Genome‐wide association studies reveal genetic basis of ionomic variation in cassava

Genome‐wide association studies reveal genetic basis of ionomic variation in cassava

SUMMARY As one of the most important food crops, cassava (Manihot esculenta) is the main dietary source of micronutrients for about 1 billion people. However, the ionomic variation in cassava and the underlying genetic mechanisms remain unclear so far. Herein, genome‐wide association studies were pe...

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Bibliographic Details
Published in:The Plant journal : for cell and molecular biology 2022-12, Vol.112 (5), p.1212-1223
Main Authors: Yin, Hongyan, Yan, Yu, Hu, Wei, Liu, Guoyin, Zeng, Hongqiu, Wei, Yunxie, Shi, Haitao
Format: Article
Language:eng
Subjects:
Accumulation
Calcium
Cassava
Cassava (Manihot esculenta)
Chromosomes
Diet
gene expression
Genetic diversity
Genetic Variation
Genome-Wide Association Study
Genomes
ionomic variation
Magnesium
Manihot - genetics
Manihot - metabolism
Manihot esculenta
Micronutrients
N accumulation
Nitrogen
Nucleotides
Phosphorus
Plant Breeding
Polymorphism, Single Nucleotide - genetics
promoter
Single-nucleotide polymorphism
tRNA
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Summary:SUMMARY As one of the most important food crops, cassava (Manihot esculenta) is the main dietary source of micronutrients for about 1 billion people. However, the ionomic variation in cassava and the underlying genetic mechanisms remain unclear so far. Herein, genome‐wide association studies were performed to reveal the specific single nucleotide polymorphisms (SNPs) that affect the ionomic variation in cassava. We identified 164 SNPs with P‐values lower than the threshold located in 88 loci associated with divergent ionomic variations. Among them, 13 SNPs are related to both calcium (Ca) and magnesium (Mg), and many loci for different ionomic traits seem to be clustered on specific chromosome regions. Moreover, we identified the peak SNPs in the promoter regions of Sc10g003170 (encoding methionyl‐tRNA synthetase [MetRS]) and Sc18g015190 (encoding the transcriptional regulatory protein AlgP) for nitrogen (N) and phosphorus (P) accumulation, respectively. Notably, these two SNPs (chr10_32807962 and chr18_31343738) were directly correlated with the transcript levels of Sc10g003170 (MetRS) and Sc18g015190 (AlgP), which positively modulated N accumulation and P concentration in cassava, respectively. Taken together, this study provides important insight into the genetic basis of cassava natural ionomic variation, which will promote genetic breeding to improve nutrient use and accumulation of elements in cassava. Significance Statement Genome‐wide association studies identified 164 loci associated with divergent ionomic variations, especially the peak SNPs (chr10_32807962 and chr18_31343738) in the promoter region of Sc10g003170 (MetRS) and Sc18g015190 (AlgP), which positively regulated N accumulation and P concentration in cassava, respectively
ISSN:0960-7412
1365-313X