Single- and multi-locus genome-wide association study reveals genomic regions of thirteen yield-related traits in common wheat DOI Creative Commons

Yuxia Lv,

Lei Dong,

X. Wang

et al.

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

Published: Nov. 25, 2024

Abstract Genetic dissection of yield-related traits can be used to improve wheat yield through molecular design breeding. In this study, we genotyped 245 varieties and measured 13 plant height-, grain- spike-related traits, in seven environments, identified 778 loci for these by genome-wide association study (GWAS) using single- multi-locus models. Among them, nine were major loci, which novel, including Qph/lph.ahau-7A height (PH) leaf pillow (LPH), Qngps/sps.ahau-1A number grains per spike (NGPS) spikelet (SPS), Qsd.ahau-2B.1 Qsd.ahau-5A.2 density (SD), Qlph.ahau-7B.2 LPH, Qgl.ahau-7B.3 grain length (GL), Qsl.ahau-3A.3 (SL). Through marker development, re-GWAS, gene annotation cloning, sequence variation, haplotype, expression analyses, confirmed two novel potential candidate genes, TraesCS7A02G118000 (named TaF-box-7A) TraesCS1A02G190200 TaBSK2-1A) underlying PH-related respectively. Furthermore, reported favorable haplotypes, TaF-box-Hap1 associated with low PH LPH TaBSK2-Hap3 high NGPS SPS. summary, findings are valuable improving enriching our understanding the complex genetic mechanisms traits.

Language: Английский

Harnessing landrace diversity empowers wheat breeding DOI Creative Commons
Shifeng Cheng, Cong Feng, Luzie U. Wingen

et al.

Nature, Journal Year: 2024, Volume and Issue: 632(8026), P. 823 - 831

Published: June 17, 2024

Abstract Harnessing genetic diversity in major staple crops through the development of new breeding capabilities is essential to ensure food security 1 . Here we examined and phenotypic A. E. Watkins landrace collection 2 bread wheat ( Triticum aestivum ), a global cereal, by whole-genome re-sequencing 827 landraces 208 modern cultivars in-depth field evaluation spanning decade. We found that are derived from two seven ancestral groups maintain very long-range haplotype integrity. The remaining five represent untapped sources, providing access landrace-specific alleles haplotypes for breeding. Linkage disequilibrium-based association genetics analyses link genomes thousands identified high-resolution quantitative trait loci significant marker–trait associations. Using these structured germplasm, genotyping informatics resources, revealed many Watkins-unique beneficial can confer superior traits wheat. Furthermore, assessed effects 44,338 haplotypes, introgressed 143 prioritized context cultivars, bridging gap between current This study establishes framework systematically utilizing crop improvement achieve sustainable security.

Language: Английский

Citations

29
Calcium signaling-mediated transcriptional reprogramming during abiotic stress response in plants DOI

Huimin Ren,

Yuting Zhang,

Minyi Zhong

et al.

Theoretical and Applied Genetics, Journal Year: 2023, Volume and Issue: 136(10)

Published: Sept. 20, 2023

Language: Английский

Citations

25
Genomics-guided landscape unlocks superior alleles and genes for yellow rust resistance in wheat DOI Creative Commons
Jianhui Wu, Shengwei Ma, Jianqing Niu

et al.

Research Square (Research Square), Journal Year: 2025, Volume and Issue: unknown

Published: March 11, 2025

Abstract Yellow rust (YR), caused by Puccinia striiformis f. sp. tritici (Pst), poses a significant threat to wheat production worldwide. Breeding resistant cultivar is crucial for managing this disease. However, understanding of the genetic mechanisms underlying YR resistance remains fragmented. To address this, we conducted comprehensive analysis with variome data from 2,191 accessions worldwide and over 47,000 response records across multiple environments pathogen races. Through genome-wide association studies, established landscape 431 loci, providing rich resource (R) gene deployment. Furthermore, cloned genes corresponding three namely Yr5x effective against Pst races, Yr6/Pm5 that conferred two species, YrKB (TaEDR2-B) conferring broad-spectrum without yield penalty. These findings offer valuable insights into basis in lay foundation engineering durable disease resistance.

Language: Английский

Citations

1
Tagging large CNV blocks in wheat boosts digitalization of germplasm resources by ultra-low-coverage sequencing DOI Creative Commons

Jianxia Niu,

Wenxi Wang,

Zihao Wang

et al.

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

Published: July 1, 2024

Abstract Background The massive structural variations and frequent introgression highly contribute to the genetic diversity of wheat, while huge complex genome polyploid wheat hinders efficient genotyping abundant varieties towards accurate identification, management, exploitation germplasm resources. Results We develop a novel workflow that identifies 1240 high-quality large copy number variation blocks (CNVb) in at pan-genome level, demonstrating CNVb can serve as an ideal DNA fingerprinting marker for discriminating varieties, with accuracy validated by PCR assay. then construct digitalized map across 1599 global accessions. Key markers are linked trait-associated introgressions, such 1RS·1BL translocation 2N v S translocation, beneficial alleles, end-use quality allele Glu-D1d (Dx5 + Dy10) semi-dwarf r-e-z allele. Furthermore, we demonstrate these tagged promote stable cost-effective strategy evaluating resources ultra-low-coverage sequencing data, competing SNP array applications new management collections gene banks, describing manner. also user-friendly interactive platform, WheatCNVb ( http://wheat.cau.edu.cn/WheatCNVb/ ), exploring profiles over ever-increasing accessions, propose QR-code-like representation individual digital fingerprint. This platform allows uploading comparison stored varieties. Conclusions CNVb-based approach provides low-cost high-throughput enabling modern breeding precise practical decision-making.

Language: Английский

Citations

7
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
Natural variant of Rht27, a dwarfing gene, enhances yield potential in wheat DOI
X. Liu, Shusong Zheng, Shuiquan Tian

et al.

Theoretical and Applied Genetics, Journal Year: 2024, Volume and Issue: 137(6)

Published: May 11, 2024

Language: Английский

Citations

4
Genetic dissection of flag leaf morphology traits and fine mapping of a novel QTL (Qflw.sxau-6BL) in bread wheat (Triticum aestivum L.) DOI

Ling Qiao,

Xingwei Zheng, Jiajia Zhao

et al.

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

Published: Jan. 1, 2025

Language: Английский

Citations

0
The allelic mutation of NBS-LRR gene causes premature senescence in wheat DOI Creative Commons
Lin Qiu, Rui Fang,

Yong Jia

et al.

Plant Science, Journal Year: 2025, Volume and Issue: unknown, P. 112395 - 112395

Published: Jan. 1, 2025

Language: Английский

Citations

0
Population-scale gene expression analysis reveals the contribution of expression diversity to the modern wheat improvement DOI Open Access
Zhimeng Zhang, Shengwei Ma,

Mou Yin

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2025, Volume and Issue: unknown

Published: Feb. 23, 2025

Abstract Changes in gene expression are crucial for crop breeding, yet population genomics has primarily focused on sequence polymorphisms rather than diversity. The strategy of using single genome reference RNA-seq analysis could not handle introgression bias, especially hexaploidy wheat. Here, we conducted 328 wheat lines, including representative diverse landraces and elite cultivars from China the United States, to investigate role variation shaping agronomic traits. Using pan-genome resources, identified 20,615 more transcripts ‘Chinese Spring’ alone. We constructed a pan-gene atlas regulatory map through eQTL analysis, demonstrating that genes introgressed wild relatives were under tight genetic control. Genes responding environmental stress show higher activity after into genome, how long-term breeding selection impacted regulation targeted introgression. Multi-omics modeling 231 high-confidence candidate 34 field traits seedling resistance phenotypes 8 powdery mildew isolates. More one fifth those candidates have no homolog genome. By utilizing indexed KN9204 EMS library, 80% showed significant trait difference between type mutant lines. Furthermore, directional shifts which changed by improvement demonstrated distinct adaptations local environments. Our study correct bias reads mapping studies revealed patterns within their mechanisms, highlighted impact world’s most important crop.

Language: Английский

Citations

0
Decoding cellular transcriptional regulatory networks governing wheat inflorescence development DOI Creative Commons
Jun Xiao, Xuemei Liu, Xuelei Lin

et al.

Research Square (Research Square), Journal Year: 2025, Volume and Issue: unknown

Published: March 12, 2025

Abstract In wheat, inflorescence architecture critically determines yield potential, yet its structural complexity and asynchronous development have hindered cellular-resolution studies of spikelet floret formation. Here, we integrate spatial transcriptomics, high-sensitivity multiplexed error-robust fluorescence in situ hybridization (MERFISH), snRNA-seq across six developmental stages to generate a spatiotemporal atlas the wheat inflorescence. We identified 20 cell types, spatially resolved into three categories: 1) proliferating cells within spikelet, marked by active division; 2) supporting along central axis, including pith, cortex, vasculature; 3) developmental located both inside at base spikelets. The multi-omics approach enabled identification rare type ovary. Trajectory inference revealed that spikelets florets originate from two temporally distinct sub-clusters proliferating cells (R7), each defined high expression regulators. These findings challenge conventional model sequential meristem transitions (inflorescence-spikelet-floret) in wheat. Integration time-series snATAC-seq delineated cellular transcriptional regulatory networks (cTRNs) governing formation, mediated auxin cytokinin signaling, driven MADS-box transcription factors. Cell identity was maintained type-specific accessible chromatin regions (csACRs), which are enriched for SNPs associated with spike-related traits. For instance, csACRs WFZP DUO1 promoters affect TaNAC30 binding, regulating supernumerary phenotypes. Our work provides mechanistic framework identifies cTRN nodes as potential targets optimizing yield-related architecture.

Language: Английский

Citations

0