ORIGINAL RESEARCH article
Front. Plant Sci.
Sec. Functional and Applied Plant Genomics
Volume 16 - 2025 | doi: 10.3389/fpls.2025.1654904
This article is part of the Research TopicGrowth and Development in Horticultural Crops: Mechanisms, Regulation, and InnovationView all articles
Genome-wide association study and genome prediction of tallness trait in spinach tallness phenotyping
Provisionally accepted
Ibtisam Alatawi1Haizheng Xiong1
Hanan Alkabkabi1
KENANI CHIWINA1
Beiquan Mou2Qun Luo1Yuejun Qu1Renjie Du1
Awais Riaz1
Derrick J Harrison1
Ainong Shi1*- 1University of Arkansas, Fayetteville, United States
- 2USDA-ARS, Salinas, United States
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Plant height is a critical agronomic trait in spinach (Spinacia oleracea L.), influencing both mechanical harvesting efficiency and overall yield. In this study, plant height variation was evaluated in 307 United States Department of Agriculture (USDA) germplasm accessions, which were phenotyped and genotyped using 15,058 single-nucleotide polymorphisms (SNPs) obtained from whole-genome resequencing. A genome-wide association study (GWAS) was conducted using the General Linear Model (GLM), Mixed Linear Model (MLM), Multiple Loci Mixed Model (MLMM), Fixed and Random Model Circulating Probability Unification (FarmCPU), and Bayesian-information and Linkage-disequilibrium Iteratively Nested Keyway (BLINK) models implemented in the Genomic Association and Prediction Integrated Tool version 3 (GAPIT3). Ten SNPs were significantly associated with plant height: (i) SOVchr1_10780051 (10,780,051 bp) on chromosome (chr) 1; (ii) SOVchr2_68062488 (68,062,488 bp) on chr 2; (iii) SOVchr4_38323167 (38,323,167 bp), SOVchr4_188084317 (188,084,317 bp), and SOVchr4_188084338 (188,084,338 bp) on chr 4; (iv) SOVchr5_70192260 (70,192,260 bp) and SOVchr5_105368320 (105,368,320 bp) on chr 5; and (v) SOVchr6_8139833 (8,139,833 bp), SOVchr6_90951127 (90,951,127 bp), and SOVchr6_91175684 (91,175,684 bp) on chr 6. Genomic prediction (GP) models were applied to estimate genomic estimated breeding values (GEBV) for plant height, achieving an r-value of 0.55 using GWAS-derived SNP markers in cross-population prediction. The integration of GWAS and GP provides insights into the genetic architecture of plant height in spinach and supports marker-assisted breeding strategies to enhance crop management and economic returns.
Keywords: genome-wide association study (GWAS), genomic prediction (GP), Plant height, single-nucleotide polymorphism (SNP), Spinacia oleracea L., spinach, Tallness
Received: 27 Jun 2025; Accepted: 11 Sep 2025.
Copyright: © 2025 Alatawi, Xiong, Alkabkabi, CHIWINA, Mou, Luo, Qu, Du, Riaz, Harrison and Shi. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
* Correspondence: Ainong Shi, University of Arkansas, Fayetteville, United States
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