Computational protocol: Analysis on genetic diversification and heterosis in autotetraploid rice

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Protocol publication

[…] Agronomic traits data was analyzed using SPSS and the statistical significances were determined using Paired-T test by SPSS version 17.0. Levels of heterosis were measured as heterobeltiosis, which is the superiority of a hybrid over the better parent, and competitive heterosis, which is calculated by comparing autotetraploid rice hybrids with their corresponding diploid hybrids. Correlation analysis between the genetic distance and heterobeltiosis was performed with SPSS version 17.0.Number of effective alleles per locus (Ae), expected heterozygosity (He) and Shannon’s information index (I) were calculated to measure the genetic variation in diploid and autotetraploid rice. Analyses of these computations were assessed using the program POPGENE version 1.32 (Yeh et al. ). Polymorphism information content (PIC) was calculated according to the formula: PICi = 1-∑P2ij (j = 1) (Anderson et al. ) and genetic distance was estimated according to the method of Nei (). Neighbor-joining (NJ) tree was constructed by Software NTSYS version 2.10e (Exeter Software, Setauket, NY USA) on the basis of similarity measures (Rohlf ), and MEGA V4.0 was used to observe the NJ tree (Tamura et al. ). […]

Pipeline specifications

Software tools POPGENE, MEGA-V
Applications Population genetic analysis, GWAS
Organisms Oryza sativa