Genome-wide association analysis of wheat stem traits using 55K microarrays
Wheat lodging poses a severe threat to yield and quality, with the morphological and structural traits of the basal second internode being critical determinants of stem strength and lodging resistance. We conducted phenotypic analysis on 239 wheat varieties (lines) collected from around the world. T...
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Frontiers Media S.A.
2025-07-01
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| Series: | Frontiers in Plant Science |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fpls.2025.1635721/full |
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| author | Wei Wang Na Sun Kai Zhao JiKun Song Hui Fang Guiqiang Fan Yonghong Gao Tianrong Huang Yindeng Ding |
| author_facet | Wei Wang Na Sun Kai Zhao JiKun Song Hui Fang Guiqiang Fan Yonghong Gao Tianrong Huang Yindeng Ding |
| author_sort | Wei Wang |
| collection | DOAJ |
| description | Wheat lodging poses a severe threat to yield and quality, with the morphological and structural traits of the basal second internode being critical determinants of stem strength and lodging resistance. We conducted phenotypic analysis on 239 wheat varieties (lines) collected from around the world. This analysis was complemented by genotyping using the wheat 55K SNP chip. Genome-wide association analysis (GWAS) was executed employing the MLM (Q+K) algorithm within the TASSLE software suite. The findings unveiled pronounced phenotypic variability in the stem diameter of the second internode across disparate temporal intervals, characterized by a coefficient of variation spanning from 11.31% to 13.95%, alongside robust inter-year correlations. Furthermore, the genome-wide linkage disequilibrium (LD) decay distance was ascertained to 3 Mb. Analyses of population structure, phylogenetic dendrograms, and principal components revealed that the intrinsic population structure of the 239 wheat varieties (lines) was markedly simplified, segregating into three discernible subgroups. GWAS analysis identified 118 SNPs significantly associated with the stem diameter of the second internode (P ≤ 0.001). Notably, among these loci, three SNPs (AX-111557672, AX-94584919, and AX-109819835) overlapped with previously reported associations, while the remaining 115 SNPs represented novel discoveries distributed across chromosomes 1A, 1B, 1D, 2A, 2B, 2D, 3A, 3B, 4A, 4B, 4D, 5A, 5B, 6A, 6B, 6D, 7A, 7B, and 7D. These newly identified loci exhibited substantial phenotypic variance explained, ranging from 8.09% to 29.14% for individual SNPs. Subsequent rigorous screening of loci showing significant phenotypic impacts and stability across diverse environmental contexts culminated in the identification of seven candidate genes implicated in the stem diameter of the second internode. This investigation provides new SNPs markers for enhancing lodging resistance in wheat, highlighting substantial practical implications. |
| format | Article |
| id | doaj-art-ff47774a986542559ca6493ff818b242 |
| institution | Kabale University |
| issn | 1664-462X |
| language | English |
| publishDate | 2025-07-01 |
| publisher | Frontiers Media S.A. |
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| series | Frontiers in Plant Science |
| spelling | doaj-art-ff47774a986542559ca6493ff818b2422025-08-20T03:56:03ZengFrontiers Media S.A.Frontiers in Plant Science1664-462X2025-07-011610.3389/fpls.2025.16357211635721Genome-wide association analysis of wheat stem traits using 55K microarraysWei Wang0Na Sun1Kai Zhao2JiKun Song3Hui Fang4Guiqiang Fan5Yonghong Gao6Tianrong Huang7Yindeng Ding8School of Computer Science and Information Engineering, Anyang Institute of Technology, Anyang, ChinaYili Prefecture Institute of Agricultural Science, Yining, ChinaSchool of Computer Science and Information Engineering, Anyang Institute of Technology, Anyang, ChinaCotton Research Institute, Chinese Academy of Agricultural Sciences, AnYang, ChinaInstitute of Crops, Xinjiang Academy of Agricultural Sciences, Xinjiang, ChinaInstitute of Crops, Xinjiang Academy of Agricultural Sciences, Xinjiang, ChinaInstitute of Crops, Xinjiang Academy of Agricultural Sciences, Xinjiang, ChinaInstitute of Crops, Xinjiang Academy of Agricultural Sciences, Xinjiang, ChinaInstitute of Crops, Xinjiang Academy of Agricultural Sciences, Xinjiang, ChinaWheat lodging poses a severe threat to yield and quality, with the morphological and structural traits of the basal second internode being critical determinants of stem strength and lodging resistance. We conducted phenotypic analysis on 239 wheat varieties (lines) collected from around the world. This analysis was complemented by genotyping using the wheat 55K SNP chip. Genome-wide association analysis (GWAS) was executed employing the MLM (Q+K) algorithm within the TASSLE software suite. The findings unveiled pronounced phenotypic variability in the stem diameter of the second internode across disparate temporal intervals, characterized by a coefficient of variation spanning from 11.31% to 13.95%, alongside robust inter-year correlations. Furthermore, the genome-wide linkage disequilibrium (LD) decay distance was ascertained to 3 Mb. Analyses of population structure, phylogenetic dendrograms, and principal components revealed that the intrinsic population structure of the 239 wheat varieties (lines) was markedly simplified, segregating into three discernible subgroups. GWAS analysis identified 118 SNPs significantly associated with the stem diameter of the second internode (P ≤ 0.001). Notably, among these loci, three SNPs (AX-111557672, AX-94584919, and AX-109819835) overlapped with previously reported associations, while the remaining 115 SNPs represented novel discoveries distributed across chromosomes 1A, 1B, 1D, 2A, 2B, 2D, 3A, 3B, 4A, 4B, 4D, 5A, 5B, 6A, 6B, 6D, 7A, 7B, and 7D. These newly identified loci exhibited substantial phenotypic variance explained, ranging from 8.09% to 29.14% for individual SNPs. Subsequent rigorous screening of loci showing significant phenotypic impacts and stability across diverse environmental contexts culminated in the identification of seven candidate genes implicated in the stem diameter of the second internode. This investigation provides new SNPs markers for enhancing lodging resistance in wheat, highlighting substantial practical implications.https://www.frontiersin.org/articles/10.3389/fpls.2025.1635721/fullwheatstem thicknesscollapseGWAScandidate genes |
| spellingShingle | Wei Wang Na Sun Kai Zhao JiKun Song Hui Fang Guiqiang Fan Yonghong Gao Tianrong Huang Yindeng Ding Genome-wide association analysis of wheat stem traits using 55K microarrays Frontiers in Plant Science wheat stem thickness collapse GWAS candidate genes |
| title | Genome-wide association analysis of wheat stem traits using 55K microarrays |
| title_full | Genome-wide association analysis of wheat stem traits using 55K microarrays |
| title_fullStr | Genome-wide association analysis of wheat stem traits using 55K microarrays |
| title_full_unstemmed | Genome-wide association analysis of wheat stem traits using 55K microarrays |
| title_short | Genome-wide association analysis of wheat stem traits using 55K microarrays |
| title_sort | genome wide association analysis of wheat stem traits using 55k microarrays |
| topic | wheat stem thickness collapse GWAS candidate genes |
| url | https://www.frontiersin.org/articles/10.3389/fpls.2025.1635721/full |
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