Frontiers in Plant Science | Functional and Applied Plant Genomics

Original Research

Published on 13 Jun 2025

Complete sequencing of the mitochondrial genome of tea plant Camellia sinensis cv. ‘Baihaozao’: multichromosomal structure, phylogenetic relationships, and adaptive evolutionary analysis

in Functional and Applied Plant Genomics

Zhiyin Chen
Zixu Wang
Wei Zhou
Sijie Liu
Yuxin Xiao
Yihui Gong

Frontiers in Plant Science

doi 10.3389/fpls.2025.1604404

1,945 views
3 citations

Editorial

Published on 10 Jun 2025

Editorial: Improving yield and quality of cereal crops: exploring and utilizing genes for green and efficient traits

in Functional and Applied Plant Genomics

Hao Zhou
Yuqing He
Ming Luo

Frontiers in Plant Science

doi 10.3389/fpls.2025.1617702

1,264 views

Original Research

Published on 09 Jun 2025

A BERT-based rice enhancer identification model combined with sequence-representation differential entropy interpretation

in Functional and Applied Plant Genomics

Yajing Pu
Xintong Hao
Zhaoqi Zheng
Huiyan Ma
Zhibin Lv

Frontiers in Plant Science

doi 10.3389/fpls.2025.1618174

2,205 views

Original Research

Published on 06 Jun 2025

GWAS and RNA-seq reveal novel loci and genes of low-nitrogen tolerance in cucumber (Cucumis sativus L.)

in Functional and Applied Plant Genomics

Huaxiang Wu
Huiming Yan
Bowen Li
Yike Han
Nan Liu
Mengyu Fan
Yahan Liu
Mingjie Lyu
Shengli Du
Aimin Wei

Frontiers in Plant Science

doi 10.3389/fpls.2025.1602360

3,142 views
2 citations

Original Research

Published on 05 Jun 2025

Comparative transcriptomics in B73-teosinte near-isogenic maize lines reveals key defense signaling and phytoalexins in response to Cercospora zeina infection

in Functional and Applied Plant Genomics

Xiaomeng Sun
Ruiyu Zhang
Zongping Wang
Haotian Zhang
Hairun Wen
Junli Zhang
Naibin Yu
Zhe Wang
Huanhuan Tai
Qin Yang

Frontiers in Plant Science

doi 10.3389/fpls.2025.1580016

1,875 views

Original Research

Published on 05 Jun 2025

IRGL-RRI: interpretable graph representation learning for plant RNA–RNA interaction discovery

in Functional and Applied Plant Genomics

Qingquan Liao
Xuchong Liu
Wei Zhao
Yu Tong
Fangzheng Xu
Xinxin Liu
Yifan Chen

Frontiers in Plant Science

doi 10.3389/fpls.2025.1617495

1,714 views

Review

Published on 04 Jun 2025

Research progress of NAC transcription factors in woody plants

in Functional and Applied Plant Genomics

Huan Zhang
Jia Zhao
Tongxing Zhang
Guiying Wang
Zhixiao Han
Yuemei Meng
Jingran Bi
Yachao Ren
Minsheng Yang

Frontiers in Plant Science

doi 10.3389/fpls.2025.1592898

2,573 views
2 citations

Mini Review

Published on 03 Jun 2025

Foundation models in plant molecular biology: advances, challenges, and future directions

in Functional and Applied Plant Genomics

Feng Xu
Tianhao Wu
Qian Cheng
Xiangfeng Wang
Jun Yan

Frontiers in Plant Science

doi 10.3389/fpls.2025.1611992

6,777 views
1 citation

Original Research

Published on 30 May 2025

Systematic identification and analysis of WRKY transcription factors reveals the role of MrWRKY14 in Myrica rubra

in Functional and Applied Plant Genomics

Xiurun Fan
Minghui Chen
Huiling Zhang
Yumeng Liu
Meng Yang
Chengyang Ye
Hailing Gu
Kai Xu
Boping Wu

Frontiers in Plant Science

doi 10.3389/fpls.2025.1602750

2,160 views
3 citations

Original Research

Published on 30 May 2025

Intensifying cropping sequences in the US Central Great Plains: an in silico analysis of a sorghum–wheat sequence

in Functional and Applied Plant Genomics

Lucia Marziotte
Ana J. P. Carcedo
Daniel Rodriguez
Laura Mayor
P. V. Vara Prasad
Ignacio A. Ciampitti

Frontiers in Plant Science

doi 10.3389/fpls.2025.1525128

1,616 views

Original Research

Published on 23 May 2025

Genome-wide identification and development of SSR molecular markers for genetic diversity studies in Ilex asprella

in Functional and Applied Plant Genomics

Jingchun Li
Changqian Quan
Rongchang Wei
Fan Wei
Qing Ma
Yuquan Huang
Meihua Xu
Danfeng Tang

Frontiers in Plant Science

doi 10.3389/fpls.2025.1582154

2,347 views
3 citations

Original Research

Published on 21 May 2025

Integrated metabolome-transcriptome analyses reveal key pathways regulating staminate catkin development and pollen maturation in Betula platyphylla

in Functional and Applied Plant Genomics

Xinying Liu
Jiayuan Shi
Jingyun Zhang
Bello Hassan Jakada
HuiLing Guo
Kehao Zeng
Xingguo Lan

Frontiers in Plant Science

doi 10.3389/fpls.2025.1581560

1,520 views

Original Research

Published on 16 May 2025

Selection and validation of reference genes for quantitative real-time PCR during the developmental stages of seeds in Sophora davidii

in Functional and Applied Plant Genomics

Jingjing Li
Shanrong Han
Zongren Xu
Bin Deng
Na Zheng
Yaqiong Su
Ziyao Qiao
Yun Yang
Hong Zhang
Zongsuo Liang

Frontiers in Plant Science

doi 10.3389/fpls.2025.1485586

1,654 views

Data Report

Published on 16 May 2025

Transcriptome map and genome annotation of flax line 3896

in Functional and Applied Plant Genomics

Daiana A. Zhernova
Alexander A. Arkhipov
Tatiana A. Rozhmina
Alexander A. Zhuchenko
Nadezhda L. Bolsheva
Elizaveta A. Sigova
Ekaterina M. Dvorianinova
Elena V. Borkhert
Elena N. Pushkova
Nataliya V. Melnikova

Frontiers in Plant Science

doi 10.3389/fpls.2025.1520832

2,015 views

Original Research

Published on 14 May 2025

Characterization analyses of MADS-box genes highlighting their functions with seed development in Ricinus communis

in Functional and Applied Plant Genomics

Jing Sun
Zekun Zhou
Fanqing Meng
Mengyun Wen
Aizhong Liu
Anmin Yu

Frontiers in Plant Science

doi 10.3389/fpls.2025.1589915

1,764 views
2 citations

Original Research

Published on 13 May 2025

Identification of key genes associated with mesocotyl length through a genome-wide association study in rice

in Functional and Applied Plant Genomics

Li Xue
Sen Wang
Qiuyu Zhang
Bing Han
Di Cui
Longzhi Han
Jianxin Deng
Xiaoding Ma

Frontiers in Plant Science

doi 10.3389/fpls.2025.1546580

2,543 views

Original Research

Published on 12 May 2025

StSN2 enhances tuber formation in potato via upregulating of the ABA signaling pathway

in Functional and Applied Plant Genomics

Shifeng Liu
Yichen Wang
Luopin Li
Lang Yan
Xiyao Wang
Qiang Wang
Xianjun Lai

Frontiers in Plant Science

doi 10.3389/fpls.2025.1566237

2,504 views
3 citations

Original Research

Published on 12 May 2025

Genome-wide identification of the HD-ZIP IV gene family in Pogostemon cablin and its association with glandular hair development

in Functional and Applied Plant Genomics

Shuqi Xie
Yiling Li
Huiting Liao
Wenyi Chen
Yuqi Zhang
Xiaoming Yan
Hongyi Zhang
Mengling He
Hanjing Yan

Frontiers in Plant Science

doi 10.3389/fpls.2025.1580351

1,733 views

Original Research

Published on 09 May 2025

Prolonged heat stress in Brassica napus during flowering negatively impacts yield and alters glucosinolate and sugars metabolism

in Functional and Applied Plant Genomics

Mariam Kourani
Maria Anastasiadi
John P. Hammond
Fady Mohareb

Frontiers in Plant Science

doi 10.3389/fpls.2025.1507338

3,332 views
5 citations

Original Research

Published on 09 May 2025

Genome-wide analysis of the laccase gene family in tossa jute (Corchorus olitorius): insights into stem development, lignification, and responses to abiotic stress

in Functional and Applied Plant Genomics

Deepak Kumar Jha
Subhadarshini Parida
Seema Pradhan
Nrisingha Dey
Shuvobrata Majumder

Frontiers in Plant Science

doi 10.3389/fpls.2025.1568674

2,813 views
1 citation

Original Research

Published on 09 May 2025

QTL mapping of flowering time in Brassica napus: a study on the interplay between temperature and day length after vernalization

in Functional and Applied Plant Genomics

Eva Heinrich
Antje Schierholt
Christian Möllers

Frontiers in Plant Science

doi 10.3389/fpls.2025.1513353

1,816 views

Editorial

Published on 08 May 2025

Editorial: Insights in functional and applied plant genomics: 2023

in Functional and Applied Plant Genomics

Huihui Li

Frontiers in Plant Science

doi 10.3389/fpls.2025.1615289

1,554 views

Editorial

Published on 25 Apr 2025

Editorial: Soybean breeding for abiotic stress tolerance: towards sustainable agriculture

in Functional and Applied Plant Genomics

Huatao Chen
Li Song
Henry T. Nguyen
Donghe Xu
Chengfu Su

Frontiers in Plant Science

doi 10.3389/fpls.2025.1578039

2,072 views
1 citation

Original Research

Published on 24 Apr 2025

Identification and characterization of Csa-miR159s and their expression patterns under different abiotic stresses in cucumber (Cucumis sativus L.)

in Functional and Applied Plant Genomics

Zhenxiang Zhao
Wenhong Ao
Weirong Luo
Yaoguang Sun
Vijay Yadav Tokala
Junjun Liu
Shenshen Zhi
Yongdong Sun

Frontiers in Plant Science

doi 10.3389/fpls.2025.1518406

1,774 views

622 articles

articles

Complete sequencing of the mitochondrial genome of tea plant Camellia sinensis cv. ‘Baihaozao’: multichromosomal structure, phylogenetic relationships, and adaptive evolutionary analysis

Editorial: Improving yield and quality of cereal crops: exploring and utilizing genes for green and efficient traits

A BERT-based rice enhancer identification model combined with sequence-representation differential entropy interpretation

GWAS and RNA-seq reveal novel loci and genes of low-nitrogen tolerance in cucumber (Cucumis sativus L.)

Comparative transcriptomics in B73-teosinte near-isogenic maize lines reveals key defense signaling and phytoalexins in response to Cercospora zeina infection

IRGL-RRI: interpretable graph representation learning for plant RNA–RNA interaction discovery

Research progress of NAC transcription factors in woody plants

Foundation models in plant molecular biology: advances, challenges, and future directions

Systematic identification and analysis of WRKY transcription factors reveals the role of MrWRKY14 in Myrica rubra

Intensifying cropping sequences in the US Central Great Plains: an in silico analysis of a sorghum–wheat sequence

Genome-wide identification and development of SSR molecular markers for genetic diversity studies in Ilex asprella

Integrated metabolome-transcriptome analyses reveal key pathways regulating staminate catkin development and pollen maturation in Betula platyphylla

Selection and validation of reference genes for quantitative real-time PCR during the developmental stages of seeds in Sophora davidii

Transcriptome map and genome annotation of flax line 3896

Characterization analyses of MADS-box genes highlighting their functions with seed development in Ricinus communis

Identification of key genes associated with mesocotyl length through a genome-wide association study in rice

StSN2 enhances tuber formation in potato via upregulating of the ABA signaling pathway

Genome-wide identification of the HD-ZIP IV gene family in Pogostemon cablin and its association with glandular hair development

Prolonged heat stress in Brassica napus during flowering negatively impacts yield and alters glucosinolate and sugars metabolism

Genome-wide analysis of the laccase gene family in tossa jute (Corchorus olitorius): insights into stem development, lignification, and responses to abiotic stress

QTL mapping of flowering time in Brassica napus: a study on the interplay between temperature and day length after vernalization

Editorial: Insights in functional and applied plant genomics: 2023

Editorial: Soybean breeding for abiotic stress tolerance: towards sustainable agriculture

Identification and characterization of Csa-miR159s and their expression patterns under different abiotic stresses in cucumber (Cucumis sativus L.)