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

Yin, Hongyan; Yan, Yu; Hu, Wei; Liu, Guoyin; Zeng, Hongqiu; Wei, Yunxie; Shi, Haitao

doi:10.1111/tpj.16006

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

Journal Article · Fri Oct 28 00:00:00 EDT 2022 · The Plant Journal

DOI:https://doi.org/10.1111/tpj.16006· OSTI ID:1895187

Yin, Hongyan ^[1]; Yan, Yu ^[2]; Hu, Wei ^[3]; Liu, Guoyin ^[2]; Zeng, Hongqiu ^[2]; Wei, Yunxie ^[2]; ^[2]

Key Laboratory of Biotechnology of Salt Tolerant Crops of Hainan Province Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources (Provincial Ministry Building State Key Laboratory Breeding Base), Sanya Nanfan Research Institute, College of Tropical Crops, Collaborative Innovation Center of Nanfan and High‐Efficiency Tropical Agriculture, Hainan University Hainan Province Sanya and Haikou China
Key Laboratory of Biotechnology of Salt Tolerant Crops of Hainan Province Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources (Provincial Ministry Building State Key Laboratory Breeding Base), Sanya Nanfan Research Institute, College of Tropical Crops, Collaborative Innovation Center of Nanfan and High‐Efficiency Tropical Agriculture, Hainan University Hainan Province Sanya and Haikou China, Hainan Yazhou Bay Seed Laboratory Hainan Province Sanya China
Key Laboratory of Biology and Genetic Resources of Tropical Crops Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences 571101 Hainan Province Haikou Xueyuan Road 4 China

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.

View Accepted Manuscript (Publisher)

Sponsoring Organization:: USDOE

OSTI ID:: 1895187

Journal Information:: The Plant Journal, Journal Name: The Plant Journal Journal Issue: 5 Vol. 112; ISSN 0960-7412

Publisher:: Wiley-BlackwellCopyright Statement

Country of Publication:: United Kingdom

Language:: English

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