Brown planthopper (BPH), one of the most important pests of the rice (Oryza sativa) crop, becomes catastrophic under severe infestations and causes up to 60% yield loss. The highly disastrous BPH biotype in the Indian sub-continent is Biotype 4, which also known as the South Asian Biotype. Though many resistance genes were mapped until now, the utility of the resistance genes in the breeding programs is limited due to the breakdown of resistance and emergence of new biotypes. Hence, to identify the resistance genes for this economically important pest, we have used a multi-parent advanced generation intercross (MAGIC) panel consisting of 391 lines developed from eight indica founder parents. The panel was phenotyped at the controlled conditions for two consecutive years. A set of 27,041 cured polymorphic single nucleotide polymorphism (SNPs) and across-year phenotypic data were used for the identification of marker–trait associations. Genome-wide association analysis was performed to find out consistent associations by employing four single and two multi-locus models. Sixty-one SNPs were consistently detected by all six models. A set of 190 significant marker-associations identified by fixed and random model circulating probability unification (FarmCPU) were considered for searching resistance candidate genes. The highest number of annotated genes were found in chromosome 6 followed by 5 and 1. Ninety-two annotated genes identified across chromosomes of which 13 genes are associated BPH resistance including NB-ARC (nucleotide binding in APAF-1, R gene products, and CED-4) domain-containing protein, NHL repeat-containing protein, LRR containing protein, and WRKY70. The significant SNPs and resistant lines identified from our study could be used for an accelerated breeding program to develop new BPH resistant cultivars.

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Rice blast is one of the most widespread diseases threatening rice production and crop damage account for a major loss to rice farmers worldwide. To identify genetic regions associated with leaf blast resistance, a genome-wide association study was performed with 391 MAGIC indica rice accessions developed at IRRI, Philippines. Evaluation of leaf blast severity was performed in the uniform blast nursery (UBN) during 2016 and 2017 at ICAR-IIRR, Hyderabad, India. Genome Wide Association Study was performed using six different statistical models with GBS data on 27041 single nucleotide polymorphisms (SNPs) distributed on all 12 rice chromosomes. Seven common associated SNPs on chromosome 3, 8 and 12 were identified with all the models. Farm CPU and Blink gave similar results and detected 31 associated SNPs on chromosome 3, 8 and 12. Highest number of annotated genes were identified on chromosome 12 followed by 8 and 3. Chromosome 12 harboring a major cluster of blast resistant genes and at least 20 blast resistant genes were mapped on this chromosome. Candidate genes identified in associated SNP regions on chromosome 12 in our study are encoding disease resistance genes; stripe rust resistance protein, MLA12, NBS-LRR disease resistance protein, NB-ARC domain containing protein, CC-NBS-LRR resistance protein MLA13, indicating the possibility of developing casual SNPs/QTNs for leaf blast resistance in rice from these regions.

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