scholarly journals QTL mapping of physiological traits at the booting stage in rice under low temperature combined with nitrogen fertilization

2019 ◽  
Vol 55 (No. 4) ◽  
pp. 146-155
Author(s):  
Shu Ming Yang ◽  
Fei Fei Zhang ◽  
Su Hua Zhang ◽  
Gui Yong Li ◽  
Li Qiong Zeng ◽  
...  
Keyword(s):  
Composite Interval Mapping ◽  
Molecular Mechanisms ◽  
Cold Water ◽  
Flag Leaf ◽  
Chilling Stress ◽  
Interval Mapping ◽  
Physiological Traits ◽  
Environment Interaction ◽  
Nitrogen Application ◽  
Cold Tolerant

Further dissection of physiological molecular mechanisms is indispensable to alleviate rice yield losses resulting from cold injury. By using 105 near-isogenic lines (NILs) derived from a backcross between cv. Lijiangxintuanheigu (LTH) and cv. Towada, we detected quantitative trait loci (QTLs) for physiological traits of the rice flag leaf, based on polymorphic simple sequence repeat (SSR) markers, inclusive composite interval mapping (ICIM), mixed composite interval mapping (MCIM) approaches and phenotypic value subjected to combine with cold-water stress and three nitrogen application rates. By using ICIM, a total of 34 QTLs with additive effects (A-QTLs) were identified on chromosomes 1, 3, 4, 5, 6, 7 and 10, and the phenotypic variation (R<sup>2</sup>) explained by each QTL ranged from 8.46 to 29.14%. By using MCIM, 20 A-QTLs and 14 pairs of QTLs with epistatic × environment interaction effects (Epistatic QTLs) were detected, the contribution of environment interaction (H<sup>2</sup>AE) was 0.87 to 7.36%, while the contribution rates of E-QTL were from 0.97 to 3.58%. Fourteen A-QTLs were detected by ICIM and MCIM, which may serve as a basis for fine-mapping and candidate gene studies, and providing strategies for the development of cold-tolerant rice cultivars and nitrogen application to alleviate chilling stress.  

Inclusive composite-interval mapping reveals quantitative trait loci for plant architectural traits in sorghum (Sorghum bicolor)

2019 ◽  
Vol 70 (8) ◽  
pp. 659
Author(s):  
Huawen Zhang ◽  
Runfeng Wang ◽  
Bin Liu ◽  
Erying Chen ◽  
Yanbing Yang ◽  
...  
Keyword(s):  
Quantitative Trait Loci ◽  
Sorghum Bicolor ◽  
Quantitative Trait ◽  
Composite Interval Mapping ◽  
Recombinant Inbred Lines ◽  
Interval Mapping ◽  
Environment Interaction ◽  
Trait Loci ◽  
Inclusive Composite Interval Mapping ◽  
Architectural Traits

Architecture-efficient sorghum (Sorghum bicolor (L.) Moench) has erect leaves forming a compact canopy that enables highly effective utilisation of solar radiation; it is suitable for high-density planting, resulting in an elevated overall production. Development of sorghum ideotypes with optimal plant architecture requires knowledge of the genetic basis of plant architectural traits. The present study investigated seven production-related architectural traits by using 181 sorghum recombinant inbred lines (RILs) with contrasting architectural phenotypes developed from the cross Shihong 137 × L-Tian. Parents along with RILs were phenotyped for plant architectural traits for two consecutive years (2012, 2013) at two locations in the field. Analysis of variance revealed significant (P ≤ 0.05) differences among RILs for architectural traits. All traits showed medium to high broad-sense heritability estimates (0.43–0.94) and significant (P ≤ 0.05) genotype × environment effects. We employed 181 simple sequence repeat markers to identify quantitative trait loci (QTLs) and the effects of QTL × environment interaction based on the inclusive composite interval mapping algorithm. In total, 53 robust QTLs (log of odds ≥4.68) were detected for these seven traits and explained 2.11–12.11% of phenotypic variation. These QTLs had small effects of QTL × environment interaction and yet significant epistatic effects, indicating that they could stably express across environments but influence phenotypes through strong interaction with non-allelic loci. The QTLs and linked markers need to be verified through function and candidate-gene analyses. The new knowledge of the genetic regulation of architectural traits in the present study will provide a theoretical basis for the genetic improvement of architectural traits in sorghum.

Combining ability for physiological traits in spring wheat over environments

2004 ◽  
Vol 52 (1) ◽  
pp. 63-68 ◽  
Author(s):  
S. N. Sharma ◽  
U. Menon ◽  
R. S. Sain
Keyword(s):  
Leaf Area ◽  
Spring Wheat ◽  
Combining Ability ◽  
Gene Action ◽  
Flag Leaf ◽  
Physiological Traits ◽  
Environment Interaction ◽  
Additive Gene Action ◽  
Additive Gene ◽  
Peduncle Length

Combining ability analysis was carried out in the F1 and F2 generations of a 10 × 10 parents half diallel for peduncle length and flag leaf area in spring wheat under three environments. The mean squares for both general combining ability (GCA) and specific combining ability (SCA) were significant for peduncle length in both the generations, indicating the involvement of both additive and non-additive gene actions in the inheritance. However, the high values of GCA variance showed the greater importance of additive gene action in the inheritance of this trait. Flag leaf area was observed to be controlled by non-additive gene action. The environment played a significant role in the expression of both the traits. The GCA × environment interaction exhibited greater sensitivity in all cases than the SCA × environment interaction. The varieties Kharchia 65 and Durgapura 65 emerged as desirable general combiners for peduncle length, whereas Pavon and Moncho had high mean performance for flag leaf area. These parents could be used as donors in future breeding to develop a physiologically efficient wheat genotype with high production. The crosses Moncho × Brochis and Durgapura 65 × Raj 821 were the most desirable specific combinations for flag leaf area and Kharchia 65 × Chiroca for both the traits. Desirable transgressive segregants can be expected from these crosses. Diallel selective mating or bi-parental crossing could be useful for the genetic improvement of these physiological traits.

scholarly journals Deciphering the Genetic Architecture of Plant Height in Soybean Using Two RIL Populations Sharing a Common M8206 Parent

Plants ◽  
2019 ◽  
Vol 8 (10) ◽  
pp. 373 ◽  
Author(s):  
Yongce Cao ◽  
Shuguang Li ◽  
Guoliang Chen ◽  
Yanfeng Wang ◽  
Javaid Akhter Bhat ◽  
...  
Keyword(s):  
Plant Height ◽  
Quantitative Trait ◽  
Composite Interval Mapping ◽  
Mixed Model ◽  
Interval Mapping ◽  
Interaction Effects ◽  
Epistatic Effect ◽  
Environment Interaction ◽  
Additive Effects ◽  
Yield And Quality

Plant height (PH) is an important agronomic trait that is closely related to soybean yield and quality. However, it is a complex quantitative trait governed by multiple genes and is influenced by environment. Unraveling the genetic mechanism involved in PH, and developing soybean cultivars with desirable PH is an imperative goal for soybean breeding. In this regard, the present study used high-density linkage maps of two related recombinant inbred line (RIL) populations viz., MT and ZM evaluated in three different environments to detect additive and epistatic effect quantitative trait loci (QTLs) as well as their interaction with environments for PH in Chinese summer planting soybean. A total of eight and 12 QTLs were detected by combining the composite interval mapping (CIM) and mixed-model based composite interval mapping (MCIM) methods in MT and ZM populations, respectively. Among these QTLs, nine QTLs viz., QPH-2, qPH-6-2MT, QPH-6, qPH-9-1ZM, qPH-10-1ZM, qPH-13-1ZM, qPH-16-1MT, QPH-17 and QPH-19 were consistently identified in multiple environments or populations, hence were regarded as stable QTLs. Furthermore, Out of these QTLs, three QTLs viz., qPH-4-2ZM, qPH-15-1MT and QPH-17 were novel. In particular, QPH-17 could detect in both populations, which was also considered as a stable and major QTL in Chinese summer planting soybean. Moreover, eleven QTLs revealed significant additive effects in both populations, and out of them only six showed additive by environment interaction effects, and the environment-independent QTLs showed higher additive effects. Finally, six digenic epistatic QTLs pairs were identified and only four additive effect QTLs viz., qPH-6-2MT, qPH-19-1MT/QPH-19, qPH-5-1ZM and qPH-17-1ZM showed epistatic effects. These results indicate that environment and epistatic interaction effects have significant influence in determining genetic basis of PH in soybean. These results would not only increase our understanding of the genetic control of plant height in summer planting soybean but also provide support for implementing marker assisted selection (MAS) in developing cultivars with ideal plant height as well as gene cloning to elucidate the mechanisms of plant height.

QTL analysis of soybean oil content under 17 environments

2014 ◽  
Vol 94 (2) ◽  
pp. 245-261 ◽  
Author(s):  
Zhaoming Qi ◽  
Xue Han ◽  
Meng Hou ◽  
Dawei Xin ◽  
Zhongyu Wang ◽  
...  
Keyword(s):  
Soybean Oil ◽  
Qtl Analysis ◽  
Composite Interval Mapping ◽  
Oil Content ◽  
Interval Mapping ◽  
Complex Nature ◽  
Environment Interaction ◽  
Plant Materials ◽  
Multiple Interval Mapping ◽  
Main Effects

Qi, Z., Han, X., Hou, M., Xin, D., Wang, Z., Zhu, R., Hu, Z., Jiang, H., Li, C., Liu, C., Hu, G. and Chen, Q. 2014. QTL analysis of soybean oil content under 17 environments. Can. J. Plant Sci. 94: 245–261. Soybean oil content is a key trait driver of successful soybean quality. Due to its complex nature, less stable quantitative trait loci (QTL) are known. The goal of this study was to identify important and stable QTL affecting soybean oil content using recombination inbred lines (RILs) derived from a cross between Charleston and Dongnong594. The plant materials were planted in three environments across 9 yr in China. The genetic effects were then partitioned into additive main effects (A), epistatic main effects (AA) and their environment interaction effects (AE and AAE) by using composite interval mapping, multiple interval mapping and composite interval mapping in a mixed linear model. Fifty-six QTL were identified on 15 of 20 soybean chromosomes excluding LG C1, D2, E, M and O by composite interval mapping and multiple interval mapping methods. Seven oil content QTL detected on LG A1, 1 on LG A2, 5 on LG B1, 4 on LG B2, 8 on LG C2, 11 on LG D1a, 2 on LG D1b, 4 on LG F, 5 on LG G, 2 on LG H, 1 on LG I, 1 on LG J, 1 on LG K, 2 on LG L and 2 on LG N. Eight QTL showed a good stability across 17 environments. The additive main-effect QTL contributed more phenotypic variation than the epistasis and environmental interaction. This indicated that it is feasible to improve soybean oil content by marker-assisted selection.

scholarly journals Comparative Transcriptome Analysis Provides Insights into the Seed Germination in Cotton in Response to Chilling Stress

2020 ◽  
Vol 21 (6) ◽  
pp. 2067 ◽  
Author(s):  
Qian Shen ◽  
Siping Zhang ◽  
Shaodong Liu ◽  
Jing Chen ◽  
Huijuan Ma ◽  
...  
Keyword(s):  
Molecular Mechanisms ◽  
Tricarboxylic Acid Cycle ◽  
Glyoxylate Cycle ◽  
Chilling Stress ◽  
Enrichment Analysis ◽  
Tca Cycle ◽  
Zeatin Riboside ◽  
Cotton Species ◽  
Tolerant Variety ◽  
Cold Tolerant

Gossypium hirsutum L., is a widely cultivated cotton species around the world, but its production is seriously threatened by its susceptibility to chilling stress. Low temperature affects its germination, and the underlying molecular mechanisms are rarely known, particularly from a transcriptional perspective. In this study, transcriptomic profiles were analyzed and compared between two cotton varieties, the cold-tolerant variety KN27-3 and susceptible variety XLZ38. A total of 7535 differentially expressed genes (DEGs) were identified. Among them, the transcripts involved in energy metabolism were significantly enriched during germination based on analysis of Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways, such as glycolysis/gluconeogenesis, tricarboxylic acid cycle (TCA cycle), and glyoxylate cycle (GAC). Results from further GO enrichment analysis show the earlier appearance of DNA integration, meristem growth, cotyledon morphogenesis, and other biological processes in KN27-3 compared with XLZ38 under chilling conditions. The synthesis of asparagine, GDP-mannose, and trehalose and the catabolic process of raffinose were activated. DEGs encoding antioxidants (spermidine) and antioxidase (CAT1, GPX4, DHAR2, and APX1) were much more up-regulated in embryos of KN27-3. The content of auxin (IAA), cis-zeatin riboside (cZR), and trans-zeatin riboside (tZR) in KN27-3 are higher than that in XLZ38 at five stages (from 12 h to 54 h). GA3 was expressed at a higher level in KN27-3 from 18 h to 54 h post imbibition compared to that in XLZ38. And abscisic acid (ABA) content of KN27-3 is lower than that in XLZ38 at five stages. Results from hormone content measurements and the related gene expression analysis indicated that IAA, CTK, and GA3 may promote germination of the cold-tolerant variety, while ABA inhibits it. These results expand the understanding of cottonseed germination and physiological regulations under chilling conditions by multiple pathways.

scholarly journals Time-Related Mapping of Quantitative Trait Loci Underlying Tiller Number in Rice

Genetics ◽  
1999 ◽  
Vol 151 (1) ◽  
pp. 297-303 ◽  
Author(s):  
Wei-Ren Wu ◽  
Wei-Ming Li ◽  
Ding-Zhong Tang ◽  
Hao-Ran Lu ◽  
A J Worland
Keyword(s):  
Quantitative Trait Loci ◽  
Quantitative Trait ◽  
Composite Interval Mapping ◽  
Interval Mapping ◽  
Tiller Number ◽  
Multiple Trait ◽  
Phenotypic Data ◽  
Recombinant Inbred Population ◽  
Trait Loci ◽  
Final Observation

Abstract Using time-related phenotypic data, methods of composite interval mapping and multiple-trait composite interval mapping based on least squares were applied to map quantitative trait loci (QTL) underlying the development of tiller number in rice. A recombinant inbred population and a corresponding saturated molecular marker linkage map were constructed for the study. Tiller number was recorded every 4 or 5 days for a total of seven times starting at 20 days after sowing. Five QTL were detected on chromosomes 1, 3, and 5. These QTL explained more than half of the genetic variance at the final observation. All the QTL displayed an S-shaped expression curve. Three QTL reached their highest expression rates during active tillering stage, while the other two QTL achieved this either before or after the active tillering stage.

Bayesian Mapping of Multiple Quantitative Trait Loci From Incomplete Inbred Line Cross Data

Genetics ◽  
1998 ◽  
Vol 148 (3) ◽  
pp. 1373-1388
Author(s):  
Mikko J Sillanpää ◽  
Elja Arjas
Keyword(s):  
Quantitative Trait Loci ◽  
Quantitative Trait ◽  
Composite Interval Mapping ◽  
Backcross Progeny ◽  
Random Variable ◽  
Interval Mapping ◽  
Mapping Method ◽  
Structure Mapping ◽  
Standard Interval ◽  
Trait Loci

Abstract A novel fine structure mapping method for quantitative traits is presented. It is based on Bayesian modeling and inference, treating the number of quantitative trait loci (QTLs) as an unobserved random variable and using ideas similar to composite interval mapping to account for the effects of QTLs in other chromosomes. The method is introduced for inbred lines and it can be applied also in situations involving frequent missing genotypes. We propose that two new probabilistic measures be used to summarize the results from the statistical analysis: (1) the (posterior) QTL-intensity, for estimating the number of QTLs in a chromosome and for localizing them into some particular chromosomal regions, and (2) the location wise (posterior) distributions of the phenotypic effects of the QTLs. Both these measures will be viewed as functions of the putative QTL locus, over the marker range in the linkage group. The method is tested and compared with standard interval and composite interval mapping techniques by using simulated backcross progeny data. It is implemented as a software package. Its initial version is freely available for research purposes under the name Multimapper at URL http://www.rni.helsinki.fi/~mjs.

scholarly journals Cold-water immersion following sprint interval training does not alter endurance signaling pathways or training adaptations in human skeletal muscle

2017 ◽  
Vol 313 (4) ◽  
pp. R372-R384 ◽  
Author(s):  
James R. Broatch ◽  
Aaron Petersen ◽  
David J. Bishop
Keyword(s):  
Mitochondrial Biogenesis ◽  
Molecular Mechanisms ◽  
Cold Water ◽  
P53 Protein ◽  
Water Immersion ◽  
Interval Training ◽  
Cold Water Immersion ◽  
Peroxisome Proliferator ◽  
Sprint Interval Training ◽  
Single Session

We investigated the underlying molecular mechanisms by which postexercise cold-water immersion (CWI) may alter key markers of mitochondrial biogenesis following both a single session and 6 wk of sprint interval training (SIT). Nineteen men performed a single SIT session, followed by one of two 15-min recovery conditions: cold-water immersion (10°C) or a passive room temperature control (23°C). Sixteen of these participants also completed 6 wk of SIT, each session followed immediately by their designated recovery condition. Four muscle biopsies were obtained in total, three during the single SIT session (preexercise, postrecovery, and 3 h postrecovery) and one 48 h after the last SIT session. After a single SIT session, phosphorylated (p-)AMPK, p-p38 MAPK, p-p53, and peroxisome proliferator-activated receptor-γ coactivator-1α ( PGC-1α) mRNA were all increased ( P < 0.05). Postexercise CWI had no effect on these responses. Consistent with the lack of a response after a single session, regular postexercise CWI had no effect on PGC-1α or p53 protein content. Six weeks of SIT increased peak aerobic power, maximal oxygen consumption, maximal uncoupled respiration (complexes I and II), and 2-km time trial performance ( P < 0.05). However, regular CWI had no effect on changes in these markers, consistent with the lack of response in the markers of mitochondrial biogenesis. Although these observations suggest that CWI is not detrimental to endurance adaptations following 6 wk of SIT, they question whether postexercise CWI is an effective strategy to promote mitochondrial biogenesis and improvements in endurance performance.

scholarly journals Overexpression of SgGH3.1 from Fine-Stem Stylo (Stylosanthes guianensis var. intermedia) Enhances Chilling and Cold Tolerance in Arabidopsis thaliana

Genes ◽  
2021 ◽  
Vol 12 (9) ◽  
pp. 1367
Author(s):  
Ming Jiang ◽  
Long-Long Ma ◽  
Huai-An Huang ◽  
Shan-Wen Ke ◽  
Chun-Sheng Gui ◽  
...  
Keyword(s):  
Arabidopsis Thaliana ◽  
Cold Stress ◽  
Stress Responses ◽  
Molecular Mechanisms ◽  
Transcriptome Profiling ◽  
Pasture Legumes ◽  
Cold Tolerant ◽  
Whole Transcriptome ◽  
Altered Sensitivity ◽  
Exogenous Iaa

Stylosanthes (stylo) species are commercially significant tropical and subtropical forage and pasture legumes that are vulnerable to chilling and frost. However, little is known about the molecular mechanisms behind stylos’ responses to low temperature stress. Gretchen-Hagen 3 (GH3) proteins have been extensively investigated in many plant species for their roles in auxin homeostasis and abiotic stress responses, but none have been reported in stylos. SgGH3.1, a cold-responsive gene identified in a whole transcriptome profiling study of fine-stem stylo (S. guianensis var. intermedia) was further investigated for its involvement in cold stress tolerance. SgGH3.1 shared a high percentage of identity with 14 leguminous GH3 proteins, ranging from 79% to 93%. Phylogenetic analysis classified SgGH3.1 into Group Ⅱ of GH3 family, which have been proven to involve with auxins conjugation. Expression profiling revealed that SgGH3.1 responded rapidly to cold stress in stylo leaves. Overexpression of SgGH3.1 in Arabidopsis thaliana altered sensitivity to exogenous IAA, up-regulated transcription of AtCBF1-3 genes, activated physiological responses against cold stress, and enhanced chilling and cold tolerances. This is the first report of a GH3 gene in stylos, which not only validated its function in IAA homeostasis and cold responses, but also gave insight into breeding of cold-tolerant stylos.

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