African Journal of
Biotechnology

  • Abbreviation: Afr. J. Biotechnol.
  • Language: English
  • ISSN: 1684-5315
  • DOI: 10.5897/AJB
  • Start Year: 2002
  • Published Articles: 12487

Full Length Research Paper

Genome-wide association analysis identifies resistance loci for bacterial blight in diverse East African rice germplasm

Moses Okello
  • Moses Okello
  • Faculty of Agriculture and Environmental Sciences, Muni University P. O. Box 725 Arua, Uganda.
  • Google Scholar
Ochwo S. Mildred
  • Ochwo S. Mildred
  • Makerere University P. O. Box 7062, Kampala, Uganda.
  • Google Scholar
Jimmy Lamo
  • Jimmy Lamo
  • National Agricultural Research Organization P. O. Box 295 Berkeley Rd. Entebbe, Uganda.
  • Google Scholar
Geoffrey Onaga
  • Geoffrey Onaga
  • Makerere University P. O. Box 7062, Kampala, Uganda.
  • Google Scholar
Thomas L. Odong
  • Thomas L. Odong
  • Makerere University P. O. Box 7062, Kampala, Uganda.
  • Google Scholar
Geoffrey Tusiime
  • Geoffrey Tusiime
  • Makerere University P. O. Box 7062, Kampala, Uganda.
  • Google Scholar
Phinehas Tukamuhabwa
  • Phinehas Tukamuhabwa
  • Makerere University P. O. Box 7062, Kampala, Uganda.
  • Google Scholar
Settumba B. Mukasa
  • Settumba B. Mukasa
  • Makerere University P. O. Box 7062, Kampala, Uganda.
  • Google Scholar
Peter Wasswa
  • Peter Wasswa
  • Makerere University P. O. Box 7062, Kampala, Uganda.
  • Google Scholar
Jonathan Ogwal
  • Jonathan Ogwal
  • University of Bath, Faculty of Computer Science, Claverton Down, Bath BA2 7PB, UK.
  • Google Scholar
Ricardo Oliva
  • Ricardo Oliva
  • World Vegetable Centre P. O. Box 42, Shanhua, Tainan 74151, Taiwan.
  • Google Scholar


  •  Received: 14 April 2023
  •  Accepted: 31 July 2023
  •  Published: 31 August 2023

Abstract

Xanthomonas oryzae pv. oryzae (Xoo), the causal agent of rice bacterial blight disease has been extensively characterized, and loci against different races identified. Many rice cultivars have been developed and utilized to combat the disease, however, due to the rapid evolution of Xoo, several resistances have broken down. The continuous challenge of ever-evolving Xoo and the breakdown of resistance in cultivated rice varieties make it even more important to discover new loci to enable sustainable durable deployment of broad-spectrum resistance genes in elite breeding lines. African germplasm can be exploited as reservoirs of useful genetic variation for bacterial blight (BB) resistance. This study was conducted to identify loci associated with BB resistance and new genetic donors for the breeding program. To identify candidate sources of resistance for advancing breeding, four virulent strains of Xoo (PXO99, MAI1, BAI3, and Xoo3-1) were used to screen 78 East African accessions by genome-wide association studies. The diverse accessions' core genetic base exhibited high resistance to the Xoo strains. 50.63% of the accessions were highly resistant to the Philippines strain PX099, while 20.25% were highly susceptible to the virulent West African strain MAI1. Two novel resistant loci significantly associated hotspots were identified using 1901 SNPs. The two hits were located on chromosome 12 (Xa25) and Chr. 6 (Xa7, Xa27, Xa33). Novel loci were identified that gives a useful basis for more investigation and a wide core genetic pool of high resistance for broad-spectrum resistance for genetic improvement.

 

Key words: Genome-wide association, Oryza sativa, bacterial blight (BB), Xanthomonas oryzae, disease resistance.