Selection of transcripts related to low-temperature tolerance using RNA sequencing from F2 plants between japonica and indica rice (Oryza sativa L.) cultivars

Commercial lowbush blueberry production involves management of what have long been considered highly diverse populations of naturally occurring clones. Wide phenotypic variation evident in fields has often been anecdotally equated with variation in yield, cultural requirements, etc., however this has not been tested rigorously. Interest in selection of clones with superior low-temperature tolerance prompted this study to estimate population-wide variation within the species. Thirty six clones of Vacciniun angustifolium exhibiting most of the typical phenotypic classes were selected from two commercial production fields in Maine. Plants were evaluated for low-temperature tolerance of reproductive and vascular tissues on a monthly basis from November through April. In addition, variation in relative time of anthesis, flower structure, and floral low-temperature tolerance were determined. Results are discussed with respect to potential for selection of superior clones for both fruit production and ornamental use.

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Identification of candidate genes for low temperature tolerance during germination of maize using a genome-wide association study and RNA-sequencing

10.21203/rs.3.rs-19588/v1 ◽

2020 ◽

Author(s):

Hong Zhang ◽

Jiayue Zhang ◽

Qingyu Xu ◽

Dandan Wang ◽

Hong Di ◽

...

Keyword(s):

Signal Transduction ◽

Low Temperature ◽

Candidate Genes ◽

Rna Sequencing ◽

Temperature Tolerance ◽

Genome Wide Association ◽

Phenotypic Traits ◽

Agricultural Crop ◽

Low Temperature Tolerance ◽

Genome Wide

Abstract Background: Maize ( Zea mays L.) is the largest agricultural crop in the world based on acreage and yield, however, it is inherently sensitive to low temperatures. The growth and yield of maize can be affected by low temperature during its whole growth period, particularly during germination. Therefore, it is urgent to identify the new gene(s) related to the low temperature tolerance during maize germination. Results: In this study, 14 phenotypic traits related to seed germination were used to explore the genetic architecture of maize through genome-wide association analysis (GWAS). A total of 30 single nucleotide polymorphisms (SNPs) associated with low temperature tolerance were detected (–log10( P ) > 4); 14 candidate genes were detected as being directly associated with these SNPs and 81 candidate genes were identified when the screen was extended to a distance of 30 kb from these SNPs. The candidate genes were predicted by conjoint analysis with RNA-sequencing (RNA-seq) to evaluate whole-genome gene expression levels. A total of nine differentially expressed genes (DEGs) (|log2foldchange|≥0.585， P <0.05) were found within distance of 30 kb, including two DEGs ( GRMZM2G101383 and GRMZM2G402584 ), which were associated with SNPs directly. The differential expression of these candidate genes was verified using qRT-PCR. The Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) terms of DEGs GRMZM2G052129 and GRMZM2G038964 were, ‘fatty acid metabolic process’, ‘Mitogen-activated protein kinase (MAPK) signal transduction’, and so on, which are related to the fluidity of the cell membrane and low temperature signal transduction. Conclusion: Therefore, further functional analysis of GRMZM2G052129 and GRMZM2G038964 will provide valuable information for understanding the genetic mechanism of low temperature tolerance during germination in maize.

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