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Meloidogyne graminicola is one of the most important plant-parasitic nematodes in rice. Breeding for natural resistance and tolerance is considered one of the most economical and sustainable approaches to control this damaging pathogen. Quantitative trait loci (QTL) mapping was carried out in a recombinant inbred line (RIL) population derived from a cross between the Asian rice genotypes IR78877-208-B-1-2 and Dinorado. IR78877-208-B-1-2 is an aerobic rice genotype that is resistant and tolerant to M. graminicola. Dinorado is a traditional upland rice genotype from the Philippines that is characterized by its aroma and prized for its cooking quality. The host response of 300 F4 lines derived from this cross was evaluated in both nematode infested and non-infested concrete beds in the dry seasons of 2013 and 2014. Five genotypes were found consistently resistant while 13 genotypes were consistently partially resistant to M. graminicola. QTL mapping for M. graminicola resistance/tolerance, yield-contributing traits, and yield revealed four main effect QTLs (qJ2RS2.1, qJ2GRT2.1, qJ2RS3.1, and qJ2GRT3.1) associated with reduced nematode reproduction on chromosomes 2 and 3 and two QTLs (qGR3.1 and qGR5.1) associated with reduced root galling on chromosomes 3 and 5. Twenty main effect QTLs associated with yield-contributing traits and yield were also found. Our study further identified co-locating QTLs associated with nematode resistance, yield-contributing traits, and yield on chromosomes 3 and 5. QTLs harboring candidate genes, such as OsBAK1, OsDST, OsIPT4, and DUF26, for higher grain yield and tolerance to abiotic and biotic stress, were identified. These QTLs and the RILs that are consistently resistant and tolerant to M. graminicola, and which are high-yielding in nematode-infested fields, can be utilized in breeding programs to improve the resistance and tolerance of Asian rice to this important pathogen. [ABSTRACT FROM AUTHOR]

Background: The root-knot nematode Meloidogyne graminicola is an obligate biotrophic pathogen considered to be the most damaging nematode species that causes significant yield losses to upland and rainfed lowland rice production in South and Southeast Asia. Mapping and identification of quantitative trait loci (QTL) for resistance to and tolerance for M. graminicola may offer a safe and economic management option to farmers. In this study, resistance to and tolerance for M. graminicola in Asian rice ( Oryza sativa L.) were studied in a mapping population consisting of 300 recombinant inbred lines (RILs) derived from IR78877–208-B-1-2, an aerobic rice genotype with improved resistance to and tolerance for M. graminicola , and IR64, a popular, high-yielding rice mega-variety susceptible to M. graminicola. RILs were phenotyped for resistance and tolerance in the dry seasons of 2012 and 2013. QTL analysis was performed using 131 single nucleotide polymorphism (SNP) and 33 simple sequence repeat (SSR) markers. Results: Three QTLs with main effects on chromosomes 4 ( qMGR 4.1 ), 7 ( qMGR 7.1 ) and 9 ( qMGR 9.1 ) and two epistatic interactions ( qMGR 3.1 / qMGR 11.1 and qMGR 4.2 / qMGR 8. 1) associated with nematode reproduction that were consistent in the two seasons were detected. A QTL affecting root galling was found on chromosomes 4 ( qGR 4.1 ) and 8 ( qGR 8.1 ), and QTLs for nematode tolerance were found on chromosomes 5 ( qYR 5.1 ) and 11 ( qYR 11.1 ). These QTLs were consistent in both seasons. A QTL for grain yield was found on chromosome 10 ( qGYLD 10.1 ), a QTL affecting filled grains per panicle was detected on chromosome 11 ( qFG 11.1 ) and a QTL for fresh root weight was found on chromosomes 2 ( qFRWt 2.1 ), 8 ( qFRWt 8.1 ) and 12 ( qFRWt 12.1 ) in both seasons. The donor of the alleles for qMGR 4.1 , qMGR 7.1 , qMGR 9.1 , qGR 4.1 , qGR 8.1 , qYR 5.1 and qFRWt 2.1 was IR78877–208-B-1-2, whereas for qYR 11.1 , qGYLD 10.1 and qFG 11.1 , qFRWt 8.1 and qFRWt 12.1 was IR64. Lines having favorable alleles for resistance, tolerance and yield provided better yield under nematode-infested conditions and could be a starting point of marker-assisted breeding (MAB) for the improvement of M. graminicola resistance and tolerance in Asian rice. Conclusion: This study identified a total of 12 QTLs with main effects and two epistatic interactions in the 1st season and 2nd season related to M. graminicola resistance and tolerance, and other agronomic traits such as plant yield, percentage of filled grains, and fresh and dry root weight. Rice genotypes that have the favorable alleles for resistance ( qMGR 4.1 , qMGR 7.1 , qMGR 9.1 , qGR 4.1 , qGR 8.1 ) and tolerance ( qYR 5.1 , and qYR 11.1 ,) QTLs, and which are either resistant or partially resistant and tolerant, were also selected. These selected genotypes and the identified QTLs are vital information in designing MAB for the improvement of high-yielding rice genotypes but are susceptible to M. graminicola infection. [ABSTRACT FROM AUTHOR]