snpReady: a tool to assist breeders in genomic analysis

Granato, Ítalo Stefanine Correia; Galli, Giovanni; Couto, Evellyn Giselly de Oliveira; Souza, Massaine Bandeira e; Mendonça, Leandro Freitas; Fritsche‐Neto, Roberto

doi:10.1007/s11032-018-0844-8

Cited by 121 publications

(95 citation statements)

References 23 publications

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“…Population genetic analysis of SNP marker data was done in R studio (v. 1.1.463) interface in R statistical software (v. 3.6.3) by application of various predesigned packages [ 30 , 31 ]. Marker minor allele frequency (MAF), polymorphic information content (PIC), and, effective population size (N e ) was calculated using SnpReady (v. 0.9.6) R package [ 32 ]. Calculation of the genetic characteristics of accessions, i .…”

Section: Methodsmentioning

confidence: 99%

Genetic structure of a germplasm for hybrid breeding in rye (Secale cereale L.)

Vendelbo

Sarup²,

Orabi³

et al. 2020

PLoS ONE

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Rye (Secale cereale L.) responds strongly to changes in heterozygosity with hybrids portraying strong heterosis effect on all developmental and yielding characteristics. In order to achieve the highest potential heterosis effect parental lines must originate from genetically distinct gene pools. Here we report the first comprehensive SNP-based population study of an elite germplasm using fertilization control system for hybrid breeding in rye that is genetically different to the predominating P-type. In total 376 inbred lines from Nordic Seed Germany GmbH were genotyped for 4419 polymorphic SNPs. The aim of this study was to confirm and quantify the genetic separation of parental populations, unveil their genetic characteristics and investigate underlying population structures. Through a palette of complimenting analysis, we confirmed a strong genetic differentiation (F ST = 0.332) of parental populations validating the germplasms suitability for hybrid breeding. These were, furthermore, found to diverge considerably in several features with the maternal population portraying a strong population structure characterized by a narrow genetic profile, small effective population size and high genome-wise linkage disequilibrium. We propose that the employed male-sterility system putatively constitutes a population determining parameter by influencing the rate of introducing novel genetic variation to the parental populations. Functional analysis of linkage blocks led to identification of a conserved segment on the distal 4RL chromosomal region annotated to the Rfp3 male-fertility restoration 'Pampa' type gene. Findings of our study emphasized the immediate value of comprehensive population studies on elite breeding germplasms as a prerequisite for application of genomic-based breeding techniques, introgression of novel material and to support breeder decisionmaking.

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Section: Methodsmentioning

confidence: 99%

Genetic structure of a germplasm for hybrid breeding in rye (Secale cereale L.)

Vendelbo

Sarup²,

Orabi³

et al. 2020

PLoS ONE

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“…To improve the efficiency of phasing and imputation, we considered genotyping data of all available bovine animals in the in-house database, which includes a large number of pairs and trios from other projects. Genome-wide relationships between individuals were estimated using a unified additive relationship (UAR) matrix [40] implemented in the R package snpReady [41] and applied to 46,678 SNP genotypes of 3457 animals. Diversity, phylogeny and population structure analyses require samples of representative and least related animals in each breed.…”

Section: Haplotyping and Unified Additive Relationships (Uar)mentioning

confidence: 99%

Genomic diversity and population structure of the indigenous Greek and Cypriot cattle populations

et al. 2020

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Background: The indigenous cattle populations from Greece and Cyprus have decreased to small numbers and are currently at risk of extinction due to socioeconomic reasons, geographic isolation and crossbreeding with commercial breeds. This study represents the first comprehensive genome-wide analysis of 10 indigenous cattle populations from continental Greece and the Greek islands, and one from Cyprus, and compares them with 104 international breeds using more than 46,000 single nucleotide polymorphisms (SNPs). Results: We estimated several parameters of genetic diversity (e.g. heterozygosity and allelic diversity) that indicated a severe loss of genetic diversity for the island populations compared to the mainland populations, which is mainly due to the declining size of their population in recent years and subsequent inbreeding. This high inbreeding status also resulted in higher genetic differentiation within the Greek and Cyprus cattle group compared to the remaining geographical breed groups. Supervised and unsupervised cluster analyses revealed that the phylogenetic patterns in the indigenous Greek breeds were consistent with their geographical origin and historical information regarding crosses with breeds of Anatolian or Balkan origin. Cyprus cattle showed a relatively high indicine ancestry. Greek island populations are placed close to the root of the tree as defined by Gir and the outgroup Yak, whereas the mainland breeds share a common historical origin with Buša. Unsupervised clustering and D-statistics analyses provided strong support for Bos indicus introgression in almost all the investigated local cattle breeds along the route from Anatolia up to the southern foothills of the Alps, as well as in most cattle breeds along the Apennine peninsula to the southern foothills of the Alps. Conclusions: All investigated Cyprus and Greek breeds present complex mosaic genomes as a result of historical and recent admixture events between neighbor and well-separated breeds. While the contribution of some mainland breeds to the genetic diversity pool seems important, some island and fragmented mainland breeds suffer from a severe decline of population size and loss of alleles due to genetic drift. Conservation programs that are a compromise between what is feasible and what is desirable should focus not only on the still highly diverse mainland breeds but also promote and explore the conservation possibilities for island breeds.

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“…Additionally, all heterozygous loci that remained in the data were considered as missing values. Then, all the missing values in the genotypic matrix were imputed [24]. The residual heterozygosity was considered as a missing value because of the presence of chimerism in D 0 cells after artificial chromosome doubling during DH in maize [13,14].…”

Section: Methodsmentioning

confidence: 99%

“…Quality control, conversion of SNP markers into numerical algorithms and imputation of missing values were carried out by the raw.data function of snp Ready package [24] of R software 3.5.0 (R Development Core Team, 2018). The genotypic data file used in this study is available in ( doi :10.17632/98t8nxgw5s.2 ) .…”

Section: Methodsmentioning

confidence: 99%

Effect of F1 and F2 generations on genetic variability and working steps of doubled haploid production in maize

Couto¹,

Cury²,

Souza³

et al. 2019

PLoS ONE

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For doubled haploid (DH) production in maize, F1 generation has been the most frequently used for haploid induction due to facility in the process. However, using F2 generation would be a good alternative to increase genetic variability owing to the additional recombination in meiosis. Our goals were to compare the effect of F1 and F2 generations on DH production in tropical germplasm, evaluating the R1-navajo expression in seeds, the working steps of the methodology, and the genetic variability of the DH lines obtained. Sources germplasm in F1 and F2 generations were crossed with the tropicalized haploid inducer LI-ESALQ. After harvest, for both induction crosses were calculated the haploid induction rate (HIR), diploid seed rate (DSR), and inhibition seed rate (ISR) using the total number of seeds obtained. In order to study the effectiveness of the DH working steps in each generation, the percentage per se and the relative percentage were verified. In addition, SNP markers were obtained for genetic variability studies. Results showed that the values for HIR, ISR, and DSR were 1.23%, 23.48%, and 75.21% for F1 and 1.78%, 15.82%, and 82.38% for F2, respectively. The effectiveness of the DH working step showed the same percentage per se value (0.4%) for F1 and F2, while the relative percentage was 27.2% for F1 and 22.4% for F2. Estimates of population parameters in DH lines from F1 were higher than F2. Furthermore, population structure and kinship analyses showed that one additional generation was not sufficient to create new genotype subgroups. Additionally, the relative efficiency of the response to selection in the F1 was 31.88% higher than F2 due to the number of cycles that are used to obtain the DH. Our results showed that in tropical maize, the use of F1 generation is recommended due to a superior balance between time and genetic variability.

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snpReady: a tool to assist breeders in genomic analysis

Cited by 121 publications

References 23 publications

Genetic structure of a germplasm for hybrid breeding in rye (Secale cereale L.)

Genetic structure of a germplasm for hybrid breeding in rye (Secale cereale L.)

Genomic diversity and population structure of the indigenous Greek and Cypriot cattle populations

Effect of F1 and F2 generations on genetic variability and working steps of doubled haploid production in maize

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