Article
Agriculture, Dairy & Animal Science
Chunqin Wu, Liyan Dong, Xiantong Gan, Fangben Gan, Wenwu Xu, Lizhi Lu
Summary: This study measured and conducted genome-wide association studies on growth traits of Yandang partridge chickens. It identified a significant locus associated with Keel length and identified a potential candidate haplotype. Additionally, the study introduced a bootstrap testing method for verifying GWAS reliability with small experimental samples.
ANIMAL BIOTECHNOLOGY
(2023)
Article
Fisheries
Xin He, Yushan Liao, Zexin Yang, Hongxing Liu, Shi Wang, Yongbo Bao
Summary: The blood clam Tegillarca granosa is a commercially important bivalve species. This study conducted genome-wide association studies and identified 39 SNP markers associated with the growth traits of T. granosa. Additionally, 27 candidate genes potentially involved in T. granosa growth were identified. Enrichment analysis highlighted the role of transmembrane transport, immune system function, protein family metabolism, and JAK-STAT signaling pathways in T. granosa growth.
Article
Plant Sciences
F. Taranto, S. Esposito, F. Fania, R. Sica, S. Marzario, G. Logozzo, T. Gioia, P. De Vita
Summary: The recent increase in genomic data for durum wheat has allowed for a better understanding of the effects of breeding on genetic structures and the identification of useful DNA markers for selection. In this study, 123 durum wheat accessions were evaluated for agronomic traits, and association mapping analysis revealed 28 QTNs related to plant morphology and kernel-related traits. The study also found strong associations for traits such as yellow berry and flowering time, providing valuable information for durum wheat breeding and genetics.
FRONTIERS IN PLANT SCIENCE
(2023)
Article
Agronomy
Xukai Li, Zhiyong Shi, Jianhua Gao, Xingchun Wang, Kai Guo
Summary: Haplotype blocks reduce genotyping effort and assist in mapping candidate genes. The CandiHap software allows rapid and robust haplotype analysis and candidate identification from sequencing data. It can be used on various operating systems and any species.
MOLECULAR BREEDING
(2023)
Article
Plant Sciences
Xin Hu, Jianfang Zuo
Summary: Glume hairiness is an important trait in wheat and is related to stress resistance. In this study, a candidate gene for glume hairiness, TaELD1-1A, was identified through GWAS analysis and gene expression analysis.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Agriculture, Dairy & Animal Science
Martina Macri, Maria Gracia Luigi-Sierra, Dailu Guan, Juan Vicente Delgado, Javier Fernandez Alvarez, Marcel Amills, Amparo Martinez Martinez
Summary: Hematological traits are important indicators of health status. In humans, the genomic architecture of blood traits has been extensively studied, but the association between marker genotypes and hematological traits in goats has not been investigated yet.
Article
Agriculture, Multidisciplinary
Zhi-peng Zhang, Zhen Li, Fang He, Ji-juan Lue, Bin Xie, Xiao-yu Yi, Jia-min Li, Jing Li, Jing-han Song, Zhi-en Pu, Jian Ma, Yuan-ying Peng, Guo-yue Chen, Yu-ming Wei, You-liang Zheng, Wei Li
Summary: This study evaluated nine crucial agronomic traits in a natural population of wheat varieties and landraces in Sichuan, China. The results showed that different traits varied between the landraces and the breeding varieties. Through genome-wide association study analysis, several quantitative trait loci (QTLs) were identified, and three important QTLs were analyzed in detail. The findings provide valuable insights for the genetic improvement of wheat yield.
JOURNAL OF INTEGRATIVE AGRICULTURE
(2023)
Article
Genetics & Heredity
Javaid Akhter Bhat, Kehinde Adewole Adeboye, Showkat Ahmad Ganie, Rutwik Barmukh, Dezhou Hu, Rajeev K. K. Varshney, Deyue Yu
Summary: Identifying the genetic components underlying yield-related traits in soybean is crucial for improving its production. This study used GWAS and GP analyses to identify stable QTL regions and putative genes regulating soybean yield. Haplotype analysis revealed diverse allelic combinations controlling phenotypic variation. The study also demonstrated the possibility of obtaining accurate breeding values at an earlier generation.
FRONTIERS IN GENETICS
(2022)
Article
Fisheries
Sila Sukhavachana, Wansuk Senanan, Suriyan Tunkijjanukij, Supawadee Poompuang
Summary: Genomic selection is an effective strategy to improve growth performance and processing traits in aquaculture. This study evaluated the utility of low-density SNPs for genomic prediction of harvest traits in Asian seabass and found that trait-specific panels significantly improved prediction accuracy.
Article
Agronomy
Salem Marzougui, Mongi Ben Younes
Summary: This study identified 24 marker-trait associations (MTAs) related to heading date, plant height, and spike-related phenotypes in barley. These associations provide valuable information for breeding programs aiming to improve these traits in barley and develop varieties better adapted to semi-arid climates.
Article
Agronomy
Rui Ren, Wei Liu, Min Yao, Yuan Jia, Luyao Huang, Wenqian Li, Xin He, Mei Guan, Zhongsong Liu, Chunyun Guan, Wei Hua, Xinghua Xiong, Lunwen Qian
Summary: This study identified candidate genes related to plant height in rapeseed through genome-wide association analysis, and further analyzed the relationship between these genes and plant height. The results showed that these genes are interconnected with hormone genes and transcription factors, forming a network regulating the plant height of rapeseed.
MOLECULAR BREEDING
(2022)
Article
Plant Sciences
Annamalai Anandan, Siddharth Panda, S. Sabarinathan, Anthony J. Travis, Gareth J. Norton, Adam H. Price
Summary: The study highlights the advantages of the direct seeded rice (DSR) system in terms of saving freshwater resources, reducing labor requirements, and increasing productivity and resource use efficiency, while reducing greenhouse gas emissions. Early root vigor is crucial for ensuring good crop growth, water and nutrient uptake, and weed competition in the DSR system. Genome-wide association studies identified genetic regions and candidate genes related to root architecture and nutrient acquisition. Additionally, a new QTL controlling root length at 14 days was discovered.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Plant Sciences
Behailu Mulugeta, Kassahun Tesfaye, Rodomiro Ortiz, Eva Johansson, Teklehaimanot Hailesilassie, Cecilia Hammenhag, Faris Hailu, Mulatu Geleta
Summary: The growing global demand for wheat for food is rising due to population growth and climate change. A genome-wide association study (GWAS) using 10,045 SNP markers was conducted to identify genomic regions associated with grain yield and related traits in Ethiopian durum wheat. The study revealed high heritability estimates and identified novel marker-trait associations (MTAs) that could potentially improve durum wheat production globally. The research also highlighted the importance of the Ethiopian durum wheat gene pool in this improvement.
FRONTIERS IN PLANT SCIENCE
(2023)
Article
Plant Sciences
Clara Pons, Joan Casals, Matthijs Brower, Adriana Sacco, Alessandro Riccini, Patrick Hendrickx, Maria del Rosario Figas, Josef Fisher, Silvana Grandillo, Andrea Mazzucato, Salvador Soler, Dani Zamir, Mathilde Causse, Maria Jose Diez, Richard Finkers, Jaime Prohens, Antonio Jose Monforte, Antonio Granell
Summary: European traditional tomato varieties have shown excellent agronomic performance and stability, even outperforming modern varieties. Genome-wide association studies have identified 141 QTLs associated with agro-morphological traits and revealed the genetic basis of stability. This study enhances our understanding of the genetic diversity available in European traditional tomato germplasm.
JOURNAL OF EXPERIMENTAL BOTANY
(2023)
Article
Plant Sciences
Hui Zhang, Lisa Dean, Ming Li Wang, Phat Dang, Marshall Lamb, Charles Chen
Summary: This research conducted a principal component analysis to identify the main traits related to peanut flavor. Genome-wide association studies revealed significant quantitative trait loci associated with total sugars and sucrose, and candidate genes for these traits were identified. The findings contribute valuable knowledge about the genetic control of peanut flavor.
FRONTIERS IN PLANT SCIENCE
(2023)
Article
Genetics & Heredity
Xiaolan Zhang, Pengjia Bao, Na Ye, Xuelan Zhou, Yongfeng Zhang, Chunnian Liang, Xian Guo, Min Chu, Jie Pei, Ping Yan
Summary: In this study, a mRNA-lncRNA co-expression network was constructed using differentially expressed mRNAs and long noncoding RNAs during the yak hair follicles cycle. Four temporally specific modules associated with the hair follicles cycle of yak were identified, enriched in pathways such as Wnt and PI3K-Akt. Hub genes like FER, HOXC13, and key lncRNAs were identified for specific expression in skin tissue. Immunofluorescence staining and Western blotting results showed DLX3 and OVOL1 may play important roles in hair follicle development.
Article
Agriculture, Dairy & Animal Science
Xiaoyun Wu, Wondossen Ayalew, Min Chu, Jie Pei, Chunnian Liang, Pengjia Bao, Xian Guo, Ping Yan
Summary: In this study, the RNA editome of the yak mammary gland during the lactation period and dry period was characterized. The findings revealed RNA editing sites associated with mammary gland development-related pathways. This research provides novel insights into the RNA editing function in the mammary gland of yaks.
Article
Genetics & Heredity
Lin Xiong, Jie Pei, Xiaoyun Wu, Pengjia Bao, Xian Guo, Ping Yan
Summary: This study revealed that female yaks have higher levels of UFAs and PUFAs in their subcutaneous fat compared to male yaks, indicating a potentially healthier choice for consumers. Further research showed that the transcriptional regulation by PPARD plays a key role in regulating UFAs, especially PUFA content in yaks of different sexes.
Article
Agriculture, Dairy & Animal Science
Xingdong Wang, Jie Pei, Lin Xiong, Shaoke Guo, Mengli Cao, Yandong Kang, Pengjia Bao, Xiaoyun Wu, Min Chu, Chunnian Liang, Ping Yan, Xian Guo
Summary: In mammals, the testis-specific serine/threonine kinase (TSSK) is crucial for spermatogenesis and male fertility. This study successfully cloned multiple alternative spliceosomes of the TSSK4 gene in yak testis tissue, providing a foundation for future investigations into the function of each spliceosome.
Article
Agriculture, Dairy & Animal Science
Yandong Kang, Shaoke Guo, Xingdong Wang, Mengli Cao, Jie Pei, Ruiwu Li, Pengjia Bao, Jiefeng Wang, Jiebu Lamao, Dangzhi Gongbao, Ji Lamao, Chunnian Liang, Ping Yan, Xian Guo
Summary: Kecai yaks, an important genetic resource in Gansu Province, China, were found to be an independent group within the Chinese yak population. They exhibit excellent production performance and high fecundity, making them valuable for future utilization. The genetic analysis of Kecai yaks also revealed genes associated with adaptation to alpine environments and muscle fat deposition.
Article
Food Science & Technology
Lin Xiong, Jie Pei, Xingdong Wang, Shaoke Guo, Xian Guo, Ping Yan
Summary: This study investigated the differences in fatty acids in yak's meat under graze feeding and stall feeding, suggesting that grazed yak's meat is healthier for consumers. Transcriptomic and lipidomics analysis identified key genes regulating fatty acid content in yak meat.
Article
Biochemistry & Molecular Biology
Jie Pei, Lin Xiong, Shaoke Guo, Xingdong Wang, Pengjia Bao, Xiaoyun Wu, Ping Yan, Xian Guo
Summary: Single-cell RNA sequencing was used to investigate the molecular characteristics of various cell types in the yak ovarian cortex, and a cellular atlas was successfully constructed. Differential gene expression analysis identified differentially expressed genes in endothelial cells, immune cells, stromal cells, smooth muscle cells, oocytes, macrophages, epithelial cells, and granulosa cells. The cellular atlas revealed the biological characteristics of the ovarian cortex at the cellular molecular level and provided insights into female reproductive biology via cellular communications in the yak.
Article
Biochemistry & Molecular Biology
Mengli Cao, Jie Pei, Lin Xiong, Shaoke Guo, Xingdong Wang, Yandong Kang, Xian Guo
Summary: This study analyzed the distribution of open chromatin regions (OCRs) in the testes of cattle-yak and yaks, and found that OCRs in both cattle-yak and yaks displayed similar genome distribution, with a preference for intergenic regions, introns, and promoters. Pathway enrichment analysis revealed that differential OCR-related genes were involved in spermatogenesis and multiple signaling pathways. Integrating ATAC-seq and mRNA-seq data showed a positive correlation between gene expression levels and chromatin openness. Additionally, several transcription factors related to spermatogenesis were identified, suggesting their potential contribution to the stagnation of spermatogenesis in cattle-yak.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biochemistry & Molecular Biology
Jie Pei, Lin Xiong, Shaoke Guo, Xingdong Wang, Yongfu La, Min Chu, Chunnian Liang, Ping Yan, Xian Guo
Summary: By employing single-cell RNA sequencing, researchers have successfully established a cellular atlas of the yak ovary, which includes different cell types with specific molecular signatures and functions. They have also constructed a cell-to-cell communication network, revealing the reproductive adaptation mechanism of yaks in high-altitude environments.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Agriculture, Dairy & Animal Science
Xinyi Li, Chun Huang, Modian Liu, Rongfeng Dai, Xiaoyun Wu, Xiaoming Ma, Min Chu, Pengjia Bao, Jie Pei, Xian Guo, Ping Yan, Chunnian Liang
Summary: This study identified the correlation between copy number variation (CNV) of the SOX6 gene and growth traits in Ashidan yaks. It was found that SOX6-CNV significantly affected the chest girth and withers height of yaks at different ages, suggesting its potential as a new marker for yak breeding. The study provides important insights for genetic breeding of yaks.
Article
Agriculture, Dairy & Animal Science
Ziqiang Ding, Lin Xiong, Xingdong Wang, Shaoke Guo, Mengli Cao, Yandong Kang, Yongfu La, Pengjia Bao, Jie Pei, Xian Guo
Summary: In this study, key genes regulating the development of the epididymal cauda and sperm maturation in yak were identified using RNA-seq and proteomics. These findings provide a theoretical basis for improving the reproductive potential of yak.
Article
Food Science & Technology
Lin Xiong, Jie Pei, Pengjia Bao, Xingdong Wang, Shaoke Guo, Mengli Cao, Yandong Kang, Ping Yan, Xian Guo
Summary: The utilization of yak milk is still in a primary stage, and the nutrition composition of yak colostrum is not systematically characterized at present. In this study, the lipids, fatty acids, amino acids and their derivatives, and metabolites in yak colostrum and mature milk were analyzed using various methods. The results showed that yak colostrum has higher nutritive value compared to yak and cow mature milk. These research findings can serve as a theoretical basis for the development of commercial products using yak colostrum.
Article
Agriculture, Dairy & Animal Science
Shaoke Guo, Jie Pei, Xingdong Wang, Mengli Cao, Lin Xiong, Yandong Kang, Ziqiang Ding, Yongfu La, Min Chu, Pengjia Bao, Xian Guo
Summary: This study investigates the mechanism of m(6)A RNA modification in yak testis development and spermatogenesis. The results show that the m(6)A level significantly increases after sexual maturity in yaks. Functional analysis reveals that m(6)A modification mainly regulates spermatogenesis and is involved in various signaling pathways. Key regulatory factors of testis development and spermatogenesis are also identified.
Article
Biochemistry & Molecular Biology
Xingdong Wang, Jie Pei, Lin Xiong, Shaoke Guo, Mengli Cao, Yandong Kang, Ziqiang Ding, Yongfu La, Chunnian Liang, Ping Yan, Xian Guo
Summary: This study conducted a comprehensive and unbiased single-cell transcriptomic analysis of spermatogenesis in sexually mature 4-year-old yaks using scRNA-seq. The analysis revealed the presence of six somatic cell types and various germ cells in yak testis. Functional enrichment analysis showed that highly expressed genes in yak testicular somatic cells were significantly enriched in cAMP signaling pathway, PI3K-Akt signaling pathway, MAPK signaling pathway, and ECM receptor interactions. Immunohistochemical techniques identified candidate marker genes for spermatogonial stem cells and Sertoli cells.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Lin Xiong, Jie Pei, Pengjia Bao, Xingdong Wang, Shaoke Guo, Mengli Cao, Yandong Kang, Ping Yan, Xian Guo
Summary: This study explores the effect of feeding systems on fat deposition in yaks through transcriptomics and lipidomics. It evaluates the thickness of subcutaneous fat and detects differences in transcriptomes and lipidomes between yaks under stall and graze feeding. The study reveals differences in lipid metabolism and identifies key genes and pathways involved in fat deposition.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)