Performing whole-genome association analysis of winter wheat plant height using the 55K chip DOI Creative Commons

Yindeng Ding,

Guiqiang Fan,

Yonghong Gao

et al.

Frontiers in Plant Science, Journal Year: 2025, Volume and Issue: 15

Published: Jan. 17, 2025

Plant height is a critical agronomic that affects both plant architecture and yield. To decipher the genetic mechanisms underlying winter wheat identify candidate genes associated with this trait, we conducted phenotypic analysis on 239 varieties (lines) collected from around world. This was complemented by genotyping using 55K SNP chip. A Wholegenome association (GWAS) of utilizing MLM (Q+K) model within TASSLE software. The results revealed significant variation in across different years, coefficients ranging 0.96% to 1.97%. Additionally, there strong correlation measurements between years. GWAS identified 44 markers significantly various environments (P ≤ 0.00001), predominantly distributed chromosomes 1B, 1D, 2A, 2B, 2D, 3B, 3D, 4A, 4B, 6B, 6D, 7D, explaining individual variance rates 5.00% 11.11%. Further, mining loci substantial effects stability multiple environments, seven related have been identified. study provides new resources for improving height.

Language: Английский

Systematic identification of wheat spike developmental regulators by integrated multi-omics, transcriptional network, GWAS, and genetic analyses DOI Creative Commons
Xuelei Lin, Yongxin Xu, Dongzhi Wang

et al.

Molecular Plant, Journal Year: 2024, Volume and Issue: 17(3), P. 438 - 459

Published: Feb. 2, 2024

Language: Английский

Citations

18
TaTPP‐7A positively feedback regulates grain filling and wheat grain yield through T6P‐SnRK1 signalling pathway and sugar–ABA interaction DOI Creative Commons
Hongxia Liu,

Xuemei Si,

Zhenyu Wang

et al.

Plant Biotechnology Journal, Journal Year: 2023, Volume and Issue: 21(6), P. 1159 - 1175

Published: Feb. 8, 2023

Grain size and filling are two key determinants of grain thousand-kernel weight (TKW) crop yield, therefore they have undergone strong selection since cereal was domesticated. Genetic dissection the traits will improve yield potential in crops. A quantitative trait locus significantly associated with wheat TKW detected on chromosome 7AS flanked by a simple sequence repeat marker Wmc17 Chinese 262 mini-core collection genome-wide association study. Combined bulked segregant RNA-sequencing (BSR-seq) analysis an F2 genetic segregation population extremely different traits, candidate trehalose-6-phosphate phosphatase gene located at 135.0 Mb (CS V1.0), designated as TaTPP-7A, identified. This specifically expressed developing grains strongly influenced size. Overexpression (OE) TaTPP-7A enhanced greatly. Detailed revealed that OE increased expression levels starch synthesis- senescence-related genes involved abscisic acid (ABA) ethylene pathways. Moreover, most sucrose metabolism regulation-related were potentially regulated SnRK1. In addition, is crucial domestication- breeding-targeted it feedback regulates lysis, flux, utilization endosperm mainly through T6P-SnRK1 pathway sugar-ABA interaction. Thus, we confirmed T6P signalling central regulatory system for allocation source-sink interactions propose trehalose components great to increase yields

Language: Английский

Citations

39
Genomic insights into the genetic basis of cotton breeding in China DOI Creative Commons
Yiqian Li, Zhanfeng Si,

Guoping Wang

et al.

Molecular Plant, Journal Year: 2023, Volume and Issue: 16(4), P. 662 - 677

Published: Feb. 2, 2023

The excellent Upland cotton (Gossypium hirsutum) cultivars developed since 1949 have made a huge contribution to production in China, the world's largest producer and consumer of cotton. However, genetic genomic basis for improvements these remains largely unclear. In this study, we selected 16 with important historical status Chinese breeding constructed multiparent, advanced generation, intercross (MAGIC) population comprising 920 recombinant inbred lines. A genome-wide association study using MAGIC identified 54 loci associated lint yield fiber quality. Of them, 25 (46.30%) pleiotropic cause simultaneous changes and/or quality traits, revealing complex trade-offs linkage drags agronomic traits. Deep sequencing data 11 introduced ancestor publicly available resequencing datasets 839 China during past 70 years were integrated explore distribution origin elite or alleles. Interestingly, 85% alleles fixed from different American ancestors, consistent practices China. seven native that are responsible Fusarium wilt resistance, early maturing, good-quality fiber, other characteristics not found ancestors but greatly contributed wide cultivation. Taken together, results provide further improving reveal composition is narrow mainly derived varieties.

Language: Английский

Citations

31
Whole-genome sequencing of diverse wheat accessions uncovers genetic changes during modern breeding in China and the United States DOI
Jianqing Niu, Shengwei Ma, Shusong Zheng

et al.

The Plant Cell, Journal Year: 2023, Volume and Issue: 35(12), P. 4199 - 4216

Published: Aug. 30, 2023

Breeding has dramatically changed the plant architecture of wheat (Triticum aestivum), resulting in development high-yielding varieties adapted to modern farming systems. However, how breeding shaped genomic this crop remains poorly understood. Here, we performed a comprehensive comparative analysis whole-genome resequencing panel 355 common accessions (representing diverse landraces and cultivars from China United States) at phenotypic levels. The genetic diversity was clearly reduced compared landraces. Consistent with these changes, most phenotypes States were significantly altered. Of 21 agronomic traits investigated, 8 showed convergent changes between 2 countries. Moreover, 207 loci associated traits, more than half overlapped regions that evidence selection. distribution selected Chinese American suggests for increased productivity accomplished by pyramiding both shared region-specific variants. This work provides framework understand adaptation agricultural production environments, as well guidelines optimizing strategies design better varieties.

Language: Английский

Citations

30
Genome resources for the elite bread wheat cultivar Aikang 58 and mining of elite homeologous haplotypes for accelerating wheat improvement DOI Creative Commons
Jizeng Jia,

Guangyao Zhao,

Danping Li

et al.

Molecular Plant, Journal Year: 2023, Volume and Issue: 16(12), P. 1893 - 1910

Published: Oct. 28, 2023

Language: Английский

Citations

29
Grain yield improvement by genome editing of TaARF12 that decoupled peduncle and rachis development trajectories via differential regulation of gibberellin signalling in wheat DOI Creative Commons

Xingchen Kong,

Fang Wang, Zhenyu Wang

et al.

Plant Biotechnology Journal, Journal Year: 2023, Volume and Issue: 21(10), P. 1990 - 2001

Published: Aug. 17, 2023

Summary Plant breeding is constrained by trade‐offs among different agronomic traits the pleiotropic nature of many genes. Genes that contribute to two or more favourable with no penalty on yield are rarely reported, especially in wheat. Here, we describe editing a wheat auxin response factor TaARF12 using CRISPR/Cas9 rendered shorter plant height larger spikes. Changes architecture enhanced grain number per spike up 14.7% significantly higher thousand‐grain weight and 11.1% increase under field trials. Weighted Gene Co‐Expression Network Analysis (WGCNA) spatial–temporal transcriptome profiles revealed hub genes: RhtL1 , DELLA domain‐free Rht‐1 paralog, which was up‐regulated peduncle, TaNGR5 an organ size regulator rachis, taarf12 plants. The up‐regulation peduncle suggested repression GA signalling, whereas may promote response, working model supported differential expression patterns biogenesis genes tissues. Thus, complemented reduction spikes gave yield. Manipulation represent new strategy trait pyramiding for improvement

Language: Английский

Citations

25
Genetic basis of geographical differentiation and breeding selection for wheat plant architecture traits DOI Creative Commons
Yangyang Liu,

Kuocheng Shen,

Changbin Yin

et al.

Genome biology, Journal Year: 2023, Volume and Issue: 24(1)

Published: May 12, 2023

Abstract Background Plant architecture associated with increased grain yield and adaptation to the local environments is selected during wheat ( Triticum aestivum ) breeding. The internode length of individual stems tiller plants are important for determination plant architecture. However, few studies have explored genetic basis these traits. Results Here, we conduct a genome-wide association study (GWAS) dissect geographical differentiation traits in 306 worldwide accessions including both landraces traditional varieties. We determine changes haplotypes genomic regions frequency 831 that either introduced from other countries or developed China last two decades. identify 83 loci one trait, while remaining 247 pleiotropic. also find 163 under strong selective sweep. GWAS results demonstrate independent regulation consistent plants. This makes it possible obtain ideal haplotype combinations four internodes. distribution explains observed differences among accessions. Conclusion provides insights into It will facilitate gene functional analysis molecular design

Language: Английский

Citations

23
Deciphering the Transcriptional Regulatory Network Governing Starch and Storage Protein Biosynthesis in Wheat for Breeding Improvement DOI Creative Commons
Long Zhao, Jinchao Chen,

Zhaoheng Zhang

et al.

Advanced Science, Journal Year: 2024, Volume and Issue: 11(33)

Published: June 28, 2024

Starch and seed storage protein (SSP) composition profoundly impact wheat grain yield quality. To unveil regulatory mechanisms governing their biosynthesis, transcriptome, epigenome profiling is conducted across key endosperm developmental stages, revealing that chromatin accessibility, H3K27ac, H3K27me3 collectively regulate SSP starch genes with varying impact. Population transcriptome phenotype analyses highlight accessible promoter regions' crucial role as a genetic variation resource, influencing quality in core collection of accessions. Integration time-serial RNA-seq ATAC-seq enables the construction hierarchical transcriptional network identifying 42 high-confidence novel candidates. These candidates exhibit overlap regions associated size traits, functional significance validated through expression-phenotype association analysis among accessions loss-of-function mutants. Functional abscisic acid insensitive 3-A1 (TaABI3-A1) genome editing knock-out lines demonstrates its promoting accumulation while repressing biosynthesis regulation. Excellent TaABI3-A1

Language: Английский

Citations

14
TabHLH27 orchestrates root growth and drought tolerance to enhance water use efficiency in wheat DOI
Dongzhi Wang, Xiuxiu Zhang, Yuan Cao

et al.

Journal of Integrative Plant Biology, Journal Year: 2024, Volume and Issue: 66(7), P. 1295 - 1312

Published: May 2, 2024

ABSTRACT Cultivating high‐yield wheat under limited water resources is crucial for sustainable agriculture in semiarid regions. Amid scarcity, plants activate drought response signaling, yet the delicate balance between tolerance and development remains unclear. Through genome‐wide association studies transcriptome profiling, we identified a atypical basic helix‐loop‐helix (bHLH) transcription factor (TF), TabHLH27‐A1, as promising quantitative trait locus candidate both relative root dry weight spikelet number per spike wheat. TabHLH27‐A1/B1/D1 knock‐out reduced tolerance, yield, use efficiency (WUE). TabHLH27‐A1 exhibited rapid induction with polyethylene glycol (PEG) treatment, gradually declining over days. It activated stress genes such TaCBL8‐B1 TaCPI2‐A1 while inhibiting growth like TaSH15‐B1 TaWRKY70‐B1 short‐term PEG stimulus. The distinct transcriptional regulation of involved diverse interacting factors TaABI3‐D1 TabZIP62‐D1. Natural variations influence its responses to stress, Hap‐II associated stronger larger system, more spikelets, higher WUE Significantly, excellent was selected during breeding process China, introgression allele improved grain especially water‐limited conditions. Our study highlights TabHLH27‐A1's role balancing providing genetic manipulation enhancing

Language: Английский

Citations

10
Effects and molecular mechanisms of polyethylene microplastic oxidation on wheat grain quality DOI
Yan Yan,

Huijie Yang,

Yuan Du

et al.

Journal of Hazardous Materials, Journal Year: 2024, Volume and Issue: 474, P. 134816 - 134816

Published: June 5, 2024

Language: Английский

Citations

9