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 Integration of gene-based markers in a pearl millet genetic map for identification of candidate genes underlying drought tolerance quantitative trait loci

2012 ◽  
Vol 12 (1) ◽  
pp. 9 ◽  
Author(s):  
Deepmala Sehgal ◽  
Vengaldas Rajaram ◽  
Ian Peter Armstead ◽  
Vincent Vadez ◽  
Yash Pal Yadav ◽  
...  
Keyword(s):  
Quantitative Trait Loci ◽  
Drought Tolerance ◽  
Candidate Genes ◽  
Pearl Millet ◽  
Genetic Map ◽  
Quantitative Trait ◽  
Trait Loci ◽  
Gene Based Markers

scholarly journals Genome-Wide Detection of Major and Epistatic Effect QTLs for Seed Protein and Oil Content in Soybean Under Multiple Environments Using High-Density Bin Map

2019 ◽  
Vol 20 (4) ◽  
pp. 979 ◽  
Author(s):  
Benjamin Karikari ◽  
Shuguang Li ◽  
Javaid Bhat ◽  
Yongce Cao ◽  
Jiejie Kong ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Oil Content ◽  
Seed Protein ◽  
Average Distance ◽  
Epistatic Effect ◽  
High Density ◽  
Environment Interaction ◽  
Potential Candidate ◽  
Main Effect ◽  
Main Effect Qtls

Seed protein and oil content are the two important traits determining the quality and value of soybean. Development of improved cultivars requires detailed understanding of the genetic basis underlying the trait of interest. However, it is prerequisite to have a high-density linkage map for precisely mapping genomic regions, and therefore the present study used high-density genetic map containing 2267 recombination bin markers distributed on 20 chromosomes and spanned 2453.79 cM with an average distance of 1.08 cM between markers using restriction-site-associated DNA sequencing (RAD-seq) approach. A recombinant inbred line (RIL) population of 104 lines derived from a cross between Linhefenqingdou and Meng 8206 cultivars was evaluated in six different environments to identify main- and epistatic-effect quantitative trait loci (QTLs)as well as their interaction with environments. A total of 44 main-effect QTLs for protein and oil content were found to be distributed on 17 chromosomes, and 15 novel QTL were identified for the first time. Out of these QTLs, four were major and stable QTLs, viz., qPro-7-1, qOil-8-3, qOil-10-2 and qOil-10-4, detected in at least two environments plus combined environment with R2 values >10%. Within the physical intervals of these four QTLs, 111 candidate genes were screened for their direct or indirect involvement in seed protein and oil biosynthesis/metabolism processes based on gene ontology and annotation information. Based on RNA sequencing (RNA-seq) data analysis, 15 of the 111 genes were highly expressed during seed development stage and root nodules that might be considered as the potential candidate genes. Seven QTLs associated with protein and oil content exhibited significant additive and additive × environment interaction effects, and environment-independent QTLs revealed higher additive effects. Moreover, three digenic epistatic QTLs pairs were identified, and no main-effect QTLs showed epistasis. In conclusion, the use of a high-density map identified closely linked flanking markers, provided better understanding of genetic architecture and candidate gene information, and revealed the scope available for improvement of soybean quality through marker assisted selection (MAS).

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 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 Consumption of a Double-Fortified Salt Affects Perceptual, Attentional, and Mnemonic Functioning in Women in a Randomized Controlled Trial in India

2017 ◽  
Vol 147 (12) ◽  
pp. 2297-2308 ◽  
Author(s):  
Michael J Wenger ◽  
Laura E Murray-Kolb ◽  
Julie EH Nevins ◽  
Sudha Venkatramanan ◽  
Gregory A Reinhart ◽  
...  
Keyword(s):  
Iron Deficiency ◽  
Iron Status ◽  
Controlled Trial ◽  
Reproductive Age ◽  
Deficiency Anemia ◽  
Control Group ◽  
Attention And Memory ◽  
Double Blind ◽  
Iron Deficient ◽  
Mnemonic Function

Abstract Background: Iron deficiency and iron deficiency anemia have been shown to have negative effects on aspects of perception, attention, and memory. Objective: The purpose of this investigation was to assess the extent to which increases in dietary iron consumption are related to improvements in behavioral measures of perceptual, attentional, and mnemonic function. Methods: Women were selected from a randomized, double-blind, controlled food-fortification trial involving ad libitum consumption of either a double-fortified salt (DFS) containing 47 mg potassium iodate/kg and 3.3 mg microencapsulated ferrous fumarate/g (1.1 mg elemental Fe/g) or a control iodized salt. Participants' blood iron status (primary outcomes) and cognitive functioning (secondary outcomes) were assessed at baseline and after 10 mo at endline. The study was performed on a tea plantation in the Darjeeling district of India. Participants (n = 126; 66% iron deficient and 49% anemic at baseline) were otherwise healthy women of reproductive age, 18–55 y. Results: Significant improvements were documented for iron status and for perceptual, attentional, and mnemonic function in the DFS group (percentage of variance accounted for: 16.5%) compared with the control group. In addition, the amount of change in perceptual and cognitive performance was significantly (P < 0.05) related to the amount of change in blood iron markers (mean percentage of variance accounted for: 16.0%) and baseline concentrations of blood iron markers (mean percentage of variance accounted for: 25.0%). Overall, there was evidence that the strongest effects of change in iron status were obtained for perceptual and low-level attentional function. Conclusion: DFS produced measurable and significant improvements in the perceptual, attentional, and mnemonic performance of Indian female tea pickers of reproductive age. This trial was registered at clinicaltrials.gov as NCT01032005.

Hypothermia in iron deficiency due to altered triiodothyronine metabolism

1980 ◽  
Vol 239 (5) ◽  
pp. R377-R381 ◽  
Author(s):  
E. Dillman ◽  
C. Gale ◽  
W. Green ◽  
D. G. Johnson ◽  
B. Mackler ◽  
...  
Keyword(s):  
Oxygen Consumption ◽  
Iron Deficiency ◽  
Ambient Temperature ◽  
The Other ◽  
Other Hand ◽  
Iron Deficient ◽  
Catecholamine Response ◽  
Cutaneous Vasoconstriction

Iron-deficient rats become hypothermic and have an excessive catecholamine response when exposed to an ambient temperature of 4 degrees C. This is not due to changes in body insulation, since thickness is unaltered, since differences persist after removal of hair, and since cutaneous vasoconstriction is intact. On the other hand, oxygen consumption of iron-deficient animals at 4 degrees C is reduced, 39 +/- 3 ml . kg-1 . min-1 compared to 63 +/- 2 in control animals. Thyroxine (T4) values at 4 degrees C were 4.34 +/- 0.20 microgram/dl sera as compared to control values of 3.6 +/- 0.32. Triiodothyronine (T3) values of iron-deficient animals in the cold were 48 +/- 6.8 ng/dl as compared to 72 +/- 5.6 in control animals. Treatment of iron-deficient animals with iron was shown to normalize the plasma T3 response at 4 degrees C within 6 days. Thyroidectomized iron-deficient animals injected with T3 did not show hypothermia at 4 degrees C, whereas thyroidectomized iron-deficient animals injected with T4 showed hypothermia, increased catecholamines, and decreased T3 levels as compared to non-iron-deficient animals similarly treated. It is proposed that iron deficiency impairs conversion of T4 to T3 and that this is primarily responsible for the hypothermia observed.

Poor efficacy of oral iron replacement therapy in pediatric patients with heart failure

2021 ◽  
pp. 1-8
Author(s):  
Kriti Puri ◽  
Joseph A. Spinner ◽  
Jacquelyn M. Powers ◽  
Susan W. Denfield ◽  
Hari P. Tunuguntla ◽  
...  
Keyword(s):  
Heart Failure ◽  
Iron Deficiency ◽  
Transferrin Saturation ◽  
Systolic Heart Failure ◽  
Oral Iron ◽  
Wilcoxon Test ◽  
Iron Therapy ◽  
Oral Iron Therapy ◽  
Iron Deficient ◽  
Iron Replacement

Abstract Introduction: Iron deficiency is associated with worse outcomes in children and adults with systolic heart failure. While oral iron replacement has been shown to be ineffective in adults with heart failure, its efficacy in children with heart failure is unknown. We hypothesised that oral iron would be ineffective in replenishing iron stores in ≥50% of children with heart failure. Methods: We performed a single-centre retrospective cohort study of patients aged ≤21 years with systolic heart failure and iron deficiency who received oral iron between 01/2013 and 04/2019. Iron deficiency was defined as ≥2 of the following: serum iron <50 mcg/dL, serum ferritin <20 ng/mL, transferrin >300 ng/mL, transferrin saturation <15%. Iron studies and haematologic indices pre- and post-iron therapy were compared using paired-samples Wilcoxon test. Results: Fifty-one children with systolic heart failure and iron deficiency (median age 11 years, 49% female) met inclusion criteria. Heart failure aetiologies included cardiomyopathy (51%), congenital heart disease (37%), and history of heart transplantation with graft dysfunction (12%). Median dose of oral iron therapy was 2.9 mg/kg/day of elemental iron, prescribed for a median duration of 96 days. Follow-up iron testing was available for 20 patients, of whom 55% (11/20) remained iron deficient despite oral iron therapy. Conclusions: This is the first report on the efficacy of oral iron therapy in children with heart failure. Over half of the children with heart failure did not respond to oral iron and remained iron deficient.

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.

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