mildew Resistance ◽  
Mildew Resistance

scholarly journals Identification of Novel Loci and Candidate Genes for Resistance to Powdery Mildew in a Resequenced Cucumber Germplasm

Genes ◽  
2021 ◽  
Vol 12 (4) ◽  
pp. 584
Author(s):  
Xiaoping Liu ◽  
Xingfang Gu ◽  
Hongwei Lu ◽  
Panna Liu ◽  
Han Miao ◽  
...  
Keyword(s):  
Powdery Mildew ◽  
Candidate Genes ◽  
Yield Loss ◽  
Genome Wide Association Study ◽  
Natural Infection ◽  
Disease Index ◽  
Potential Contribution ◽  
Homologous Genes ◽  
Genome Wide ◽  
S Genes

Powdery mildew (PM) is one of the most serious diseases in cucumber and causes huge yield loss. Multiple quantitative trait loci (QTLs) for PM resistance have been reported in previous studies using a limited number of cucumber accessions. In this study, a cucumber core germplasm (CG) consisting of 94 resequenced lines was evaluated for PM resistance in four trials across three years (2013, 2014, and 2016). These trials were performed on adult plants in the field with natural infection. Using genome-wide association study (GWAS), 13 loci (pmG1.1, pmG1.2, pmG2.1, pmG2.2, pmG3.1, pmG4.1, pmG4.2, pmG5.1, pmG5.2, pmG5.3, pmG5.4, pmG6.1, and pmG6.2) associated with PM resistance were detected on all chromosomes except for Chr.7. Among these loci, ten were mapped to chromosomal intervals where QTLs had been reported in previous studies, while, three (pmG2.1, pmG3.1, and pmG4.1) were novel. The loci of pmG2.1, pmG5.2, pmG5.3 showed stronger signal in four trials. Based on the annotation of homologous genes in Arabidopsis and pairwise LD correlation analysis, candidate genes located in the QTL intervals were predicted. SNPs in these candidate genes were analyzed between haplotypes of highly resistant (HR) and susceptible (HS) CG lines, which were defined based on combing disease index data of all trials. Furthermore, candidate genes (Csa5G622830 and CsGy5G015660) reported in previous studies for PM resistance and cucumber orthologues of several PM susceptibility (S) genes (PMR5, PMR-6, and MLO) that are colocalized with certain QTLs, were analyzed for their potential contribution to the QTL effect on both PM and DM in the CG population. This study shows that the CG germplasm is a very valuable resource carrying known and novel QTLs for both PM and DM resistance, which can be exploited in cucumber breeding.

scholarly journals Quantitative Trait Loci Mapping Of Philippine Downy Mildew Resistance Gene In Maize (Zea Mays L.)

Zuriat ◽  
2015 ◽  
Vol 13 (1) ◽  
Author(s):  
D. Ruswandi ◽  
D. M. Hautea ◽  
A. L. Carpena ◽  
R. M. Lantican ◽  
A. M. Salazar ◽  
...  
Keyword(s):  
Downy Mildew ◽  
Inbred Line ◽  
Zea Mays L ◽  
Disease Incidence ◽  
Downy Mildew Resistance ◽  
Generation Mean Analysis ◽  
Cross Combination ◽  
Phenotypic Data ◽  
First Time ◽  
Line P

An experiment to locate QTL conferring resistance against Peronosclerospora philippinensis causing Philippine downy mildew was observed in a BC1F2 population developed from a cross between the susceptible inbred line Pi 23 and the resistant inbred line P 345. Phenotypic data were collected in Los Baños, UPLB for disease incidence. A total of four regions were associated with disease incidence. Some of QTL associated with disease incidence have been reported previously, and the remaining QTL are described here for the first time. The results on QTL analysis using molecular markers also agree with the previous study using classical generation mean analysis of the cross combination Pi 23 x P 345.

scholarly journals Effectiveness of Azoxystrobin in the Control of Erysiphe Cichoracearum and Pseudoperonospora Cubensis on Cucumber

2008 ◽  
Vol 48 (2) ◽  
pp. 147-159 ◽  
Author(s):  
Theerthagiri Anand ◽  
Angannan Chandrasekaran ◽  
Sasthamoorthy Kuttalam ◽  
Govindasamy Senthilraja ◽  
Thiruvengadam Raguchander ◽  
...  
Keyword(s):  
Powdery Mildew ◽  
Downy Mildew ◽  
Field Trial ◽  
Field Studies ◽  
Field Trials ◽  
Optimum Dose ◽  
Pseudoperonospora Cubensis ◽  
Erysiphe Cichoracearum ◽  
Cucumber Downy Mildew ◽  
Phytotoxic Effect

Effectiveness of Azoxystrobin in the Control ofErysiphe CichoracearumandPseudoperonospora Cubensison CucumberThe bioefficacy of azoxystrobin (Amistar 25 SC) was tested against cucumber downy mildew and powdery mildew diseases. The two season trials of field studies revealed that the disease progression of cucumber downy mildew and powdery mildew was successfully arrested by azoxystrobin. Spraying of azoxystrobin at various doses (31.25, 62.50 and 125g a.s./ha) revealed that 125 g a.s./ha (500 ml/ha) was considered as the optimum dose for the control of these diseases of cucumber. The treatment also recorded the highest yield of 13.23 and 14.46 tonnes/ha in the first and second season, respectively. No phytotoxic effect of azoxystrobin was observed in the both field trials even at four times of the recommended dose 125 g a.s./ha. The persistence of azoxystrobin at 250 and 500 g a.s./ha was observed up to seven days after last spraying. However, the persistence of azoxystrobin at 31.25, 62.50 and 125 a.s./ha was observed up to three to five days after last spraying. The safe waiting period for the harvest of cucumber fruits was 1.53 days in the first field trial and 2.37 days in the second field trial, respectively at azoxystrobin 125 g a.s./ha. The residues of azoxystrobin were at below detectable level (BDL) in the harvested cucumber fruits.

scholarly journals Genome-Wide Detection of Genetic Loci and Candidate Genes for Body Conformation Traits in Duroc × Landrace × Yorkshire Crossbred Pigs

2021 ◽  
Vol 12 ◽  
Author(s):  
Hui Zhang ◽  
Zhanwei Zhuang ◽  
Ming Yang ◽  
Rongrong Ding ◽  
Jianping Quan ◽  
...  
Keyword(s):  
Body Weight ◽  
Candidate Genes ◽  
Genetic Architecture ◽  
Genome Wide Association Study ◽  
Body Height ◽  
Gene Set Enrichment Analysis ◽  
Phenotypic Data ◽  
Body Conformation ◽  
Genome Wide ◽  
A Genome

The Duroc × (Landrace × Yorkshire) hybrid pigs (DLY) are the most popular commercial pigs, providing consumers with the largest source of pork. In order to gain more insights into the genetic architecture of economically important traits in pigs, we performed a genome-wide association study (GWAS) using the GeneSeek Porcine 50 K SNP Chip to map the genetic markers and genes associated with body conformation traits (BCT) in 311 DLY pigs. The quantitative traits analyzed included body weight (BW), carcass length (CL), body length (BL), body height (BH), and body mass index (BMI). BMI was defined as BMICL, BMIBL, and BMIBH, respectively, based on CL, BL, and BH phenotypic data. We identified 82 SNPs for the seven traits by GEMMA-based and FarmCPU-based GWASs. Both methods detected two quantitative trait loci (QTL) on SSC8 and SSC17 for body conformation traits. Several candidate genes (such as TNFAIP3, KDM4C, HSPG2, BMP2, PLCB4, and GRM5) were found to be associated with body weight and body conformation traits in pigs. Notably, the BMP2 gene had pleiotropic effects on CL, BL, BH, BMICL, and BMIBL and is proposed as a strong candidate gene for body size due to its involvement in growth and bone development. Furthermore, gene set enrichment analysis indicated that most of the pathway terms are associated with regulation of cell growth, negative regulation of cell population proliferation, and chondrocyte differentiation. We anticipate that these results further advance our understanding of the genetic architecture of body conformation traits in the popular commercial DLY pigs and provide new insights into the genetic architecture of BMI in pigs.

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