Evidence map›Paper›PMID 41073899›Full record

ArticleBMC plant biology2025

Combining QTL mapping and RNA-Seq reveals candidate genes controlling flag leaf width in foxtail millet.

Zhilan Wang, Mengmeng Shen, Huan Yang, Xiaofen Du, Kangni Han, Hongpo Wu, Xiangrui Dai, Shichao Lian, Yuxin Li, Yanfang Li and 2 more

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PubMed Full text at PMC Publisher
In one paragraph

Article in BMC plant biology, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.

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1citing papers in PubMed
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1 · What the graph read from it

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3 · Its place in the literature

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1 citing paper in PubMed.

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4 · The record

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5 · Who and what money

Authors and funding

12 authors.

Zhilan Wang *Shanxi Houji Laboratory, Millet Research Institute, Shanxi Agricultural University, Changzhi, 046011, China.
Mengmeng Shen *Shanxi Houji Laboratory, Millet Research Institute, Shanxi Agricultural University, Changzhi, 046011, China.
Huan YangShanxi Houji Laboratory, Millet Research Institute, Shanxi Agricultural University, Changzhi, 046011, China.
Xiaofen DuShanxi Houji Laboratory, Millet Research Institute, Shanxi Agricultural University, Changzhi, 046011, China.
Kangni HanShanxi Houji Laboratory, Millet Research Institute, Shanxi Agricultural University, Changzhi, 046011, China.
Hongpo WuShanxi Houji Laboratory, Millet Research Institute, Shanxi Agricultural University, Changzhi, 046011, China.
Xiangrui DaiShanxi Houji Laboratory, Millet Research Institute, Shanxi Agricultural University, Changzhi, 046011, China.
Shichao LianShanxi Houji Laboratory, Millet Research Institute, Shanxi Agricultural University, Changzhi, 046011, China.
Yuxin LiShanxi Houji Laboratory, Millet Research Institute, Shanxi Agricultural University, Changzhi, 046011, China.
Yanfang LiShanxi Houji Laboratory, Millet Research Institute, Shanxi Agricultural University, Changzhi, 046011, China.
Linyi ZhangShanxi Houji Laboratory, Millet Research Institute, Shanxi Agricultural University, Changzhi, 046011, China.
Jun WangShanxi Houji Laboratory, Millet Research Institute, Shanxi Agricultural University, Changzhi, 046011, China. 128wan@163.com.

Funding

National Key R&D Program of China 2023YFD1202704the Central Guidance on Local Science and Technology Development Fund of Shanxi Province, China YDZJSX2024D047the Establishment and Construction Plan for Key Laboratories in Changzhi City 2024sy005the Modern Agriculture Industry Technology System Construction Project of Shanxi Province, China 2025CYJSTX04-01the Shanxi Province Agricultural Key Core Technology Research, China NYGG19the Shanxi Province Science and Technology Innovation Team Project, China 2015013001-09
6 · The paper itself

Abstract

backgroundThe flag leaf, a crucial component of plant architecture, significantly influences final grain yield in crops, including foxtail millet (Setaria italica L.). Optimizing flag leaf size is considered an effective strategy for enhancing grain yield potential under higher planting densities. However, the genetic mechanism underlying flag leaf size, particularly flag leaf width (FLW), remains largely unknown under varying planting densities in foxtail millet.

resultsAn FLW phenotype variation analysis was conducted across multiple planting densities using a recombinant inbred line (RIL) population derived from Heizhigu (narrow leaf) and Changnong 35 (wide leaf). Based on a high-density genetic map with 3795 Bin markers, 11 flag leaf width (FLW) QTLs were identified on chromosomes 3, 5, and 6, explaining 2.35%-36.06%. Among these, qFLW5-2 was a major QTL, detected consistently across 3 environments and explaining a large proportion of FLW variation. The QTL was further validated with 9 InDel markers with its candidate region across different planting densities. Moreover, RNA-seq revealed 2,293 and 2,338 differentially expressed genes (DEGs) between biparents at heading stage and grain filling stage, respectively. There were 11 and 9 DEGs within the location range of qFLW5-2 among 2 comparison groups (HZG-H_vs_CN35-H and HZG-G_vs_CN35-G). Combining QTL mapping and RNA-seq, we speculated that Seita.5g134600 (encoding an auxin responsive protein Aux/IAA) and Seita.5G123900 (encoding a cytochrome P450 family protein) as key candidate genes for qFLW5-2. Furthermore, variation analysis confirmed that the lines or germplasm with Seita.5G134600

conclusionsThis study elucidates genetic and molecular mechanism regulating flag leaf growth and development in foxtail millet. The results provide a theoretical foundation for improving plant architecture and facilitating molecular marker-assisted breeding in this crop.

Indexed as

Genes, PlantPlant LeavesQuantitative Trait LociSetaria PlantChromosome MappingPhenotypeRNA-SeqCandidate geneFlag leaf widthFoxtail milletQTL mappingRNA-seq

Identifiers

PMID41073899
PMCPMC12512300

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LicenceCC BY-NC-ND
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.