<scp>mmod</scp>: an R library for the calculation of population differentiation statistics

Winter, David J.

doi:10.1111/j.1755-0998.2012.03174.x

Cited by 295 publications

(213 citation statements)

References 32 publications

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“…Genetic differentiation between seed increase groups was estimated with Jost's D across 29 260 RAD-seq SNPs using the 'D_Jost' function in the R package mmod (Jost, 2008;Winter, 2012).…”

Section: Resultsmentioning

confidence: 99%

Ecological characteristics andin situgenetic associations for yield-component traits of wildMiscanthusfrom eastern Russia

Clark

Dzyubenko

et al. 2016

Ann Bot

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Background and aims Miscanthus is a genus of perennial C 4 grasses native to East Asia. It includes the emerging ligno-cellulosic biomass crop M. Âgiganteus, a hybrid between M. sinensis and M. sacchariflorus. Biomass yield and cold tolerance are of particular interest in Miscanthus, given that this crop is more temperate adapted than its C 4 relatives maize, sorghum and sugarcane.Methods A plant exploration was conducted in eastern Russia, at the northern extreme of the native range for Miscanthus, with collections including 174 clonal germplasm accessions (160 M. sacchariflorus and 14 M. sinensis) from 47 sites. Accessions were genotyped by restriction site-associated DNA sequencing (RAD-seq) and plastid microsatellites.Key Results Miscanthus sinensis was found in maritime climates near Vladivostok (43Á6 N) and on southern Sakhalin Island (46Á6 N). Miscanthus sacchariflorus was found inland at latitudes as high as 49Á3 N, where M. sinensis was absent. Most M. sacchariflorus accessions were diploid, but approx. 2 % were tetraploids. Molecular markers revealed little population structure (Jost's D < 0Á007 among diploid groups) but high genetic diversity (expected heterozygosity ¼ 0Á14) within the collection of Russian M. sacchariflorus. Genome-wide association (GWA) analysis for traits measured at the collection sites revealed three M. sacchariflorus single nucleotide polymorphisms (SNPs) significantly associated with the number of stems per unit area, one with height and one with basal stem diameter; three were near or within previously described sorghum quantitative trait loci for related traits.Conclusions This new Miscanthus germplasm collection from eastern Russia will be useful for breeding Miscanthus and sugarcane cultivars with improved adaptation to cold. Moreover, a strategy is proposed to facilitate the rapid utilization of new germplasm collections: by implementing low-cost SNP genotyping to conduct GWA studies of phenotypic data obtained at collection sites, plant breeders can be provided with actionable information on which accessions have desirable traits and alleles.

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“…Genetic differentiation between seed increase groups was estimated with Jost's D across 29 260 RAD-seq SNPs using the 'D_Jost' function in the R package mmod (Jost, 2008;Winter, 2012).…”

Section: Resultsmentioning

confidence: 99%

Ecological characteristics andin situgenetic associations for yield-component traits of wildMiscanthusfrom eastern Russia

Clark

Dzyubenko

et al. 2016

Ann Bot

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“…The p -value adjustment for multiple samples was carried out by Benjamini–Hochberg (BH) correction with the p.adjust function of R. F -statistics for population analysis ( F IT , F IS ) [86,88,89] were estimated for each sample category or individual DNA marker using R packages hierfstat [90] and pegas [91] in combination with adegenet [92]. Additionally, Hedrick’s G'' ST [88], which is an equivalent of F ST extended to multiallelic DNA markers, was estimated globally or pairwise using the mmod package of R [93] in combination with adegenet [92]. …”

Section: Methodsmentioning

confidence: 99%

Hybrid Origins of Citrus Varieties Inferred from DNA Marker Analysis of Nuclear and Organelle Genomes

et al. 2016

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Most indigenous citrus varieties are assumed to be natural hybrids, but their parentage has so far been determined in only a few cases because of their wide genetic diversity and the low transferability of DNA markers. Here we infer the parentage of indigenous citrus varieties using simple sequence repeat and indel markers developed from various citrus genome sequence resources. Parentage tests with 122 known hybrids using the selected DNA markers certify their transferability among those hybrids. Identity tests confirm that most variant strains are selected mutants, but we find four types of kunenbo (Citrus nobilis) and three types of tachibana (Citrus tachibana) for which we suggest different origins. Structure analysis with DNA markers that are in Hardy–Weinberg equilibrium deduce three basic taxa coinciding with the current understanding of citrus ancestors. Genotyping analysis of 101 indigenous citrus varieties with 123 selected DNA markers infers the parentages of 22 indigenous citrus varieties including Satsuma, Temple, and iyo, and single parents of 45 indigenous citrus varieties, including kunenbo, C. ichangensis, and Ichang lemon by allele-sharing and parentage tests. Genotyping analysis of chloroplast and mitochondrial genomes using 11 DNA markers classifies their cytoplasmic genotypes into 18 categories and deduces the combination of seed and pollen parents. Likelihood ratio analysis verifies the inferred parentages with significant scores. The reconstructed genealogy identifies 12 types of varieties consisting of Kishu, kunenbo, yuzu, koji, sour orange, dancy, kobeni mikan, sweet orange, tachibana, Cleopatra, willowleaf mandarin, and pummelo, which have played pivotal roles in the occurrence of these indigenous varieties. The inferred parentage of the indigenous varieties confirms their hybrid origins, as found by recent studies.

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“…We used the R package mmod (version 1.3.2) [98] to measure several differentiation statistics for the SNPs passing quality filters, including G ST [54], G’ ST [99], Jost’s D [100], and ϕ ST [101]. SNPs that differed significantly (α < 0.05, Bonferroni correction for multiple comparisons) between populations were identified using Fisher’s exact test using base functions in the R statistical framework (version 3.2.4) [102].…”

Section: Methodsmentioning

confidence: 99%

Genomic adaptation to agricultural environments: cabbage white butterflies (Pieris rapae) as a case study

2017

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BackgroundAgricultural environments have long presented an opportunity to study evolution in action, and genomic approaches are opening doors for testing hypotheses about adaptation to crops, pesticides, and fertilizers. Here, we begin to develop the cabbage white butterfly (Pieris rapae) as a system to test questions about adaptation to novel, agricultural environments. We focus on a population in the north central United States as a unique case study: here, canola, a host plant, has been grown during the entire flight period of the butterfly over the last three decades.ResultsFirst, we show that the agricultural population has diverged phenotypically relative to a nonagricultural population: when reared on a host plant distantly related to canola, the agricultural population is smaller and more likely to go into diapause than the nonagricultural population. Second, drawing from deep sequencing runs from six individuals from the agricultural population, we assembled the gut transcriptome of this population. Then, we sequenced RNA transcripts from the midguts of 96 individuals from this canola agricultural population and the nonagricultural population in order to describe patterns of genomic divergence between the two. While population divergence is low, 235 genes show evidence of significant differentiation between populations. These genes are significantly enriched for cofactor and small molecule metabolic processes, and many genes also have transporter or catalytic activity. Analyses of population structure suggest the agricultural population contains a subset of the genetic variation in the nonagricultural population.ConclusionsTaken together, our results suggest that adaptation of cabbage whites to an agricultural environment occurred at least in part through selection on standing genetic variation. Both the phenotypic and genetic data are consistent with the idea that this pest has adapted to an abundant and predictable agricultural resource through a narrowing of niche breadth and loss of genetic variants rather than de novo gain of adaptive alleles. The present research develops genomic resources to pave the way for future studies using cabbage whites as a model contributing to our understanding of adaptation to agricultural environments.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-017-3787-2) contains supplementary material, which is available to authorized users.

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mmod: an R library for the calculation of population differentiation statistics

Cited by 295 publications

References 32 publications

Ecological characteristics andin situgenetic associations for yield-component traits of wildMiscanthusfrom eastern Russia

Ecological characteristics andin situgenetic associations for yield-component traits of wildMiscanthusfrom eastern Russia

Hybrid Origins of Citrus Varieties Inferred from DNA Marker Analysis of Nuclear and Organelle Genomes

Genomic adaptation to agricultural environments: cabbage white butterflies (Pieris rapae) as a case study

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