Ruixin Zhang

Overexpression of SeTIP2;3 and SePIP1;4 from Salicornia europaea Enhances Drought Tolerance in Arabidopsis

Ruixin Zhang, Yujie Li, Jiashou Shen, Guangxin Cui et autres

Aquaporins (AQPs) are key channels for water and small molecule transport across membranes, and represent early targets of stress signaling pathways in plants. Salicornia europaea is a typical halophyte adapted to saline-alkaline and nutrient-poor soils. However, studies on AQPs from S. europaea …

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Integrating GWAS and Machine Learning to Dissect the Genetic Basis of Flowering Time and Vernalization-Type Differentiation in Brassica napus

Ye Hua, Zhen Huang, Xiaoyue Zhu, Ruixin Zhang et autres

Flowering time is an important trait affecting regional adaptation and yield stability in rapeseed (Brassica napus). To dissect the genetic basis of flowering time and vernalization-type differentiation in B. napus, this study integrated genome-wide SNPs, flowering-time phenotypes, vernalization types, and geographic origin …

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The Zinc-Finger Protein MsCCCH20 Is Predicted to Regulate Salt-Stress Response in Alfalfa (Medicago sativa L.) by Binding to Conserved 3′UTR Motifs

Meng Wang, Xiaoyue Zhu, Huixin Jiang, Lina Dong et autres

Soil salinization is a source of major abiotic stress that severely limits the production of alfalfa (Medicago sativa L.), a globally critical forage legume for sustainable livestock production. Its complex autotetraploid genome and self-incompatibility greatly hinder salt tolerance genetic improvement, while the …

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Engineering Pitfalls in AI Coding Tools: An Empirical Study of Bugs in Claude Code, Codex, and Gemini CLI

Ruixin Zhang, Wuyang Dai, Hung Viet Pham, Gias Uddin et autres

The rapid integration of Large Language Models (LLMs) into software development workflows has given rise to a new class of AI-assisted coding tools, such as Claude-Code, Codex, and Gemini CLIs. While promising significant productivity gains, the engineering process of building these tools, …

Engineering Pitfalls in AI Coding Tools: An Empirical Study of Bugs in Claude Code, Codex, and Gemini CLI

Ruixin Zhang, Wuyang Dai, Hung Viet Pham, Gias Uddin et autres

The rapid integration of Large Language Models (LLMs) into software development workflows has given rise to a new class of AI-assisted coding tools, such as Claude-Code, Codex, and Gemini CLIs. While promising significant productivity gains, the engineering process of building these tools, …

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Enhancing Genomic Selection for Soybean Drought Tolerance via Integration of Epistasis and AlphaFold2 Prediction

Ruixin Zhang, Xiaoyue Zhu, Lina Dong, Changhong Guo et autres

Soybean is a globally important economic and food crop, whose production is often constrained by drought stress, posing a serious threat to yield and quality. Genomic selection (GS) has become a core technology in modern breeding, effectively enhancing breeding efficiency. However, conventional …

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Integrating GWAS and genomic selection with SNP and SV markers for enhanced prediction of complex traits in common carp

Xiaoyue Zhu, Yuhan Fu, Zhipeng Sun, Ruixin Zhang et autres

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Integrating Genome-Wide Association Study (GWAS) and Marker-Assisted Selection for Enhanced Predictive Performance of Soybean Cold Tolerance

Y. J. Xue, Xiaofei Tang, Xiaoyue Zhu, Ruixin Zhang et autres

(L.) Merr.), as a crucial source of oil and protein globally, is widely cultivated in many countries. Low-temperature stress has become one of the major environmental factors affecting soybean production, especially in colder regions, making the improvement of cold tolerance traits in …

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High-Copy SINE Transposons Facilitate Broad Ecological Adaptation in White Clover (Trifolium repens)

Hong Wei, Meng Wang, Jun Tian, Xiaoyue Zhu et autres

Recent advances in plant genomics have characterized transposable elements (TEs) as key contributors to genome structure and gene regulation. This study focuses on the remarkably high abundance of short interspersed nuclear elements (SINEs) in the genus Trifolium. Using the allotetraploid horticultural plant …

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Leveraging GWAS-Identified Markers in Combination with Bayesian and Machine Learning Models to Improve Genomic Selection in Soybean

Y. J. Xue, Xiaofei Tang, Xiaoyue Zhu, Ruixin Zhang et autres

(L.) Merr.) is one of the most important global economic crops, extensively utilized in the production of food, animal feed, and industrial raw materials. As the demand for soybeans continues to rise, improving both the yield and quality of soybeans has become …

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A Framework Integrating GWAS and Genomic Selection to Enhance Prediction Accuracy of Economical Traits in Common Carp

Zhipeng Sun, Yingmei Fu, Xiaoyue Zhu, Ruixin Zhang et autres

Common carp (Cyprinus carpio) is one of the most significant fish species worldwide, with its natural distribution spanning Europe and Asia. To conduct a genome-wide association study (GWAS) and compare the prediction accuracy of genomic selection (GS) models for the growth traits …

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Genomic Selection in Alfalfa Across Multiple Ploidy Levels: A Comparative Study Using Machine Learning and Bayesian Methods

Xiaoyue Zhu, Ruixin Zhang, Tianxiang Zhang, Changhong Guo et autres

Agronomic traits and quality traits of alfalfa are of great importance to the feed industry. Genomic selection (GS) based on genotyping-by-sequencing (GBS) data, if it achieves moderate to high accuracy, has the potential to significantly shorten breeding cycles for complex traits and …

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