Systematic mining and functional analysis of factors regulating wheat spike development for breeding selection DOI Creative Commons
Xuelei Lin, Yongxin Xu, Dongzhi Wang

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2022, Volume and Issue: unknown

Published: Nov. 11, 2022

Abstract The spike architecture of wheat plays a crucial role in determining grain number, making it key trait to optimize breeding programs. In this study, through multi-omic approach, we analyzed the transcriptome and epigenome profiles shoot apex at eight developmental stages, revealing coordinated changes chromatin accessibility H3K27me3 abundance during flowering transition. We constructed core transcriptional regulatory network (TRN) that drives formation, experimentally validated multi-layer module involving TaSPL15, TaAGLG1, TaFUL2. By integrating TRN with genome-wide association analysis (GWAS), identified 227 transcription factors (TFs), including 42 known functions 185 unknown functions. Further investigation 61 novel TFs using multiple homozygous mutant lines uncovered 36 altered or time, such as TaMYC2-A1, TaMYB30-A1, TaWRKY37-A1. Of particular interest, downstream repressed by WFZP, was found regulate fertile spikelet number. Notably, domestication process China, excellent haplotype TaMYB30-A1 containing C allele WFZP binding site enriched, leading improved agronomic traits. Our study presents high-confidence regulators offers an effective strategy for understanding genetic basis development, practical impact applications.

Language: Английский

Identification of Whirly transcription factors in Triticeae species and functional analysis of TaWHY1-7D in response to osmotic stress DOI Creative Commons
Hao Liu, Xiaoyu Wang, Wenbo Yang

et al.

Frontiers in Plant Science, Journal Year: 2023, Volume and Issue: 14

Published: Dec. 5, 2023

Osmotic stress poses a threat to the production and quality of crops. Whirly transcription factors have been investigated enhance tolerance. In this study, total 18 genes were identified from six Triticeae species, which classified into Whirly1 Whirly2 . The exon–intron structure, conserved motif, chromosomal location, collinearity, regulatory network also analyzed. Real-time PCR results indicated that TaWHY1 exhibited higher expression levels in leaf sheaths leaves during seedling stage, while TaWHY2 predominantly expressed roots. Under PEG stress, TaWHY1-7A , TaWHY2-6A TaWHY2-6B TaWHY2-6D increased, TaWHY1-7D was reduced, TaWHY1-4A had no significant change. All TaWHY significantly up-regulated response NaCl treatment. addition, mainly enhanced tolerance oxidative yeast cells. TaWHY2s improved sensitive TaWHYs slightly d -sorbitol stress. heterologous greatly drought salt transgenic Arabidopsis conclusion, these provide foundation for further functional study aimed at improving osmotic wheat.

Language: Английский

Citations

4
Integrated multi-omics reveals contrasting epigenetic patterns in leaf and root morphogenesis in Aegilops speltoides DOI Creative Commons
Ling-Feng Miao, Zhe Chen,

Lifeng Gao

et al.

The Crop Journal, Journal Year: 2024, Volume and Issue: unknown

Published: Oct. 1, 2024

Language: Английский

Citations

1
Omics big data for crop improvement: Opportunities and challenges DOI Creative Commons

Naresh Vasupalli,

Javaid Akhter Bhat, Priyanka Jain

et al.

The Crop Journal, Journal Year: 2024, Volume and Issue: unknown

Published: Nov. 1, 2024

Language: Английский

Citations

1
Transcriptional regulatory network reveals key transcription factors for regulating agronomic traits in soybean DOI Creative Commons
Jiao Wu,

Mang-Mang Wang,

Yi-Jian Guan

et al.

Genome biology, Journal Year: 2024, Volume and Issue: 25(1)

Published: Dec. 18, 2024

Transcription factors (TFs) bind regulatory genomic regions to orchestrate spatio-temporal expression of target genes. Global dissection the cistrome is critical for elucidating transcriptional networks underlying complex agronomic traits in crops. Here, we generate a comprehensive genome-wide binding map 148 TFs using DNA affinity purification sequencing soybean. We find TF sites (TFBSs) exhibit elevated chromatin accessibility and contain more rare alleles than other regions. Intriguingly, methylation variations at TFBSs partially contribute bias among whole genome duplication paralogs. Furthermore, construct soybean gene network (SoyGRN) by integrating TF-target interactions with diverse datasets encompassing expression, TFBS motifs, accessibility, evolutionarily conserved regulation. SoyGRN comprises 2.44 million 3188 51,665 successfully identify key governing seed coat color oil content prioritize candidate genes within quantitative trait loci associated various SoyGRN. To accelerate utilization SoyGRN, develop an interactive webserver ( www.soytfbase.cn ) community explore functional involved Overall, our study unravels intricate landscape provides valuable resource dissecting regulators control improvement.

Language: Английский

Citations

1
Systematic mining and functional analysis of factors regulating wheat spike development for breeding selection DOI Creative Commons
Xuelei Lin, Yongxin Xu, Dongzhi Wang

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2022, Volume and Issue: unknown

Published: Nov. 11, 2022

Abstract The spike architecture of wheat plays a crucial role in determining grain number, making it key trait to optimize breeding programs. In this study, through multi-omic approach, we analyzed the transcriptome and epigenome profiles shoot apex at eight developmental stages, revealing coordinated changes chromatin accessibility H3K27me3 abundance during flowering transition. We constructed core transcriptional regulatory network (TRN) that drives formation, experimentally validated multi-layer module involving TaSPL15, TaAGLG1, TaFUL2. By integrating TRN with genome-wide association analysis (GWAS), identified 227 transcription factors (TFs), including 42 known functions 185 unknown functions. Further investigation 61 novel TFs using multiple homozygous mutant lines uncovered 36 altered or time, such as TaMYC2-A1, TaMYB30-A1, TaWRKY37-A1. Of particular interest, downstream repressed by WFZP, was found regulate fertile spikelet number. Notably, domestication process China, excellent haplotype TaMYB30-A1 containing C allele WFZP binding site enriched, leading improved agronomic traits. Our study presents high-confidence regulators offers an effective strategy for understanding genetic basis development, practical impact applications.

Language: Английский

Citations

4