scholarly journals Genome prediction accuracy of common bean via Bayesian models

2018 ◽  
Vol 48 (8) ◽  
Author(s):  
Leiri Daiane Barili ◽  
Naine Martins do Vale ◽  
Fabyano Fonseca e Silva ◽  
José Eustáquio de Souza Carneiro ◽  
Hinayah Rojas de Oliveira ◽  
...  
Keyword(s):  
Common Bean ◽  
Prediction Accuracy ◽  
Bayesian Models ◽  
Snp Markers ◽  
Genomic Information ◽  
Stay Green ◽  
Single Nucleotide ◽  
Genome Prediction ◽  
Heritability Estimation ◽  
Selection Of

ABSTRACT: We aimed to apply genomic information based on SNP (single nucleotide polymorphism) markers for the genetic evaluation of the traits “stay-green” (SG), plant architecture (PA), grain aspect (GA) and grain yield (GY) in common bean through Bayesian models. These models were compared in terms of prediction accuracy and ability for heritability estimation for each one of the mentioned traits. A total of 80 cultivars were genotyped for 377 SNP markers, whose effects were estimated by five different Bayesian models: Bayes A (BA), B (BB), C (BC), LASSO (BL) e Ridge regression (BRR). Although, prediction accuracies calculated by means of cross-validation have been similar within each trait, the BB model stood out for the trait SG, whereas the BRR was indicated for the remaining traits. The heritability estimates for the traits SG, PA, GA and GY were 0.61, 0.28, 0.32 and 0.29, respectively. In summary, the Bayesian methods applied here were effective and ease to be implemented. The used SNP markers can help in the early selection of promising genotypes, since incorporating genomic information increase the prediction accuracy of the estimated genetic merit.

scholarly journals GWAS findings improved genomic prediction accuracy of lipid profile traits: Tehran Cardiometabolic Genetic Study

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Mahdi Akbarzadeh ◽  
Saeid Rasekhi Dehkordi ◽  
Mahmoud Amiri Roudbar ◽  
Mehdi Sargolzaei ◽  
Kamran Guity ◽  
...  
Keyword(s):  
Lipid Profile ◽  
Genetic Study ◽  
Prediction Accuracy ◽  
Significant Snps ◽  
Snp Markers ◽  
Linear Unbiased Prediction ◽  
Genetic Prediction ◽  
Heritability Estimation ◽  
Precise Prediction ◽  
Best Linear Unbiased

AbstractIn recent decades, ongoing GWAS findings discovered novel therapeutic modifications such as whole-genome risk prediction in particular. Here, we proposed a method based on integrating the traditional genomic best linear unbiased prediction (gBLUP) approach with GWAS information to boost genetic prediction accuracy and gene-based heritability estimation. This study was conducted in the framework of the Tehran Cardio-metabolic Genetic study (TCGS) containing 14,827 individuals and 649,932 SNP markers. Five SNP subsets were selected based on GWAS results: top 1%, 5%, 10%, 50% significant SNPs, and reported associated SNPs in previous studies. Furthermore, we randomly selected subsets as large as every five subsets. Prediction accuracy has been investigated on lipid profile traits with a tenfold and 10-repeat cross-validation algorithm by the gBLUP method. Our results revealed that genetic prediction based on selected subsets of SNPs obtained from the dataset outperformed the subsets from previously reported SNPs. Selected SNPs’ subsets acquired a more precise prediction than whole SNPs and much higher than randomly selected SNPs. Also, common SNPs with the most captured prediction accuracy in the selected sets caught the highest gene-based heritability. However, it is better to be mindful of the fact that a small number of SNPs obtained from GWAS results could capture a highly notable proportion of variance and prediction accuracy.

DNA Fingerprinting of Vegetable Soybean Cultivar ‘Zhexian No.9’ Using 101 New Developed HRM-Based SNP Markers

2019 ◽  
Author(s):  
X. J. Fu ◽  
J. X. Pei ◽  
Y. T. Zheng ◽  
D. D. Guo ◽  
Q. H. Yang ◽  
...  
Keyword(s):  
High Resolution Melting ◽  
Snp Markers ◽  
Soybean Cultivar ◽  
Polymorphic Markers ◽  
Nucleotide Polymorphisms ◽  
Analysis Method ◽  
Vegetable Soybean ◽  
Genomic Information ◽  
Single Nucleotide ◽  
Plant Genomes

Single nucleotide polymorphisms (SNPs) have been proved to be powerful markers in genetic analysis due to their high abundance and polymorphism in plant genomes. The recently developed high-resolution melting (HRM) analysis method provides a novel, quick, and close-tube PCR approach to analyze SNP variations. In present study, 101 HRM-based SNP markers from 20 soybean chromosomes were developed for genotyping vegetable soybean cultivar ‘Zhexian No.9’ with ‘Williams 82’ as reference. 33.7% of these markers were polymorphic between ‘Zhexian No.9’ and ‘Williams 82’. Polymorphic markers were found on 85% (17 of 20) of the soybean chromosomes when comparing ‘Zhexian No.9’ and ‘Williams 82’. Finally, an array of 101 in-sequence nucleotide letters was generated as the first precise SNP fingerprint of ‘Zhexian No.9’. The described marker-developing methodology could be used in other crops with known genomic information.

scholarly journals Effects of single nucleotide polymorphism ascertainment on population structure inferences

2021 ◽  
Author(s):  
Kotaro Dokan ◽  
Sayu Kawamura ◽  
Kosuke M Teshima
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Population Structure ◽  
Natural Populations ◽  
Snp Markers ◽  
Ascertainment Bias ◽  
Snp Discovery ◽  
Nucleotide Polymorphism ◽  
Frequency Spectra ◽  
Single Nucleotide ◽  
Selection Of

Abstract Single nucleotide polymorphism (SNP) data are widely used in research on natural populations. Although they are useful, SNP genotyping data are known to contain bias, normally referred to as ascertainment bias, because they are conditioned by already confirmed variants. This bias is introduced during the genotyping process, including the selection of populations for novel SNP discovery and the number of individuals involved in the discovery panel and selection of SNP markers. It is widely recognized that ascertainment bias can cause inaccurate inferences in population genetics and several methods to address these bias issues have been proposed. However, especially in natural populations, it is not always possible to apply an ideal ascertainment scheme because natural populations tend to have complex structures and histories. In addition, it was not fully assessed if ascertainment bias has the same effect on different types of population structure. Here we examine the effects of bias produced during the selection of population for SNP discovery and consequent SNP marker selection processes under three demographic models: the island, stepping-stone, and population split models. Results show that site frequency spectra and summary statistics contain biases that depend on the joint effect of population structure and ascertainment schemes. Additionally, population structure inferences are also affected by ascertainment bias. Based on these results, it is recommended to evaluate the validity of the ascertainment strategy prior to the actual typing process because the direction and extent of ascertainment bias vary depending on several factors.

scholarly journals Impact of inclusion rates of crossbred phenotypes and genotypes in nucleus selection programs

2020 ◽  
Vol 98 (12) ◽  
Author(s):  
Garrett M See ◽  
Benny E Mote ◽  
Matthew L Spangler
Keyword(s):  
Data Collection ◽  
Genetic Correlation ◽  
Snp Markers ◽  
Breeding Value ◽  
Single Nucleotide ◽  
Data Collection Strategy ◽  
Inclusion Rate ◽  
Genetic Evaluations ◽  
The Impact ◽  
Selection Of

Abstract Numerous methods have been suggested to incorporate crossbred (CB) phenotypes and genotypes into swine selection programs, yet little research has focused on the implicit trade-off decisions between generating data at the nucleus or commercial level. The aim of this study was to investigate the impact of altering the proportion of purebred (PB) and CB phenotypes and genotypes in genetic evaluations on the response to selection of CB performance. Assuming CB and PB performance with moderate heritabilities (h2=0.4), a three-breed swine crossbreeding scheme was simulated and selection was practiced for six generations, where the goal was to increase CB performance. Phenotypes, genotypes, and pedigrees for three PB breeds (25 and 175 mating males and females for each breed, respectively), F1 crosses (400 mating females), and terminal cross progeny (2,500) were simulated. The genome consisted of 18 chromosomes with 1,800 quantitative trait loci and 72k single nucleotide polymorphism (SNP) markers. Selection was performed in PB breeds using estimated breeding value for each phenotyping/genotyping strategy. Strategies investigated were: 1) increasing the proportion of CB with genotypes, phenotypes, and sire pedigree relationships, 2) decreasing the proportion of PB phenotypes and genotypes, and 3) altering the genetic correlation between PB and CB performance (rpc). Each unique rpc scenario and data collection strategy was replicated 10 times. Results showed that including CB data improved the CB performance regardless of  rpc or data collection strategy compared with when no CB data were included. Compared with using only PB information, including 10% of CB progeny per generation with sire pedigrees and phenotypes increased the response in CB phenotype by 134%, 55%, 33%, 23%, and 21% when rpc was 0.1, 0.3, 0.5, 0.7, and 0.9, respectively. When the same 10% of CB progeny were also genotyped, CB performance increased by 243%, 54%, 38%, 23%, and 20% when the rpc was 0.1, 0.3, 0.5, 0.7, and 0.9, respectively, compared with when no CB data were utilized. Minimal change was observed in the average CB phenotype when PB phenotypes were included or proportionally removed when CB were genotyped. Removal of both PB phenotypes and genotypes when CB were genotyped greatly reduced the response in CB performance. In practice, the optimal inclusion rate of CB and PB data depends upon the genetic correlation between CB and PB animals and the expense of additional CB data collection compared with the economic benefit associated with increased CB performance.

scholarly journals Efficiency of using SNP markers in the MSTN gene in the selection of the Pushkin breed chickens

2020 ◽  
Vol 23 (8) ◽  
pp. 993-998 ◽  
Author(s):  
N. V. Dementeva ◽  
A. B. Vakhrameev ◽  
T. A. Larkina ◽  
O. V. Mitrofanova
Keyword(s):  
Molecular Genetic ◽  
Live Weight ◽  
Snp Markers ◽  
Experimental Population ◽  
Adult Bird ◽  
Nucleotide Polymorphisms ◽  
Poultry Industry ◽  
Single Nucleotide ◽  
Low Efficiency ◽  
Selection Of

In the poultry industry, indicators reflecting the growth rate of young stock and the exterior characteristics of chickens are important benchmarks for breeding. Traditional selection based on phenotypic evaluation is characterized by low efficiency with a low character inheritance ratio and is difficult to apply in small groups of animals and birds bred in bioresource collections. The use of molecular genetic markers associated with economically important traits makes it possible to carry out early selection of birds. This entails an increase in the profitability of the poultry industry. Recently, single nucleotide polymorphisms (SNPs) have served as convenient markers for selection purposes. For five generations (P1–P5), an experimental selection of hens of the Pushkin breed was carried out for live weight. It was based on selection for single nucleotide polymorphism rs313744840 in the MSTN gene. As a result, a significant increase in the frequency of allele A in this gene, from 0.11 to 0.50, took place. The association of SNP markers with meat qualities in the experimental group led to changes in the exterior profile of an adult bird at 330 days of age. The individuals with the AA and AG genotypes had the greatest live weight and longest body. As a result of selection, the bird on average became larger due to an increase in the number of heterozygous individuals with long bodies and large chest girths. The depth of the chest and the width of the pelvis increased due to an increase in the frequency of allele A in the experimental population. A tendency towards an increase in these indicators with the substitution of G with A in the genotype was found. Saturation of the population with desirable alleles led to an increase in the average live weight of the chickens. Analysis of the exterior parameters of adult birds showed that this growth is achieved by increasing the depth and volume of the bird body, and not by increasing the length of the limbs. Thus, marker selection carried out for five generations in the experimental population of Pushkin breed chickens to increase body weight has reliably (p < 0.001) changed the exterior profile of adult birds.

scholarly journals Development and characterization of 57 SNP markers in Misgurnus anguillicaudatus

2021 ◽  
Author(s):  
Guiyun Huang ◽  
Fengying Gao ◽  
Zhigang Liu ◽  
Jianmeng Cao ◽  
Gang Chen ◽  
...  
Keyword(s):  
Snp Markers ◽  
Freshwater Species ◽  
Nucleotide Polymorphisms ◽  
Misgurnus Anguillicaudatus ◽  
Population Genetic Analysis ◽  
Single Nucleotide ◽  
Natural Resource Conservation ◽  
Hardy Weinberg Equilibrium ◽  
Selection Of

Abstract The dojo loach Misgurnus anguillicaudatus is an endemic freshwater species to Asia. The effective conservation and molecular-aided selection of M. anguillicaudatus have been limited without sufficient molecular markers. In this study, 112 novel single nucleotide polymorphisms (SNPs) were screened based on 2b-RAD sequencing database, and 57 SNP markers were developed and characterized by genotyping 40 individuals using SNaPshot method. The observed heterozygosity (Ho) ranged from 0.025 to 0.675, while the expected heterozygosity (He) varied from 0.025 to 0.500. The minor allele frequency (MAF) ranged from 0.013 to 0.500. Among these SNPs, 18 loci were found to deviate significantly from the Hardy–Weinberg equilibrium after Bonferroni correction (P < 0.05). The first set of SNP markers developed from M. anguillicaudatus will provide valuable information in further population genetic analysis and natural resource conservation.

scholarly journals Genetics and Mapping of the Cl Gene for Circumlineated Pattern in Common Bean Using AFLP-based Bulk Segregant Analysis and SNP-based Bidirectional Selective Genotyping

2014 ◽  
Vol 139 (2) ◽  
pp. 213-218
Author(s):  
Luwbia Aranda ◽  
Timothy G. Porch ◽  
Mark J. Bassett ◽  
Laura Lara ◽  
Perry B. Cregan
Keyword(s):  
Common Bean ◽  
Genome Sequence ◽  
Bulk Segregant Analysis ◽  
Snp Markers ◽  
Selective Genotyping ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Precipitation Line ◽  
Single Nucleotide ◽  
The Common

Circumlineatus (cl) in common bean (Phaseolus vulgaris L.) is identified by a precipitation line in the seedcoat at the boundary of the white and colored zones. Cl is recessive and is expressed in partly colored seedcoats (t) with restricted patterns such as virgarcus. In this study, amplified fragment length polymorphism (AFLP) and single nucleotide polymorphism (SNP) markers, and the common bean genome sequence were used in combination with bulk segregant analysis and bidirectional selective genotyping to identify the genetic location of Cl. Markers were identified that cosegregated with Cl using Cl/Cl and cl/cl F3 and F5 progeny bulks from the cross t z cl G b v virgarcus BC3 5-593 × t zsel Cl G b v sellatus BC3 5-593. Two bands from an AFLP primer combination, which yielded unambiguous polymorphisms between the bulks, were cloned and sequenced. The two sequences were used to interrogate the common bean whole genome sequence identifying a region also found through cosegregation analysis using bidirectional selective genotyping with SNPs. Thus, the Cl gene was localized on Pv09 using cosegregating AFLP and SNP markers, and the physical location was confirmed with the whole genome sequence.

Molecular Characterization of Parental Lines and Validation of Snp Markers for Disease Resistance in Common Bean

2021 ◽  
Author(s):  
Lucas Matias Gomes-Messias ◽  
Rosana Pereira Vianello ◽  
Joney Pereira Monteiro-Júnior ◽  
Luana Alves Rodrigues ◽  
Ana Paula Simplício Mota ◽  
...  
Keyword(s):  
Disease Resistance ◽  
Common Bean ◽  
Molecular Characterization ◽  
High Efficiency ◽  
Snp Markers ◽  
Molecular Tools ◽  
Breeding Programs ◽  
Efficiency Of Selection ◽  
Selection Of

Abstract The implementation of molecular tools that help the early selection of genotypes carrying target alleles increases efficiency and reduces the time and costs of breeding programs. The present study aimed the molecular characterization and validation of SNPs targeting disease resistance alleles for assisted selection. A total of 376 common bean lines with contrasting responses for anthracnose and angular leaf spot resistance were used, as well as 149 F2 plants from the cross between BRS Cometa x SEL 1308 (carrying the Anthracnose resistance gene Co-42). Seven of the ten SNP markers evaluated showed potential for assisted breeding: snpPV0025 (Phg-2), snpPV0027 (Phg-5), snpPV0079 (Phg-5), snpPV0046 (Co-u), snpPV0068 (Co-42), snpPV0070 (Co-42) and snpP8282v3-817 (Co-42). Markers snpPV0070 and snpP8282v3-817 showed high efficiency of selection (99.7 and 99.8%, respectively). These markers exhibit great potential to assist in the selection at different stages of the breeding program and may be readily incorporated into marker-assisted selection.

scholarly journals QTL Mapping for Grain Zinc and Iron Concentrations in Bread Wheat

2021 ◽  
Vol 8 ◽  
Author(s):  
Yue Wang ◽  
Xiaoting Xu ◽  
Yuanfeng Hao ◽  
Yelun Zhang ◽  
Yuping Liu ◽  
...  
Keyword(s):  
Recombinant Inbred Lines ◽  
Snp Array ◽  
Snp Markers ◽  
Environment Interaction ◽  
Single Nucleotide ◽  
Wide Range ◽  
Grain Zinc ◽  
Hidden Hunger ◽  
Range Of Variation ◽  
Selection Of

Deficiency of micronutrient elements, such as zinc (Zn) and iron (Fe), is called “hidden hunger,” and bio-fortification is the most effective way to overcome the problem. In this study, a high-density Affymetrix 50K single-nucleotide polymorphism (SNP) array was used to map quantitative trait loci (QTL) for grain Zn (GZn) and grain Fe (GFe) concentrations in 254 recombinant inbred lines (RILs) from a cross Jingdong 8/Bainong AK58 in nine environments. There was a wide range of variation in GZn and GFe concentrations among the RILs, with the largest effect contributed by the line × environment interaction, followed by line and environmental effects. The broad sense heritabilities of GZn and GFe were 0.36 ± 0.03 and 0.39 ± 0.03, respectively. Seven QTL for GZn on chromosomes 1DS, 2AS, 3BS, 4DS, 6AS, 6DL, and 7BL accounted for 2.2–25.1% of the phenotypic variances, and four QTL for GFe on chromosomes 3BL, 4DS, 6AS, and 7BL explained 2.3–30.4% of the phenotypic variances. QTL on chromosomes 4DS, 6AS, and 7BL might have pleiotropic effects on both GZn and GFe that were validated on a germplasm panel. Closely linked SNP markers were converted to high-throughput KASP markers, providing valuable tools for selection of improved Zn and Fe bio-fortification in breeding.

scholarly journals Identification of ‘Haryejosaeng’ mandarin by multiplex SNP genotyping

2020 ◽  
Author(s):  
Seong-Beom Jin ◽  
Ho Bang Kim ◽  
Suk Man Park ◽  
Min Ju Kim ◽  
Seok-Beom Kang ◽  
...  
Keyword(s):  
Multiplex Pcr ◽  
Negative Control ◽  
Snp Markers ◽  
Accurate Identification ◽  
Single Nucleotide ◽  
Satsuma Mandarin ◽  
Bud Mutation ◽  
Melting Analysis ◽  
Nucellar Embryo ◽  
Selection Of

Abstract BackgroundMost of the satsuma mandarin (Citrus unshiu Marc.) cultivars grown on Jeju Island farms, Korea, are difficult to improve through hybridization because of polyembryony and male sterility. Therefore, their improvement has mostly been based on the selection of nucellar embryo and bud mutation. These cultivars are supplied to breeders and farms at the seedling stage, which renders their identification based only on morphological traits. In addition, because these seedlings originate from nucellar embryo and bud mutation selection, they are genetically very similar. Therefore, the present study was carried out to develop markers that can specifically and rapidly distinguish ‘Haryejosaeng,’ which is generally supplied to breeders, from other satsuma mandarin cultivars that are planted on farms.ResultsPolymerase chain reaction (PCR) was performed to distinguish ‘Haryejosaeng’ from other 8 cultivars (‘Haryejosaeng’- breeder’s stock, ‘Miyagawa wase,’ ‘Okitsu wase,’ ‘Yura wase,’ ‘Miyamoto wase,’ ‘Ueno wase,’ ‘Yonezawa wase,’ and ‘Nichinan 1 gou’) using 6 single nucleotide polymorphism (SNP) markers specific for ‘Haryejosaeng’ and one SNP primer pair, which was used as the negative control. Using a multiplex PCR, SNP markers P1 (HL-SNP-SCAF_2-23997586-F and HL-SNP-SCAF_2-23997586-R), P2 (HL-SNP-SCAF_2-36059523-F and HL-SNP-SCAF_2-36059523-R), and P5 (HL-SNP-SCAF_9-30793978-F and HL-SNP-SCAF_9-30793978-R) simultaneously yielded 165, 150, and 526 bp amplicons, respectively, for Haryejosaeng only. The SNP markers were further validated by high-resolution melting analysis. The multiplex PCR based on P1/P5 and P2/P5 was also used to identify ‘Haryejosaeng’ on a farm growing 17 different cultivars of satsuma mandarin.ConclusionsWe developed specific molecular markers for accurate identification of ‘Haryejosaeng,’ which can be performed by multiplex PCR to save time and cost associated with the supply of ‘Haryejosaeng’ to farms.

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