Yingjun Zhang

China National Environmental Monitoring Center

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Lijing Sun

Hebei Academy of Agriculture and Forestry Sciences

Mengyun Hu

Hebei Academy of Agriculture and Forestry Sciences

Pei-Nan Wang

Hebei Academy of Agriculture and Forestry Sciences

Xianchun Xia

Institute of Crop Sciences

Qianying Li

Suizhou Central Hospital

Liangjie Lv

Hebei Academy of Agriculture and Forestry Sciences

Jiacong Huang

Nanjing Institute of Geography and Limnology

Zhonghu He

Chinese Academy of Agricultural Sciences

Junfeng Gao

Nanjing Institute of Geography and Limnology

Xiyong Chen

Guangxi University

Cooperative Institutions

Chinese Academy of Sciences

University of Chinese Academy of Sciences

Chinese Academy of Agricultural Sciences

Hebei Academy of Agriculture and Forestry Sciences

Institute of Genetics and Developmental Biology

Institute of Crop Sciences

Nanjing Institute of Geography and Limnology

Ministry of Agriculture and Rural Affairs

Peking University

Jilin University

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Genome-wide association study of yield-related traits in common wheat (Triticum aestivum L.) under normal and drought treatment conditions

Frontiers in Plant Science (2023)

Jie Zhao Lijing Sun Huimin Gao Mengyun Hu Liming Mu

The primary goal of modern wheat breeding is to develop new high-yielding and widely adaptable varieties. We analyzed four yield-related agronomic traits in 502 wheat accessions under normal conditions (NC) and drought treatment (DT) conditions over three years. The genome-wide association analysis identified 51 yield-related and nine drought-resistance-related QTL, including 13 for the thousand-grain weight (TGW), 30 for grain length (GL), three for grain width (GW), five for spike length (SL) and nine for stress tolerance index (STI) QTL in wheat. These QTL, containing 72 single nucleotide polymorphisms (SNPs), explained 2.23 - 7.35% of the phenotypic variation across multiple environments. Eight stable SNPs on chromosomes 2A, 2D, 3B, 4A, 5B, 5D, and 7D were associated with phenotypic stability under NC and DT conditions. Two of these stable SNPs had association with TGW and STI. Several novel QTL for TGW, GL and SL were identified on different chromosomes. Three linked SNPs were transformed into kompetitive allele-specific PCR (KASP) markers. These results will facilitate the discovery of promising SNPs for yield-related traits and/or drought stress tolerance and will accelerate the development of new wheat varieties with desirable alleles.

Common wheat

Drought Tolerance

Genome-wide Association Study

10.3389/fpls.2022.1098560

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Identification and molecular characterization of mutant line deficiency in three waxy proteins of common wheat (Triticum aestivum L.)

Research Square (Research Square) (2019)

Qian Liu Yaping Hu Mengyun Hu Lijing Sun Xiyong Chen

Abstract Background: Starch is the main component of wheat (Triticum aestivum L.) grain and a key factor in determining wheat processing quality. The Wx gene encodes the granule bound starch synthase I (GBSS I) and is the sole gene responsible for amylose synthesis. Results: A waxy mutant (Wx-null) was isolated by screening M3 seeds derived from 1.0% EMS mutagenized materials with I2-KI staining of endosperm starch. SDS-PAGE electrophoresis confirmed that the Wx-null line lacked all three waxy proteins. DNA sequencing revealed three SNPs and a 3-bp InDel in the first exon, and a 16-bp InDel at the junction region of the first Wx-A1 intron from the Wx-null line. Six SNPs were identified in Wx-B1 gene of Wx-null line compared to the wild-type Gao 8901, including four missense mutations. One nonsense mutation was found at position 857 in the fourth exon, which resulted in a premature stop codon. Expression levels of Wx genes were dramatically reduced in the Wx-null line. Nonsense-mediated mRNA decay (NMD) may be triggered to degrade the non-functional Wx mRNA. There were no detectable differences in granule size and morphology between Wx-null and wild-type, but the Wx-null line contained a larger proportion of B-type starch granules. The amylose content of the Wx-null line (0.22%) was remarkably lower compared to the wild-type Gao 8901 (20.82%). Total starch is also lower in the Wx-null line. Conclusions: All three waxy proteins were non-functional in the Wx-null line. NMD may be the cause for reduced expression levels of Wx genes in the Wx-null line. The Wx-null line exhibited more B-type starch granules, dramatically lower amylose content, and decreased total starch. The Wx-null line may provide a potential waxy material with high agronomic performance in wheat breeding programs.

Starch synthase

Null allele

Wild type

10.21203/rs.2.18059/v1

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Molecular characterisation of the NAM-1 genes in bread wheat in Australia

Crop and Pasture Science (2018)

Rongchang Yang Angéla Juhász Yujuan Zhang Xueyan Chen Yingjun Zhang

The wheat NAM-B1 and NAM-A1 genes are positively associated with grain protein content (GPC) in wheat. We conducted molecular characterisation of the NAM-1 genes in 51 Australian wheat varieties (Triticum aestivum L.), with the aim of improving GPC and nitrogen-usage efficiency in Australian wheat. In summary, the wild type NAM-B1 gene, which originated from Israel, was identified in two Australian wheat varieties. Five varieties contained a deletion allele, whereas the majority (43) harboured a non-functional NAM-B1 allele and one variety contained both functional and non-functional alleles. Twenty-six Australian wheat varieties contained the NAM-A1a haplotype, which was similar to its well-characterised homoeolog NAM-B1 wild type and associated with high GPC. The NAM-D1 gene in the 51 wheat varieties was also characterised, and no gene variation in the exon regions was noted; only two single-nucleotide polymorphisms in introns 1 and 2 were found among the 51 varieties.

Common wheat

Plant Breeding

10.1071/cp18273

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Boosting wheat functional genomics via an indexed EMS mutant library of KN9204

Plant Communications (2023)

Dongzhi Wang Yongpeng Li Haojie Wang Yongxin Xu Yiman Yang

A better understanding of wheat functional genomics can improve targeted breeding for better agronomic traits and environmental adaptation. However, the lack of gene-indexed mutants and the low transformation efficiency of wheat limit in-depth gene functional studies and genetic manipulation for breeding. In this study, we created a library for KN9204, a popular wheat variety in northern China, with a reference genome, transcriptome, and epigenome of different tissues, using ethyl methyl sulfonate (EMS) mutagenesis. This library contains a vast developmental diversity of critical tissues and transition stages. Exome capture sequencing of 2090 mutant lines using KN9204 genome-designed probes revealed that 98.79% of coding genes had mutations, and each line had an average of 1383 EMS-type SNPs. We identified new allelic variations for crucial agronomic trait-related genes such as Rht-D1, Q, TaTB1, and WFZP. We tested 100 lines with severe mutations in 80 NAC transcription factors (TFs) under drought and salinity stress and identified 13 lines with altered sensitivity. Further analysis of three lines using transcriptome and chromatin accessibility data revealed hundreds of direct NAC targets with altered transcription patterns under salt or drought stress, including SNAC1, DREB2B, CML16, and ZFP182, factors known to respond to abiotic stress. Thus, we have generated and indexed a KN9204 EMS mutant library that can facilitate functional genomics research and offer resources for genetic manipulation of wheat.

Functional Genomics

10.1016/j.xplc.2023.100593

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Genetic dissection of grain morphology and yield components in a wheat line with defective grain filling

Theoretical and Applied Genetics (2023)

Bingyan Liu Lingli Li Chao Fu Yingjun Zhang Bin Bai

Plant biochemistry

Morphology

Line (geometry)

10.1007/s00122-023-04410-1

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Cloning and Analysis of Replicase Polyprotein-Encoding ORF1 of Transmissible Gastroenteritis Virus SC-Y Strain

Xumu shouyi xuebao (2007)

Yingjun Zhang

In this study,the complete sequence of the replicase polyprotein-encoding ORF1 of TGEV SC-Y strain was obtained by RT-PCR,the entire nucleotide sequence was determined(GenBank Accession No.DQ390461).Results showed that there were two partially over lapping open reading frames in replicase polyprotein-encoding ORF1 of SC-Y strain,the ORF1a contains 12 053 nucleotides encoding a polypeptide of 4 018 amino acids,the ORF1b contains 8 036 nucleotides encoding 2 678 amino acids.The sequences were compared among different TGEV strains and other coronary viruses.The results showed that the SC-Y has the highest homology with PUR46-MAD strain,the ORF1a and ORF1b nucleotide sequences had 99.5% and 99.8%,amino acid sequences had 99.2% and 99.8% respectively.The ORF1b is highly conserved among the different coronaviruses.

Homology

Strain (injury)

Source

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Transcriptome and Proteome Analysis Revealed the Influence of High-Molecular-Weight Glutenin Subunits (HMW-GSs) Deficiency on Expression of Storage Substances and the Potential Regulatory Mechanism of HMW-GSs

Foods (2023)

Yun Zhao Jie Zhao Mengyun Hu Lijing Sun Qian Liu

The processing quality of wheat is affected by seed storage substances, such as protein and starch. High-molecular-weight glutenin subunits (HMW-GSs) are the major components of wheat seed storage proteins (SSPs); they are also key determinators of wheat end-use quality. However, the effects of HMW-GSs absence on the expression of other storage substances and the regulation mechanism of HMW-GSs are still limited. Previously, a wheat transgenic line LH-11 with complete deletions of HMW-GSs was obtained through introducing an exogenous gene Glu-1Ebx to the wild-type cultivar Bobwhite by transgenic approach. In this study, comparative seed transcriptomics and proteomics of transgenic and non-transgenic lines at different seed developmental stages were carried out to explore the changes in genes and proteins and the underlying regulatory mechanism. Results revealed that a number of genes, including genes related to SSPs, carbohydrates metabolism, amino acids metabolism, transcription, translation, and protein process were differentially enriched. Seed storage proteins displayed differential expression patterns between the transgenic and non-transgenic line, a major rise in the expression levels of gliadins were observed at 21 and 28 days post anthesis (DPA) in the transgenic line. Changes in expressions of low-molecular-weight glutenins (LMW-GSs), avenin-like proteins (ALPs), lipid transfer proteins (LTPs), and protease inhibitors (PIs) were also observed. In addition, genes related to carbohydrate metabolism were differentially expressed, which probably leads to a difference in starch component and deposition. A list of gene categories participating in the accumulation of SSPs was proposed according to the transcriptome and proteome data. Six genes from the MYB and eight genes from the NAC transcription families are likely important regulators of HMW-GSs accumulation. This study will provide data support for understanding the regulatory network of wheat storage substances. The screened candidate genes can lay a foundation for further research on the regulation mechanism of HMW-GSs.

Glutenin

Proteome

Glutelin

10.3390/foods12020361

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Cloning and characterization of EgGDSL, a gene associated with oil content in oil palm

Scientific Reports (2018)

Yingjun Zhang Bin Bai May Lee Yuzer Alfiko Antonius Suwanto

Abstract Oil palm ( Elaeis guineensis , Jacq.) is a key tropical oil crop, which provides over one third of the global vegetable oil production, but few genes related to oil yield have been characterized. In this study, a GDSL esterase/lipase gene, which was significantly associated with oil content, was isolated from oil palm and designated as EgGDSL . Its functional characterization was carried out through ectopic expression in Arabidopsis ecotype Col-0. It was shown that expression of EgGDSL in Arabidopsis led to the increased total fatty acid content by 9.5% compared with the wild type. Further analysis of the fatty acid composition revealed that stearic acid (18:0) increased in the seeds of the transgenic lines, but the levels of linoleic acid (18:2) plus 11-eicosenoic acid drastically declined. Quantitative real-time PCR (qPCR) revealed that in oil palm, EgGDSL was highly expressed in mesocarp followed by leaf, and the expression level was very low in the root. The expression level of EgGDSL gene began to increase at two months after flowering (MAF) and reached its peak by four MAF, then declined rapidly, and reached its lowest level during the mature period (6 MAF). The EgGDSL gene was more highly expressed in oil palm trees with high oil content than that with low oil content, demonstrating that the transcription level of EgGDSL correlated with the amount of oil accumulation. The gene may be valuable for engineering fatty acid metabolism in crop improvement programmes and for marker-assisted breeding.

Elaeis guineensis

Vegetable oil

10.1038/s41598-018-29492-6

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Identification and molecular characterization of mutant line deficiency in three waxy proteins of common wheat (Triticum aestivum L.)

Scientific Reports (2021)

Qian Liu Yaping Hu Mengyun Hu Lijing Sun Xiyong Chen

Abstract Starch is the main component of wheat ( Triticum aestivum L.) grain and a key factor in determining wheat processing quality. The Wx gene is the gene responsible for amylose synthesis. An ethyl methanesulfonate (EMS) mutagenized population was generated using common wheat cv. Gao 8901, a popular and high-quality cultivar in China. A waxy mutant (Wx-null) was isolated by screening M3 seeds with KI-I 2 staining of endosperm starch. No obvious waxy proteins in Wx-null line were detected using Sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE). DNA sequencing revealed three SNPs and a 3-bp InDel in the first exon, and a 16-bp InDel at the junction region of the first Wx-A1 intron from the Wx-null line. Six SNPs were identified in Wx-B1 gene of Wx-null line compared to the wild-type Gao 8901, including four missense mutations. One nonsense mutation was found at position 857 in the fourth exon, which resulted in a premature stop codon. Expression levels of Wx genes were dramatically reduced in the Wx-null line. There were no detectable differences in granule size and morphology between Wx-null and wild-type, but the Wx-null line contained more B-type starch granules. The amylose content of the Wx-null line (0.22%) was remarkably lower compared to the wild-type Gao 8901 (24.71%). Total starch is also lower in the Wx-null line. The Wx-null line may provide a potential waxy material with high agronomic performance in wheat breeding programs.

Common wheat

Null allele

Starch synthase

10.1038/s41598-021-82865-2

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Citations (12)

Genome-Wide Linkage Mapping for Preharvest Sprouting Resistance in Wheat Using 15K Single-Nucleotide Polymorphism Arrays

Frontiers in Plant Science (2021)

Lingli Li Yingjun Zhang Yong Zhang Ming Li Dengan Xu

Preharvest sprouting (PHS) significantly reduces grain yield and quality. Identification of genetic loci for PHS resistance will facilitate breeding sprouting-resistant wheat cultivars. In this study, we constructed a genetic map comprising 1,702 non-redundant markers in a recombinant inbred line (RIL) population derived from cross Yangxiaomai/Zhongyou9507 using the wheat 15K single-nucleotide polymorphism (SNP) assay. Four quantitative trait loci (QTL) for germination index (GI), a major indicator of PHS, were identified, explaining 4.6-18.5% of the phenotypic variances. Resistance alleles of

Marker-Assisted Selection

Preharvest

Epistasis

10.3389/fpls.2021.749206

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Citations (17)