scholarly journals Genetic Architecture and Candidate Genes for Pubescence Length and Density and Its Relationship With Resistance to Common Cutworm in Soybean

2022 ◽  
Vol 12 ◽  
Author(s):  
Yawei Li ◽  
Li Chu ◽  
Xiaofeng Liu ◽  
Nannan Zhang ◽  
Yufei Xu ◽  
...  
Keyword(s):  
Drought Tolerance ◽  
Candidate Genes ◽  
Insect Resistance ◽  
Gene Annotation ◽  
Wild Soybean ◽  
Deep Understanding ◽  
Phenotypic Variance ◽  
Common Cutworm ◽  
And Cluster Analysis ◽  
The Relationship

Soybean pubescence plays an important role in insect resistance, drought tolerance, and other stresses. Hence, a deep understanding of the molecular mechanism underlying pubescence is a prerequisite to a deeper understanding of insect resistance and drought tolerance. In the present study, quantitative trait loci (QTL) mapping of pubescence traits was performed using a high-density inter-specific linkage map of one recombinant inbred line (RIL) population, designated NJRINP. It was observed that pubescence length (PL) was negatively correlated with pubescence density (PD). A total of 10 and 9 QTLs distributed on six and five chromosomes were identified with phenotypic variance (PV) of 3.0–9.9% and 0.8–15.8% for PL and PD, respectively, out of which, eight and five were novel. Most decreased PL (8 of 10) and increased PD (8 of 9) alleles were from the wild soybean PI 342618B. Based on gene annotation, Protein ANalysis THrough Evolutionary Relationships and literature search, 21 and 12 candidate genes were identified related to PL and PD, respectively. In addition, Glyma.12G187200 from major QTLs qPL-12-1 and qPD-12-2, was identified as Ps (sparse pubescence) before, having an expression level of fivefold greater in NN 86-4 than in PI 342618B, hence it might be the candidate gene that is conferring both PL and PD. Based on gene expression and cluster analysis, three and four genes were considered as the important candidate genes of PL and PD, respectively. Besides, leaves with short and dense (SD) pubescence, which are similar to the wild soybean pubescence morphology, had the highest resistance to common cutworm (CCW) in soybean. In conclusion, the findings in the present study provide a better understanding of genetic basis and candidate genes information of PL and PD and the relationship with resistance to CCW in soybean.

scholarly journals Improved Genetic Map Identified Major QTLs for Drought Tolerance- and Iron Deficiency Tolerance-Related Traits in Groundnut

Genes ◽  
2020 ◽  
Vol 12 (1) ◽  
pp. 37
Author(s):  
Manish K. Pandey ◽  
Sunil S. Gangurde ◽  
Vinay Sharma ◽  
Santosh K. Pattanashetti ◽  
Gopalakrishna K. Naidu ◽  
...  
Keyword(s):  
Iron Deficiency ◽  
Drought Tolerance ◽  
Candidate Genes ◽  
Genetic Map ◽  
Deep Understanding ◽  
Soil Conditions ◽  
Glycosyl Hydrolases ◽  
Iron Deficient ◽  
Main Effect ◽  
Main Effect Qtls

A deep understanding of the genetic control of drought tolerance and iron deficiency tolerance is essential to hasten the process of developing improved varieties with higher tolerance through genomics-assisted breeding. In this context, an improved genetic map with 1205 loci was developed spanning 2598.3 cM with an average 2.2 cM distance between loci in the recombinant inbred line (TAG 24 × ICGV 86031) population using high-density 58K single nucleotide polymorphism (SNP) “Axiom_Arachis” array. Quantitative trait locus (QTL) analysis was performed using extensive phenotyping data generated for 20 drought tolerance- and two iron deficiency tolerance-related traits from eight seasons (2004–2015) at two locations in India, one in Niger, and one in Senegal. The genome-wide QTL discovery analysis identified 19 major main-effect QTLs with 10.0–33.9% phenotypic variation explained (PVE) for drought tolerance- and iron deficiency tolerance- related traits. Major main-effect QTLs were detected for haulm weight (20.1% PVE), SCMR (soil plant analytical development (SPAD) chlorophyll meter reading, 22.4% PVE), and visual chlorosis rate (33.9% PVE). Several important candidate genes encoding glycosyl hydrolases; malate dehydrogenases; microtubule-associated proteins; and transcription factors such as MADS-box, basic helix-loop-helix (bHLH), NAM, ATAF, and CUC (NAC), and myeloblastosis (MYB) were identified underlying these QTL regions. The putative function of these genes indicated their possible involvement in plant growth, development of seed and pod, and photosynthesis under drought or iron deficiency conditions in groundnut. These genomic regions and candidate genes, after validation, may be useful to develop molecular markers for deploying genomics-assisted breeding for enhancing groundnut yield under drought stress and iron-deficient soil conditions.

scholarly journals RcTGA1 and glucosinolate biosynthesis pathway involvement in the defence of rose against the necrotrophic fungus Botrytis cinerea

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Penghua Gao ◽  
Hao Zhang ◽  
Huijun Yan ◽  
Qigang Wang ◽  
Bo Yan ◽  
...  
Keyword(s):  
Disease Resistance ◽  
Gene Annotation ◽  
Infected Plant ◽  
Grey Mould ◽  
Cascade Reactions ◽  
Postharvest Quality ◽  
Rna Seq ◽  
Protein Activity ◽  
Phenylpropanoid Biosynthesis ◽  
And Cluster Analysis

Abstract Background Rose is an important economic crop in horticulture. However, its field growth and postharvest quality are negatively affected by grey mould disease caused by Botrytis c. However, it is unclear how rose plants defend themselves against this fungal pathogen. Here, we used transcriptomic, metabolomic and VIGS analyses to explore the mechanism of resistance to Botrytis c. Result In this study, a protein activity analysis revealed a significant increase in defence enzyme activities in infected plants. RNA-Seq of plants infected for 0 h, 36 h, 60 h and 72 h produced a total of 54 GB of clean reads. Among these reads, 3990, 5995 and 8683 differentially expressed genes (DEGs) were found in CK vs. T36, CK vs. T60 and CK vs. T72, respectively. Gene annotation and cluster analysis of the DEGs revealed a variety of defence responses to Botrytis c. infection, including resistance (R) proteins, MAPK cascade reactions, plant hormone signal transduction pathways, plant-pathogen interaction pathways, Ca2+ and disease resistance-related genes. qPCR verification showed the reliability of the transcriptome data. The PTRV2-RcTGA1-infected plant material showed improved susceptibility of rose to Botrytis c. A total of 635 metabolites were detected in all samples, which could be divided into 29 groups. Metabonomic data showed that a total of 59, 78 and 74 DEMs were obtained for T36, T60 and T72 (T36: Botrytis c. inoculated rose flowers at 36 h; T60: Botrytis c. inoculated rose flowers at 60 h; T72: Botrytis c. inoculated rose flowers at 72 h) compared to CK, respectively. A variety of secondary metabolites are related to biological disease resistance, including tannins, amino acids and derivatives, and alkaloids, among others; they were significantly increased and enriched in phenylpropanoid biosynthesis, glucosinolates and other disease resistance pathways. This study provides a theoretical basis for breeding new cultivars that are resistant to Botrytis c. Conclusion Fifty-four GB of clean reads were generated through RNA-Seq. R proteins, ROS signalling, Ca2+ signalling, MAPK signalling, and SA signalling were activated in the Old Blush response to Botrytis c. RcTGA1 positively regulates rose resistance to Botrytis c. A total of 635 metabolites were detected in all samples. DEMs were enriched in phenylpropanoid biosynthesis, glucosinolates and other disease resistance pathways.

scholarly journals PSVII-37 Late-Breaking Abstract: CNV analysis of indigenous sheep reveals genes linked to disease resistance and adaptation

2020 ◽  
Vol 98 (Supplement_4) ◽  
pp. 339-339
Author(s):  
Annelin Molotsi
Keyword(s):  
Candidate Genes ◽  
Copy Number ◽  
Structural Changes ◽  
Gene Annotation ◽  
Smallholder Farmers ◽  
Copy Number Variations ◽  
Ovis Aries ◽  
Matrix Composition ◽  
Low Input ◽  
Gene Group

Abstract Smallholder farmers often make use of low-input systems, suggesting that robust and adaptable individuals are needed in these systems that have good production and reproduction in these low-input systems. One of the reasons certain individuals may be more adaptable or have higher production outputs could be due to the presence of advantageous mutations or genetic structural variants. Genetic variants, namely copy number variations (CNVs), are structural changes to the DNA and are larger than a single nucleotide. In this study, 47 sheep were investigated for the presence of CNVs. A total of 206 CNVs passed quality control. These CNVs were compared to the NCBI RefSeq Ovis aries: Oar_v4.0 to identify candidate genes located within or overlapping the copy number variations identified. Gene annotation analysis was carried out on the identified candidate genes. Gene annotation assigned the candidate genes to two gene groups. The first gene group were protein coding genes responsible for interferons that are the natural defences individuals have against viral and bacterial infection. The second gene group was found to be responsible for a variety of biological functions including transport, metabolic precursors, neurogenesis, signalling as well as bone and cartilage matrix composition along with a number of other important functions. This indicates that CNVs could have various effects on important biological process which could possibly influence an individual’s survival or even production and reproduction. This highlights the need for CNV studies to determine the influence of these CNVs and how they can be utilised in breeding programmes to improve adaptation and production outputs.

scholarly journals A note on genetic parameters and accuracy of estimated breeding values in honey bees

2019 ◽  
Vol 51 (1) ◽  
Author(s):  
Evert W. Brascamp ◽  
Piter Bijma
Keyword(s):  
Honey Bees ◽  
Variance Components ◽  
Genetic Parameters ◽  
Additive Genetic Variance ◽  
Breeding Value ◽  
Phenotypic Variance ◽  
Breeding Values ◽  
Estimated Breeding Values ◽  
Additive Genetic Relationship ◽  
The Relationship

Abstract Background In honey bees, observations are usually made on colonies. The phenotype of a colony is affected by the average breeding value for the worker effect of the thousands of workers in the colony (the worker group) and by the breeding value for the queen effect of the queen of the colony. Because the worker group consists of multiple individuals, interpretation of the variance components and heritabilities of phenotypes observed on the colony and of the accuracy of selection is not straightforward. The additive genetic variance among worker groups depends on the additive genetic relationship between the drone-producing queens (DPQ) that produce the drones that mate with the queen. Results Here, we clarify how the relatedness between DPQ affects phenotypic variance, heritability and accuracy of the estimated breeding values of replacement queens. Second, we use simulation to investigate the effect of assumptions about the relatedness between DPQ in the base population on estimates of genetic parameters. Relatedness between DPQ in the base generation may differ considerably between populations because of their history. Conclusions Our results show that estimates of (co)variance components and derived genetic parameters were seriously biased (25% too high or too low) when assumptions on the relationship between DPQ in the statistical analysis did not agree with reality.

Rapid identification of a stripe rust resistance gene YrXK in Chinese wheat line Xike01015 using specific locus amplified fragment (SLAF) sequencing

Plant Disease ◽  
2021 ◽  
Author(s):  
Cai Sun ◽  
Yike Liu ◽  
Qiang Li ◽  
Baotong Wang ◽  
Shuhui Chen ◽  
...  
Keyword(s):  
Stripe Rust ◽  
Puccinia Striiformis ◽  
Gene Annotation ◽  
Dominant Gene ◽  
Rapid Identification ◽  
Wheat Breeding ◽  
Stripe Rust Resistance ◽  
Phenotypic Variance ◽  
F2 Population ◽  
Chinese Wheat

Wheat stripe rust, an airborne fungal disease and caused by Puccinia striiformis Westend. f. sp. tritici (Pst), is one of the most devastating diseases on wheat. It is the most effective and economical measure for the diseases control to identify high-level resistance genes and apply in wheat breeding. Chinese wheat cultivar Xike01015 presents high levels of all stage resistance (ASR) to the current predominant Pst race CYR33. In this study, a single dominant gene, designated as YrXk, was identified in Xike01015 conferring resistance to CYR33 with genetic analysis of F2 and BC1 population from cross of Mingxian169 (susceptible) and Xike01015. The specific length amplified fragment sequencing (SLAF-seq) strategy was used to construct linkage map in the F2 population. QTL analysis mapped YrXk to a 12.4 Mb segment on chromosome1BS, explaining over 86.96% phenotypic variance. Gene annotation in the QTL region identified three differential expressed candidate genes , TraesCS1B02G168600.1, TraesCS1B02G170200.1, and TraesCS1B02G172400.1. The qRT-PCR results displayed that TraesCS1B02G170200.1 and TraesCS1B02G168600.1 significantly up-regulated and down-regulated, respectively, and TraesCS1B02G170200.1 slightly up-regulated after changed with CYR33 in the seedling stage, which indicating these genes may function in wheat resistance to stripe rust. The results of this study can be used in wheat breeding for improving resistance to stripe rust.

Prioritisation of candidate genes in QTL regions for seed germination and early seedling growth in bread wheat (Triticum aestivum) under salt-stress conditions

2021 ◽  
Vol 72 (1) ◽  
pp. 1
Author(s):  
Elham Rezaei ◽  
Eslam Majidi Hervan ◽  
Amin Azadi ◽  
Alireza Etminan ◽  
Hossein Ramshini
Keyword(s):  
Triticum Aestivum ◽  
Salt Stress ◽  
Candidate Genes ◽  
Metabolic Process ◽  
Stress Conditions ◽  
Phenotypic Variance ◽  
Fresh Weight ◽  
Main Effect ◽  
Early Seedling ◽  
Go Terms

Salinity and drought are major abiotic stresses affecting wheat (Triticum aestivum L.) production throughout the world, and discovery of loci for traits affecting yield under salinity may lead to the breeding for salt-tolerant plants. In the present study, 186 F10 recombinant inbred line (RIL) populations were evaluated under salt-stress conditions in order to identify main-effect and epistatic-effect quantitative trait loci (QTLs) for 15 traits in wheat during the germination and early-seedling stages. In total, 61 main-effect QTLs on 15 chromosomes and 21 epistatic interactions on 12 chromosomes were detected through composite interval mapping (CIM) and a mixed-model-based CIM method. Two major QTLs for primary-leaf fresh weight and coleoptile fresh weight were detected on chromosome (or linkage group) 5B2 and 2D, respectively, which contributed ~44% and 43% of the phenotypic variance. Additionally, 12 QTL clusters including different traits were detected on 1A1, 3A, 4A, 2B1, 3B, 5B1 and 2D1. Candidate genes were identified within QTL regions and gene ontology (GO) enrichment analysis was performed. In total, 9134 candidate genes were grouped into 274 GO terms (including 79 GO terms involved in the ‘biological process’ category). These genes directly or indirectly play a vital role such as lipid localisation, biological regulation, fatty acid biosynthetic process, cellular process, DNA conformation change, translational elongation, carbohydrate metabolic process, Fe ion homeostasis, hydrogen peroxide metabolic process, and pigment biosynthetic process at the germination and early-seedling stages under salt-stress conditions.

scholarly journals Transcriptomic analysis of sweet potato under dehydration stress identifies candidate genes for drought tolerance

Plant Direct ◽  
2018 ◽  
Vol 2 (10) ◽  
pp. e00092 ◽  
Author(s):  
Kin H. Lau ◽  
María del Rosario Herrera ◽  
Emily Crisovan ◽  
Shan Wu ◽  
Zhangjun Fei ◽  
...  
Keyword(s):  
Drought Tolerance ◽  
Candidate Genes ◽  
Sweet Potato ◽  
Transcriptomic Analysis ◽  
Dehydration Stress

Work Values and Its Impact on Managerial Effectiveness: A Relationship Study in Indian Context

2016 ◽  
Vol 20 (4) ◽  
pp. 300-311 ◽  
Author(s):  
Geeta Rana ◽  
Renu Rastogi ◽  
Pooja Garg
Keyword(s):  
Regression Analysis ◽  
Work Values ◽  
Deep Understanding ◽  
Global Competition ◽  
Managerial Effectiveness ◽  
Research Attention ◽  
Indian Context ◽  
Relationship Study ◽  
The Impact ◽  
The Relationship

Competent managers are very important assets to any organization as they drive it to success through the challenges of global competition. Managerial effectiveness has gained much research attention in recent years due to its importance to the organization as a whole. The purpose of this study is to test the impact of work values on managerial effectiveness in Indian organizations. To this end, a survey was conducted on a sample of 300 managers working in different organizations in India. The article employs factor analysis, Pearson’s r and step-wise multiple regression analysis to determine the effect of work values on managerial effectiveness. Findings indicate that work values have a positive and significant relationship with managerial effectiveness. The study provides valuable implications for practitioners and researchers by providing a deep understanding of the relationship between work values and managerial effectiveness, and between the dimensions and aspects of the two constructs. Practitioners could use the findings of the study to identify which work values influence managerial effectiveness most and work towards incorporating those values in the organizational culture.

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