Genome-Wide Identification of Circular RNAs in Response to Low-Temperature Stress in Tomato Leaves

Low temperature inhibits rapid germination and successful seedling establishment of rapeseed (Brassica napus L.), leading to significant productivity losses. Little is known about the genetic diversity for seed vigor under low-temperature conditions in rapeseed, which motivated our investigation of 13 seed germination- and emergence-related traits under normal and low-temperature conditions for 442 diverse rapeseed accessions. The stress tolerance index was calculated for each trait based on performance under non-stress and low-temperature stress conditions. Principal component analysis of the low-temperature stress tolerance indices identified five principal components that captured 100% of the seedling response to low temperature. A genome-wide association study using ~8 million SNP (single-nucleotide polymorphism) markers identified from genome resequencing was undertaken to uncover the genetic basis of seed vigor related traits in rapeseed. We detected 22 quantitative trait loci (QTLs) significantly associated with stress tolerance indices regarding seed vigor under low-temperature stress. Scrutiny of the genes in these QTL regions identified 62 candidate genes related to specific stress tolerance indices of seed vigor, and the majority were involved in DNA repair, RNA translation, mitochondrial activation and energy generation, ubiquitination and degradation of protein reserve, antioxidant system, and plant hormone and signal transduction. The high effect variation and haplotype-based effect of these candidate genes were evaluated, and high priority could be given to the candidate genes BnaA03g40290D, BnaA06g07530D, BnaA09g06240D, BnaA09g06250D, and BnaC02g10720D in further study. These findings should be useful for marker-assisted breeding and genomic selection of rapeseed to increase seed vigor under low-temperature stress.

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Genome-Wide Analysis of NAC Gene Family in Betula pendula

Forests ◽

10.3390/f10090741 ◽

2019 ◽

Vol 10 (9) ◽

pp. 741 ◽

Cited By ~ 8

Author(s):

Song Chen ◽

Xin Lin ◽

Dawei Zhang ◽

Qi Li ◽

Xiyang Zhao ◽

...

Keyword(s):

Low Temperature ◽

Gene Family ◽

Temperature Stress ◽

Betula Pendula ◽

Low Temperature Stress ◽

Specific Expression ◽

Genome Wide ◽

Nac Gene Family ◽

Cold Responses ◽

Insight Into

NACs (NAM, ATAF1/2, and CUC2) are plant-specific transcription factors that play diverse roles in various plant developmental processes. In this study, we identified the NAC gene family in birch (Betula pendula) and further analyzed the function of BpNACs. Phylogenetic analysis reveals that the 114 BpNACs can be divided into seven subfamilies. We investigated the expression levels of these BpNACs in different tissues of birch including roots, xylem, leaves, and flowers, and the results showed that the BpNACs seem to be expressed higher in xylem and roots than leaves and flowers. In addition to tissue-specific expression analysis, we investigated the expression of BpNACs under low-temperature stress. A total of 21 BpNACs were differentially expressed under low-temperature stress, of which 17 were up-regulated, and four were down-regulated. Using the gene expression data, we reconstructed the gene co-expression network for the 21 low-temperature-responsive BpNACs. In conclusion, our results provide insight into the evolution of NAC genes in the B. pendula genome, and provide a basis for understanding the molecular mechanism for BpNAC-mediated cold responses in birch.

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Genome-wide analyses of banana fasciclin-like AGP genes and their differential expression under low-temperature stress in chilling sensitive and tolerant cultivars

Plant Cell Reports ◽

10.1007/s00299-020-02524-0 ◽

2020 ◽

Vol 39 (6) ◽

pp. 693-708 ◽

Cited By ~ 1

Author(s):

Jian Meng ◽

Bei Hu ◽

Ganjun Yi ◽

Xiaoquan Li ◽

Houbin Chen ◽

...

Keyword(s):

Low Temperature ◽

Differential Expression ◽

Temperature Stress ◽

Low Temperature Stress ◽

Genome Wide

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Assessment of cold stress tolerance in maize through quantitative trait locus, genome-wide association study and transcriptome analysis

Notulae Botanicae Horti Agrobotanici Cluj-Napoca ◽

10.15835/nbha49412525 ◽

2021 ◽

Vol 49 (4) ◽

pp. 12525

Author(s):

Syed F.A. GILLANI ◽

Adnan RASHEED ◽

Gai YUHONG ◽

Wei JIAN ◽

Wang Y. XIA ◽

...

Keyword(s):

Low Temperature ◽

Association Study ◽

Temperature Stress ◽

Genome Wide Association Study ◽

Grain Filling ◽

Low Temperature Stress ◽

Genome Wide Association ◽

Ps Ii ◽

Genome Wide ◽

Trait Locus

Genome-wide association study (GWAS) has become a widely accepted strategy for decoding genotype phenotype associations in many species thanks to advances in next-generation sequencing (NGS) technologies. Maize is an ideal crop for GWAS and significant progress has been made in the last decade. This review summarizes current GWAS efforts in maize functional genomics research and discusses future prospects in the omics era. The general goal of GWAS is to link genotypic variations to corresponding differences in phenotype using the most appropriate statistical model in a given population. The current review also presents perspectives for optimizing GWAS design and analysis. GWAS analysis of data from RNA, protein, and metabolite-based omics studies is discussed, along with new models and new population designs that will identify causes of phenotypic variation that have been hidden to date. The detailed that low temperature in maize seedlings altogether restricts germination and seedlings' development and destabilizes the cancer prevention agent safeguard component. Cold pressure adversely influences root morphology, photosystem II (PS II) effectiveness, chlorophyll substance, and leaf region. A short scene of low temperature stress (for example, under 10 °C for 7 days) during the V6–V9 maize development stages can fundamentally defer the anthesis commencement. Among the morphological reactions by focused on maize plants, low temperature stress causes strange tuft development in maize, along these lines influencing the fertilization and grain filling measures. Hence, problematic temperatures can cause a genuine yield decrease if happening at basic conceptive stages, as plants allocate over half of their photosynthesis to foster grains during this stage until physiological development. Low temperature stress fundamentally diminishes the plant stature and absolute yield biomass of maize. Leaf improvement turns out to be delayed in chilly focused on plants because of a drawn-out cell cycle and diminished pace of mitosis. The joint and continuous efforts of the whole community will enhance our understanding of maize quantitative traits and boost crop molecular breeding designs.

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