Frontiers in Plant Science | Functional and Applied Plant Genomics

Original Research

Published on 21 Nov 2025

Integrating machine learning and the GGE biplot for identification of climate-suitable grasspea genotypes

in Functional and Applied Plant Genomics

Surendra Barpete
Arpita Das
Mangla Parikh
Sonika Yumnam
Muhammad Aasim
Seyid Amjad Ali
Akanksha Singh
Ashutosh Kumar Yadav
Narayana Bhat Devate
Smita Kaul

Frontiers in Plant Science

doi 10.3389/fpls.2025.1647903

753 views

Original Research

Published on 20 Nov 2025

Conserved regions upstream of BRC1B regulate bud dormancy in tomato

in Functional and Applied Plant Genomics

Gül Hatinoğlu
Froukje van der Wal
Gerco C. Angenent
Ruud A. de Maagd
Richard G.H. Immink

Frontiers in Plant Science

doi 10.3389/fpls.2025.1702139

824 views

Original Research

Published on 20 Nov 2025

Genome-wide identification and characterization of ALOG domain genes in Rosa

in Functional and Applied Plant Genomics

Feng Chen
Bo Lv
Jiaqi Guo
Jurong Song
Cong Guo
Jie Yang
Jianguo Lin
Yuanyuan Yang
Fayun Xiang

Frontiers in Plant Science

doi 10.3389/fpls.2025.1690365

643 views

Original Research

Published on 20 Nov 2025

Multilayered defense responses in sugarcane against Pratylenchus zeae revealed by comparative transcriptomics

in Functional and Applied Plant Genomics

Pedro M. S. Confort
Tiarla Graciane Souto
Jonathan F. Macedo
Silvana Creste
Claudia Barros Monteiro-Vitorello

Frontiers in Plant Science

doi 10.3389/fpls.2025.1703046

644 views

Original Research

Published on 19 Nov 2025

High-density genetic map construction using whole-genome resequencing of the Cymbidium eburneum(‘Duzhan Chun’) × Cymbidium insigne (‘Meihua Lan’) F1 population and localization of flower color genes

in Functional and Applied Plant Genomics

Yu Han
Yutong Cui
Yu Chen
Dandan Rao
Erhuan Wu
Rongcun Gan
Tengmin Li
Mi Tian

Frontiers in Plant Science

doi 10.3389/fpls.2025.1685531

809 views

Original Research

Published on 19 Nov 2025

A novel NAC transcription factor mediates negative regulation of early ethylene production and ripening in tomato fruits

in Functional and Applied Plant Genomics

Jiawei Li
Junwen Han
Tong Li
Daoyun Chen
Kenji Miura
Lazaro Eustaquio Pereira Peres
Hiroshi Ezura
Ning Wang

Frontiers in Plant Science

doi 10.3389/fpls.2025.1696915

745 views

Original Research

Published on 19 Nov 2025

MTMixG-Net: mixture of Transformer and Mamba network with a dual-path gating mechanism for plant gene expression prediction

in Functional and Applied Plant Genomics

Fei Guo
Wenjuan Li
Aihong Lu
Rongzhen Feng
Wu Fang

Frontiers in Plant Science

doi 10.3389/fpls.2025.1718258

427 views

Data Report

Accepted on 17 Nov 2025

Whole-Genome Sequencing of Russian Poplars to Understand Relationships within the Genus Populus L

in Functional and Applied Plant Genomics

Elena V. Borkhert
Elena N. Pushkova
George S. Krasnov
Yuri A. Nasimovich
Ramil A. Murataev
Peter M. Evlakov
Andrey V. Klimov
Marina V. Kostina
Boris V. Proshkin
Daiana A. Krupskaya (Zhernova)

Frontiers in Plant Science

246 views

Opinion

Published on 17 Nov 2025

Rethinking de novo genes in plants: mechanisms, methodological progress, and future prospects

in Functional and Applied Plant Genomics

Man Luo
Haibo Wu
Dinghua Zhan
Guangcai Chen
Yunpeng Cao

Frontiers in Plant Science

doi 10.3389/fpls.2025.1724832

1,104 views

Original Research

Published on 14 Nov 2025

Identification of chalcone isomerase family genes and roles of DnCHI1 in flavonoid metabolism in Dendrobium nobile

in Functional and Applied Plant Genomics

Ling-ling Chang
Yu-xin Zhou
Ling-rong Wang
Lei Liu
Zhen-jian Li

Frontiers in Plant Science

doi 10.3389/fpls.2025.1687738

847 views

Original Research

Published on 05 Nov 2025

Integrated RNA-seq and snRNA-seq analysis identifies PR10 tandem gene cluster governing early defense against Fusarium wilt in sea island cotton

in Functional and Applied Plant Genomics

Baojun Liu
Shu Wang
Yujia Zhang
Gang Liu
Ziyi Liu
Aixing Gu
Jianyu Bai

Frontiers in Plant Science

doi 10.3389/fpls.2025.1622223

1,243 views

Original Research

Published on 31 Oct 2025

Differential gene expression and phenotypic variation across tissues between Saccharum officinarum and Saccharum spontaneum

in Functional and Applied Plant Genomics

Qin-Nan Wang
Sheng-Ren Sun
Jun-Lv Chen
Jing-Ru Zhou
Yuan-Xia Qin
Wei Zhang
Li-Yu Chen
San-Ji Gao

Frontiers in Plant Science

doi 10.3389/fpls.2025.1696921

1,024 views

Original Research

Published on 31 Oct 2025

Comprehensive identification, characterization, and expression analysis of m6A methylation transferase gene family in maize (Zea mays L.)

in Functional and Applied Plant Genomics

Chunlei Li
Ming He
Xinyi Liu
Qingxue Lv
Xiaoming Yu
Xiaoxue Fan
Xia Bai
Jie Cong
Chuanbo Sun

Frontiers in Plant Science

doi 10.3389/fpls.2025.1673408

1,111 views

Original Research

Accepted on 27 Oct 2025

Pan-Genomic Insights into LTP Gene Family Evolution across Diploid Cotton Species

in Functional and Applied Plant Genomics

Yanghan Lu
Lishuang Guo
Zhengya Wei
Yujun Li
Yue Zhang
Juyun Zheng
Baohua Wang
Zhonghua Zhou
Haodong Chen

Frontiers in Plant Science

284 views

Review

Published on 27 Oct 2025

Perspectives on the utilization of Aegilops species containing the U genome in wheat breeding: a review

in Functional and Applied Plant Genomics

Ekaterina D. Badaeva
Maida Jazmin González Franco
Olga Razumova
Nadezhda A. Tereshchenko
Mikhail Divashuk

Frontiers in Plant Science

doi 10.3389/fpls.2025.1661257

1,188 views

Original Research

Published on 23 Oct 2025

Study on mechanism of temperature-modulated polyphenolic biosynthesis in cigar tobacco leaves

in Functional and Applied Plant Genomics

Jiahao Kang
Bo Fu
Xiaoxiao Yan
Menglan Xiao
Weili Yang
Mingqin Zhao

Frontiers in Plant Science

doi 10.3389/fpls.2025.1693512

777 views

Original Research

Published on 21 Oct 2025

Hydrogen sulfide enhances salt tolerance in sorghum by activating the chloroplastic AsA–GSH cycle to sustain photosynthesis

in Functional and Applied Plant Genomics

Chang Liu
Sitong Liu
Xin Hu
Xiaolong Shi
Chunjuan Liu
Lu Sun
Yufei Zhou

Frontiers in Plant Science

doi 10.3389/fpls.2025.1664076

940 views

Original Research

Published on 14 Oct 2025

Prediction of harvest-related traits in barley using high-throughput phenotyping data and machine learning

in Functional and Applied Plant Genomics

Hans Tietze
Lamis Abdelhakim
Barbora Pleskačová
Ayelet Kurtz-Sohn
Eyal Fridman
Zoran Nikoloski
Klára Panzarová

Frontiers in Plant Science

doi 10.3389/fpls.2025.1686506

2,096 views

Original Research

Published on 14 Oct 2025

Yield and yield component trait analysis with DArT genotyping for GWAS in soybean grown in drought conditions of Kazakhstan

in Functional and Applied Plant Genomics

Aigul Amangeldiyeva
Raushan Yerzhebayeva
Shynar Mazkirat
Svetlana Didorenko
Sholpan Bastaubayeva
Bekzhan Maikotov
Rinat Kassenov
Assel Jenisbayeva
Yuri Shavrukov

Frontiers in Plant Science

doi 10.3389/fpls.2025.1674201

1,353 views

Original Research

Published on 14 Oct 2025

Comparative analysis of chloroplast genomes in Carica species reveals evolutionary relationships of papaya and the development of efficient molecular markers

in Functional and Applied Plant Genomics

Yajin Chen
Xiaoxi Du
Lei Pan
Qiyuan Huang
Zhigang Hao

Frontiers in Plant Science

doi 10.3389/fpls.2025.1686914

1,964 views

Original Research

Published on 13 Oct 2025

Re-calibration of flow cytometry standards for plant genome size estimation

in Functional and Applied Plant Genomics

Abhishek Soni
Robert J. Henry

Frontiers in Plant Science

doi 10.3389/fpls.2025.1548766

2,054 views

Original Research

Published on 09 Oct 2025

Fine mapping of the major-effect QTL qPHS4.1 revealed a CsDOG1 gene controlling pre-harvest sprouting in cucumber (Cucumis sativus L.)

in Functional and Applied Plant Genomics

Mingming Cao
Qiang Deng
Huizhe Wang
Changyue Liu
Haiyan Zhao
Ruihuan Yang

Frontiers in Plant Science

doi 10.3389/fpls.2025.1701268

1,710 views
1 citation

Review

Published on 08 Oct 2025

Research progress on the synergistic regulation of MYB transcription factor-mediated developmental plasticity and stress responses in rice

in Functional and Applied Plant Genomics

Wenyan Peng
Yi Zhang
Hongjun Xie
Yinghong Yu
Mingdong Zhu

Frontiers in Plant Science

doi 10.3389/fpls.2025.1668800

1,658 views

Original Research

Published on 08 Oct 2025

Genome-wide identification of GH17 family genes and their expression patterns associated with bud dormancy-regrowth regulation in Prunus persica

in Functional and Applied Plant Genomics

Xuehui Zhao
Haifeng Xie
Yifei Han
Jiaqi Zhang
Yihua Qi
Zejie Zhang
Maoxiang Sun
Meiying Liu
Fen Wang
Qingjie Wang

Frontiers in Plant Science

doi 10.3389/fpls.2025.1693135

1,499 views

622 articles

articles

Integrating machine learning and the GGE biplot for identification of climate-suitable grasspea genotypes

Conserved regions upstream of BRC1B regulate bud dormancy in tomato

Genome-wide identification and characterization of ALOG domain genes in Rosa

Multilayered defense responses in sugarcane against Pratylenchus zeae revealed by comparative transcriptomics

High-density genetic map construction using whole-genome resequencing of the Cymbidium eburneum(‘Duzhan Chun’) × Cymbidium insigne (‘Meihua Lan’) F1 population and localization of flower color genes

A novel NAC transcription factor mediates negative regulation of early ethylene production and ripening in tomato fruits

MTMixG-Net: mixture of Transformer and Mamba network with a dual-path gating mechanism for plant gene expression prediction

Whole-Genome Sequencing of Russian Poplars to Understand Relationships within the Genus Populus L

Rethinking de novo genes in plants: mechanisms, methodological progress, and future prospects

Identification of chalcone isomerase family genes and roles of DnCHI1 in flavonoid metabolism in Dendrobium nobile

Integrated RNA-seq and snRNA-seq analysis identifies PR10 tandem gene cluster governing early defense against Fusarium wilt in sea island cotton

Differential gene expression and phenotypic variation across tissues between Saccharum officinarum and Saccharum spontaneum

Comprehensive identification, characterization, and expression analysis of m6A methylation transferase gene family in maize (Zea mays L.)

Pan-Genomic Insights into LTP Gene Family Evolution across Diploid Cotton Species

Perspectives on the utilization of Aegilops species containing the U genome in wheat breeding: a review

Study on mechanism of temperature-modulated polyphenolic biosynthesis in cigar tobacco leaves

Hydrogen sulfide enhances salt tolerance in sorghum by activating the chloroplastic AsA–GSH cycle to sustain photosynthesis

Prediction of harvest-related traits in barley using high-throughput phenotyping data and machine learning

Yield and yield component trait analysis with DArT genotyping for GWAS in soybean grown in drought conditions of Kazakhstan

Comparative analysis of chloroplast genomes in Carica species reveals evolutionary relationships of papaya and the development of efficient molecular markers

Re-calibration of flow cytometry standards for plant genome size estimation

Fine mapping of the major-effect QTL qPHS4.1 revealed a CsDOG1 gene controlling pre-harvest sprouting in cucumber (Cucumis sativus L.)

Research progress on the synergistic regulation of MYB transcription factor-mediated developmental plasticity and stress responses in rice

Genome-wide identification of GH17 family genes and their expression patterns associated with bud dormancy-regrowth regulation in Prunus persica