scholarly journals Integrative QTL Identification, Fine Mapping and Candidate Gene Analysis of a Major Locus qLTG3a for Seed Low-Temperature Germinability in Rice

Rice ◽  
2021 ◽  
Vol 14 (1) ◽  
Author(s):  
Zhaoyuan Pan ◽  
Bin Tan ◽  
Guiyuan Cao ◽  
Rongqi Zheng ◽  
Meng Liu ◽  
...  
Keyword(s):  
Low Temperature ◽  
Expression Patterns ◽  
Physical Region ◽  
Genetic Distances ◽  
Progeny Testing ◽  
Genetic Dissection ◽  
Substitution Lines ◽  
Rice Varieties ◽  
Negative Effect ◽  
Cropping Seasons

AbstractLow-temperature germinability (LTG) is an important agronomic trait that can affect the planting time, planting area, and grain yield of staple crops, such as rice. However, the genetic mechanism of LTG is still unclear. In this study, a multi-parental permanent population with 208 single segment substitution lines (SSSLs) was used to conduct a genetic dissection for LTG across four cropping seasons. LTG was a typical quantitative trait with a high combined broad-sense heritability of 0.71. By comparison with the recipient parent, Huajingxian74, 24 SSSLs were identified as carrying LTG QTLs, which were further merged into integrated QTLs with shorter genetic distances by substitution mapping. Finally, 14 LTG QTLs were mapped on ten chromosomes, including seven positive-effect and seven negative-effect QTLs, with additive effect contributions ranging from 19.2 to 39.9%. qLTG3a, a main-effect and novel QTL, was confirmed by bulk segregant analysis using an F2 segregating population, and five key recombinants were selected to develop F3 populations for progeny testing. Marker-trait association analysis fine mapped qLTG3a to a 332.7-kb physical region between markers M6026 and M6341. Within this interval, 40 annotated genes were revealed, and three genes (Os03g0213300, Os03g0214400, and Os03g0214600) were considered as pivotal candidate genes for qLTG3a based on their sequence variations and expression patterns. Besides low temperature, qLTG3a can also enhance seed germination under standard temperature and osmotic stress. In summary, this study identified some genetic factors regulating LTG and opened a new window for breeding elite direct-seeded rice varieties. It will help reduce the climate risk in the production process of rice, which is of great significance to ensuring food security.

scholarly journals Meta-QTL and ortho-MQTL analyses identified genomic regions controlling rice yield, yield-related traits and root architecture under water deficit conditions

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Bahman Khahani ◽  
Elahe Tavakol ◽  
Vahid Shariati ◽  
Laura Rossini
Keyword(s):  
Water Deficit ◽  
Root Architecture ◽  
Agronomic Traits ◽  
Heading Date ◽  
Dry Weight ◽  
Genetic Dissection ◽  
Rice Varieties ◽  
Average Confidence ◽  
Stable Qtls ◽  
Genomic Regions

AbstractMeta-QTL (MQTL) analysis is a robust approach for genetic dissection of complex quantitative traits. Rice varieties adapted to non-flooded cultivation are highly desirable in breeding programs due to the water deficit global problem. In order to identify stable QTLs for major agronomic traits under water deficit conditions, we performed a comprehensive MQTL analysis on 563 QTLs from 67 rice populations published from 2001 to 2019. Yield and yield-related traits including grain weight, heading date, plant height, tiller number as well as root architecture-related traits including root dry weight, root length, root number, root thickness, the ratio of deep rooting and plant water content under water deficit condition were investigated. A total of 61 stable MQTLs over different genetic backgrounds and environments were identified. The average confidence interval of MQTLs was considerably refined compared to the initial QTLs, resulted in the identification of some well-known functionally characterized genes and several putative novel CGs for investigated traits. Ortho-MQTL mining based on genomic collinearity between rice and maize allowed identification of five ortho-MQTLs between these two cereals. The results can help breeders to improve yield under water deficit conditions.

scholarly journals Genome-Wide Association Study (GWAS) For Cold Tolerance at The Bud Burst Stage in Rice Using SNP Markers

2021 ◽  
Author(s):  
Caijing Li ◽  
Jindong Liu ◽  
Jianxin Bian ◽  
Tao Jin ◽  
Baoli Zou ◽  
...  
Keyword(s):  
Low Temperature ◽  
Association Study ◽  
Cold Tolerance ◽  
Genetic Basis ◽  
Genome Wide Association Study ◽  
Genome Wide Association ◽  
Bud Burst ◽  
Rice Varieties ◽  
Rice Landraces ◽  
Genome Wide

Abstract Background: Rice is a crop that is very sensitive to low temperature, and its morphological development and production are greatly affected by low temperature. Therefore, understanding the genetic basis of cold tolerance in rice is of great significance for mining favorable genes and cultivating excellent rice varieties. However, there were limited studies focusing on cold tolerance at the bud burst stage, therefore, considerable attention should be paid to the genetic basis of cold tolerance at the bud burst stage (CTBB).Results: In this study, a natural population consisting of 211 rice landraces collected from 15 provinces of China and other countries were firstly used to evaluate the cold tolerance at the bud burst stage. Population structure analysis showed that this population divided into three groups and was rich in genetic diversity. Our evaluation results confered that the japonica rice was more tolerance to cold at the bud burst stage than indica rice. Genome-wide association study (GWAS) were performed through the phenotypic data of 211 rice landraces and 36,727 SNPs dataset under a mixed linear model, and 12 QTLs (P < 0.0001) were identified according to the seedling survival rate (SSR) treated at 4 ℃, in which there are five QTLs (qSSR2-2, qSSR3-1, qSSR3-2, qSSR3-3 and qSSR9) which were co-located with previous studies, and seven QTLs (qSSR2-1, qSSR3-4, qSSR3-5, qSSR3-6, qSSR3-7, qSSR4 and qSSR7) which were reported for the first time. Among these QTLs, qSSR9, harboring the highest-peak SNP, explained biggest phenotypic variation. Through bioinformatics analysis, five genes (LOC_Os09g12440, LOC_Os09g12470, LOC_Os09g12520, LOC_Os09g12580 and LOC_Os09g12720) were nominated as candidates for qSSR9. Conclusion: This natural population consisting of 211 rice landraces with high density SNPs will serve as a better choice for identifying rice QTLs/genes in future, and the detected QTLs associated with cold tolerance in rice bud burst stage will be conducive to further mining favorable genes and breeding of rice varieties under cold stress.

scholarly journals Identification of candidate genes controlling chilling tolerance of rice in the cold region at the booting stage by BSA-Seq and RNA-Seq

2020 ◽  
Vol 7 (11) ◽  
pp. 201081
Author(s):  
Zhenhua Guo ◽  
Lijun Cai ◽  
Zhiqiang Chen ◽  
Ruiying Wang ◽  
Lanming Zhang ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Bulked Segregant Analysis ◽  
Expression Patterns ◽  
Enrichment Analysis ◽  
Chilling Tolerance ◽  
Pathway Enrichment Analysis ◽  
Potential Candidate ◽  
Rice Varieties ◽  
Booting Stage ◽  
F2 Population

Rice is sensitive to low temperatures, specifically at the booting stage. Chilling tolerance of rice is a quantitative trait loci that is governed by multiple genes, and thus, its precise identification through the conventional methods is an arduous task. In this study, we investigated the candidate genes related to chilling tolerance at the booting stage of rice. The F2 population was derived from Longjing25 (chilling-tolerant) and Longjing11 (chilling-sensitive) cross. Two bulked segregant analysis pools were constructed. A 0.82 Mb region containing 98 annotated genes on chromosomes 6 and 9 was recognized as the candidate region associated with chilling tolerance of rice at the booting stage. Transcriptomic analysis of Longjing25 and Longjing11 revealed 50 differentially expressed genes (DEGs) on the candidate intervals. KEGG pathway enrichment analysis of DEGs was performed. Nine pathways were found to be enriched, which contained 10 DEGs. A total of four genes had different expression patterns or levels between Longjing25 and Longjing11. Four out of the 10 DEGs were considered as potential candidate genes for chilling tolerance. This study will assist in the cloning of the candidate genes responsible for chilling tolerance and molecular breeding of rice for the development of chilling-tolerant rice varieties.

Morphological and molecular evaluation for germinability in rice varieties under low-temperature and anaerobic conditions

2017 ◽  
Vol 20 (1) ◽  
pp. 21-27 ◽  
Author(s):  
Do Yoon Hyun ◽  
MyeongWon Oh ◽  
Yu-Mi Choi ◽  
Sukyeung Lee ◽  
Myung-Chul Lee ◽  
...  
Keyword(s):  
Low Temperature ◽  
Anaerobic Conditions ◽  
Rice Varieties ◽  
Molecular Evaluation

scholarly journals Evaluation of the lipid fraction of pyrochars organic matter in the aspect of negative effects on soil

2020 ◽  
Vol 17 ◽  
pp. 00156
Author(s):  
Rodion Okunev ◽  
Elena Smirnova ◽  
Kamil Giniyatullin ◽  
Irina Guseva
Keyword(s):  
Organic Matter ◽  
Low Temperature ◽  
Pyrolysis Temperature ◽  
Lipid Fraction ◽  
Total Content ◽  
Negative Effects ◽  
Polycyclic Aromatic ◽  
Negative Effect ◽  
Pahs Concentration ◽  
Low Temperature Pyrolysis

The evaluation of the possible negative effect of pyrochars on soils based on the analysis of the content of lipid fraction and polycyclic aromatic hydrocarbons (PAHs) of organic matter was evaluated. Eight species of pyrochar were obtained from the crop and wood residues (linden, willow, corn, millet) by two pyrolysis regimes: low-temperature pyrolysis (<400°C) and high-temperature pyrolysis (400–600°C). The largest amount of lipid fraction (from 0.54 to 2.78%) and PAHs were found in pyrochars obtained at a low pyrolysis temperature. The total content of PAHs in the studied samples ranged from 8.49 to 603.21 μg/kg. According to the PAHs content, pyrochar was the most adverse for application to the soil, obtained from the residues of millet of low-temperature pyrolysis, however, at a high pyrolysis temperature, the safest product with the lowest PAHs concentration and a significant amount of lipid fraction was formed. Using an incubation experiment by measuring substrate-induced respiration in soil-pyrochar mixtures, it was shown that the application of this meliorant can also increase the emission of carbon dioxide from soils in a short time. The results of the experiments showed that it is necessary to precisely control the conditions of pyrolysis and carefully select the material for pyrochar in order to obtain the products with most favourable amounts of lipid fraction and PAHs content.

scholarly journals Divergent selection and genetic introgression shape the genome landscape of heterosis in hybrid rice

2020 ◽  
Vol 117 (9) ◽  
pp. 4623-4631 ◽  
Author(s):  
Zechuan Lin ◽  
Peng Qin ◽  
Xuanwen Zhang ◽  
Chenjian Fu ◽  
Hanchao Deng ◽  
...  
Keyword(s):  
Hybrid Rice ◽  
Field Trials ◽  
Hybrid Breeding ◽  
Genetic Introgression ◽  
Rice Varieties ◽  
Rice Landraces ◽  
Rice Hybrid ◽  
Negative Effect ◽  
Two Populations ◽  
Positive Effect

The successful application of heterosis in hybrid rice has dramatically improved rice productivity, but the genetic mechanism for heterosis in the hybrid rice remains unclear. In this study, we generated two populations of rice F1hybrids with present-day commercial hybrid parents, genotyped the parents with 50k SNP chip and genome resequencing, and recorded the phenotype of ∼2,000 hybrids at three field trials. By integrating these data with the collected genotypes of ∼4,200 rice landraces and improved varieties that were reported previously, we found that the male and female parents have different levels of genome introgressions from other rice subpopulations, includingindica,aus, andjaponica, therefore shaping heterotic loci in the hybrids. Among the introgressed exogenous genome, we found that heterotic loci, includingGhd8/DTH8,Gn1a, andIPA1existed in wild rice, but were significantly divergently selected among the rice subpopulations, suggesting these loci were subject to environmental adaptation. During modern rice hybrid breeding, heterotic loci were further selected by removing loci with negative effect and fixing loci with positive effect and pyramid breeding. Our results provide insight into the genetic basis underlying the heterosis of elite hybrid rice varieties, which could facilitate a better understanding of heterosis and rice hybrid breeding.

The Effect of Surface Self-Nanocrystallization on Low-Temperature Gas Carburization for AISI 316L Steel

2019 ◽  
Vol 795 ◽  
pp. 137-144
Author(s):  
Zhe Liu ◽  
Ya Wei Peng ◽  
Jian Ming Gong ◽  
Chao Ming Chen
Keyword(s):  
Stainless Steel ◽  
Elastic Modulus ◽  
Austenitic Stainless Steel ◽  
Low Temperature ◽  
Surface Hardness ◽  
Electron Probe Micro Analyzer ◽  
Gas Carburizing ◽  
316L Steel ◽  
Negative Effect ◽  
Effect Of Surface

In this work, the effect of surface self-nanocrystallization on low-temperature gas carburizing for AISI316L austenitic stainless steel has been studied. The surface ultrasonic rolling processing (SURP) was used to prepare nanostructured surface layers, and then the un-SURP and SURP samples were treated by LTGC at 470 °C for 10 h, 20 h and 30 h. In order to analyze the effect of surface self-nanocrystallization on low-temperature gas carburizing, optical microscopy (OM), atomic force microscope (AFM), scanning electron probe micro-analyzer (EPMA) and nano-indentation analyzer were used. The results show depth of SURP-induced plastic deformation layer was about 330 μm. Meanwhile, the surface hardness and elastic modulus were increased but the surface roughness decreased obviously after SURP. After low-temperature gas carburizing, according to the results of the thickness, carbon concentration, nano-hardness and elastic modulus of the carburized layer, the conclusion is that surface self-nanocrystallization carried by SURP has a negative effect on the low-temperature gas carburizing for AISI316L austenitic stainless steel and with the increase of carburizing time, the greater the adverse effect on carburizing.

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