Multiple Genome Wide Association Mapping Models Identify Quantitative Trait Nucleotides for Brown Planthopper (Nilaparvata lugens) Resistance in MAGIC Indica Population of Rice

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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Not AvailableThe brown planthopper Nilaparvatalugens (Stål) is a major insect pest that is primarily present in Asia causing a significant impact on rice crop. Seventy-three rice genotypes were evaluated for molecular diversity based on known BPH resistance loci. A total number of 108 alleles were detected by 39 polymorphic markers with an average of 2.37 alleles per locus. The allele frequency which is useful in estimating the frequency of alleles, ranged from 0.054 to 0.9726, while the expected heterozygosity varied between 0.054 (RM494) and 0.688 (RM231) with an average of 0.431.The Polymorphic Information Content (PIC) values provided an estimation of the marker’s discriminating power by ranged from 0.066 (RM496) to 0.621 (RM231) suggesting moderate level of polymorphism for the selected BPH specific SSR markers among the germplasm lines. Accounting the major allele frequency, heterozygosity and PIC content, the marker RM231 associated with QBph3.1 and regarded as the most informative one along with RM19291, RM335, RM469, RM518, RM8213, RM228, RH078 and RM589 for dissecting the molecular diversity of germplasm lines with respect to BPH resistance. Based on the marker data, the genotypes were classified into seven clusters that distinguished the lines clustering as resistant and susceptible separately. The information about the genetic diversity of these lines will be extremely useful for proper selection of parents related to BPH reaction, especially for gene mapping and for marker assisted selection.Not Availabl

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Not AvailableSoil phosphorus (P) deficiency is one of the major challenges for the cultivation of rice worldwide because it limits the growth and productivity of the crop. Therefore, the ability to grow in P-deficit soils is an important trait for rice cultivation. O . rufipogon Griff., a wild relative of rice, is a source of genetic variation for low phosphorus tolerance. The present study was undertaken to identify low P stress-tolerant introgression lines by analysing stress tolerance indices of 40 introgression lines of O. rufipogon. The populations were screened under low soil P and normal soil P plots for two growing seasons. Based on yield under stress and normal conditions, we computed different stress indices, including stress tolerance index (STI), tolerance index, yield reduction ratio (YR), stress susceptibility index, yield stability index (YSI), yield index, per cent yield reduction and geometric mean productivity (GMP). The studies of correlation analysis, principal component analysis and clustering revealed that STI, YSI and GMP were ideal indices for the selection of genotypes that performed well under both stress and normal conditions. Based on these indices, introgression lines (IL-24, IL-29 and IL-32) were identified as promising low P tolerant lines, which exhibited better grain yield under both stress (YS) and normal (YP) conditions. These pre-breeding lines serve as valuable genetic resources for low P tolerance in rice breeding programmes across the world.Not Availabl