Multiple Genome Wide Association Mapping Models Identify Quantitative Trait Nucleotides for Brown Planthopper (<i>Nilaparvata lugens</i>) Resistance in MAGIC <i>Indica</i> Population of Rice
Vanisri Satturu,
Jhansi Lakshmi Vattikuti,
Durga Sai J,
Arvind Kumar,
Rakesh Kumar Singh,
Srinivas Prasad M,
Hein Zaw,
Mona Liza Jubay,
Lakkakula Satish,
Abhishek Rathore,
Sreedhar Mulinti,
Ishwarya Lakshmi VG,
Abdul Fiyaz R.,
Animikha Chakraborty,
Nepolean Thirunavukkarasu
Affiliations
Vanisri Satturu
Institute of Biotechnology, Professor Jayashankar Telangana State Agricultural University, Rajendranagar, Hyderabad 500030, India
Jhansi Lakshmi Vattikuti
Entomology, Pathology and Plant breeding Division, Indian Institute of Rice Research (ICAR-IIRR), Rajendranagar, Hyderabad 500030, India
Durga Sai J
Institute of Biotechnology, Professor Jayashankar Telangana State Agricultural University, Rajendranagar, Hyderabad 500030, India
Arvind Kumar
Plant Breeding Division, International Rice Research Institute (IRRI)-South Asia Hub (SAH), Patancheru, Hyderabad 502324, India
Rakesh Kumar Singh
Plant Breeding Division, International Rice Research Institute (IRRI), Metro Manila 1226, Philippines
Srinivas Prasad M
Entomology, Pathology and Plant breeding Division, Indian Institute of Rice Research (ICAR-IIRR), Rajendranagar, Hyderabad 500030, India
Hein Zaw
Plant Breeding Division, International Rice Research Institute (IRRI), Metro Manila 1226, Philippines
Mona Liza Jubay
Plant Breeding Division, International Rice Research Institute (IRRI), Metro Manila 1226, Philippines
Lakkakula Satish
Department of Biotechnology Engineering, Ben-Gurion University of the Negev, Beer Sheva 84105, Israel
Abhishek Rathore
Agriculture Statistics Division, International Crops Research for the Semi-Arid Tropics (ICRISAT), Patancheru, Hyderabad 502324, India
Sreedhar Mulinti
MFPI-Quality Control Lab, Professor Jayashankar Telangana State Agricultural University, Rajendranagar, Hyderabad 500030, India
Ishwarya Lakshmi VG
Institute of Biotechnology, Professor Jayashankar Telangana State Agricultural University, Rajendranagar, Hyderabad 500030, India
Abdul Fiyaz R.
Entomology, Pathology and Plant breeding Division, Indian Institute of Rice Research (ICAR-IIRR), Rajendranagar, Hyderabad 500030, India
Animikha Chakraborty
Plant Breeding Division, Indian Institute of Millets Research (ICAR-IIMR), Rajendranagar, Hyderabad 500030, India
Nepolean Thirunavukkarasu
Plant Breeding Division, Indian Institute of Millets Research (ICAR-IIMR), Rajendranagar, Hyderabad 500030, India
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.
