Genome-wide SNP discovery, linkage mapping, and analysis of QTL for morpho-physiological traits in rice during vegetative stage under drought stress

2021 ◽  
Author(s):  
Rizky Dwi Satrio ◽  
Miftahul Huda Fendiyanto ◽  
Ence Darmo Jaya Supena ◽  
Sony Suharsono ◽  
Miftahudin Miftahudin
Keyword(s):  
Drought Stress ◽  
Linkage Mapping ◽  
Physiological Traits ◽  
Vegetative Stage ◽  
Snp Discovery ◽  
Genome Wide

scholarly journals Molecular Markers Associated with Agro-Physiological Traits under Terminal Drought Conditions in Bread Wheat

2020 ◽  
Vol 21 (9) ◽  
pp. 3156 ◽  
Author(s):  
Sajid Shokat ◽  
Deepmala Sehgal ◽  
Prashant Vikram ◽  
Fulai Liu ◽  
Sukhwinder Singh
Keyword(s):  
Drought Stress ◽  
Genome Wide Association Study ◽  
Genomic Analysis ◽  
Kernel Weight ◽  
Physiological Traits ◽  
Breeding Lines ◽  
Terminal Stage ◽  
Terminal Drought ◽  
Genome Wide ◽  
Population Structure Analysis

Terminal drought stress poses a big challenge to sustain wheat grain production in rain-fed environments. This study aimed to utilize the genetically diverse pre-breeding lines for identification of genomic regions associated with agro-physiological traits at terminal stage drought stress in wheat. A total of 339 pre-breeding lines panel derived from three-way crosses of ‘exotics × elite × elite’ lines were evaluated in field conditions at Obregon, Mexico for two years under well irrigated as well as drought stress environments. Drought stress was imposed at flowering by skipping the irrigations at pre and post anthesis stage. Results revealed that drought significantly reduced grain yield (Y), spike length (SL), number of grains spikes−1 (NGS) and thousand kernel weight (TKW), while kernel abortion (KA) was increased. Population structure analysis in this panel uncovered three sub-populations. Genome wide linkage disequilibrium (LD) decay was observed at 2.5 centimorgan (cM). The haplotypes-based genome wide association study (GWAS) identified significant associations of Y, SL, and TKW on three chromosomes; 4A (HB10.7), 2D (HB6.10) and 3B (HB8.12), respectively. Likewise, associations on chromosomes 6B (HB17.1) and 3A (HB7.11) were found for NGS while on chromosome 3A (HB7.12) for KA. The genomic analysis information generated in the study can be efficiently utilized to improve Y and/or related parameters under terminal stage drought stress through marker-assisted breeding.

scholarly journals Interactive Effects of Organic Fertilizers and Drought Stress on Growth and Nutrient Content of Brassica juncea at Vegetative Stage

2021 ◽  
Vol 13 (24) ◽  
pp. 13948
Author(s):  
Addisie Geremew ◽  
Laura Carson ◽  
Selamawit Woldesenbet ◽  
Charles Carpenter ◽  
Elisha Peace ◽  
...  
Keyword(s):  
Water Stress ◽  
Drought Stress ◽  
Brassica Juncea ◽  
Nutrient Concentration ◽  
Nutrient Content ◽  
Leafy Vegetables ◽  
Organic Fertilizers ◽  
Physiological Traits ◽  
Vegetative Stage ◽  
Change Scenario

With the ongoing climate change scenario and alarmingly increased land degradation, understanding complex interactions of drought stress and organic fertilizers on morpho-physiological traits and dynamics of nutrient concentration is pivotal for sustainable production leafy vegetables such as mustard (Brassica juncea). Thus, this study evaluated the effect of drought stress and organic fertilizers on B. juncea growth, physiology, and dynamics of nutrient concentration at the vegetative stage. The plants were exposed to three water stress levels (well-watered (100% field capacity, FC), mild (50% FC), and severe (25% FC) supplemented with three organic fertilizers (chitosan, ultra green, and home-grown natural vegetable foods) either individually or in combination during the vegetative growth stage. Water stress had a negative effect on growth and physiological traits, and macro- and micronutrients of mustard. However, the ameliorative effects of fertilizer application were revealed by improved plant height, leaf area, relative water content, membrane stability index, and chlorophyll content from 9.7% to 26.9%, 28% to 32.72%, 7.97% to 39.51%, 7.93% to 39.66%, and 29.68% to 56.53%, respectively. Analysis of variance revealed a significant effect of soil moisture level, fertilizer type and their interaction on content of macronutrients (Ca, K, P, N, C, S, Na, Mg) and micronutrients (Fe, Zn) in mustard leaves. However, there was no significant effect detected for Cu across all factors as well the interaction effect on Mn. Overall, our results indicated that application of organic fertilizers enables mustard plant to withstand the deleterious effect of drought stress, resulting in improved growth and physiological traits as well as leaf nutrient content.

Genome-wide linkage mapping of QTL for physiological traits in a Chinese wheat population using the 90K SNP array

Euphytica ◽  
2016 ◽  
Vol 209 (3) ◽  
pp. 789-804 ◽  
Author(s):  
Fengmei Gao ◽  
Jindong Liu ◽  
Li Yang ◽  
Xiaoxia Wu ◽  
Yonggui Xiao ◽  
...  
Keyword(s):  
Linkage Mapping ◽  
Snp Array ◽  
Physiological Traits ◽  
Wheat Population ◽  
Genome Wide ◽  
Chinese Wheat ◽  
90K Snp Array

The Impact of Drought Stress on some Morpho-Physiological Traits and RAPD Markers in Wheat Genotypes

2015 ◽  
Vol 4 (1) ◽  
pp. 27-37 ◽  
Author(s):  
Bayoumi Y. ◽  
Amal Abd EL-Mageed ◽  
Enas Ibrahim ◽  
Soad Mahmoud ◽  
I. El-Demardash ◽  
...  
Keyword(s):  
Drought Stress ◽  
Rapd Markers ◽  
Physiological Traits ◽  
Wheat Genotypes ◽  
The Impact

High-density linkage mapping for agronomic and physiological traits of rice (Oryza sativa L.) under reproductive-stage salt stress

2021 ◽  
Vol 100 (2) ◽  
Author(s):  
Mostafa Ahmadizadeh ◽  
Nadali Babaeian-Jelodar ◽  
Ghasem Mohammadi-Nejad ◽  
Nadali Bagheri ◽  
Rakesh Kumar Singh
Keyword(s):  
Oryza Sativa ◽  
Salt Stress ◽  
Linkage Mapping ◽  
Oryza Sativa L ◽  
High Density ◽  
Reproductive Stage ◽  
Physiological Traits

scholarly journals Genome wide identification and characterization of light-harvesting Chloro a/b binding (LHC) genes reveals their potential role in enhancing drought tolerance in Gossypium hirsutum

2021 ◽  
Vol 4 (1) ◽  
Author(s):  
Teame Gereziher MEHARI ◽  
Yanchao XU ◽  
Richard Odongo MAGWANGA ◽  
Muhammad Jawad UMER ◽  
Joy Nyangasi KIRUNGU ◽  
...  
Keyword(s):  
Drought Stress ◽  
Gossypium Hirsutum ◽  
Abiotic Stresses ◽  
Substitution Rate ◽  
Synonymous Substitution ◽  
Synonymous Substitution Rate ◽  
Drought Tolerant ◽  
Genome Wide ◽  
Identification And Characterization

Abstract Background Cotton is an important commercial crop for being a valuable source of natural fiber. Its production has undergone a sharp decline because of abiotic stresses, etc. Drought is one of the major abiotic stress causing significant yield losses in cotton. However, plants have evolved self-defense mechanisms to cope abiotic factors like drought, salt, cold, etc. The evolution of stress responsive transcription factors such as the trihelix, a nodule-inception-like protein (NLP), and the late embryogenesis abundant proteins have shown positive response in the resistance improvement to several abiotic stresses. Results Genome wide identification and characterization of the effects of Light-Harvesting Chloro a/b binding (LHC) genes were carried out in cotton under drought stress conditions. A hundred and nine proteins encoded by the LHC genes were found in the cotton genome, with 55, 27, and 27 genes found to be distributed in Gossypium hirsutum, G. arboreum, and G. raimondii, respectively. The proteins encoded by the genes were unevenly distributed on various chromosomes. The Ka/Ks (Non-synonymous substitution rate/Synonymous substitution rate) values were less than one, an indication of negative selection of the gene family. Differential expressions of genes showed that majority of the genes are being highly upregulated in the roots as compared with leaves and stem tissues. Most genes were found to be highly expressed in MR-85, a relative drought tolerant germplasm. Conclusion The results provide proofs of the possible role of the LHC genes in improving drought stress tolerance, and can be explored by cotton breeders in releasing a more drought tolerant cotton varieties.

Genome-wide investigation on transcriptional responses to drought stress in wild and cultivated rice

2021 ◽  
pp. 104555
Author(s):  
Mu-Fan Geng ◽  
Xiu-Hua Wang ◽  
Mei-Xia Wang ◽  
Zhe Cai ◽  
Qing-Lin Meng ◽  
...  
Keyword(s):  
Drought Stress ◽  
Cultivated Rice ◽  
Transcriptional Responses ◽  
Genome Wide

scholarly journals Comprehensive analysis and identification of drought-responsive candidate NAC genes in three semi-arid tropics (SAT) legume crops

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Sadhana Singh ◽  
Himabindu Kudapa ◽  
Vanika Garg ◽  
Rajeev K. Varshney
Keyword(s):  
Drought Stress ◽  
Candidate Genes ◽  
Developmental Stages ◽  
Biological Activities ◽  
Expression Patterns ◽  
Genome Wide ◽  
Legume Crops ◽  
Root Tissues ◽  
Semi Arid ◽  
Comprehensive Study

Abstract Background Chickpea, pigeonpea, and groundnut are the primary legume crops of semi-arid tropics (SAT) and their global productivity is severely affected by drought stress. The plant-specific NAC (NAM - no apical meristem, ATAF - Arabidopsis transcription activation factor, and CUC - cup-shaped cotyledon) transcription factor family is known to be involved in majority of abiotic stresses, especially in the drought stress tolerance mechanism. Despite the knowledge available regarding NAC function, not much information is available on NAC genes in SAT legume crops. Results In this study, genome-wide NAC proteins – 72, 96, and 166 have been identified from the genomes of chickpea, pigeonpea, and groundnut, respectively, and later grouped into 10 clusters in chickpea and pigeonpea, while 12 clusters in groundnut. Phylogeny with well-known stress-responsive NACs in Arabidopsis thaliana, Oryza sativa (rice), Medicago truncatula, and Glycine max (soybean) enabled prediction of putative stress-responsive NACs in chickpea (22), pigeonpea (31), and groundnut (33). Transcriptome data revealed putative stress-responsive NACs at various developmental stages that showed differential expression patterns in the different tissues studied. Quantitative real-time PCR (qRT-PCR) was performed to validate the expression patterns of selected stress-responsive, Ca_NAC (Cicer arietinum - 14), Cc_NAC (Cajanus cajan - 15), and Ah_NAC (Arachis hypogaea - 14) genes using drought-stressed and well-watered root tissues from two contrasting drought-responsive genotypes of each of the three legumes. Based on expression analysis, Ca_06899, Ca_18090, Ca_22941, Ca_04337, Ca_04069, Ca_04233, Ca_12660, Ca_16379, Ca_16946, and Ca_21186; Cc_26125, Cc_43030, Cc_43785, Cc_43786, Cc_22429, and Cc_22430; Ah_ann1.G1V3KR.2, Ah_ann1.MI72XM.2, Ah_ann1.V0X4SV.1, Ah_ann1.FU1JML.2, and Ah_ann1.8AKD3R.1 were identified as potential drought stress-responsive candidate genes. Conclusion As NAC genes are known to play role in several physiological and biological activities, a more comprehensive study on genome-wide identification and expression analyses of the NAC proteins have been carried out in chickpea, pigeonpea and groundnut. We have identified a total of 21 potential drought-responsive NAC genes in these legumes. These genes displayed correlation between gene expression, transcriptional regulation, and better tolerance against drought. The identified candidate genes, after validation, may serve as a useful resource for molecular breeding for drought tolerance in the SAT legume crops.

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