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

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.

scholarly journals Joint transcriptomic and metabolomic analysis reveals the mechanism of low-temperature tolerance in Hosta ventricosa

PLoS ONE ◽  
2021 ◽  
Vol 16 (11) ◽  
pp. e0259455
Author(s):  
QianQian Zhuang ◽  
Shaopeng Chen ◽  
ZhiXin Jua ◽  
Yue Yao
Keyword(s):  
Signal Transduction ◽  
Low Temperature ◽  
Temperature Tolerance ◽  
Differentially Expressed ◽  
Metabolomic Analysis ◽  
Temperature Changes ◽  
Low Temperature Tolerance ◽  
Content Ratio ◽  
Temperature Damage ◽  
Hosta Ventricosa

Hosta ventricosa is a robust ornamental perennial plant that can tolerate low temperatures, and which is widely used in urban landscaping design in Northeast China. However, the mechanism of cold-stress tolerance in this species is unclear. A combination of transcriptomic and metabolomic analysis was used to explore the mechanism of low-temperature tolerance in H. ventricosa. A total of 12 059 differentially expressed genes and 131 differentially expressed metabolites were obtained, which were mainly concentrated in the signal transduction and phenylpropanoid metabolic pathways. In the process of low-temperature signal transduction, possibly by transmitting Ca2+ inside and outside the cell through the ion channels on the three cell membranes of COLD, CNGCs and CRLK, H. ventricosa senses temperature changes and stimulates SCRM to combine with DREB through the MAPK signal pathway and Ca2+ signal sensors such as CBL, thus strengthening its low-temperature resistance. The pathways of phenylpropanoid and flavonoid metabolism represent the main mechanism of low-temperature tolerance in this species. The plant protects itself from low-temperature damage by increasing its content of genistein, scopolentin and scopolin. It is speculated that H. ventricosa can also adjust the content ratio of sinapyl alcohol and coniferyl alcohol and thereby alter the morphological structure of its cell walls and so increase its resistance to low temperatures.When subjected to low-temperature stress, H. ventricosa perceives temperature changes via COLD, CNGCs and CRLK, and protection from low-temperature damage is achieved by an increase in the levels of genistein, scopolentin and scopolin through the pathways of phenylpropanoid biosynthesis and flavonoid biosynthesis.

scholarly journals QTL Mapping Low-Temperature Germination Ability in the Maize IBM Syn10 DH Population

Plants ◽  
2022 ◽  
Vol 11 (2) ◽  
pp. 214
Author(s):  
Qinghui Han ◽  
Qingxiang Zhu ◽  
Yao Shen ◽  
Michael Lee ◽  
Thomas Lübberstedt ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Low Temperature ◽  
Candidate Genes ◽  
Temperature Tolerance ◽  
Bhlh Transcription Factor ◽  
Rna Seq ◽  
Dh Population ◽  
Low Temperature Tolerance ◽  
Germination Ability ◽  
Upregulated Genes

Chilling injury poses a serious threat to seed emergence of spring-sowing maize in China, which has become one of the main climatic limiting factors affecting maize production in China. It is of great significance to mine the key genes controlling low-temperature tolerance during seed germination and study their functions for breeding new maize varieties with strong low-temperature tolerance during germination. In this study, 176 lines of the intermated B73 × Mo17 (IBM) Syn10 doubled haploid (DH) population, which comprised 6618 bin markers, were used for QTL analysis of low-temperature germination ability. The results showed significant differences in germination related traits under optimum-temperature condition (25 °C) and low-temperature condition (10 °C) between two parental lines. In total, 13 QTLs were detected on all chromosomes, except for chromosome 5, 7, 10. Among them, seven QTLs formed five QTL clusters on chromosomes 1, 2, 3, 4, and 9 under the low-temperature condition, which suggested that there may be some genes regulating multiple germination traits at the same time. A total of 39 candidate genes were extracted from five QTL clusters based on the maize GDB under the low-temperature condition. To further screen candidate genes controlling low-temperature germination, RNA-Seq, in which RNA was extracted from the germination seeds of B73 and Mo17 at 10 °C, was conducted, and three B73 upregulated genes and five Mo17 upregulated genes were found by combined analysis of RNA-Seq and QTL located genes. Additionally, the variations of Zm00001d027976 (GLABRA2), Zm00001d007311 (bHLH transcription factor), and Zm00001d053703 (bZIP transcription factor) were found by comparison of amino sequence between B73 and Mo17. This study will provide a theoretical basis for marker-assisted breeding and lay a foundation for further revealing molecular mechanism of low-temperature germination tolerance in maize.

scholarly journals Joint Transcriptomic and Metabolomic Analysis Reveals the Mechanism of Low Temperature Tolerance in Hosta Ventricosa

2021 ◽  
Author(s):  
QianQian Zhuang ◽  
Shaopeng Chen ◽  
ZhiXin Jua ◽  
Yao Yue
Keyword(s):  
Signal Transduction ◽  
Low Temperature ◽  
Low Temperatures ◽  
Temperature Tolerance ◽  
Differentially Expressed ◽  
Metabolomic Analysis ◽  
Temperature Changes ◽  
Low Temperature Tolerance ◽  
Temperature Damage ◽  
Hosta Ventricosa

Abstract Background: Hosta ventricosa is a robust ornamental perennial plant that can tolerate low temperatures, and which is widely used in urban landscaping design in Northeast China. However, the mechanism of cold stress tolerance in this species is unclear. Methods:This study used a combination of transcriptomic and metabolomic analysis to explore the mechanism of low temperature tolerance in H. ventricosa.Results: A total of 12 059 differentially expressed genes (DEGs) and 131 differentially expressed metabolites were obtained, which were mainly concentrated in the signal transduction and phenylpropanoid metabolic pathways. In the process of low temperature signal transduction, H. ventricosa is mainly through the ion channels on the three cell membranes of COLD, CNGCs and CRLK to transmit Ca2+ inside and outside the cell to sense temperature changes, and stimulate SCRM to combine with DREB through the MAPK signal pathway and Ca2+ signal sensors such as CBL. Strengthen the low temperature resistance of H. ventricosa. The pathways of phenylpropanoid and flavonoid metabolism represent the main mechanism of low temperature tolerance in this species. The plant protects itself from low temperature damage by increasing its content of genistein, scopolentin and scopolin. It is speculated that H. ventricosa can also adjust the content ratio of sinapyl alcohol and coniferyl alcohol and thereby alter the morphological structure of its cell walls and so increase its resistance to low temperatures.Conclusions: In H. ventricosa that is subjected to low temperature stress, temperature changes are perceived through COLD, CNGCs and CRLK, and protection from low temperature damage is achieved by an increase in the levels of genistein, scopolentin and scopolin through the pathways of phenylpropanoid biosynthesis and flavonoid biosynthesis.

scholarly journals Genome-Wide Association Study towards Genomic Predictive Power for High Production and Quality of Milk in American Alpine Goats

2020 ◽  
Vol 2020 ◽  
pp. 1-12
Author(s):  
Y. Tilahun ◽  
T. A. Gipson ◽  
T. Alexander ◽  
M. L. McCallum ◽  
P. R. Hoyt
Keyword(s):  
Association Study ◽  
Candidate Genes ◽  
Predictive Power ◽  
Genome Wide Association Study ◽  
Genome Wide Association ◽  
Breeding Value ◽  
Phenotypic Traits ◽  
Nucleotide Polymorphisms ◽  
Genome Wide ◽  
Dairy Traits

This paper reports an exploratory study based on quantitative genomic analysis in dairy traits of American Alpine goats. The dairy traits are quality-determining components in goat milk, cheese, ice cream, etc. Alpine goat phenotypes for quality components have been routinely recorded for many years and deposited in the Council on Dairy Cattle Breeding (CDCB) repository. The data collected were used to conduct an exploratory genome-wide association study (GWAS) from 72 female Alpine goats originating from locations throughout the U.S. Genotypes were identified with the Illumina Goat 50K single-nucleotide polymorphisms (SNP) BeadChip. The analysis used a polygenic model where the dropping criterion was a call rate≥0.95. The initial dataset was composed of ~60,000 rows of SNPs and 21 columns of phenotypic traits and composed of 53,384 scaffolds containing other informative data points used for genomic predictive power. Phenotypic association with the 50K BeadChip revealed 26,074 reads of candidate genes. These candidate genes segregated as separate novel SNPs and were identified as statistically significant regions for genome and chromosome level trait associations. Candidate genes associated differently for each of the following phenotypic traits: test day milk yield (13,469 candidate genes), test day protein yield (25,690 candidate genes), test day fat yield (25,690 candidate genes), percentage protein (25,690 candidate genes), percentage fat (25,690 candidate genes), and percentage lactose content (25,690 candidate genes). The outcome of this study supports elucidation of novel genes that are important for livestock species in association to key phenotypic traits. Validation towards the development of marker-based selection that provides precision breeding methods will thereby increase the breeding value.

scholarly journals Genome-Wide Association Study and Transcriptome Differential Expression Analysis of the Feather Rate in Shouguang Chickens

2020 ◽  
Vol 11 ◽  
Author(s):  
Xiayi Liu ◽  
Zhou Wu ◽  
Junying Li ◽  
Haigang Bao ◽  
Changxin Wu
Keyword(s):  
Differential Expression ◽  
Candidate Genes ◽  
Rna Sequencing ◽  
Expression Analysis ◽  
Differential Expression Analysis ◽  
Serine Phosphorylation ◽  
Differentially Expressed ◽  
Genome Wide Association ◽  
Sequencing Analysis ◽  
Genome Wide

The feather rate phenotype in chicks, including early-feathering and late-feathering phenotypes, are widely used as a sexing system in the poultry industry. The objective of this study was to obtain candidate genes associated with the feather rate in Shouguang chickens. In the present study, we collected 56 blood samples and 12 hair follicle samples of flight feathers from female Shouguang chickens. Then we identified the chromosome region associated with the feather rate by genome-wide association analysis (GWAS). We also performed RNA sequencing and analyzed differentially expressed genes between the early-feathering and late-feathering phenotypes using HISAT2, StringTie, and DESeq2. We identified a genomic region of 10.0–13.0 Mb of chromosome Z, which is statistically associated with the feather rate of Shouguang chickens at one-day old. After RNA sequencing analysis, 342 differentially expressed known genes between the early-feathering (EF) and late-feathering (LF) phenotypes were screened out, which were involved in epithelial cell differentiation, intermediate filament organization, protein serine kinase activity, peptidyl-serine phosphorylation, retinoic acid binding, and so on. The sperm flagellar 2 gene (SPEF2) and prolactin receptor (PRLR) gene were the only two overlapping genes between the results of GWAS and differential expression analysis, which implies that SPEF2 and PRLR are possible candidate genes for the formation of the chicken feathering phenotype in the present study. Our findings help to elucidate the molecular mechanism of the feather rate in chicks.

scholarly journals Genome-Wide Association Study of Maize Aboveground Dry Matter Accumulation at Seedling Stage

2021 ◽  
Vol 11 ◽  
Author(s):  
Xianju Lu ◽  
Jinglu Wang ◽  
Yongjian Wang ◽  
Weiliang Wen ◽  
Ying Zhang ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Dry Matter ◽  
Association Studies ◽  
Genome Wide Association ◽  
Phenotypic Traits ◽  
Pathway Enrichment Analysis ◽  
Dry Matter Accumulation ◽  
Genome Wide Association Studies ◽  
Genome Wide ◽  
Maize Varieties

Dry matter accumulation and partitioning during the early phases of development could significantly affect crop growth and productivity. In this study, the aboveground dry matter (DM), the DM of different organs, and partition coefficients of a maize association mapping panel of 412 inbred lines were evaluated at the third and sixth leaf stages (V3 and V6). Further, the properties of these phenotypic traits were analyzed. Genome-wide association studies (GWAS) were conducted on the total aboveground biomass and the DM of different organs. Analysis of GWAS results identified a total of 1,103 unique candidate genes annotated by 678 significant SNPs (P value &lt; 1.28e–6). A total of 224 genes annotated by SNPs at the top five of each GWAS method and detected by multiple GWAS methods were regarded as having high reliability. Pathway enrichment analysis was also performed to explore the biological significance and functions of these candidate genes. Several biological pathways related to the regulation of seed growth, gibberellin-mediated signaling pathway, and long-day photoperiodism were enriched. The results of our study could provide new perspectives on breeding high-yielding maize varieties.

scholarly journals A Genome-Wide Association Study Identifies Candidate Genes Associated With Shell Color in Bay Scallop Argopecten irradians irradians

2021 ◽  
Vol 8 ◽  
Author(s):  
Xinghai Zhu ◽  
Junhao Zhang ◽  
Xiujiang Hou ◽  
Pingping Liu ◽  
Jia Lv ◽  
...  
Keyword(s):  
Association Study ◽  
Candidate Genes ◽  
Genome Wide Association Study ◽  
Genome Wide Association ◽  
Phenotypic Traits ◽  
Argopecten Irradians ◽  
Shell Color ◽  
Genome Wide ◽  
A Genome ◽  
Bay Scallop

Molluscan shell color has consistently drawn attention for its abundant diversity and commercial use in shellfish breeding projects. Recently, two new strains of bay scallop (Argopecten irradians irradians) with different shell colors as marked phenotypic traits have been artificially bred to improve their economic values; however, the inheritance mechanism of their shell pigmentation is still unclear. In this study, a genome-wide association study (GWAS) was conducted to determine the genetic basis of shell color in bay scallops utilizing 29,036 high-quality single-nucleotide polymorphisms (SNPs) derived from 80 purple-red (PP) and 80 black-brown (BP) shell color individuals. The result of the GWAS showed that 469 SNPs (p &lt;1.72E−6) significantly associated with shell color were mainly distributed in chromosome 7. The top three SNPs (i.e., chr7-12764003, chr7-13213864, and chr7-11899306) are located in the genic region of G-protein-coupled receptor-like 101 (GRL101), polyketide synthase 1 (PKS1), and phosphoinositide phospholipase C (PLC1), which have been widely reported to be involved in pigmentation. Successfully, the top three SNPs were verified in another non-breeding bay scallop population. Furthermore, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses obtained 38 GO terms covering 297 genes and aggregating pathways involving 252 annotated genes. Specifically, the expression profiles of the top three identified candidate genes were detected in mantles of PP and BP individuals by real-time quantitative reverse transcription PCR. The significantly higher expression levels of GRL101 (6.43-fold) and PLC1 (6.48-fold) in PP, and PKS1 (12.02-fold) in BP implied that GRL101 and PLC1 potentially functioned in PP shell coloration, and black pigmentation in BP might be principally regulated by PKS1. Our data provide valuable information for deciphering the phenotype differences of shell color in the bay scallop.

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