Expected Genotype Quality and Diploidized Marker Data from Genotyping‐by‐Sequencing of <i>Urochloa</i> spp. Tetraploids

Matias, Filipe Inácio; Meireles, Karem Guimarães Xavier; Nagamatsu, Sheila Tiemi; Barrios, S. C. L.; Valle, Cacilda Borges do; Carazzolle, Marcelo Falsarella; Fritsche‐Neto, Roberto; Endelman, Jeffrey B.

doi:10.3835/plantgenome2019.01.0002

Cited by 19 publications

(23 citation statements)

References 66 publications

(72 reference statements)

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“…S2). Setaria italica allowed more alignments for Urochloa spp., which were relatively well distributed across the genome, following what was observed by Matias et al (2019).…”

Section: Gwas Analyses For the Different Seasonssupporting

confidence: 61%

“…(Si) (Bennetzen et al, 2012), Sorghum bicolor (L.) Moench. (Sb) (DOE-JGI, 2018b), Oryza sativa L. (Os) (Ouyang et al, 2006), Zea mays L. (Zm) (Schnable et al, 2009), and the Urochloa mock reference (Um) (Matias et al, 2019). Default alignment parameters were used in the software Burrows-Wheeler Alignment tool (Li and Durbin, 2009), SAMtools Li, 2011) and Picard (http:// broadinstitute.github.io/picard/).…”

Section: Genotypingmentioning

confidence: 99%

“…The average depth was 18 reads per marker by sample. Remaining missing data were imputed using the Random Forest package (Liaw and Wiener, 2002), where all markers with r 2 ³0.1 were used as predictors, and 300 trees were considered, following the recommendation of Matias et al (2019). Consequently, we selected 26,535 SNPs with diploid and tetraploid dosage configurations.…”

Section: Genotypingmentioning

confidence: 99%

“…For significant SNPs found on the Urochloa mock reference (Matias et al, 2019), a sequence of 50 nucleotide positions from both sides of significant SNPs was selected from the respective reference and compared with the information available in genomic data banks using the Basic Local Alignment Search Tool (BLAST) (Altschul et al, 1990). For the significant SNPs found on the other references (annotated genomes), a window of 1 kb was evaluated to determined candidate genes.…”

Section: Gene Annotationmentioning

confidence: 99%

“…S1). These markers came from centroids in the Um genome reference (Matias et al, 2019) originated from the GBS-SNP-CROP approach (Melo et al, 2016). Although there were no candidate genes on these regions, the last part of both sequences showed the same final nucleotide sequence.…”

Section: Gwas Analyses For the Different Seasonsmentioning

confidence: 99%

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Association Mapping Considering Allele Dosage: An Example of Forage Traits in an Interspecific Segmental Allotetraploid Urochloa spp. Panel

et al. 2019

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The breeding process in tropical segmental allopolyploid forage Urochloa is challenging due to the complex genetic control of the traits. Knowledge about genes associated with forage traits, expressed in the different cutting seasons, are extremely useful to support breeding programs and development of new cultivars. Thus, the aims of our study were (i) to identify genomic regions related to forage traits through genome‐wide association studies (GWAS), and (ii) to verify the influence of allele dosage on these results. A panel of 272 genotypes of Urochloa spp. [U. brizantha (Hoscht. ex A. Rich.) R. Webster × U. ruziziensis (Hoscht. ex A. Rich.) R. Webster] was evaluated in both the wet and dry seasons. The GWAS analyses were performed with 26,535 single nucleotide polymorphisms (SNPs) obtained by genotyping‐by‐sequencing (GBS) using diploid and tetraploid allele dosage configurations. Furthermore, we evaluated scenarios including additive, dominance, and epistatic effects. Seven candidate genomic regions associated with the main forage traits of Urochloa spp. were identified. The importance of the diploid and tetraploid molecular configuration in GWAS analyses for segmental allopolyploid species was demonstrated to identify the genomic behavior of important regions. Results demonstrated that it is possible to identify the same regions using both ploidy configurations; however, in some cases, the allele substitution effect can be biased mainly for regions with dominance and epistatic effects. Finally, this study contributes to the understanding of genetic control of tropical forage traits and genomics to accelerate the selection and reduce the cost to release new cultivars.

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“…S2). Setaria italica allowed more alignments for Urochloa spp., which were relatively well distributed across the genome, following what was observed by Matias et al (2019).…”

Section: Gwas Analyses For the Different Seasonssupporting

confidence: 61%

Section: Genotypingmentioning

confidence: 99%

Section: Genotypingmentioning

confidence: 99%

Section: Gene Annotationmentioning

confidence: 99%

Section: Gwas Analyses For the Different Seasonsmentioning

confidence: 99%

See 3 more Smart Citations

Association Mapping Considering Allele Dosage: An Example of Forage Traits in an Interspecific Segmental Allotetraploid Urochloa spp. Panel

et al. 2019

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Urochloa spp. multivariate performance: Similarities and divergences among intra‐ and interspecific populations

et al. 2020

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Multivariate analysis is a tool that breeders can use to compare populations and select genotypes for specific purposes. This study used principal component analysis to compare three intraspecific and three interspecific populations of Urochloa spp. based on insect resistance, agronomic, and seed production characteristics. This multivariate strategy exposed completely different profiles and important differences among these populations despite their close genomic ancestry. In general, interspecific populations had greater variability than intraspecific populations for agronomic traits, seed production, and spittlebug resistance. Consequently, crosses among different species, whenever possible, are a better option to obtain new Urochloa breeding populations. However, the breeding of intraspecific populations is also an excellent option to improve specific traits related to each species, which can then be used to speed the breeding in the interspecific programs. Multivariate analysis demonstrated substantial variability within progenies of the interspecific Urochloa populations that can be used to improve insect resistance and productivity of tropical pastures.

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Using probabilistic genotypes in linkage analysis of polyploids

et al. 2021

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Key message In polyploids, linkage mapping is carried out using genotyping with discrete dosage scores. Here, we use probabilistic genotypes and we validate it for the construction of polyploid linkage maps. Abstract Marker genotypes are generally called as discrete values: homozygous versus heterozygous in the case of diploids, or an integer allele dosage in the case of polyploids. Software for linkage map construction and/or QTL analysis usually relies on such discrete genotypes. However, it may not always be possible, or desirable, to assign definite values to genotype observations in the presence of uncertainty in the genotype calling. Here, we present an approach that uses probabilistic marker dosages for linkage map construction in polyploids. We compare our method to an approach based on discrete dosages, using simulated SNP array and sequence reads data with varying levels of data quality. We validate our approach using experimental data from a potato (Solanum tuberosum L.) SNP array applied to an F1 mapping population. In comparison to the approach based on discrete dosages, we mapped an additional 562 markers. All but three of these were mapped to the expected chromosome and marker position. For the remaining three markers, no physical position was known. The use of dosage probabilities is of particular relevance for map construction in polyploids using sequencing data, as these often result in a higher level of uncertainty regarding allele dosage.

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Expected Genotype Quality and Diploidized Marker Data from Genotyping‐by‐Sequencing of Urochloa spp. Tetraploids

Cited by 19 publications

References 66 publications

Association Mapping Considering Allele Dosage: An Example of Forage Traits in an Interspecific Segmental Allotetraploid Urochloa spp. Panel

Association Mapping Considering Allele Dosage: An Example of Forage Traits in an Interspecific Segmental Allotetraploid Urochloa spp. Panel

Urochloa spp. multivariate performance: Similarities and divergences among intra‐ and interspecific populations

Using probabilistic genotypes in linkage analysis of polyploids

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