QTL-seq reveals a major root-knot nematode resistance locus on chromosome 11 in rice (Oryza sativa L.)

Zobaida Lahari, Antonio Ribeiro, Partha Talukdar, Brennan Martin, Zeynab Heidari, Godelieve Gheysen, Adam H. Price* (Corresponding Author), Roshi Shrestha

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

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The root-knot nematode Meloidogyne graminicola is a serious pest in rice affecting production in many rice growing areas. Natural host resistance is an attractive control strategy because the speed of the parasite’s life cycle and the broad host range it attacks make other control measures challenging. Although resistance has been found in the domesticated African rice Oryza glaberrima and the wild rice species O. longistaminata, the introgression of resistance genes to Asian rice O. sativa is challenging. Resistance due to a major gene in O. sativa would greatly aid breeding. Recently two accessions resistant to M. graminicola have been identified in a screen of 332 diverse O. sativa cultivars. In this study, these two resistant cultivars, LD 24 (an indica from Sri Lanka) and Khao Pahk Maw (an aus from Thailand), were crossed with a moderately susceptible cultivar, Vialone Nano (a temperate japonica from Italy). Approximately 175 F2 progeny of both populations were screened for susceptibility to M. graminicola infection. Between 20-23 individuals with highest and lowest galls per plants were pooled to make susceptible and resistant bulks which were sequenced to conduct bulked segregant analysis using the QTL-seq method. This revealed a nematode resistance locus from 23 Mbp to the bottom of rice chromosome 11 in both crosses suggesting a rare introgression of the same locus is responsible for resistance in both cultivars. While this information can be used in marker-assisted breeding, analysis of available SNP data revealed candidate loci and genes worthy of further investigation for gene identification.
Original languageEnglish
Article number117
Early online date14 Jun 2019
Publication statusPublished - 1 Jul 2019

Bibliographical note

Open Access via Springer Compact Agreement.

This project was funded by FAACE-JPI NET project “GreenRice” (Sustainable and environmental friendly rice cultivation systems in Europe); BBSRC award BB/M018415/1. The authors would like to acknowledge the support of the Maxwell computer cluster funded by the University of Aberdeen for sequencing work and the financial support of GOA 01GB3013 from Ghent University.


  • M. graminicola
  • O. sativa
  • QTL-seq
  • bulk segregant analysis
  • nematode resistance genes
  • Nematode resistance genes
  • Bulk segregant analysis


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