Computational protocol: Effect of multiple allelic combinations of genes on regulating grain size in rice

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Protocol publication

[…] The eleven markers were scored as present (1) or absent (0) to generate a binary matrix for each individual and used to infer the assessment of genetic distance and similarity coefficients. An unweighted neighbour joining un-rooted tree was constructed using computer software programme Darwin []. The Polymorphism information content (PIC) refers to the relative value of each marker regarding the amount of polymorphism exhibited. The estimation of major allele frequency, allele per locus, gene diversity, heterozygosity, PIC value of the markers was determined using PIC calculator (http://www.liv.ac.uk/~kempsj/pic.html); [] and POWERMARKER Ver3.25 program []. [...] The association between grain size (GL, GW, GLWR and TGW) and 10 selected markers of 7 genes were analyzed using the general linear model (GLM) model in TASSEL5 software []. To study the presence of genetic structure for grain size, population structure analysis was performed using the program STRUCTURE version 2.3.4 []. The model was run based on an admixture model with correlated allele frequencies and the number of sub groups (K) in the clusters was determined by simulating different K-values (K = 1 to 10) with 5 independent runs and run length of 100,000 burn-in period and 100,000 MCMC. The optimal K-value was determined through the ΔK method [] using Structure Harvester ver. 0.6.193 application []. The Principal Coordinate Analysis (PCoA) was calculated from the generated binary data of markers with the GenAlEx 6.502 []. The genotypic data of genes corresponding to the grain size were converted into binary matrix which was used to determine the analysis of molecular variance (AMOVA) for separation of the total molecular variance between and within groups and significant FST using GenAlEx 6.502 []. All other statistical analysis was conducted using statistical package XLSTAT (https://www.xlstat.com). […]

Pipeline specifications

Software tools DARwin, PowerMarker, TASSEL, Structure Harvester, GenAlEx
Applications Phylogenetics, Population genetic analysis
Organisms Oryza sativa