Shaoyan Wu^1,2, Jie Tian^1,2, Yiyan Wang^1,2, Muhammad Arif^1,2, Shuyao Wang^1,2, Jing Wang^1,2, Zhuoyao Yang^1,2, Ruhong Xu^1,2,*, Luhua Li^1,2,*

Phyton-International Journal of Experimental Botany, Vol.94, No.12, pp. 3913-3924, 2025, DOI:10.32604/phyton.2025.072229 - 29 December 2025

Abstract Wheat grain morphology, particularly grain length (GL) and width (GW), is a key determinant of yield. To improve the suboptimal grain dimensions of the local anthocyanin-rich variety Guizi 1 (GZ1), we crossed it with Zhongyan 96-3 (ZY96-3), an elite germplasm known for faster grain filling and superior grain size. A genotyping-by-sequencing (GBS) approach was applied to an F₂ population of 110 individuals derived from GZ1 × ZY96-3, resulting in the identification of 23,134 high-quality SNPs. Most of the SNPs associated with GL and GW were clustered on chromosomes 2B, 3A, and 3B. QTL mapping for GL… More >

Qunlu Liu^1,#, Fiza Liaquat^1,2,#, Qiqi Tang¹, Jun Yang^3,4, Shuai Qiu⁵, Amber Malik², Kang Ye^3,4, Kai Gao⁵, Jun Qin^3,4,*

Phyton-International Journal of Experimental Botany, Vol.94, No.11, pp. 3539-3562, 2025, DOI:10.32604/phyton.2025.071989 - 01 December 2025

Abstract Hydrangea macrophylla is a popular ornamental shrub with a lot of economic and aesthetic value. It is known for its different flower shapes (lacecap and mophead) and the way its flowers change color depending on the pH of the soil. Even though it is important for gardening, we still don’t know much about the molecular processes that lead to flower growth. The purpose of this study was to find and study SNP-related genes and transcription factors that are connected to the growth of H. macrophylla flowers. Genome-wide SNP analysis identified 11 SNPs associated with MYB transcription factors… More >

Jiexiong Xu^*

Phyton-International Journal of Experimental Botany, Vol.94, No.8, pp. 2365-2383, 2025, DOI:10.32604/phyton.2025.067124 - 29 August 2025

Abstract Background: Rice grain morphology—including traits such as awn length, hull color, size, and shape—is of central importance to yield, quality, and domestication, yet comprehensive quantification at scale has remained challenging. A promising solution has been provided by the integration of high-throughput imaging with genomic analysis. Methods: A standardized 2D image-processing pipeline was established to extract four categories of traits—awn length, hull color, projected grain area, and shape descriptors via PCA of normalized contours—from high-resolution photographs of 229 Oryza sativa japonica landraces. Genome-wide association analyses were then performed using a mixed linear model to control for population… More >

Jiawei Shi^1,2,3,#, Zhen Wang^1,2,3,#, Ying Bai^1,2,3, Shiying Li^1,2,3, Xin Zhang^1,2,3, Tianshu Liu^1,2,3, Liu Hong^1,2,3, Li Cui^1,2,3, Yi Zhang^1,2,3, Jing Ma^1,2,3, Juanjuan Liu^1,2,3, Jing Zhang^1,2,3, Haiyan Cao^1,2,3,*, Jing Wang^1,2,3,*

Congenital Heart Disease, Vol.20, No.2, pp. 213-229, 2025, DOI:10.32604/chd.2025.064950 - 30 April 2025

Abstract Background: Tetralogy of Fallot (TOF), the predominant cyanotic congenital heart defect, arises from multifactorial gene-environment interactions disrupting cardiac developmental networks. This study investigated TOF-specific transcriptional alterations and identified high-confidence candidate genes. Methods: Based on GSE36761 transcriptome data, a weighted gene co-expression network analysis (WGCNA) and protein-protein interaction (PPI) network were conducted to identify TOF-related sub-network and Hub genes. The potential biological functions among these genes were revealed by enrichment analysis. Genetic, epigenetic and transcriptional alteration in the Hub genes were analyzed with leveraged public resources: a methylation dataset (GSE62629) and two single-cell datasets (EGAS00001003996 and GSE126128). Results:… More >

Pengcheng Li^1,2,#, Tianze Zhu^1,#, Yunyun Wang^1,2, Shuangyi Yin¹, Xinjie Zhu¹, Minggang Ji¹, Wenye Rui¹, Houmiao Wang¹, Zefeng Yang^1,2,*, Chenwu Xu^1,2,*

Phyton-International Journal of Experimental Botany, Vol.93, No.7, pp. 1441-1453, 2024, DOI:10.32604/phyton.2024.052219 - 30 July 2024

Abstract The nutritional composition and overall quality of maize kernels are largely determined by the key chemical components: protein, oil, and starch. Nevertheless, the genetic basis underlying these nutritional quality traits during grain filling remains poorly understood. In this study, the concentrations of protein, oil, and starch were studied in 204 recombinant inbred lines resulting from a cross between DH1M and T877 at four different stages post-pollination. All the traits exhibited considerable phenotypic variation. During the grain-filling stage, the levels of protein and starch content generally increased, whereas oil content decreased, with significant changes observed between… More >

Jianyu Lu¹, Qingping Jiang¹, Tongyu Liu¹, Yangyang Zhou¹, Mengtong Liu¹, Jing Qu², Yiyong Ma^2,*, Shuyan Guan^2,*

Phyton-International Journal of Experimental Botany, Vol.91, No.6, pp. 1199-1209, 2022, DOI:10.32604/phyton.2022.019298 - 14 February 2022

Abstract Maize flowering is an important agronomic character, which is controlled by quantitative trait loci (QTL). Over the years, a large number of flowering-related QTL have been found in maize and exist in public databases. However, combining these data, re-analyzing and mining candidate loci and fine mapping of flowering-related traits to reduce confidence intervals has become a hot issue in maize. In this study, the QTL of 6 important agronomic traits of maize flowering were collected from 15 published articles, including flowering period (DA), Days to tasseling (DTT), Days to silking (DS), Days to pollen shedding More >

Xihua Liu¹, Min Luo¹, Xiaofei Chen¹, Changjun Ding^2,*

Phyton-International Journal of Experimental Botany, Vol.90, No.6, pp. 1697-1709, 2021, DOI:10.32604/phyton.2021.015295 - 28 June 2021

Abstract Bamboos are one of the most beautiful and useful plants on Earth. The genetic background and population structure of bamboos are well known, which helps accelerate the process of artificial domestication of bamboo. Partial sequences of six genes involved in nitrogen use efficiency in 32 different bamboo species were analyzed for occurrence of single nucleotide polymorphisms (SNPs). The nucleotide diversity θw and total nucleotide polymorphisms π_T of the sequenced DNA regions was 0.05137 and 0.03332, respectively. Both πnonsyn /πsyn and Ka/Ks values were <1. The nucleotide sequences of these six genes were inferred to be relatively… More >

Linjun Cai^1,#, Junhua Liu^2,#, Han Yun¹, Dan Du¹, Xiaolong Zhong¹, Zhenlin Yang¹, Xianchun Sang¹, Changwei Zhang^1,*

Phyton-International Journal of Experimental Botany, Vol.90, No.4, pp. 1103-1117, 2021, DOI:10.32604/phyton.2021.015532 - 27 April 2021

Abstract Leaf color mutants are ideal materials for studying many plant physiological and metabolic processes such as photosynthesis, photomorphogenesis, hormone physiology and disease resistance. In this study, the genetically stable yellow-green leaf mutant ygl16 was identified from mutated “Xinong 1B”. Compared with the wild type, the pigment concentration and photosynthetic capacity of the ygl16 decreased significantly. The ultrastructural observation showed that the distribution of thylakoid lamellae was irregular in ygl16 chloroplasts, and the grana and matrix lamellae were blurred and loose in varied degrees, and the chloroplast structure was disordered, while the osmiophilic corpuscles increased. The results of More >

Qi Zhang^1,#, Pengtao Li^2,#, Aiying Liu¹, Shaoqi Li¹, Quanwei Lu², Qun Ge¹, Junwen Li¹, Wankui Gong¹, Xiaoying Deng¹, Haihong Shang^1,3, Yuzhen Shi^1,*, Youlu Yuan^1,3,*

Phyton-International Journal of Experimental Botany, Vol.90, No.3, pp. 837-858, 2021, DOI:10.32604/phyton.2021.014437 - 30 March 2021

Abstract Cotton is the most widely cultivated commercial crop producing natural fiber around the world. As a critical trait for fiber quality, fiber strength principally determined during the secondary wall thickening period. Based on the developed BC₅F_3:5 CSSLs (chromosome segment substitution lines) from Gossypium hirsutum CCRI36 × G. barbadense Hai 1, the superior MBI9915 was chosen to construct the secondary segregated population BC₇F₂ with its recurrent parent CCRI36, which was subsequently subjected to Bulk segregant RNA-sequencing (BSR-seq) for rapid identification of candidate genes related to fiber strength. A total of 4 fiber-transcriptome libraries were separately constructed and sequenced, including… More >

Lin Zhang^1,2,*, Yiting Zou¹, Zhong Bian¹, Dong Xie¹, Hadi Yeilaghi¹, Xiaolei Fan^1,2, Dongsheng Zhao^1,2, Qiaoquan Liu^1,2,*

Phyton-International Journal of Experimental Botany, Vol.90, No.3, pp. 789-802, 2021, DOI:10.32604/phyton.2021.014880 - 30 March 2021

Abstract Rice panicle is the sink organ where assimilation product accumulates, and its morphology determines the rice yield. Panicle length has been suggested as a yield-related trait, but the genetic factor for its control is still limited. In this study, we carried out fine-mapping of qPL8, a QTL identified for panicle length in our previous work. Near isogenic line (NIL) with qPL8 exhibited elongated panicle without obvious effect on other panicle elements. With five key recombinants from NIL population, the locus was finally narrowed down to a 278-kb region, where 44 genes are annotated. By comparing the More >