Wheat genomic study for genetic improvement of traits in China

Xiao, Jun; Liu, Bao; Yao, Yingyin; Guo, Zifeng; Jia, Haiyan; Kong, Lingrang; Zhang, Aimin; Ma, Wujun; Ni, Zhongfu; Xu, Shengbao; Lü, Fei; Jiao, Yuannian; Yang, Wuyun; Lin, Xiaozeng; Sun, Silong; Lu, Zefu; Gao, Lifeng; Zhao, Guangyao; Cao, Shuanghe; Chen, Qian; Zhang, Kunpu; Wang, Mengcheng; Wang, Meng; Hu, Zhaorong; Guo, Weilong; Li, Guoqiang; Ma, Xin; Li, Junming; Han, Fangpu; Fu, Xiang‐Dong; Ma, Zhengqiang; Wang, Daowen; Zhang, Xueyong; Ling, Hong‐Qing; Xia, Guangmin; Tong, Yiping; Li, Yong; He, Zhonghu; Jia, Jizeng; Chong, Kang

doi:10.1007/s11427-022-2178-7

Cited by 94 publications

(72 citation statements)

References 585 publications

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“…Known factors involved in flowering time regulation and inflorescence development is highlighted from specific cluster. For instance, flowering time gene TaPPD1 in cluster2 is expressed before floral transition from SAM to DR (Boden et al, 2015;Perez-Gianmarco et al, 2020); WAPO1, required for the maintenance of SM activity, is highly expressed at SMI (Kuzay et al, 2022); TaTFL1 and WFZP, involved in terminal spikelet formation and floret fate, are expressed at GPD and FMI (Li et al, 2021;Wang et al, 2017); floral organ regulator TaAGL6 is highly expressed at FOP (Kong et al, 2022) (Figure 1D). Besides, various members of SPL family TF (TaSPL9/12, TaSPL1, TaSPL14, and TaSPL8/16) are highly expressed at different stages (Figure 1D), consistent with recent report .…”

Section: A Transcriptome and Chromatin Landscape Atlas For Wheat Spik...mentioning

confidence: 99%

“…Of the candidate TFs, we categorize them into three classes, termed as 'researched' for functional studied in wheat and 'conserved' as orthologue being studied in other species as well as 'novel' for functional unknown for wheat and other crops (Figure 4G). Among the 260 TFs, 11 factors are 'researched' in wheat, including VRN1 (Li et al, 2019), TaFUL3 (Li et al, 2019), TaAGL6 (Kong et al, 2022), TaSEP3 (Zhang et al, 2021). Another 41 factors are 'conserved', including MOC1 (Zhang et al, 2015), PAP2 (Kobayashi et al, 2010;Kobayashi et al, 2012), MADS14 (Wu et al, 2017), etc.…”

Section: Integration Of Multi-data To Systematically Screen Regulator...mentioning

confidence: 99%

“…WFZP, a homologous of rice FRIZZY PANICLE (FZP), determines the SNS and the floret meristem fate partially by VRN1 and HOMEOBOX4 (TaHOX4) (Li et al, 2021), as well as by inhibiting the repressor of spikelet formation gene TaBA1 through epigenetic modification factors TaHDA1 and TaLHP1 (Du et al, 2021). Several SQUAMOSA promoter-binding protein-like (SPL) and MADS-box TFs are involved in the floral organ formation and regulate floret fertility, such as TaSPL13-B (Li et al, 2020), TaSPL14 (Cao et al, 2021), TaAGL6-A (Kong et al, 2022). Besides of the key TFs that mediating the meristem identity switch, factors in auxin and cytokinin (CK) hemostasis also play important role in regulation of spike development in wheat, such as TaCYP78A5 and TaCKX2.1, TaCKX2.2 (Guo et al, 2022;Jablonski et al, 2020;Jablonski et al, 2021;Qi et al, 2019).…”

Section: Introductionmentioning

confidence: 99%

“…Several SQUAMOSA promoter-binding protein-like (SPL) and MADS-box TFs are involved in the floral organ formation and regulate floret fertility, such as TaSPL13-B (Li et al, 2020), TaSPL14 (Cao et al, 2021), TaAGL6-A (Kong et al, 2022). Besides of the key TFs that mediating the meristem identity switch, factors in auxin and cytokinin (CK) hemostasis also play important role in regulation of spike development in wheat, such as TaCYP78A5 and TaCKX2.1, TaCKX2.2 (Guo et al, 2022;Jablonski et al, 2020;Jablonski et al, 2021;Qi et al, 2019).…”

Section: Introductionmentioning

confidence: 99%

“…Wheat ( Triticum aestivum ) is a major crop worldwide and provides about 20% of the daily calories and proteins consumed by human population. Yield is a polygenic complex quantitative trait composed of multiple elements including fertile tiller per area, grain number per spike (GNPS) and grain weight (Xiao et al, 2022). GNPS is determinate by the architecture of spike/inflorescence, which involves the number and arrangement of spikelet and fertile florets within spikelet.…”

Section: Introductionmentioning

confidence: 99%

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Systematic mining and functional analysis of factors regulating wheat spike development for breeding selection

Lin

Wang

et al. 2022

Preprint

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Spike architecture largely affects grain number embraced, which is a key factor influencing wheat grain yield. Here, we systematically explore the genetic regulation network governing wheat spike development by integration of multi-omic data with population genetics. Transcriptome and epigenome profile of shoot apex at eight developmental stages were generated. Gain-of-chromatin accessibility and changes of H3K27me3 coordinately associate with the progressive transcriptome alteration for flowering. A core transcriptional regulation network (TRN) that likely drives various meristematic cell identities transition to form spike was constructed. Integration of the TRN and genome-wide association analysis (GWAS), 260 transcription factors (TFs) were identified, including 52 characterized factors in crops, but mostly unstudied. Multi-layer regulatory module among TaSPL6, TaMADS34 and TaMADS14 suggested by TRN was further validated experimentally. About 85 novel TFs contain high impact mutant lines in KN9204 TILLING library. Of them, 44 TFs with homozygous mutation, including NAC, bHLH, MYB, and WRKY, show altered spike architecture. In particular, TaMYB4-A positively regulates fertile spikelet number likely via regulating hormones homeostasis or signaling, while acting downstream of- and repressed by WFZP. The elite allele of TaMYB4-A, with higher expression and more fertile spikelet, was selected during breeding process in China. Collectively, we present invaluable resource of high-confidence regulators and novel strategy for understanding the genetic regulation of wheat spike development systematically.

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Section: A Transcriptome and Chromatin Landscape Atlas For Wheat Spik...mentioning

confidence: 99%

Section: Integration Of Multi-data To Systematically Screen Regulator...mentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Systematic mining and functional analysis of factors regulating wheat spike development for breeding selection

Lin

Wang

et al. 2022

Preprint

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Deciphering the Transcriptional Regulatory Network Governing Starch and Storage Protein Biosynthesis in Wheat for Breeding Improvement

Zhao,

Chen,

Zhang

et al. 2024

Advanced Science

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Starch and seed storage protein (SSP) composition profoundly impact wheat grain yield and quality. To unveil regulatory mechanisms governing their biosynthesis, transcriptome, and epigenome profiling is conducted across key endosperm developmental stages, revealing that chromatin accessibility, H3K27ac, and H3K27me3 collectively regulate SSP and starch genes with varying impact. Population transcriptome and phenotype analyses highlight accessible promoter regions’ crucial role as a genetic variation resource, influencing grain yield and quality in a core collection of wheat accessions. Integration of time‐serial RNA‐seq and ATAC‐seq enables the construction of a hierarchical transcriptional regulatory network governing starch and SSP biosynthesis, identifying 42 high‐confidence novel candidates. These candidates exhibit overlap with genetic regions associated with grain size and quality traits, and their functional significance is validated through expression‐phenotype association analysis among wheat accessions and loss‐of‐function mutants. Functional analysis of wheat abscisic acid insensitive 3‐A1 (TaABI3‐A1) with genome editing knock‐out lines demonstrates its role in promoting SSP accumulation while repressing starch biosynthesis through transcriptional regulation. Excellent TaABI3‐A1Hap1 with enhanced grain weight is selected during the breeding process in China, linked to altered expression levels. This study unveils key regulators, advancing understanding of SSP and starch biosynthesis regulation and contributing to breeding enhancement.

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Identification of genetic loci for powdery mildew resistance in bread wheat

Zhao,

Zeng,

Liu

et al. 2023

Crop Science

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Powdery mildew is a very destructive disease that threatens yield and quality of wheat. In the present study, 262 recombinant inbred lines derived from a cross between Zhongmai 578 (ZM578) with moderate resistance to powdery mildew and Jimai 22 (JM22) with high resistance to powdery mildew in the field were used to map powdery mildew resistance loci using the high‐density Illumina iSelect 50K single‐nucleotide polymorphism array. Three quantitative trait loci (QTLs) on chromosomes 2B, 5B, and 5D were identified by inclusive composite interval mapping, designated as QPm.caas‐2BL.1, QPm.caas‐5BL, and QPm.caas‐5DL, respectively, explaining 5.0%–37.0% of the phenotypic variances. The resistance allele of QPm.caas‐5BL was contributed by ZM578, whereas alleles of QPm.caas‐2BL.1 and QPm.caas‐5DL were from JM22. QPm.caas‐2BL.1, detected in all the six experimental environments, was a major and stable QTL. QPm.caas‐5DL was detected in five of the six environments and is likely to be a new QTL for powdery mildew resistance. The kompetitive allele‐specific PCR (KASP) markers Kpm‐2BL and Kpm‐5DL for QPm.caas‐2BL.1 and QPm.caas‐5DL, respectively, were validated in a diverse panel of 287 cultivars. These KASP markers, tightly linked with the QTLs, can be used for marker‐assisted breeding targeting the improvement of powdery mildew resistance in wheat.

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Wheat genomic study for genetic improvement of traits in China

Cited by 94 publications

References 585 publications

Systematic mining and functional analysis of factors regulating wheat spike development for breeding selection

Systematic mining and functional analysis of factors regulating wheat spike development for breeding selection

Deciphering the Transcriptional Regulatory Network Governing Starch and Storage Protein Biosynthesis in Wheat for Breeding Improvement

Identification of genetic loci for powdery mildew resistance in bread wheat

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