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Journal of Integrative Agriculture  2024, Vol. 23 Issue (10): 3406-3418    DOI: 10.1016/j.jia.2024.03.037
Section 1: Cotton functional genomics Advanced Online Publication | Current Issue | Archive | Adv Search |
Mining elite loci and candidate genes for root morphology-related traits at the seedling stage by genome-wide association studies in upland cotton (Gossypium hirsutum L.) 
Huaxiang Wu*, Xiaohui Song*, Muhammad Waqas-Amjid, Chuan Chen, Dayong Zhang#, Wangzhen Guo#
State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization/Engineering Research Center of Cotton Germplasm Enhancement and Application, Ministry of Education/Nanjing Agricultural University, Nanjing 210095, China
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摘要  
根系结构在植物获取水分和养分方面发挥着至关重要的作用,同时在植物适应各种环境胁迫方面扮演关键的角色。本研究利用242份陆地棉材料,研究了棉花幼苗期的6个根系形态特征,包括主根长(MRL)、根系鲜重(RFW)、总根长(TRL)、根表面积(RSA)、根体积(RV)和根平均直径(AvgD)。相关性分析表明,TRL与RSA、RV与RSA和AvgD呈正相关,而TRL与AvgD呈显著负相关。利用实验室前期鉴定的该套材料含56,010个单核苷酸多态性(SNPs)位点的基因型数据,结合根表型数据进行了全基因组关联分析(GWAS)。共鉴定出41个数量性状位点(QTLs),其中与MRL相关的QTL 9个、RFW 6个、TRL 9个、RSA 12个、RV 12个、AvgD 2个。有8个QTLs在两个或多个性状上被重复检测到。结合转录组数据分析,在这些QTLs区间筛选到17个在根组织中高表达(TPM值≥ 30)的候选基因。进一步对一个编码包含WPP结构域、具有调节根系发育功能的候选基因GH_D05G2106进行了功能验证,病毒诱导基因沉默(VIGS)试验表明,降低GH_D05G2106的表达显著抑制棉花根系发育,表明其在根系形态建成中具有正调节作用。研究结果为棉花根系发育生物学和根系相关育种研究提供了理论依据和候选基因。


Abstract  
Root system architecture plays an essential role in water and nutrient acquisition in plants, and it is significantly involved in plant adaptations to various environmental stresses.  In this study, a panel of 242 cotton accessions was collected to investigate six root morphological traits at the seedling stage, including main root length (MRL), root fresh weight (RFW), total root length (TRL), root surface area (RSA), root volume (RV), and root average diameter (AvgD).  The correlation analysis of the six root morphological traits revealed strong positive correlations of TRL with RSA, as well as RV with RSA and AvgD, whereas a significant negative correlation was found between TRL and AvgD.  Subsequently, a genome-wide association study (GWAS) was performed using the root phenotypic and genotypic data reported previously for the 242 accessions using 56,010 single nucleotide polymorphisms (SNPs) from the CottonSNP80K array.  A total of 41 quantitative trait loci (QTLs) were identified, including nine for MRL, six for RFW, nine for TRL, 12 for RSA, 12 for RV and two for AvgD.  Among them, eight QTLs were repeatedly detected in two or more traits.  Integrating these results with a transcriptome analysis, we identified 17 candidate genes with high transcript values of transcripts per million (TPM)≥30 in the roots.  Furthermore, we functionally verified the candidate gene GH_D05G2106, which encodes a WPP domain protein 2 in root development.  A virus-induced gene silencing (VIGS) assay showed that knocking down GH_D05G2106 significantly inhibited root development in cotton, indicating its positive role in root system architecture formation.  Collectively, these results provide a theoretical basis and candidate genes for future studies on cotton root developmental biology and root-related cotton breeding.


Keywords:  cotton       root-morphology traits        quantitative trait loci        candidate genes        GWAS  
Received: 17 October 2023   Accepted: 01 February 2024
Fund: 
This work was supported by the Jiangsu Natural Science Foundation, China (BK20231468), the Fundamental Research Funds for the Central Universities, China (ZJ24195012) the National Natural Science Foundation in China (31871668), the Jiangsu Key R&D Program, China (BE2022384), the Xinjiang Uygur Autonomous Region Science and Technology Support Program, China (2021E02003), and the Jiangsu Collaborative Innovation Center for Modern Crop Production Project, China (No. 10).
About author:  Huaxiang Wu, E-mail: wuhx@mail.nankai.edu.cn; Xiaohui Song, E-mail: 2018101045@njau.edu.cn; #Correspondence Wangzhen Guo, E-mail: moelab@njau.edu.cn; Dayong Zhang, Tel: +86-25-84396523, E-mail: dyzhang@njau.edu.cn * These authors contributed equally to this study.

Cite this article: 

Huaxiang Wu, Xiaohui Song, Muhammad Waqas-Amjid, Chuan Chen, Dayong Zhang, Wangzhen Guo. 2024. Mining elite loci and candidate genes for root morphology-related traits at the seedling stage by genome-wide association studies in upland cotton (Gossypium hirsutum L.) . Journal of Integrative Agriculture, 23(10): 3406-3418.

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