Genome-Wide Association Mapping of Rice Resistance Genes Against Magnaporthe oryzae Isolates from Four African Countries

Abstract

Rice blast disease is emerging as a major constraint to rice production in Africa. Although a traditional gene-tagging strategy using biparental crosses can effectively identify resistance (R) genes or quantitative trait loci (QTL) against Magnaporthe oryzae, the mapping procedure required is time consuming and requires many populations to investigate the genetics of resistance. In this report, we conducted a genome-wide association study (GWAS) to rapidly map rice genes conferring resistance against eight M. oryzae isolates from four African countries. We inoculated 162 rice cultivars, which were part of the rice diversity panel 1 (RDP1) and were previously genotyped with the 44,000 single-nucleotide polymorphism (SNP) chip, with the eight isolates. The GWAS identified 31 genomic regions associated with blast resistance (RABR) in the rice genome. In addition, we used polymerase chain reaction analysis to confirm the association between the Pish gene and a major RABR on chromosome 1 that was associated with resistance to four M. oryzae isolates. Our study has demonstrated the power of GWAS for the rapid identification of rice blast R or QTL genes that are effective against African populations of M. oryzae. The identified SNP markers associated with RABR can be used in breeding for resistance against rice blast in Africa.

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

“…RABR_3, RABR_20, RABR_22, and RABR_23 are located in the regions with the previously mapped R genes Pi-sh, Pi-y(t), Pi-6, and Pi-ta, respectively. Two of these four RABRs (RABR_3 and RABR_20) were also identified in our previous study using 162 RDP1 cultivars (Mgonja et al 2016). Three of the 25 RABRs (RABR_20, RABR_22, and RABR_23) were identified previously (Kang et al 2016).…”

“…Five days after germination, the plantlets were transplanted into sterilized soil in small pots in a growth chamber. The fungal spores were prepared and the plants were spray inoculated as previously described (Mgonja et al 2016;Park et al 2012). The six M. oryzae isolates used in this study were collected from four African countries: TZ-01 and TZ-12 were from Tanzania, UG-05 and UG-11 were from Uganda, KE-37 was from Kenya, and BF-07 was from Burkina Faso (Mgonja et al 2016).…”

“…Evaluation of rice blast resistance. The blast resistance of the 190 cultivars was evaluated as previously described (Mgonja et al 2016). In brief, disease was scored 6 days after inoculation using a 0 to 9 blast scale (Kang et al 2016), in which 0 indicates no blast symptoms (highly resistant) and 9 indicates severe blast symptoms (highly susceptible) (Zhu et al 2012).…”

“…Thus, the breeding of rice blast resistance in elite cultivars requires the use of rice germplasm that contains both major and minor genes. In our previous study (Mgonja et al 2016), we used 162 cultivars of the rice diversity panel 1 (RDP1); these cultivars were from many countries and were genotyped with 44K SNPs. We inoculated the 162 cultivars with eight M. oryzae isolates from four East Africa countries.…”

Genome‐wide association study identifies an NLR gene that confers partial resistance to Magnaporthe oryzae in rice

“…Blast resistance of the 584 accessions was evaluated as previously described (Mgonja et al , ). In brief, disease was scored 6 days after inoculation using a 0–9 blast scale, in which ‘0’ indicated no blast symptoms (highly resistant) and ‘9’ indicated severe blast symptoms (highly susceptible; Zhu et al , ).…”