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Mbe JO, Dzidzienyo DK, Abah SP, Njoku DN, Onyeka J, Tongoona P, Egesi C. Novel SNP markers and other stress-related genomic regions associated with nitrogen use efficiency in cassava. Front Plant Sci 2024; 15:1376520. [PMID: 38638347 PMCID: PMC11024350 DOI: 10.3389/fpls.2024.1376520] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Accepted: 03/15/2024] [Indexed: 04/20/2024]
Abstract
Cassava productivity is constrained by low soil nitrogen, which is predominant in most cassava-growing regions in the tropics and subtropical agroecology. Improving the low nitrogen tolerance of cassava has become an important breeding objective. The current study aimed to develop cassava varieties with improved nitrogen use efficiency by identifying genomic regions and candidate genes linked to nitrogen use efficiency in cassava. A genome-wide association study (GWAS) was performed using the Genome Association and Prediction Integrated Tool (GAPIT). A panel of 265 diverse cassava genotypes was phenotyped for 10 physiological and agronomic traits under optimum and low-nitrogen regimes. Whole-genome genotyping of these cassava cloneswas performed using the Diversity Arrays Technology (DArTseq) sequencing platform. A total of 68,814 single nucleotide polymorphisms (SNPs) were identified, which were spread across the entire 18 chromosomes of the cassava genome, of which 52 SNPs at various densities were found to be associated with nitrogen use efficiency in cassava and other yield-related traits. The putative genes identified through GWAS, especially those with significant associated SNP markers for NUE and related traits have the potential, if deployed appropriately, to develop cassava varieties with improved nitrogen use efficiency, which would translate to a reduction in the economic and environmental cost of cassava production.
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Affiliation(s)
- Joseph Okpani Mbe
- Cassava Research Program, National Root Crops Research Institute (NRCRI), Umudike, Nigeria
- West Africa Centre for Crop Improvement (WACCI), University of Ghana, Accra, Ghana
| | - Daniel Kwadjo Dzidzienyo
- West Africa Centre for Crop Improvement (WACCI), University of Ghana, Accra, Ghana
- Biotechnology Centre, College of Basic and Applied Sciences, University of Ghana, Accra, Ghana
| | - Simon Peter Abah
- Cassava Research Program, National Root Crops Research Institute (NRCRI), Umudike, Nigeria
- West Africa Centre for Crop Improvement (WACCI), University of Ghana, Accra, Ghana
| | - Damian Ndubuisi Njoku
- Cassava Research Program, National Root Crops Research Institute (NRCRI), Umudike, Nigeria
| | - Joseph Onyeka
- Cassava Research Program, National Root Crops Research Institute (NRCRI), Umudike, Nigeria
| | - Pangirayi Tongoona
- West Africa Centre for Crop Improvement (WACCI), University of Ghana, Accra, Ghana
| | - Chiedozie Egesi
- Cassava Research Program, National Root Crops Research Institute (NRCRI), Umudike, Nigeria
- Department of Plant Breeding and Genetics, Cornell University, Ithaca, NY, United States
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