scholarly journals Mapping Quantitative Trait Loci for Cold Tolerance in Rice under Germination Stage by Whole Genome Resequencing and Analysis of Candidate Genes

2020 ◽  
Author(s):  
Yinghua Pan ◽  
Lei Chen ◽  
Xinghai Yang ◽  
Lijun Gao ◽  
Baoxuan Nong ◽  
...  
Keyword(s):  
Low Temperature ◽  
Cold Stress ◽  
Wild Rice ◽  
Expression Patterns ◽  
Rice Genome ◽  
Annotation Project ◽  
Rice Genome Annotation Project ◽  
Whole Genome Resequencing ◽  
Germination Stage ◽  
Map Distance

Abstract Low-temperature stress significantly affects rice growth and causes serious loss of yield in temperate and high-altitude areas of the world. Rice lacks cold tolerance (CT) at germination stage, which reduces seedling vigor, hinders crop establishment and crop growth, and even affect direct-seeded rice. A chromosome segment substitution line (CSSL) population, including 271 lines, was derived from cold-tolerant donor wild rice Y11 (Oryza rufipogon Griff.) crossed with cold-sensitive rice variety GH998 to explore new genetic resource with CT and further investigate quantitative trait loci (QTLs) responsible for germination properties under low temperature. The germination rates of Y11 and GH998 were 95% and 73.33%, respectively, under cold stress. The range of variance of the germination rate in the CSSLs was between 0% and 98.33%. In addition, the CSSLs and parents were sequenced via whole genome resequencing. Results showed 33.46, 33.36, and 475.65 Gbp of clean data of GH998, Y11, and CSSLs, respectively. In 12 linkage groups, the general map distance was 941.49 cM, while the average map distance was 0.63 cM. On thebasis of 1484 bins, a high-density linkage map of the CSSLs was developed. The average distance of the linkage map ranged from 0.42 cM to 1.39 cM. The phenotype of CSSLs under low temperature and 615,466 single nucleotide polymorphisms (SNPs) between Y11 and GH998 were used for QTL analysis. Two QTLs, namely, low-temperature germination 8 (qLTG8) and qLTG11, were responsible for the germination ability under low temperature in rice. qLTG8 was mapped on chromosome 8, and it explained 14.55% of the total phenotypic variation explained (PVE) during the germination stage. qLTG8 was in 195.5 kb, and 32 genes were predicted based on the Rice Genome Annotation Project. qLTG11 was located on chromosome 11, and it explained 14.31% of the total PVE during the germination stage. qLTG11 was mapped at a narrow distance in 78.83 kb, and only 12 genes fall within this range according to the Rice Genome Annotation Project. The expression patterns of these 32 genes in the qLTG8 region demonstrated that LOC_Os08g01120, LOC_Os08g01140, LOC_Os08g01390, LOC_Os08g01170, and LOC_Os08g01380 were highly induced by cold stress in Y11 compared with GH998. The expression patterns of 12 genes in the qLTG11 region suggested that LOC_Os11g32880 and LOC_Os11g32940 were highly induced by cold stress in Y11 compared with GH998. This study provides an effective method, i.e., constructing CSSLs of wild rice, to explore excellent genes of wild rice and create new genetic resources. The results also provide a basis for identifying the genes underlying qLTG8 and qLTG11, indicating that QTL could be used for genetic improvement of CT in cultivar rice.

scholarly journals Transcriptomic profiling of germinating seeds under cold stress and characterization of the cold-tolerant gene LTG5 in rice

2020 ◽  
Author(s):  
yinghua Pan ◽  
Haifu Liang ◽  
Lijun Gao ◽  
Gaoxing Dai ◽  
Weiwei Chen ◽  
...  
Keyword(s):  
Low Temperature ◽  
Cold Stress ◽  
Cold Tolerance ◽  
Wild Rice ◽  
Expression Patterns ◽  
Molecular Genetic ◽  
Oryza Rufipogon ◽  
Rna Seq ◽  
Cold Tolerant ◽  
Cold Sensitive

Abstract Background: Wild rice ( Oryza rufipogon Griff.) is an important germplasm resource for rice improvement. It has superior tolerance for many abiotic stresses including cold stress, but little is known about the mechanism underlying its resistance to cold. Low temperature is one of the most prevalent factors that limit rice productivity and geographical distribution.Results: This study aimed to elucidate the molecular genetic mechanisms of wild rice in tolerating low temperature. Comprehensive transcriptome profiles of two rice genotypes (cold-sensitive ce 253 and cold-tolerant Y12-4) at the germinating stage under cold stress were comparatively analyzed. A total of 42.44–68.71 million readings were obtained, resulting in the alignment of 29128 and 30131 genes in genotypes 253 and Y12-4, respectively. Many common and differentially expressed genes (DEGs) were analyzed in cold-sensitive and cold-tolerant genotypes. Results showed more upregulated DEGs in cold-tolerant genotypes than in cold-sensitive genotypes at four stages under cold stress. Gene ontology enrichment analyses indicated more upregulated genes than downregulated ones in cold-tolerant genotypes based on cellular process, metabolic process, response stimulus, membrane part, and catalytic activity. To confirm the RNA Sequencing (RNA-seq) data, Quantitative real time polymerase chain reaction (qRT-PCR) was performed on seven randomly selected DEGs. These genes showed similar expression patterns corresponding with the RNA-Seq method. We also explored a gene for cold tolerance LTG5 , encoding a UDP-glucosyltransferase. The overexpression of LTG5 gene conferred cold tolerance to indica rice.Conclusion: Overall, our results suggested that gene resources related to cold stress from wild rice can be valuable for improving the cold tolerance of crop plants.

scholarly journals Transcriptomic profiling of germinating seeds under cold stress and characterization of the cold-tolerant gene LTG5 in rice

2020 ◽  
Author(s):  
Yinghua Pan ◽  
Haifu Liang ◽  
Lijun Gao ◽  
Gaoxing Dai ◽  
Weiwei Chen ◽  
...  
Keyword(s):  
Low Temperature ◽  
Cold Stress ◽  
Cold Tolerance ◽  
Wild Rice ◽  
Expression Patterns ◽  
Rna Seq ◽  
Cold Tolerant ◽  
Cold Sensitive ◽  
Sensitive Genotype ◽  
Tolerant Genotype

Abstract Background: Low temperature is a limiting factor of rice productivity and geographical distribution. Wild rice (Oryza rufipogon Griff.) is an important germplasm resource for rice improvement. It has superior tolerance to many abiotic stresses, including cold stress, but little is known about the mechanism underlying its resistance to cold. Results: This study elucidated the molecular genetic mechanisms of wild rice in tolerating low temperature. Comprehensive transcriptome profiles of two rice genotypes (cold-sensitive ce 253 and cold-tolerant Y12-4) at the germinating stage under cold stress were comparatively analyzed. A total of 42.44–68.71 million readings were obtained, resulting in the alignment of 29 128 and 30 131 genes in genotypes 253 and Y12-4, respectively. Many common and differentially expressed genes (DEGs) were analyzed in the cold-sensitive and cold-tolerant genotypes. Results showed more upregulated DEGs in the cold-tolerant genotype than in the cold-sensitive genotype at four stages under cold stress. Gene ontology enrichment analyses based on cellular process, metabolic process, response stimulus, membrane part, and catalytic activity indicated more upregulated genes than downregulated ones in the cold-tolerant genotype than in the cold-sensitive genotype. Quantitative real-time polymerase chain reaction was performed on seven randomly selected DEGs to confirm the RNA Sequencing (RNA-seq) data. These genes showed similar expression patterns corresponding with the RNA-Seq method. Weighted gene co-expression network analysis（WGCNA）revealed Y12-4 showed more positive genes than 253 under cold stress. We also explored the cold tolerance gene LTG5 (Low Temperature Growth 5) encoding a UDP-glucosyltransferase. The overexpression of the LTG5 gene conferred cold tolerance to indica rice. Conclusion: Gene resources related to cold stress from wild rice can be valuable for improving the cold tolerance of crops.

scholarly journals Different Responses of Cytoplasmic and Endoplasmic Reticulum Hsp90 Genes from Eogystia hippophaecola (Lepidoptera: Cossidae) to Cold Stress

Forests ◽  
2019 ◽  
Vol 10 (11) ◽  
pp. 1039
Author(s):  
Qianqian Wang ◽  
Jing Tao ◽  
Yurong Li ◽  
Yabei Xu ◽  
Xinhai Liu ◽  
...  
Keyword(s):  
Endoplasmic Reticulum ◽  
Amino Acid ◽  
Low Temperature ◽  
Cold Stress ◽  
Cold Tolerance ◽  
Response Times ◽  
Expression Patterns ◽  
Amino Acid Sequences ◽  
Sea Buckthorn ◽  
Open Reading Frames

Eogystia hippophaecola Hua, Chou, Fang et Chen (Lepidoptera: Cossidae) is an important borer pest of the sea buckthorn forest (Hippophae rhamnoides L.) in China. Its larvae, which are highly cold tolerant, mainly overwinter in sea buckthorn roots. Heat shock proteins (Hsps) are important molecular chaperones that have been linked to cold tolerance in insects. In this study, we cloned the open reading frames (ORFs) of two Hsp90 genes from E. hippophaecola, EhHsp90-1 and EhHsp90-2, and analyzed their expression under cold stress by qRT-PCR. EhHsp90-1 and EhHsp90-2 are 2154 and 2346 bp in length, respectively, encoding 717 and 781 amino acids. The deduced amino acid sequences contain the conserved signature sequences of the Hsp90 family and the C-terminus characteristic sequence of cytoplasmic or endoplasmic reticulum Hsp90 protein. Phylogenetic analysis revealed the amino acid sequences of EhHsp90-1 and EhHsp90-2 were very similar to the corresponding proteins from Lepidoptera. Under various low-temperature treatments lasting 2 h, EhHsp90-1 and EhHsp90-2 exhibited similar expression patterns, increasing first and then decreasing. At −5 °C, EhHsp90-1 was significantly up-regulated after 12 h, whereas EhHsp90-2 was up-regulated after just 1 h and reached its highest level at 2 h; however, the overall degree of upregulation was greater for EhHsp90-1. Subsequently, the expression level of EhHsp90-2 fluctuated with time. Our results suggest that the two Hsp90s play important roles in E. hippophaecola larvae response to cold stress, but that their response times and the magnitudes of their responses to low-temperature stress differed significantly, providing a theoretical basis for further studying the molecular mechanism of cold tolerance in E. hippophaecola larvae.

scholarly journals Genetic basis analysis for indica germinability under low temperature using a new RILs population genotyping by whole-genome resequencing

2020 ◽  
Author(s):  
Peng Wang ◽  
Guangliang Wu ◽  
Xin Luo ◽  
Ruiqi Liu ◽  
Andong Zhou ◽  
...  
Keyword(s):  
Cold Stress ◽  
Cold Tolerance ◽  
Genetic Map ◽  
Marker Assisted Selection ◽  
Genetic Basis ◽  
High Density ◽  
Genome Resequencing ◽  
Rice Varieties ◽  
Whole Genome Resequencing ◽  
Germination Stage

Abstract Background : Improving the cold tolerance of rice at germination stage is an important objective to maintain rice yields. However, less analyses were carried out to detect the quantitative trait loci (QTLs) associated with cold tolerance using indica/indica population. Therefore, the genetic basis of cold tolerance of the indica varieties should be provided considerable attentionResults: In this study, a recombinant inbred lines (RILs) population comprising 126 lines derived from two widely used double-cropped indica rice varieties Wufeng B (WFB) and Changhui T025 (CHT025) was used to construct a high-density linkage map based on whole-genome resequencing. The high-density genetic map included 2,578 bins on 12 linkage groups and was 1762.80 cM in length, with an average interlocus distance of 0.68 cM. On the basis of newly constructed high-density genetic map, a total of 18 additive QTLs ranging from 34.55 to 315.21 kb on Nipponbare genome and two pairs of epistatic QTLs associated with cold stress at germination stage were detected, which indicated that the genetic basis of cold tolerance of WFB and CHT025 at germination stage is manly due to additive effects of several QTLs. Otherwise, the phylogenetic analysis showed that WFB is a typical indica variety while CHT025 is an interphyletic rice variety. Most of the favorable QTLs harbouring in indica WFB showed different chromosomal region from the QTLs associating with cold stress from japonica rice in previous studies, which indicated that indica might have different cold stress genetic mechanism comparing to japonica subspecies. Furthermore, we can incorporate these favorable QTLs existing in WFB into rice varieties to breed new cold tolerance indica male sterile maintenance line via marker-assisted selection; CHT025 is a better source of these cold tolerance favorable QTLs only only for the improvement of indcia but also for japonica restorer line germinability under low temperature via marker-assisted selection.Conclusion : This population with high density genetic map will serve as better choice for identifying important quantitative traits of these two good indica germplasms, and these favorable QTLs exist in WFB and CHT025 can be used to breed new cold tolerance indica varieties via marker-assisted selection. These authors have contributed equally to this work

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