Genome-Wide Identification and Expression Analysis of NF-YA Gene Family in the Filling Stage of Wheat (Triticum aestivum L.) DOI Open Access
Yang Zhang,

Yan‐Min Xu,

Yulu Mao

et al.

International Journal of Molecular Sciences, Journal Year: 2024, Volume and Issue: 26(1), P. 133 - 133

Published: Dec. 27, 2024

The NF-YA gene family is a highly conserved transcription factor that plays crucial role in regulating plant growth, development, and responses to various stresses. Despite extensive studies multiple plants, there has been dearth of focused systematic analysis on genes wheat grains. In this study, we carried out comprehensive bioinformatics the wheat, using latest genomic data from Chinese Spring. A total 19 TaNF-YA were identified. An domains, phylogenetic relationships, structure indicated significant degree conservation among TaNF-YAs. collinearity demonstrated fragment duplication was predominant mechanism driving amplification Furthermore, cis-acting elements within promoters TaNF-YAs found be implicated grain development. Subsequently, SNP revealed genetic variation different wheat. Moreover, published RNA-seq used RNA-seqs Pinyu8155, Yaomai30, Yaomai36, Pinyu8175 performed identify influencing Finally, it NF-YAs had no self-activating activity This study provides key candidate for exploration development filling stage also lays foundation further research regulation starch protein synthesis accumulation.

Language: Английский

Global nutritional challenges and opportunities: Buckwheat, a potential bridge between nutrient deficiency and food security DOI

Rintu Jha,

Kaixuan Zhang, Yuqi He

et al.

Trends in Food Science & Technology, Journal Year: 2024, Volume and Issue: 145, P. 104365 - 104365

Published: Feb. 5, 2024

Language: Английский

Citations

33
Genomic insight into the origin, domestication, dispersal, diversification and human selection of Tartary buckwheat DOI Creative Commons
Yuqi He, Kaixuan Zhang, Yaliang Shi

et al.

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

Published: Feb. 27, 2024

Abstract Background Tartary buckwheat, Fagopyrum tataricum , is a pseudocereal crop with worldwide distribution and high nutritional value. However, the origin domestication history of this remain to be elucidated. Results Here, by analyzing population genomics 567 accessions collected reviewing historical documents, we find that buckwheat originated in Himalayan region then spread southwest possibly along migration Yi people, minority Southwestern China has long planting buckwheat. Along expansion Mongol Empire, dispersed Europe ultimately rest world. The different natural growth environments resulted adaptation, especially significant differences salt tolerance between northern southern Chinese populations. By scanning for selective sweeps using genome-wide association study, identify genes responsible differentiation, which experimentally validate. Comparative QTL analysis further shed light on genetic foundation easily dehulled trait particular variety was artificially selected Wa group known cultivating specifically steaming as staple food prevent lysine deficiency. Conclusions This study provides both comprehensive insights into of, molecular breeding for,

Language: Английский

Citations

15
Innovative computational tools provide new insights into the polyploid wheat genome DOI Creative Commons
Yongming Chen, Wenxi Wang, Zhengzhao Yang

et al.

aBIOTECH, Journal Year: 2024, Volume and Issue: 5(1), P. 52 - 70

Published: Feb. 7, 2024

Abstract Bread wheat ( Triticum aestivum ) is an important crop and serves as a significant source of protein calories for humans, worldwide. Nevertheless, its large allopolyploid genome poses constraints on genetic improvement. The complex reticulate evolutionary history the intricacy genomic resources make deciphering functional considerably more challenging. Recently, we have developed comprehensive list versatile computational tools with integration statistical models dissecting polyploid genome. Here, summarize methodological innovations applications these databases. A series step-by-step examples illustrates how can be utilized germplasm unveiling genes associated agronomic traits. Furthermore, outline future perspectives new advanced databases, taking into consideration unique features bread wheat, to accelerate genomic-assisted breeding.

Language: Английский

Citations

6
Reshaped DNA methylation cooperating with homoeolog‐divergent expression promotes improved root traits in synthesized tetraploid wheat DOI Creative Commons
Ling-Feng Miao, Weiya Xu, Yanhong Liu

et al.

New Phytologist, Journal Year: 2024, Volume and Issue: 242(2), P. 507 - 523

Published: Feb. 16, 2024

Polyploidization is a major event driving plant evolution and domestication. However, how reshaped epigenetic modifications coordinate gene transcription to generate phenotypic variations during wheat polyploidization currently elusive. Here, we profiled transcriptomes DNA methylomes of two diploid accessions (S

Language: Английский

Citations

6
Engineering the future cereal crops with big biological data: toward an intelligence-driven breeding by design DOI
Lei Liu,

Jimin Zhan,

Jianbing Yan

et al.

Journal of genetics and genomics/Journal of Genetics and Genomics, Journal Year: 2024, Volume and Issue: 51(8), P. 781 - 789

Published: March 24, 2024

Language: Английский

Citations

4
Dissection of QTLs underlying the genetic basis of drought resistance in wheat: a meta-analysis DOI

Arif Mehmood Shakir,

Miaomiao Geng,

Jiahao Tian

et al.

Theoretical and Applied Genetics, Journal Year: 2025, Volume and Issue: 138(1)

Published: Jan. 1, 2025

Language: Английский

Citations

0
WheatGP, a genomic prediction method based on CNN and LSTM DOI Creative Commons
Chunying Wang, Di Zhang, Yuexin Ma

et al.

Briefings in Bioinformatics, Journal Year: 2025, Volume and Issue: 26(2)

Published: March 1, 2025

Abstract Wheat plays a crucial role in ensuring food security. However, its complex genetic structure and trait variation pose significant challenges for breeding superior varieties. In this study, genomic prediction method wheat (WheatGP) is proposed. WheatGP designed to improve the phenotype accuracy by modeling both additive effects epistatic effects. It primarily composed of convolutional neural network (CNN) module long short-term memory (LSTM) module. The multilayer CNNs within CNN focus on capturing short-range dependencies sequence. Meanwhile, LSTM module, with unique gating mechanism, retain long-distance dependency relationships between gene loci features. Therefore, could comprehensively extract multilevel features from inputs. Compared ridge regression best linear unbiased (rrBLUP), extreme gradient boosting (XGBoost), support vector (SVR), deep (DNNGP), demonstrates clear advantage terms accuracy. yield reaches 0.73, while accuracies various agronomic traits range 0.62 0.78. also exhibits robust performance across other crop types multi-omics datasets. addition, SHapley Additive exPlanations (SHAP) employed evaluate contributions inputs predictive model. As high-performance tool wheat, opens up new possibilities achieving efficient optimized breeding.

Language: Английский

Citations

0
Wheat genomics: genomes, pangenomes, and beyond DOI
Vijay Tiwari, Gautam Saripalli, Parva Kumar Sharma

et al.

Trends in Genetics, Journal Year: 2024, Volume and Issue: 40(11), P. 982 - 992

Published: Aug. 26, 2024

Language: Английский

Citations

2
Wide hybridizations reveal the robustness of functional centromeres in Triticum–Aegilops species complex lines DOI
Yuhong Huang, Qinghua Shi, Chen Zhou

et al.

Journal of genetics and genomics/Journal of Genetics and Genomics, Journal Year: 2023, Volume and Issue: unknown

Published: Dec. 1, 2023

Language: Английский

Citations

5
Dissection of QTLs underlying the genetic basis of drought resistance in wheat: A Meta-Analysis DOI Creative Commons
Ruihui Wang,

Arif Mehmood Shakir,

Miaomiao Geng

et al.

Research Square (Research Square), Journal Year: 2024, Volume and Issue: unknown

Published: June 6, 2024

Abstract Wheat (Triticum aestivum L.) is one of the most important cereal crops, with its grain serving as a predominant staple food source on global scale. However, there are many biotic and abiotic stresses challenging stability wheat production. Among stresses, drought recognized significant stressor, poses substantial threat to production quality throughout world. Raising tolerance varieties through genetic regulation therefore considered effective ways combat challenges caused by stress. Meta-QTL analysis has demonstrated effectiveness in identifying consensus QTL regions resistance numerous instances. In this study, we present comprehensive meta-analysis aimed at unraveling basis associated agronomic traits bread wheat. Extracting data from 34 previously-published studies, aggregated corpus 1291 Quantitative Trait Loci (QTL) pertinent tolerance. Then translation map yielded compendium 49 distinct MQTLs, each diverse traits. Prominently featured among MQTLs were 1.1, 1.7, 1.8 (1D), 4.1 (4A), 4.6 (4D), 5.2 (5B), 6.6 (6B) 7.2 (7B), distinguished pivotal offering potential for application marker-assisted breeding endeavors. Altogether, total 66 putative candidate genes (CGs) related was identified. This work illustrates translational research approach transferring information published mapping studies genomic hosting major QTLs governing key agronomical

Language: Английский

Citations

1