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other·plant_genetics, agronomy, crop_science, plant_physiology, genomics·PMC10094163

Genome-Wide Association Study for Root Morphology and Phosphorus Acquisition Efficiency in Diverse Maize Panels

International Journal of Molecular Sciences · 11 authors, 5 centres

AI SUMMARY

FIDELITY 94%

POPULATION561 tropical maize inbred lines (365 from Embrapa, 196 from DTMA panel)

INTERVENTIONGrowth under low phosphorus (2.5 μM) vs. high phosphorus (250 μM) in nutrient solution

COMPARISONComparison of root morphology traits (root length, surface area, diameter), total seedling dry weight, and total P content between low- and high-P conditions

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TL;DR

This genome-wide association study (GWAS) in 561 diverse tropical maize lines identified seven SNPs significantly associated with root morphology, biomass, and phosphorus (P) content under low- and high-P conditions. Two key SNPs linked to root length and seedling dry weight under P deficiency were located near genes encoding AGC kinase and MAPKKK protein kinases, suggesting these kinases play a role in root adaptation to low P. These findings provide candidate genes and markers that could be used in breeding programs to improve phosphorus acquisition efficiency in maize, particularly for tropical soils where P is limiting.

Full summary

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**Background:** Phosphorus (P) is a critical macronutrient for plant growth, but its low availability in many soils, especially tropical soils, limits crop yields. Maize (Zea mays) is highly dependent on P fertilization, and improving P acquisition efficiency (PAE) is a key breeding goal. Root morphology traits, such as root length (RL), surface area (SA), and diameter (RD), are important for PAE, but their genetic basis is not fully understood. This study aimed to identify genetic loci associated with root morphology and P acquisition traits in a diverse panel of tropical maize lines under contrasting P levels.

**Methods:** A panel of 561 tropical maize inbred lines (365 from Embrapa, Brazil, and 196 from the DTMA project, CIMMYT/IITA) was phenotyped for RL, SA, RD, total seedling dry weight (TDW), and total P content (PCont) under low (2.5 μM) and high (250 μM) P in nutrient solution using a paper pouch system. Root images were analyzed with RootReader2D and WinRHIZO. Genotyping-by-sequencing (GBS) yielded 353,540 SNPs after imputation and filtering (MAF > 5%). Population structure was assessed via principal component analysis (PCA) on 12,700 SNPs. Linkage disequilibrium (LD) decayed to r² = 0.2 at ~1 kb. GWAS was performed using a mixed linear model (MLM) including the first five PCs and a kinship matrix (K). Significance was set at a Bonferroni-corrected threshold of –log10(p) ≥ 6.07, based on 58,708 independent LD blocks.

**Key Results:** - Broad-sense heritabilities ranged from 0.49 (PCont low-P) to 0.71 (RL both P levels). - Under low P, the Embrapa panel showed increased RL and SA and decreased RD, while the DTMA panel showed decreased RL and SA, indicating differential root plasticity. - Seven SNPs reached the Bonferroni significance threshold: - S4_3751192 (RD high-P, –log10(p)=6.44) within GRMZM2G037472 (kinesin motor domain). - S8_88600375 (RL low-P, –log10(p)=6.30) within GRMZM2G044531 (AGC kinase). - S6_34607369 (TDW low-P, –log10(p)=6.37) with no predicted gene. - S9_137746077 (TDW low-P, –log10(p)=6.43) 57 bp upstream of GRMZM2G378852 (MAPKKK). - S10_77284783 (TDW high-P, –log10(p)=6.41) within GRMZM2G110145 (cellulose synthase-like). - S8_21326857 (PCont high-P, –log10(p)=6.34) with no flanking gene. - S9_143192439 (PCont high-P, –log10(p)=6.11) within GRMZM2G104618 (uncharacterized). - The region around S8_88600375 (bin 8.03) showed high LD (r² ~0.77) with SNPs in GRMZM2G057116 (WRKY transcription factor) located ~127 kb away.

**Clinical Implications:** This study identifies candidate genes and SNPs associated with root morphology and P acquisition efficiency in tropical maize. The AGC kinase and MAPKKK genes are promising targets for marker-assisted selection to improve P efficiency, especially in low-P soils common in tropical regions. The differential root plasticity between Embrapa and DTMA panels suggests that different breeding strategies may be needed for different germplasm. These findings could accelerate the development of maize varieties with enhanced P acquisition, reducing reliance on P fertilizers and improving sustainability.

PICO

PPOPULATION

561 tropical maize inbred lines (365 from Embrapa, 196 from DTMA panel)

IINTERVENTION

Growth under low phosphorus (2.5 μM) vs. high phosphorus (250 μM) in nutrient solution

OOUTCOME

Seven SNPs reached Bonferroni significance (p < 6.07e-7) for root diameter, root length, total dry weight, and P content; candidate genes include AGC kinase, MAPKKK, WRKY transcription factor, and cellulose synthase-like protein

STUDY TYPE

other

SPECIALTY

plant_genetics

SUMMARISED BY

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FIDELITY CHECK

94% · A

ORIGINAL PAPER

PMC10094163

Genome-Wide Association Study for Root Morphology and Phosphorus Acquisition Efficiency in Diverse Maize Panels

International Journal of Molecular Sciences

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ABSTRACT

Abstract Maximizing soil exploration through modifications of the root system is a strategy for plants to overcome phosphorus (P) deficiency. Genome-wide association with 561 tropical maize inbred lines from Embrapa and DTMA panels was undertaken for root morphology and P acquisition traits under low- and high-P concentrations, with 353,540 SNPs. P supply modified root morphology traits, biomass and P content in the global maize panel, but root length and root surface area changed differentially in Embrapa and DTMA panels. This suggests that different root plasticity mechanisms exist for maize adaptation to low-P conditions. A total of 87 SNPs were associated to phenotypic traits in both P conditions at −log 10 ( p -value) ≥ 5, whereas only seven SNPs reached the Bonferroni significance. Among these SNPs, S9_137746077, which is located upstream of the gene GRMZM2G378852 that encodes a MAPKKK protein kinase, was significantly associated with total seedling dry weight, with the same allele increasing root length and root surface area under P deficiency. The C allele of S8_88600375, mapped within GRMZM2G044531 that encodes an AGC kinase, significantly enhanced root length under low P, positively affecting root surface area and seedling weight. The broad genetic diversity evaluated in this panel suggests that candidate genes and favorable alleles could be exploited to improve P efficiency in maize breeding programs of Africa and Latin America. Keywords: GWAS, root morphology, maize, P acquisition efficiency, P deficiency

CITATION EXPORT

Carlos Alexandre Gomes Ribeiro, Sylvia Morais de Sousa Tinoco, Vander Fillipe de Souza et al.. Genome-Wide Association Study for Root Morphology and Phosphorus Acquisition Efficiency in Diverse Maize Panels. International Journal of Molecular Sciences. (2023). https://doi.org/10.3390/ijms24076233

AUTHORS

11 · 5 CENTRES

Carlos Alexandre Gomes Ribeiro, Sylvia Morais de Sousa Tinoco, Vander Fillipe de Souza, Barbara França Negri, Christine Marie Gault, Maria Marta Pastina, Jurandir Vieira Magalhaes, Lauro José Moreira Guimarães, Everaldo Gonçalves de Barros, Edward S Buckler, Claudia Teixeira Guimaraes

1Programa de Pós-Graduação em Genética e Melhoramento, Universidade Federal de Viçosa, Viçosa 36570-000, Minas Gerais, Brazil
2Embrapa Milho e Sorgo, Sete Lagoas 35701-970, Minas Gerais, Brazil
3Programa de Pós-Graduação em Bioengenharia, Universidade Federal de São João del-Rei, São João del-Rei 36301-160, Minas Gerais, Brazil
4Institute for Genomic Diversity, Cornell University, Ithaca, NY 14853, USA
5USDA-ARS, Robert Holley Center, Ithaca, NY 14853, USA