Evidence map›Paper›PMID 41652531›Full record

ArticleBMC plant biology2026

Integrating QTL mapping with transcriptome analysis uncovers candidate genes of ear length in maize.

Bin Hou, Yue Zhu, Guo Chen, Yanwei Xiu, Chen Chen, Shasha Hu, Zhaohong Liu, Naeem Huzaifa, Anmureguli Tudi, Feng Teng and 5 more

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Article in BMC plant biology, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited 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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4 · The record

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5 · Who and what money

Authors and funding

15 authors.

Bin HouKey Laboratory of Oasis Ecology Agricultural of Xinjiang Production and Construction Corps, Agricultural College, Shihezi University, Shihezi, 832003, China.
Yue ZhuKey Laboratory of Oasis Ecology Agricultural of Xinjiang Production and Construction Corps, Agricultural College, Shihezi University, Shihezi, 832003, China.
Guo ChenXinjiang Key Laboratory of Crop Biotechnology, Biological Breeding Laboratory, Academy of Agricultural Sciences of Xinjiang Uyghur Autonomous Region, Urumqi, 830091, China.
Yanwei XiuKey Laboratory of Oasis Ecology Agricultural of Xinjiang Production and Construction Corps, Agricultural College, Shihezi University, Shihezi, 832003, China.
Chen ChenKey Laboratory of Oasis Ecology Agricultural of Xinjiang Production and Construction Corps, Agricultural College, Shihezi University, Shihezi, 832003, China.
Shasha HuXinjiang Production and Construction Corps Fourth Division Institute of Agricultural Sciences, Kekedala, 835219, China.
Zhaohong LiuKey Laboratory of Oasis Ecology Agricultural of Xinjiang Production and Construction Corps, Agricultural College, Shihezi University, Shihezi, 832003, China.
Naeem HuzaifaKey Laboratory of Oasis Ecology Agricultural of Xinjiang Production and Construction Corps, Agricultural College, Shihezi University, Shihezi, 832003, China.
Anmureguli TudiKey Laboratory of Oasis Ecology Agricultural of Xinjiang Production and Construction Corps, Agricultural College, Shihezi University, Shihezi, 832003, China.
Feng TengHubei Key Laboratory of Food Crop Germplasm and Genetic Improvement, Food Crops Institute, Hubei Academy of Agricultural Sciences, Wuhan, 430064, China.
Ze ZhangKey Laboratory of Oasis Ecology Agricultural of Xinjiang Production and Construction Corps, Agricultural College, Shihezi University, Shihezi, 832003, China.
Zhiqiang ZhaoXinjiang Production and Construction Corps Fourth Division Institute of Agricultural Sciences, Kekedala, 835219, China.
Guangchao KongKey Laboratory of Oasis Ecology Agricultural of Xinjiang Production and Construction Corps, Agricultural College, Shihezi University, Shihezi, 832003, China. kgch_agr@shzu.edu.cn.
Haitao JiaHubei Key Laboratory of Food Crop Germplasm and Genetic Improvement, Food Crops Institute, Hubei Academy of Agricultural Sciences, Wuhan, 430064, China. htjia@hbaas.com.
Zhenyuan PanKey Laboratory of Oasis Ecology Agricultural of Xinjiang Production and Construction Corps, Agricultural College, Shihezi University, Shihezi, 832003, China. panzhenyuandawood@163.com.

Funding

Shihezi University YZZX202402the national natural science foundation of China 32160475the Open Project of Key Laboratory in the Xinjiang Uygur Autonomous Region of China 2023D04041Xinjiang Uygur Autonomous Region XJAR-02-33XPCC 9th Division 2023JS008
6 · The paper itself

Abstract

backgroundEar length (EL) is a critical determinant of yield in maize breeding, yet its genetic underpinnings remain poorly characterized. This study aimed to identify key quantitative trait loci (QTLs) and candidate genes controlling EL to enhance our understanding of the genetic basis of ear development.

resultsTo characterize candidate genes governing EL regulation, a population consist of 318 BC4F4 lines, derived from B73 (recurrent parent) and Baimaya (BMY, donor parent) was used for EL related QTL mapping with 10 K maize SNP array in three environments. We identified 16 QTLs for EL across three environments and the best linear unbiased prediction (BLUP), among which, three QTLs were repeatedly detected, especially the major QTL qEL2.05, with an average phenotypic variation (PVE) of 9.40%, logarithm of odds (LOD) score of 7.49, and average additive effect of 0.65 cm. Further, near-isogenic lines (NILs) of qEL2.05 confirmed its effect, with qEL2.05BMY exhibiting significantly longer ears and larger inflorescence meristems than qEL2.05B73. Then, the integration of linkage mapping and transcriptome analysis of 5 mm immature ears of the NILs uncovered a candidate gene, Zm00001eb085560, which encoded an aldehyde dehydrogenase, and showed significantly up-regulated in qEL2.05BMY, and two missense variations between the NILs. Analysis of differentially expressed genes (DEGs) revealed significant enrichment in pathways related to the phosphatidylinositol signaling system, which have been reported to be related to the development of plant inflorescences. Furthermore, pyramiding the favorable alleles from the three stable QTLs enhanced EL more significantly than single alleles.

conclusionsOur findings uncover stable QTLs and a promising candidate gene governing ear length in maize. This research lays a solid foundation for future functional studies and molecular breeding aimed at improving maize yield.

Indexed as

Genes, PlantQuantitative Trait LociZea maysChromosome MappingGene Expression ProfilingPhenotypePolymorphism, Single NucleotideTranscriptomeCandidate geneEar lengthFavorable allelesQuantitative trait locusTranscriptome analysis

Identifiers

PMID41652531
PMCPMC12973922

What Socratic holds

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LicenceCC BY-NC-ND
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Registered trials

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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 Socratic graph.