A New Genotype Imputation Method with Tolerance to High Missing Rate and Rare Variants

Yang, Yumei; Wang, Qishan; Chen, Qiang; Liao, Rongrong; Zhang, Xiangzhe; Yang, Hongjie; Zheng, Yun; Zhang, Zhiwu; Pan, Yuchun

doi:10.1371/journal.pone.0101025

Cited by 27 publications

(28 citation statements)

References 36 publications

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“…Because of phase ambiguity for haplotypes and the diversity of breeds, the missing genotype rate of pig SNP data must be controlled to guarantee high accuracy of imputation (Yang et al . ). However, the critical value of the missing genotype rate that could be tolerated during ROH detection needs to be explored first to help determine the threshold for SNP filtration.…”

Section: Discussionmentioning

confidence: 97%

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Distribution of runs of homozygosity in Chinese and Western pig breeds evaluated by reduced‐representation sequencing data

Zhang

Xiao

et al. 2018

Animal Genetics

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Inbreeding, which has several causes including genetic drift, population bottlenecks, mating of close relatives and selection, can leave tracts of runs of homozygosity (ROH) along genomes. Recently, decreasing performance on reproductive traits, which might have resulted from inbreeding, has been observed in Chinese pigs. In this study, 830 individuals from Western and Chinese pig breeds were genotyped using the reducedrepresentation sequencing method. After imputation and quality control, 60 850 highconfidence SNPs were retained for ROH detection. A simulation was performed to explore the reliability of ROH detection with imputed data. Different ROH-related variables were compared between imputed and non-missing genotypes used in ROH detection. Furthermore, ROH islands were evaluated and annotated to find genes influenced by inbreeding in these pigs. The simulation results showed that imputed data with 0.7 as the average missing genotype rate and three heterozygotes allowed in a sliding window have comparable ROH detected compared with data with no missing genotypes. Compared with Western pig breeds, Chinese pigs had more autosomes covered by ROH longer than 5 Mb, indicating higher inbreeding in Chinese pigs in recent times. Genes related to reproduction, immunity, meat quality and adaptability in Chinese pigs and several genes related to growth speed and immunity in Western pigs were observed in short ROH islands. The reproduction-related gene PRM1 was found to be located in the most frequent long ROH island in Chinese pigs, which might explain the decreasing fertility in Chinese pig breeds.

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Section: Discussionmentioning

confidence: 97%

“…This was caused by low performance of the imputation method at high minor allele frequencies and is consistent with a previous study (Yang et al . ). However, the parameter ‐‐het in plink controlled mainly false‐negative detection of ROH.…”

Section: Discussionmentioning

confidence: 97%

Distribution of runs of homozygosity in Chinese and Western pig breeds evaluated by reduced‐representation sequencing data

Zhang

Xiao

et al. 2018

Animal Genetics

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“…Missing data can be addressed with imputation [108], a statistical method that replaces missing data by estimated values [97]. Yang et al [109], using simulated data, reported that the accuracy of Beagle imputation software is 0.99 for a missing rate of 10 or 30%. Therefore, to explore further the utility of missing imputed genotypes on phylogenetic analysis, we employed missing rates of 10 or 30%.…”

Section: Discussionmentioning

confidence: 99%

Genotyping-by-sequencing provides the discriminating power to investigate the subspecies of Daucus carota (Apiaceae)

et al. 2016

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BackgroundThe majority of the subspecies of Daucus carota have not yet been discriminated clearly by various molecular or morphological methods and hence their phylogeny and classification remains unresolved. Recent studies using 94 nuclear orthologs and morphological characters, and studies employing other molecular approaches were unable to distinguish clearly many of the subspecies. Fertile intercrosses among traditionally recognized subspecies are well documented. We here explore the utility of single nucleotide polymorphisms (SNPs) generated by genotyping-by-sequencing (GBS) to serve as an effective molecular method to discriminate the subspecies of the D. carota complex.ResultsWe used GBS to obtain SNPs covering all nine Daucus carota chromosomes from 162 accessions of Daucus and two related genera. To study Daucus phylogeny, we scored a total of 10,814 or 38,920 SNPs with a maximum of 10 or 30% missing data, respectively. To investigate the subspecies of D. carota, we employed two data sets including 150 accessions: (i) rate of missing data 10% with a total of 18,565 SNPs, and (ii) rate of missing data 30%, totaling 43,713 SNPs. Consistent with prior results, the topology of both data sets separated species with 2n = 18 chromosome from all other species. Our results place all cultivated carrots (D. carota subsp. sativus) in a single clade. The wild members of D. carota from central Asia were on a clade with eastern members of subsp. sativus. The other subspecies of D. carota were in four clades associated with geographic groups: (1) the Balkan Peninsula and the Middle East, (2) North America and Europe, (3) North Africa exclusive of Morocco, and (4) the Iberian Peninsula and Morocco. Daucus carota subsp. maximus was discriminated, but neither it, nor subsp. gummifer (defined in a broad sense) are monophyletic.ConclusionsOur study suggests that (1) the morphotypes identified as D. carota subspecies gummifer (as currently broadly circumscribed), all confined to areas near the Atlantic Ocean and the western Mediterranean Sea, have separate origins from sympatric members of other subspecies of D. carota, (2) D. carota subsp. maximus, on two clades with some accessions of subsp. carota, can be distinguished from each other but only with poor morphological support, (3) D. carota subsp. capillifolius, well distinguished morphologically, is an apospecies relative to North African populations of D. carota subsp. carota, (4) the eastern cultivated carrots have origins closer to wild carrots from central Asia than to western cultivated carrots, and (5) large SNP data sets are suitable for species-level phylogenetic studies in Daucus.Electronic supplementary materialThe online version of this article (doi:10.1186/s12862-016-0806-x) contains supplementary material, which is available to authorized users.

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“…The imputation analysis for the missing genotypes described below was performed with iblup (http://klab.sjtu.edu.cn/iBLUP/), which accounts for both the identity‐by‐descent and linkage disequilibrium information and can impute missing genotypes with greater accuracy than can other imputation methods, such as beagle (Yang et al . 2014). A total of 105 550 high‐confidence SNPs with minor allele frequencies (MAFs) ≥ 0.05 were obtained.…”

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confidence: 99%

Genetic diversity and population structure of six Chinese indigenous pig breeds in the Taihu Lake region revealed by sequencing data

et al. 2015

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SummaryThe Chinese indigenous pig breeds in the Taihu Lake region are the most prolific pig breeds in the world. In this study, we investigated the genetic diversity and population structure of six breeds, including Meishan, Erhualian, Mi, Fengjing, Shawutou and Jiaxing Black, in this region using whole‐genome SNP data. A high SNP with proportions of polymorphic markers ranging from 0.925 to 0.995 was exhibited by the Chinese indigenous pigs in the Taihu Lake region. The allelic richness and expected heterozygosity also were calculated and indicated that the genetic diversity of the Meishan breed was the greatest, whereas that of the Fengjing breed was the lowest. The genetic differentiation, as indicated by the fixation index, exhibited an overall mean of 0.149. Both neighbor‐joining tree and principal components analysis were able to distinguish the breeds from each other, but structure analysis indicated that the Mi and Erhualian breeds exhibited similar major signals of admixture. With this genome‐wide comprehensive survey of the genetic diversity and population structure of the indigenous Chinese pigs in the Taihu Lake region, we confirmed the rationality of the current breed classification of the pigs in this region.

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A New Genotype Imputation Method with Tolerance to High Missing Rate and Rare Variants

Cited by 27 publications

References 36 publications

Distribution of runs of homozygosity in Chinese and Western pig breeds evaluated by reduced‐representation sequencing data

Distribution of runs of homozygosity in Chinese and Western pig breeds evaluated by reduced‐representation sequencing data

Genotyping-by-sequencing provides the discriminating power to investigate the subspecies of Daucus carota (Apiaceae)

Genetic diversity and population structure of six Chinese indigenous pig breeds in the Taihu Lake region revealed by sequencing data

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