Yiran Cheng

Sichuan Agricultural University

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Xing Fan

Sichuan Agricultural University

Lina Sha

Sichuan Agricultural University

Houyang Kang

Sichuan Agricultural University

Dandan Wu

Sichuan Agricultural University

Haiqin Zhang

Sichuan Agricultural University

Jian Zeng

Sichuan Agricultural University

Yi Wang

Sichuan Agricultural University

Yonghong Zhou

Sichuan Agricultural University

Lili Xu

Sichuan Agricultural University

Wei Zhu

Sichuan Agricultural University

Cooperative Institutions

Sichuan Agricultural University

130

Chinese Academy of Sciences

Ministry of Agriculture and Rural Affairs

University of Chinese Academy of Sciences

Sichuan University

Chinese Academy of Medical Sciences & Peking Union Medical College

Chinese Academy of Agricultural Sciences

Capital Medical University

Huazhong University of Science and Technology

China Agricultural University

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Introgression of tetraploid Thinopyrum elongatum 6EL segments enhances the stripe rust resistance of adult wheat plants

Research Square (Research Square) (2023)

Chunyan Zeng Liangxi Li Zaimei He Wei Zhu Lili Xu

Abstract Preventing the widespread occurrence of stripe rust in wheat largely depends on the identification of new stripe rust resistance genes and the breeding of cultivars with durable resistance. We obtained a wheat–tetraploid Thinopyrum elongatum 6E (6D) substitution line and determined that chromosome 6E contains genetic material conferring superior resistance to stripe rust at the adult stage. In this study, three novel wheat–tetraploid Th. elongatum translocation lineswere generated from the offspring of a cross between common wheat and the 6E (6D) substitution line. Genomic in situ hybridization (GISH), fluorescence in situ hybridization chromosome painting (FISH painting), repetitive sequential FISH, and 55K SNP analyses indicated that K227-48, K242-82, and K246-6 contained 42 chromosomes and were 6ES·6DL, 2DL·6EL, and 6DS·6ELtranslocation lines, respectively. The assessment of stripe rust resistance revealed that K227-48 was susceptible to a mixture of Pst races, whereas the 6EL lines K242-82 and K246-6 exhibited adult plant resistance to stripe rust. Thus, this resistance was due to the 6EL chromosome. The overall good agronomic performance of K246-6 implies this line may be a useful germplasm resource for wheat breeding programs. Furthermore, 34 PCR-based markers for chromosome 6EL were developed using the whole-genome sequence of diploid Th. elongatum. This novel translocation line may be applicable for breeding wheat lines resistant to stripe rust. Additionally, themarkers developed in this study will enablethe accurate tracing of tetraploid Th. elongatum chromosome 6E and the mapping of additional favorable genes on 6EL.

Introgression

Germ plasm

Rust (programming language)

Common wheat

10.21203/rs.3.rs-3657512/v1

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Recent natural hybridization inElymusandCampeiostachysof Triticeae: evidence from morphological, cytological and molecular analyses

Botanical Journal of the Linnean Society (2023)

Dandan Wu Xiaoyan Liu Zheng‐Hao Yu Lu Tan Jiale Lu

Abstract Natural hybrids in Triticeae have been frequently reported from the Qinghai–Tibet plateau, but minor variation in morphological features and homoploid hybridization have made it difficult to identify the origin and genome constitution of hybrids between Elymus and Campeiostachys. Specimens were investigated using morphology, cytogenetics and phylogenetic analyses to uncover the genome constitution and origin of ten putative natural hybrids (SH01-SH10) from the Qinghai–Tibet plateau. SH01, SH02, SH03, SH05 and SH06 (2n = 5x = 35, StStHHY) originated from Campeiostachys breviaristata (2n = 6x = 42, StStHHYY) and Elymus sibiricus (2n = 4x = 28, StStHH); SH04 and SH07 (2n = 5x = 35, StStHHY) originated from C. nutans (2n = 6x = 42, StStHHYY) and E. sibiricus; SH08 (2n = 5x = 35, StStHHY) originated from C. dahurica var. tangutorum (2n = 6x = 42, StStHHYY) and E. sibiricus; and SH09 and SH10 (2n = 4x = 28, StStHH) were the homoploid hybrids of E. sibiricus and an unknown Elymus sp. (2n = 4x = 28, StStHH). Karyotype variations in SH04 and SH07 might originate from the maternal progenitor. Frequent hybridization in the Qinghai–Tibet plateau might result from factors such as genome constitution, pollination habits, overlapping flowering stage, sympatric distribution and unique ecological conditions.

Triticeae

Elymus

10.1093/botlinnean/boac057

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Confirmation of Natural Hybridization between Kengyilia (StStYYPP) and Campeiostachys (StStYYHH) (Triticeae: Poaceae) Based on Morphological and Molecular Cytogenetic Analyses

Cytogenetic and Genome Research (2022)

Yue-Chuan Luo Chen Chen Dandan Wu Jiale Lu Lina Sha

Natural hybridization has been frequently observed in Triticeae; however, few studies have investigated the origin of natural intergeneric Triticeae hybrids. In the present study, we discovered three putative hybrid Triticeae plants in the Western Sichuan Plateau of China. Morphologically, the putative hybrids were intermediate between Kengyilia melanthera (2n = 6x = 42; StStYYPP) and Campeiostachys dahurica var. tangutorum (2n = 6x = 42; StStYYHH) with greater plant height and tiller number. Cytological analyses demonstrated that the hybrids were hexaploid with 42 chromosomes (2n = 6x = 42). At metaphase I, 12.10-12.58 bivalents and 13.81-14.18 univalents per cell were observed in the hybrid plants. Genomic in situ hybridization demonstrated that the hybrids had StStYYHP genomes. Phylogenetic analysis of Acc1 sequences indicated that the hybrids were closely related to K. melanthera and C. dahurica var. tangutorum. Our morphological, cytological, and molecular analyses indicate that these hexaploid natural hybrid plants may be hybrids of K. melanthera and C. dahurica var. tangutorum.

Triticeae

Phylogenetic relationship

Elymus

10.1159/000527781

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Development, identification, and utilization of wheat–tetraploid Thinopyrum elongatum 4EL translocation lines resistant to stripe rust

Theoretical and Applied Genetics (2024)

Biran Gong Linfeng Chen Hao Zhang Wei Zhu Lili Xu

Stem rust

Rust (programming language)

10.1007/s00122-023-04525-5

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Genome-wide identification and characterization of bZIP gene family explore the responses of PsebZIP44 and PsebZIP46 in Pseudoroegneria libanotica under drought stress

BMC Plant Biology (2024)

Xunzhe Yang Xiang Li Xia Wang Chen Chen Dandan Wu

The fundamental leucine zipper (bZIP) genes play a crucial role as transcriptional coactivators in plants. Pseudoroegneria libanotica served as the maternal contributor to several species within the tribe Triticeae (Poaceae), exhibiting commendable resilience to various stressors. Consequently, bZIP genes of Pseudoroegneria libanotica response to abiotic stresses was important for further understanding of stress tolerance studies in Triticeae. A total of 108 PsebZIPs were identified in this study, and they were divided into 10 subgroups. PsebZIPs were found to be extensively involved in the biological activities within P. libanotica. The RNA-seq results revealed differential responses of PsebZIPs to drought stress in both aerial and root tissues. PsebZIP44 and PsebZIP46 were regarded as potential genes capable of responding to abiotic stress, and their varying degrees of responsiveness to drought, salinity, heavy metals, heat, and oxidative stress have been demonstrated in yeast. Homologous proteins with intact bZIP gene structures of PsebZIP44 or PsebZIP46 have not been identified in wheat. The current investigation not only provides a fundamental basis for further probing into the biological functions of PsebZIPs within P. libanotica but also reveals previously undiscovered potential genes with the ability to respond to abiotic stress. They could contribute to improving the genetic constitution of Triticeae crops, including wheat.

Identification

Drought stress

10.1186/s12870-024-05809-8

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Development of wheat-tetraploid Thinopyrum elongatum 4EL small fragment translocation lines with stripe rust resistance gene Yr4EL

Theoretical and Applied Genetics (2024)

Biran Gong Jing Gao Yangqiu Xie Hao Zhang Wei Zhu

Plant biochemistry

Rust (programming language)

Stripe rust

10.1007/s00122-024-04756-0

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Phylogeny and taxonomy of the polyploidy species that contains St genome (Triticeae; Poaceae) based on four nuclear DNA and three chloroplast genes

Research Square (Research Square) (2024)

X. Pan Tingting Zheng Yuxin Zhao Xing Fan Lina Sha

Abstract Background The genus Pseudoroegneria (Nevski) Á. Löve with the St genome accounts for more than 60% of perennial Triticeae speciation. However, the strong dominant character of the St genome results in challenging to distinguish each species even genus based on single or combined morphological traits, the phylogeny and taxonomy of the St-containing polyploid genera remain under controversy. Results In this study, we used nuclear and chloroplast DNA-based phylogenetic analyses to reveal the systematic relationships of the St-containing polyploidy species. The maximum likelihood (ML) tree based on nuclear ribosomal internal transcribed spacer region (nrITS) and three single-copy nuclear genes data (Acc1 + Pgk1 + DMC1) showed that St-containing polyploid species were separated into StStHH, StStYY, StStYYHH, StStYYPP, StStYYWW, StStPP, and StStEE genome types and polyploidy species in Caucasus, America and Australia have unique polyploidization events. The ML tree for the chloroplast DNA fragments (matK + rbcL + trnL-trnF) displayed that the P genome serves as a maternal donor of Kengyilia melanthera and K. dingqinensis from the Hengduan Mountains region, while the St or StY genome serves as the maternal donor of other St genome containing species. Herein, we reported the genome constitution of Kengyilia tibetica, K. changduensis, and K. dingqinensis with the StStYYPP genome for the first time. Conclusions The St-containing polyploid species should be treated as distinct genera according to different genome constitutions, St-containing polyploid species experienced independent allopolyploidization events in different distribution regions and the St-containing polyploid species had two relatively independent maternal origins from the P genome or St/StYgenome. Besides, the Xp genome may have contributed to the unknown Y genome formation.

Triticeae

Nuclear gene

Nuclear DNA

10.21203/rs.3.rs-4927682/v1

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CleanVul: Automatic Function-Level Vulnerability Detection in Code Commits Using LLM Heuristics

arXiv (Cornell University) (2024)

Yikun Li Ting Zhang Ratnadira Widyasari Yan Naing Tun Huy Do Minh Nguyen

Accurate identification of software vulnerabilities is crucial for system integrity. Vulnerability datasets, often derived from the National Vulnerability Database (NVD) or directly from GitHub, are essential for training machine learning models to detect these security flaws. However, these datasets frequently suffer from significant noise, typically 40% to 75%, due primarily to the automatic and indiscriminate labeling of all changes in vulnerability-fixing commits (VFCs) as vulnerability-related. This misclassification occurs because not all changes in a commit aimed at fixing vulnerabilities pertain to security threats; many are routine updates like bug fixes or test improvements. This paper introduces the first methodology that uses the Large Language Model (LLM) with a heuristic enhancement to automatically identify vulnerability-fixing changes from VFCs, achieving an F1-score of 0.82. VulSifter was applied to a large-scale study, where we conducted a crawl of 127,063 repositories on GitHub, resulting in the acquisition of 5,352,105 commits. VulSifter involves utilizing an LLM to comprehend code semantics and contextual information, while applying heuristics to filter out unrelated changes. We then developed CleanVul, a high-quality dataset comprising 11,632 functions using our LLM heuristic enhancement approach, demonstrating Correctness (90.6%) comparable to established datasets such as SVEN and PrimeVul. To evaluate the CleanVul dataset, we conducted experiments focusing on fine-tuning various LLMs on CleanVul and other high-quality datasets. Evaluation results reveal that LLMs fine-tuned on CleanVul not only exhibit enhanced accuracy but also superior generalization capabilities compared to those trained on uncleaned datasets. Specifically, models trained on CleanVul and tested on PrimeVul achieve accuracy higher than those trained and tested exclusively on PrimeVul.

Heuristics

Code (set theory)

Vulnerability

10.48550/arxiv.2411.17274

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Cadmium uptake, translocation, and redistribution affect Cd accumulation in grain of common wheat (Triticum aestivum L.) cultivars

Research Square (Research Square) (2020)

Yiran Cheng Xu Zhang Sha Wang Xue Xiao Jian Zeng

Abstract Background To study the cadmium (Cd) accumulation in wheat grain, we evaluated the grain Cd concentrations of 46 common wheat cultivars grown at two sites in Sichuan, China and selected five different grain Cd accumulators (a high-Cd accumulator ZM18, four low-Cd accumulators YM51, YM53, SM969 and CM104) to explore the physiological processes of Cd accumulation in the grain of wheat grown under varying degrees of Cd stress. Results Our results showed that the Cd concentration in grain differed among genotypes. Under low-Cd stress, the grain Cd concentration was correlated with the Cd translocation factor (TF) of roots to grain and all the Cd redistribution factors (RFs). Compared with the ZM18, the cultivars YM53 and SM969 accumulated less Cd in the grain due to low Cd redistribution from lower stems and older leaves to grain. The low-Cd accumulators YM51 and CM104 were due to low Cd transport from roots to grain, and low Cd redistribution from glumes, flag leaves, lower stems, and older leaves to grain. Under high-Cd stress, the ZM18, YM53, and SM969 accumulated significantly more Cd in the grain, root and other tissues than did YM51 and CM104. Correlation analyses showed that the grain Cd concentration of wheat under high Cd stress was positively correlated with the Cd concentration in each tissue and the TFs of roots to grains, rachis, internode 1 and flag leaves. Conclusions Cd translocation directly from roots to grain and Cd redistribution from shoots to grain determines the Cd accumulation in grain of wheat cultivars under low-Cd stress. Cd uptake by root and then synchronously transported to new shoots determined the differences of Cd accumulation in the grain of wheat cultivars under high Cd stress.

Redistribution

10.21203/rs.3.rs-22672/v1

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Additional file 2 of Biosystematics studies on Elymus breviaristatus and Elymus sinosubmuticus (Poaceae: Triticeae)

Figshare (2022)

Lu Tan Qingxiang Huang Song Yang Dandan Wu Yiran Cheng

Additional file 2.

Elymus

Triticeae

Leymus

10.6084/m9.figshare.19106177

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