Frontiers in Plant Science | Functional and Applied Plant Genomics

Opinion

Published on 11 Dec 2025

Integrated biotechnological and artificial intelligence innovations for plant improvement

in Functional and Applied Plant Genomics

Haibo Wu
Man Luo
Yubin Liu
Jinghao Yang
Yunpeng Cao

Frontiers in Plant Science

doi 10.3389/fpls.2025.1736707

1,316 views

Original Research

Published on 08 Dec 2025

Characterization of CXE genes in pineapple and their aroma-related expression during fruit ripening

in Functional and Applied Plant Genomics

Wenxin Xu
Tangxiu Li
Jing Wu
You Wang
Junting Feng
Aiping Luan
Okandze Poho Pérol Carzorel
Shuqiang He
Junhu He
Chengjie Chen

Frontiers in Plant Science

doi 10.3389/fpls.2025.1733743

1,646 views

Original Research

Published on 05 Dec 2025

Genetic variation in storage protein and starch biosynthesis genes reveals key associations with seed composition in pea (Pisum sativum)

in Functional and Applied Plant Genomics

Admas Alemu
Kavitha Anguluri
Bo Yuan
René Lametsch
Cecilia Hammenhag

Frontiers in Plant Science

doi 10.3389/fpls.2025.1679498

1,881 views

Original Research

Published on 04 Dec 2025

TPS5 and TOR signaling components are determinants of Populus balsamifera leaf morphology

in Functional and Applied Plant Genomics

Marc J. Champigny
Shankar Pahari
Charles A. Hefer
Salim N. Silim
Shawn D. Mansfield
Raju Y. Soolanayakanahally

Frontiers in Plant Science

doi 10.3389/fpls.2025.1683866

1,442 views

Original Research

Published on 03 Dec 2025

Comparing four heat-inducible promoters in stably transformed sugarcane regarding spatial and temporal control of transgene expression reveals candidates to drive stem-preferred transgene expression

in Functional and Applied Plant Genomics

Moni Qiande
Fredy Altpeter

Frontiers in Plant Science

doi 10.3389/fpls.2025.1709171

1,712 views
1 citation

Original Research

Published on 28 Nov 2025

Genome-wide association study and fine-mapping identify a major quantitative trait locus controlling hundred-seed weight in soybean

in Functional and Applied Plant Genomics

Chunlei Zhang
Huilong Hong
Rongqiang Yuan
Shiyao Zhang
Tianjiao Gao
Shuping Yan
Sobhi F. Lamlom
Honglei Ren
Zhangxiong Liu
Jiajun Wang

Frontiers in Plant Science

doi 10.3389/fpls.2025.1716186

1,507 views

Systematic Review

Published on 28 Nov 2025

Research evolution of flat peach (Prunus persica (L.) Batsch): a decadal bibliometric analysis

in Functional and Applied Plant Genomics

Abebe Misganaw Gedamu
Yong Li
Jinlong Wu
Ke Cao
Muhammad Anees
Zhaohui Wang
Suning Liu
Hongyang Xing
Pengcheng Wei
Muhammad Jehangir

Frontiers in Plant Science

doi 10.3389/fpls.2025.1710142

1,370 views

Original Research

Published on 26 Nov 2025

Genome-wide analysis of the CrRLK1L gene family in Puccinellia tenuiflora and functional study of PutFER1 in Arabidopsis underpinning salt tolerance

in Functional and Applied Plant Genomics

Gaojian Li
Yulin Peng
Yanshuang Liu
Zhen Wu
Shaojun Dai
Zhi Qin
Meihong Sun

Frontiers in Plant Science

doi 10.3389/fpls.2025.1680452

1,350 views

Original Research

Published on 26 Nov 2025

MicroRNA identification and expression analysis of wheat thermo-sensitive male sterile line BNS366 for fertility transformation

in Functional and Applied Plant Genomics

Junpeng Chen
Xue Hu
Ruilian Song
Genlou Sun
Sisi Huang
Wei Hua
Jinghuan Zhu
Daorong Zhang
Xifeng Ren

Frontiers in Plant Science

doi 10.3389/fpls.2025.1662041

1,027 views

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

1,203 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

988 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

1,457 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

1,154 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

1,179 views
1 citation

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

1,313 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

788 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

1,690 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

1,250 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

1,848 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

1,392 views
1 citation

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

1,464 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

1,741 views
1 citation

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

1,095 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

1,297 views

653 articles

articles

Integrated biotechnological and artificial intelligence innovations for plant improvement

Characterization of CXE genes in pineapple and their aroma-related expression during fruit ripening

Genetic variation in storage protein and starch biosynthesis genes reveals key associations with seed composition in pea (Pisum sativum)

TPS5 and TOR signaling components are determinants of Populus balsamifera leaf morphology

Comparing four heat-inducible promoters in stably transformed sugarcane regarding spatial and temporal control of transgene expression reveals candidates to drive stem-preferred transgene expression

Genome-wide association study and fine-mapping identify a major quantitative trait locus controlling hundred-seed weight in soybean

Research evolution of flat peach (Prunus persica (L.) Batsch): a decadal bibliometric analysis

Genome-wide analysis of the CrRLK1L gene family in Puccinellia tenuiflora and functional study of PutFER1 in Arabidopsis underpinning salt tolerance

MicroRNA identification and expression analysis of wheat thermo-sensitive male sterile line BNS366 for fertility transformation

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

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

Conserved regions upstream of BRC1B regulate bud dormancy in tomato

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

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.)

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