Genotyping-by-Sequencing-Based Genetic Analysis of African Rice Cultivars and Association Mapping of Blast Resistance Genes Against Magnaporthe oryzae Populations in Africa

Abstract

Understanding the genetic diversity of rice germplasm is important for the sustainable use of genetic materials in rice breeding and production. Africa is rich in rice genetic resources that can be utilized to boost rice productivity on the continent. A major constraint to rice production in Africa is rice blast, caused by the hemibiotrophic fungal pathogen Magnaporthe oryzae. In this report, we present the results of a genotyping-by-sequencing (GBS)-based diversity analysis of 190 African rice cultivars and an association mapping of blast resistance (R) genes and quantitative trait loci (QTLs). The 190 African cultivars were clustered into three groups based on the 184K single nucleotide polymorphisms generated by GBS. We inoculated the rice cultivars with six African M. oryzae isolates. Association mapping identified 25 genomic regions associated with blast resistance (RABRs) in the rice genome. Moreover, PCR analysis indicated that RABR_23 is associated with the Pi-ta gene on chromosome 12. Our study demonstrates that the combination of GBS-based genetic diversity population analysis and association mapping is effective in identifying rice blast R genes/QTLs that contribute to resistance against African populations of M. oryzae. The identified markers linked to the RABRs and 14 highly resistant cultivars in this study will be useful for rice breeding in Africa.

Prospects of Understanding the Molecular Biology of Disease Resistance in Rice

“…Nowadays, GWAS has been used in combination with NGS like genotyping by sequencing (GBS) to identify the SNP markers associated with resistance phenotypes in rice. Recently, an association study was performed based on 184 000 SNPs generated by GBS which helped in associating25 genomic regions with blast resistance in the rice genome [ 344 ].…”

Genome-Wide Association Study Identifies a Rice Panicle Blast Resistance Gene, Pb2, Encoding NLR Protein

“…Five rice blast resistance loci including the cloned gene Pita were first identified by GWAS, which verified the feasibility of identifying rice blast resistance loci by GWAS [ 28 ]. To date, in total more than 230 rice blast resistance-related loci distributed in all 12 chromosomes were identified by GWAS [ 29 , 30 , 31 , 32 , 33 , 34 , 35 ]. Among them, 16 resistance loci were identified through naturally occurring resistance phenotypes in the blast nurseries, which can resist the invasion of various strains [ 31 ].…”

Genetic Diversity and Population Structure of Kerala Rice Landraces Using Genotyping-By-Sequencing

“…Genotyping by sequencing (GBS) is a fast, powerful and cost-effective platform of next-generation sequencing (NGS) technology that uses enzyme-based complexity reduction to discover polymorphisms and genotypic information across the population of interest (Poland and Rife 2012). This method has been successfully used for assessing genetic diversity and population structure in several crops like large and complex genome of wheat (Manickavelu et al 2014;Alipour et al 2017;Eltaher et al 2018;Yang et al 2020), rice (Mgonja et al 2017), maize (Leng et al 2019;Yu et al 2021), rye (Schreiber et al 2019), pearl millet (Serba et al 2019), nger millet (Kumar et al 2016) etc., which demonstrated the power of GBS-SNP genotyping as an appropriate technology for high throughput genotyping in cereal crops. GBS is valued as a rapid and cost-effective high throughput genotyping to depict genomic diversity and population structure in non-referenced neglected orphan species (Peterson et al 2014;Hu et al 2015;D'Agostino et al 2018).…”