scholarly journals Rapid Mining of Candidate Genes for Verticillium Wilt Resistance in Cotton Based on BSA-Seq Analysis

2021 ◽  
Vol 12 ◽  
Author(s):  
Yanli Cui ◽  
Qun Ge ◽  
Pei Zhao ◽  
Wei Chen ◽  
Xiaohui Sang ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Verticillium Wilt ◽  
Molecular Breeding ◽  
Fiber Quality ◽  
Transcriptome Data ◽  
Virus Induced Gene Silencing ◽  
Cotton Production ◽  
Genomic Information ◽  
Important Cash Crop ◽  
Candidate Loci

Cotton is a globally important cash crop. Verticillium wilt (VW) is commonly known as “cancer” of cotton and causes serious loss of yield and fiber quality in cotton production around the world. Here, we performed a BSA-seq analysis using an F2:3 segregation population to identify the candidate loci involved in VW resistance. Two QTLs (qvw-D05-1 and qvw-D05-2) related to VW resistance in cotton were identified using two resistant/susceptible bulks from the F2 segregation population constructed by crossing the resistant cultivar ZZM2 with the susceptible cultivar J11. A total of 30stop-lost SNPs and 42 stop-gained SNPs, which included 17 genes, were screened in the qvw-D05-2 region by SnpEff analysis. Further analysis of the transcriptome data and qRT-PCR revealed that the expression level of Ghir_D05G037630 (designated as GhDRP) varied significantly at certain time points after infection with V. dahliae. The virus-induced gene silencing of GhDRP resulted in higher susceptibility of the plants to V. dahliae than the control, suggesting that GhDRP is involved in the resistance to V. dahlia infection. This study provides a method for rapid mining of quantitative trait loci and screening of candidate genes, as well as enriches the genomic information and gene resources for the molecular breeding of disease resistance in cotton.

Mulches and Nitrogen Application Improves Cotton Yield and Fiber Quality

2019 ◽  
Vol 1 (1) ◽  
pp. 09-13
Author(s):  
Hakoomat Ali ◽  
Asad Abbas ◽  
Shabir Hussain ◽  
Shoukat Ali Abid ◽  
Shazia Khaliq ◽  
...  
Keyword(s):  
Wheat Straw ◽  
Crop Residues ◽  
Fiber Quality ◽  
Fertilizer Application ◽  
Cotton Yield ◽  
Nitrogen Application ◽  
Cotton Production ◽  
Nitrogen Levels ◽  
Important Cash Crop ◽  
Wheat Straw Mulch

Cotton is an important cash crop and source of foreign exchange. Nitrogen is a critical nutrient for plant growth throughout the life span of the crop. Wheat straw mulch not only source of nitrogen supply but also improves soil fertility and reduces soil erosion. The current study was performed to investigate the effects of mulches and nitrogen application on cotton productivity and fiber quality at the Central Cotton Research Institute (CCRI), Multan. Two crop residues i.e. wheat straw and non wheat straw were used in main plots while nitrogen levels viz. 0,50, 100 and 150 kg ha-1 were randomized in subplots. The highest seed cotton yield (22.99 t ha-1) was obtained by the combination of nitrogen fertilizer application highest level (150 kg N ha-1) along with the wheat straw (20.27 t ha-1). The fiber quality was also affected by the wheat straw along with nitrogen application 150 kg N ha-1 and gave maximum results. In conclusion, wheat straw along with 150 kg ha-1 of Nitrogen application gave maximum results on cotton production as compared to non straw with low nitrogen application.

scholarly journals QTL and candidate gene identification of the node of the first fruiting branch (NFFB) by QTL-seq in upland cotton (Gossypium hirsutum L.)

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Jingjing Zhang ◽  
Xiaoyun Jia ◽  
Xiaohao Guo ◽  
Hengling Wei ◽  
Meng Zhang ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Fiber Quality ◽  
Functional Verification ◽  
Virus Induced Gene Silencing ◽  
Flower Bud ◽  
Early Maturity ◽  
Polymorphic Snps ◽  
Fruiting Branch ◽  
Early Maturing ◽  
Nucleotide Data

Abstract Background The node of the first fruiting branch (NFFB) is an important precocious trait in cotton. Many studies have been conducted on the localization of quantitative trait loci (QTLs) and genes related to fiber quality and yield, but there has been little attention to traits related to early maturity, especially the NFFB, in cotton. Results To identify the QTL associated with the NFFB in cotton, a BC4F2 population comprising 278 individual plants was constructed. The parents and two DNA bulks for high and low NFFB were whole genome sequenced, and 243.8 Gb of clean nucleotide data were generated. A total of 449,302 polymorphic SNPs and 135,353 Indels between two bulks were identified for QTL-seq. Seventeen QTLs were detected and localized on 11 chromosomes in the cotton genome, among which two QTLs (qNFFB-Dt2–1 and qNFFB-Dt3–3) were located in hotspots. Two candidate genes (GhAPL and GhHDA5) related to the NFFB were identified using quantitative real-time PCR (qRT-PCR) and virus-induced gene silencing (VIGS) experiments in this study. Both genes exhibited higher expression levels in the early-maturing cotton material RIL182 during flower bud differentiation, and the silencing of GhAPL and GhHDA5 delayed the flowering time and increased the NFFB compared to those of VA plants in cotton. Conclusions Our study preliminarily found that GhAPL and GhHDA5 are related to the early maturity in cotton. The findings provide a basis for the further functional verification of candidate genes related to the NFFB and contribute to the study of early maturity in cotton.

scholarly journals Current advances in pathogen-plant interaction between Verticillium dahliae and cotton provide new insight in the disease management

2021 ◽  
Vol 4 (1) ◽  
Author(s):  
Koffi Kibalou PALANGA ◽  
Ruixian LIU ◽  
Qun GE ◽  
Juwu GONG ◽  
Junwen LI ◽  
...  
Keyword(s):  
Biological Control ◽  
Cell Wall ◽  
Disease Management ◽  
Gene Silencing ◽  
Cotton Plant ◽  
Verticillium Wilt ◽  
Verticillium Dahliae ◽  
Fiber Quality ◽  
Phytopathogenic Fungus ◽  
Cotton Production

AbstractVerticillium wilt is the second serious vascular wilt caused by the phytopathogenic fungus Verticillium dahliae Kleb. It has distributed worldwide, causing serious yield losses and fiber quality reduction in cotton production. The pathogen has developed different mechanisms like the production of cell wall degrading enzymes, activation of virulence genes and protein effectors to succeed in its infection. Cotton plant has also evolved multiple mechanisms in response to the fungus infection, including a strong production of lignin and callose deposition to strengthen the cell wall, burst of reactive oxygen species, accumulation of defene hormones, expression of defense-related genes, and target-directed strategies like cross-kingdom RNAi for specific virulent gene silencing. This review summarizes the recent progress made over the past two decades in understanding the interactions between cotton plant and the pathogen Verticillium dahliae during the infection process. The review also discusses the achievements in the control practices of cotton verticillium wilt in recent years, including cultivation practices, biological control, and molecular breeding strategies. These studies reveal that effective management strategies are needed to control the disease, while cultural practices and biological control approaches show promising results in the future. Furthermore, the biological control approaches developed in recent years, including antagonistic fungi, endophytic bacteria, and host induced gene silencing strategies provide efficient choices for integrated disease management.

scholarly journals The Cotton Lignin Biosynthetic Gene Gh4CL30 Regulates Lignification and Phenolic Content and Contributes to Verticillium Wilt Resistance

2021 ◽  
pp. MPMI-03-20-0071
Author(s):  
Xian-Peng Xiong ◽  
Shi-Chao Sun ◽  
Qian-Hao Zhu ◽  
Xin-Yu Zhang ◽  
Yan-Jun Li ◽  
...  
Keyword(s):  
Verticillium Wilt ◽  
Expression Profiles ◽  
Lignin Biosynthesis ◽  
Biosynthesis Pathway ◽  
Virus Induced Gene Silencing ◽  
Cotton Production ◽  
Hub Genes ◽  
Time Points ◽  
Before And After ◽  
Open Access Article

Verticillium wilt is a vascular disease causing tremendous damage to cotton production worldwide. However, our knowledge of the mechanisms of cotton resistance or susceptibility to this disease is very limited. In this study, we compared the defense transcriptomes of cotton (Gossypium hirsutum) cultivars Shidalukang 1 (Verticillium dahliae resistant, HR) and Junmian 1 (V. dahliae susceptible, HS) before and after V. dahliae infection, identified hub genes of the network associated with responses to V. dahliae infection, and functionally characterized one of the hub genes involved in biosynthesis of lignin and phenolics. We identified 6,831 differentially expressed genes (DEGs) between the basal transcriptomes of HR and HS; 3,685 and 3,239 of these DEGs were induced in HR and HS, respectively, at different time points after V. dahliae infection. KEGG pathway analysis indicated that DEGs were enriched for genes involved in lignin biosynthesis. In all, 23 hub genes were identified based on a weighted gene coexpression network analysis of the 6,831 DEGs and their expression profiles at different time points after V. dahliae infection. Knockdown of Gh4CL30, one of the hub genes related to the lignin biosynthesis pathway, by virus-induced gene silencing, led to a decreased content of flavonoids, lignin, and S monomer but an increased content of G monomer, G/S lignin monomer, caffeic acid, and ferulic acid, and enhanced cotton resistance to V. dahliae. These results suggest that Gh4CL30 is a key gene modulating the outputs of different branches of the lignin biosynthesis pathway, and provide new insights into cotton resistance to V. dahliae. [Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license .

scholarly journals The Candidate Genes Underlying a Stably Expressed QTL for Low Temperature Germinability in Rice (Oryza sativa L.)

Rice ◽  
2020 ◽  
Vol 13 (1) ◽  
Author(s):  
Tifeng Yang ◽  
Lian Zhou ◽  
Junliang Zhao ◽  
Jingfang Dong ◽  
Qing Liu ◽  
...  
Keyword(s):  
Low Temperature ◽  
Differential Expression ◽  
Candidate Genes ◽  
Complex Traits ◽  
Molecular Breeding ◽  
Genome Wide Association Study ◽  
Oryza Sativa L ◽  
Sequence Comparisons ◽  
Cold Environments ◽  
Promising Source

Abstract Background Direct seeding is an efficient cultivation technique in rice. However, poor low temperature germinability (LTG) of modern rice cultivars limits its application. Identifying the genes associated with LTG and performing molecular breeding is the fundamental way to address this issue. However, few LTG QTLs have been fine mapped and cloned so far. Results In the present study, the LTG evaluation of 375 rice accessions selected from the Rice Diversity Panel 2 showed that there were large LTG variations within the population, and the LTG of Indica group was significantly higher than that of Japonica and Aus groups (p < 0.01). In total, eleven QTLs for LTG were identified through genome-wide association study (GWAS). Among them, qLTG_sRDP2–3/qLTG_JAP-3, qLTG_AUS-3 and qLTG_sRDP2–12 are first reported in the present study. The QTL on chromosome 10, qLTG_sRDP2–10a had the largest contribution to LTG variations in 375 rice accessions, and was further validated using single segment substitution line (SSSL). The presence of qLTG_sRDP2–10a could result in 59.8% increase in LTG under 15 °C low temperature. The expression analysis of the genes within qLTG_sRDP2–10a region indicated that LOC_Os10g22520 and LOC_Os10g22484 exhibited differential expression between the high and low LTG lines. Further sequence comparisons revealed that there were insertion and deletion sequence differences in the promoter and intron region of LOC_Os10g22520, and an about 6 kb variation at the 3′ end of LOC_Os10g22484 between the high and low LTG lines, suggesting that the sequence variations of the two genes could be the cause for their differential expression in high and low LTG lines. Conclusion Among the 11 QTLs identified in this study, qLTG_sRDP2–10a could also be detected in other three studies using different germplasm under different cold environments. Its large effect and stable expression make qLTG_sRDP2–10a particularly valuable in rice breeding. The two genes, LOC_Os10g22484 and LOC_Os10g22520, were considered as the candidate genes underlying qLTG_sRDP2–10a. Our results suggest that integrating GWAS and SSSL can facilitate identification of QTL for complex traits in rice. The identification of qLTG_sRDP2–10a and its candidate genes provide a promising source for gene cloning of LTG and molecular breeding for LTG in rice.

scholarly journals Genome-wide association analysis reveals genetic variations and candidate genes associated with salt tolerance related traits in Gossypium hirsutum

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Peng Xu ◽  
Qi Guo ◽  
Shan Meng ◽  
Xianggui Zhang ◽  
Zhenzhen Xu ◽  
...  
Keyword(s):  
Salt Stress ◽  
Salt Tolerance ◽  
Candidate Genes ◽  
Genetic Variations ◽  
Genome Wide Association ◽  
Cotton Production ◽  
Fresh Matter ◽  
Salt Stress Response ◽  
Genome Wide ◽  
A Genome

Abstract Background Cotton is more resistant to salt and drought stresses as compared to other field crops, which makes itself as a pioneer industrial crop in saline-alkali lands. However, abiotic stresses still negatively affect its growth and development significantly. It is therefore important to breed salt tolerance varieties which can help accelerate the improvement of cotton production. The development of molecular markers linked to causal genes has provided an effective and efficient approach for improving salt tolerance. Results In this study, a genome-wide association study (GWAS) of salt tolerance related traits at seedling stage was performed based on 2 years of phenotype identification for 217 representative upland cotton cultivars by genotyping-by-sequencing (GBS) platform. A total of 51,060 single nucleotide polymorphisms (SNPs) unevenly distributed among 26 chromosomes were screened across the cotton cultivars, and 25 associations with 27 SNPs scattered over 12 chromosomes were detected significantly (−log10p > 4) associated with three salt tolerance related traits in 2016 and 2017. Among these, the associations on chromosome A13 and D08 for relative plant height (RPH), A07 for relative shoot fresh matter weight (RSFW), A08 and A13 for relative shoot dry matter weight (RSDW) were expressed in both environments, indicating that they were likely to be stable quantitative trait loci (QTLs). A total of 12 salt-induced candidate genes were identified differentially expressed by the combination of GWAS and transcriptome analysis. Three promising genes were selected for preliminary function verification of salt tolerance. The increase of GH_A13G0171-silenced plants in salt related traits under salt stress indicated its negative function in regulating the salt stress response. Conclusions These results provided important genetic variations and candidate genes for accelerating the improvement of salt tolerance in cotton.

scholarly journals Genome-wide association analysis reveals genetic variations and candidate genes associated with salt tolerance related traits in Gossypium hirsutum

2020 ◽  
Author(s):  
Peng Xu ◽  
Qi Guo ◽  
Shan Meng ◽  
Xianggui Zhang ◽  
Zhenzhen Xu ◽  
...  
Keyword(s):  
Salt Stress ◽  
Salt Tolerance ◽  
Candidate Genes ◽  
Genetic Variations ◽  
Genome Wide Association ◽  
Cotton Production ◽  
Fresh Matter ◽  
Salt Stress Response ◽  
Genome Wide ◽  
A Genome

Abstract Background: Cotton is more resistant to salt and drought stresses as compared to other field crops, which makes itself as a pioneer industrial crop in saline-alkali lands. However, abiotic stresses still negatively affect its growth and development significantly. It is therefore important to breed salt tolerance varieties which can help accelerate the improvement of cotton production. The development of molecular markers linked to causal genes has provided an effective and efficient approach for improving salt tolerance. Results: In this study, a genome-wide association study (GWAS) of salt tolerance related traits at seedling stage was performed based on two years of phenotype identification for 217 representative upland cotton cultivars by genotyping-by-sequencing (GBS) platform. A total of 51,060 single nucleotide polymorphisms (SNPs) unevenly distributed among 26 chromosomes were screened across the cotton cultivars, and 25 associations with 27 SNPs scattered over 12 chromosomes were detected significantly (-log10p>4) associated with three salt tolerance related traits in 2016 and 2017. Among these, the associations on chromosome A13 and D08 for relative plant height (RPH), A07 for relative shoot fresh matter weight (RSFW), A08 and A13 for relative shoot dry matter weight (RSDW) were expressed in both environments, indicating that they were likely to be stable quantitative trait loci (QTLs). A total of 12 salt-induced candidate genes were identified differentially expressed by the combination of GWAS and transcriptome analysis. Three promising genes were selected for preliminary function verification of salt tolerance. The increase of GH_A13G0171-silenced plants in salt related traits under salt stress indicated its negative function in regulating the salt stress response. Conclusions: These results provided important genetic variations and candidate genes for accelerating the improvement of salt tolerance in cotton.

scholarly journals Identification of Flower-Specific Promoters through Comparative Transcriptome Analysis in Brassica napus

2019 ◽  
Vol 20 (23) ◽  
pp. 5949 ◽  
Author(s):  
Yan Li ◽  
Caihua Dong ◽  
Ming Hu ◽  
Zetao Bai ◽  
Chaobo Tong ◽  
...  
Keyword(s):  
Brassica Napus ◽  
Candidate Genes ◽  
Oilseed Rape ◽  
Agronomic Traits ◽  
Expression System ◽  
Expression Patterns ◽  
Gus Expression ◽  
Pcr Analysis ◽  
Transcriptome Data ◽  
Sclerotinia Stem Rot

Brassica napus (oilseed rape) is an economically important oil crop worldwide. Sclerotinia stem rot (SSR) caused by Sclerotinia sclerotiorum is a threat to oilseed rape production. Because the flower petals play pivotal roles in the SSR disease cycle, it is useful to express the resistance-related genes specifically in flowers to hinder further infection with S. sclerotiorum. To screen flower-specific promoters, we first analyzed the transcriptome data from 12 different tissues of the B. napus line ZS11. In total, 249 flower-specific candidate genes with high expression in petals were identified, and the expression patterns of 30 candidate genes were verified by quantitative real-time transcription-PCR (qRT-PCR) analysis. Furthermore, two novel flower-specific promoters (FSP046 and FSP061 promoter) were identified, and the tissue specificity and continuous expression in petals were determined in transgenic Arabidopsis thaliana with fusing the promoters to β-glucuronidase (GUS)-reporter gene. GUS staining, transcript expression pattern, and GUS activity analysis indicated that FSP046 and FSP061 promoter were strictly flower-specific promoters, and FSP046 promoter had a stronger activity. The two promoters were further confirmed to be able to direct GUS expression in B. napus flowers using transient expression system. The transcriptome data and the flower-specific promoters screened in the present study will benefit fundamental research for improving the agronomic traits as well as disease and pest control in a tissue-specific manner.

scholarly journals Functional Analysis of the Asian Soybean Rust Resistance Pathway Mediated by Rpp2

2011 ◽  
Vol 24 (2) ◽  
pp. 194-206 ◽  
Author(s):  
Ajay K. Pandey ◽  
Chunling Yang ◽  
Chunquan Zhang ◽  
Michelle A. Graham ◽  
Heidi D. Horstman ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Candidate Genes ◽  
Leaf Tissue ◽  
Soybean Rust ◽  
Virus Induced Gene Silencing ◽  
Resistance Response ◽  
P450 Monooxygenase ◽  
Methyl Transferase ◽  
Asian Soybean Rust ◽  
Resistance Pathway

Asian soybean rust is an aggressive foliar disease caused by the obligate biotrophic fungus Phakopsora pachyrhizi. On susceptible plants, the pathogen penetrates and colonizes leaf tissue, resulting in the formation of necrotic lesions and the development of numerous uredinia. The soybean Rpp2 gene confers resistance to specific isolates of P. pachyrhizi. Rpp2-mediated resistance limits the growth of the pathogen and is characterized by the formation of reddish-brown lesions and few uredinia. Using virus-induced gene silencing, we screened 140 candidate genes to identify those that play a role in Rpp2 resistance toward P. pachyrhizi. Candidate genes included putative orthologs to known defense-signaling genes, transcription factors, and genes previously found to be upregulated during the Rpp2 resistance response. We identified 11 genes that compromised Rpp2-mediated resistance when silenced, including GmEDS1, GmNPR1, GmPAD4, GmPAL1, five predicted transcription factors, an O-methyl transferase, and a cytochrome P450 monooxygenase. Together, our results provide new insight into the signaling and biochemical pathways required for resistance against P. pachyrhizi.

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