Genetic variability in a Holstein population using SNP markers and their use for monitoring mating strategies

Genetic variability and structure of the population were studied in 7949 registered Normande cattle in Colombia. The pedigree was deep with 18 traced generations, but there were some incomplete genealogical information for the cattle born in the more distant past. The average number of complete and equivalent complete generations was 2.42 and 5.21, respectively. The average pedigree completeness index for five generations was 0.62, which increased over time, and a significant difference between sexes was found (males: 0.82 ± 0.11; females: 0.62 ± 0.38). The average generation interval was 7.57 years. The number of founders, effective founders, ancestors, and founder genomes were 575, 115, 47, and 22.22, respectively, which suggests that an unequal use of founders and a random loss of alleles from founders occurred over time. The level of inbreeding was 0.019 and increased to 0.023, when the inbreeding coefficient was calculated by assigning inbreeding of contemporaries to founders. These levels of inbreeding lead to an effective population size of 138.5 and 117.9 and to a 0.36% and 0.42% rate of inbreeding, respectively. Out of 267 herds with more than five registered breeding animals, only one nucleus herd was present, whereas 117 and 119 were classified as multiplier and commercial herds, respectively. About 92% of calves were sired by French bulls; but the use of Colombian bulls for breeding is increasing. The Colombian Normande breed is at an acceptable level of genetic variability, although some losses of founder alleles have occurred. As the level of inbreeding has been increasing, inbreeding and mating strategies should be monitored in order to maintain the genetic diversity of the breed.

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Genetic Variability in the Italian Heavy Draught Horse from Pedigree Data and Genomic Information

Animals ◽

10.3390/ani10081310 ◽

2020 ◽

Vol 10 (8) ◽

pp. 1310

Author(s):

Enrico Mancin ◽

Michela Ablondi ◽

Roberto Mantovani ◽

Giuseppe Pigozzi ◽

Alberto Sabbioni ◽

...

Keyword(s):

Genetic Variability ◽

Genomic Structure ◽

Population Level ◽

Snp Markers ◽

Pedigree Information ◽

Pedigree Data ◽

Selection Signatures ◽

Effective Population ◽

Genomic Inbreeding ◽

Inbreeding Level

This study aimed to investigate the genetic diversity in the Italian Heavy Horse Breed from pedigree and genomic data. Pedigree information for 64,917 individuals were used to assess inbreeding level, effective population size (Ne), and effective numbers of founders and ancestors (fa/fe). Genotypic information from SNP markers were available for 267 individuals of both sexes, and it allowed estimating genomic inbreeding in two methods (observed versus expected homozygosity and from ROH) to study the breed genomic structure and possible selection signatures. Pedigree and genomic inbreeding were greatly correlated (0.65 on average). The inbreeding trend increased over time, apart from periods in which the base population enlarged, when Ne increased also. Recent bottlenecks did not occur in the genome, as fa/fe have shown. The observed homozygosity results were on average lower than expected, which was probably due to the use of French Breton stallions to support the breed genetic variability. High homozygous regions suggested that inbreeding increased in different periods. Two subpopulations were distinguished, which was probably due to the different inclusion of French animals by breeders. Few selection signatures were found at the population level, with possible associations to disease resistance. The almost low inbreeding rate suggested that despite the small breed size, conservation actions are not yet required.

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Phenotypic and molecular assessment of genetic structure and diversity in a panel of winged yam (Dioscorea alata) clones and cultivars

Scientific Reports ◽

10.1038/s41598-019-54761-3 ◽

2019 ◽

Vol 9 (1) ◽

Cited By ~ 6

Author(s):

Paterne Agre ◽

Flora Asibe ◽

Kwabena Darkwa ◽

Alex Edemodu ◽

Guillaume Bauchet ◽

...

Keyword(s):

Genetic Variability ◽

Phenotypic Variability ◽

Breeding Population ◽

Snp Markers ◽

Breeding Program ◽

Joint Analysis ◽

Phenotypic Traits ◽

Dioscorea Alata ◽

Phenotypic Data ◽

Heterotic Groups

AbstractA better understanding of the structure and extent of genetic variability in a breeding population of a crop is essential for translating genetic diversity to genetic gain. We assessed the nature and pattern of genetic variability and differentiation in a panel of 100 winged-yam (Dioscorea alata) accessions using 24 phenotypic traits and 6,918 single nucleotide polymorphism (SNP) markers. Multivariate analysis for phenotypic variability indicated that all phenotypic traits assessed were useful in discriminating the yam clones and cultivars. Cluster analysis based on phenotypic data distinguished two significant groups, while a corresponding analysis with SNP markers indicated three genetic groups. However, joint analysis for the phenotypic and genotypic data provided three clusters that could be useful for the identification of heterotic groups in the D. alata breeding program. Our analysis for phenotypic and molecular level diversity provided valuable information about overall diversity and variation in economically important traits useful for establishing crossing panels with contrasting traits of interest. The selection and hybridization of parental lines from the different heterotic groups identified would facilitate maximizing diversity and exploiting population heterosis in the D. alata breeding program.

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Genetic variability and relationships among six grass carp Ctenopharyngodon idella populations in China estimated using EST-SNP Markers

Fisheries Science ◽

10.1007/s12562-014-0709-y ◽

2014 ◽

Vol 80 (3) ◽

pp. 475-481 ◽

Cited By ~ 4

Author(s):

Lingyun Yu ◽

Junjie Bai ◽

Tingting Cao ◽

Jiajia Fan ◽

Yingchun Quan ◽

...

Keyword(s):

Genetic Variability ◽

Grass Carp ◽

Snp Markers ◽

Ctenopharyngodon Idella ◽

Grass Carp Ctenopharyngodon Idella

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Unbiased population heterozygosity estimates from genome-wide sequence data

10.1101/2020.12.20.423694 ◽

2020 ◽

Author(s):

Thomas L Schmidt ◽

Moshe Jasper ◽

Andrew R Weeks ◽

Ary A Hoffmann

Keyword(s):

Missing Data ◽

Genetic Variability ◽

Sample Size ◽

Sequence Data ◽

Snp Markers ◽

Sequence Information ◽

List Type ◽

Invasion History ◽

Sample Sizes ◽

Genome Wide

AbstractGenetic variability within populations is a key parameter for the management of threatened species and for tracking invasion history. Heterozygosity (observed and expected) is commonly used to represent genetic variability and is increasingly being estimated with single nucleotide polymorphism (SNP) markers. While many SNP markers can provide precise estimates of genetic processes, the results of ‘downstream’ analysis of these markers may depend heavily on ‘upstream’ filtering decisions.Here we explore the downstream consequences of sample size, rare allele filtering, missing data thresholds and known population structure on estimates of heterozygosity using a ddRADseq dataset of the mosquito Aedes aegypti and a DArTseq dataset of a threatened grasshopper, Keyacris scurra.We show that estimates based on polymorphic markers only (i.e. SNP heterozygosity) are always biased by sample size, regardless of other filtering considerations. By contrast, results are consistent across sample sizes when calculations consider monomorphic as well as polymorphic sequence information (i.e. genome-wide or autosomal heterozygosity). We also show that when loci with missing genotypes are included, observed and expected heterozygosity estimates diverge in proportion to the amount of missing data permitted at each locus.To ensure robust results across studies, we make two recommendations for estimating heterozygosity: (i) autosomal heterozygosity should be reported instead of (or in addition to) SNP heterozygosity; (ii) sites with any missing data should be removed when calculating heterozygosity. Applying these protocols to K. scurra, we show that autosomal heterozygosity estimates are consistent even when populations with different sample sizes and high levels of differentiation are analysed together. This should facilitate comparisons across studies and between observed and expected measures of heterozygosity.

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Genome-Wide SNP Markers for Genotypic and Phenotypic Differentiation of Melon (Cucumis melo L.) Varieties Using Genotyping-by-Sequencing

International Journal of Molecular Sciences ◽

10.3390/ijms22136722 ◽

2021 ◽

Vol 22 (13) ◽

pp. 6722

Author(s):

Do Yoon Hyun ◽

Raveendar Sebastin ◽

Gi-An Lee ◽

Kyung Jun Lee ◽

Seong-Hoon Kim ◽

...

Keyword(s):

Genetic Variability ◽

Cucumis Melo ◽

Systematic Approach ◽

Genome Wide Association Study ◽

Genotyping By Sequencing ◽

Snp Markers ◽

Phenotypic Traits ◽

Nucleotide Polymorphisms ◽

Genome Wide ◽

Cucumis Melo L

Melon (Cucumis melo L.) is an economically important horticultural crop with abundant morphological and genetic variability. Complex genetic variations exist even among melon varieties and remain unclear to date. Therefore, unraveling the genetic variability among the three different melon varieties, muskmelon (C. melo subsp. melo), makuwa (C. melo L. var. makuwa), and cantaloupes (C. melo subsp. melo var. cantalupensis), could provide a basis for evolutionary research. In this study, we attempted a systematic approach with genotyping-by-sequencing (GBS)-derived single nucleotide polymorphisms (SNPs) to reveal the genetic structure and diversity, haplotype differences, and marker-based varieties differentiation. A total of 6406 GBS-derived SNPs were selected for the diversity analysis, in which the muskmelon varieties showed higher heterozygote SNPs. Linkage disequilibrium (LD) decay varied significantly among the three melon varieties, in which more rapid LD decay was observed in muskmelon (r2 = 0.25) varieties. The Bayesian phylogenetic tree provided the intraspecific relationships among the three melon varieties that formed, as expected, individual clusters exhibiting the greatest genetic distance based on the posterior probability. The haplotype analysis also supported the phylogeny result by generating three major networks for 48 haplotypes. Further investigation for varieties discrimination allowed us to detect a total of 52 SNP markers that discriminated muskmelon from makuwa varieties, of which two SNPs were converted into cleaved amplified polymorphic sequence markers for practical use. In addition to these markers, the genome-wide association study identified two SNPs located in the genes on chromosome 6, which were significantly associated with the phenotypic traits of melon seed. This study demonstrated that a systematic approach using GBS-derived SNPs could serve to efficiently classify and manage the melon varieties in the genebank.

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Single Nucleotide Polymorphism Analysis Using KASP Assay Reveals Genetic Variability in Rotylenchulus reniformis

Plant Disease ◽

10.1094/pdis-11-18-1975-re ◽

2019 ◽

Vol 103 (8) ◽

pp. 1835-1842 ◽

Cited By ~ 4

Author(s):

Churamani Khanal ◽

Manjula T. Kularathna ◽

Jeffery D. Ray ◽

Salliana R. Stetina ◽

Edward C. McGawley ◽

...

Keyword(s):

South Carolina ◽

Genetic Variability ◽

Resistance Breeding ◽

Snp Markers ◽

Polymorphism Analysis ◽

Nucleotide Polymorphisms ◽

Reniform Nematode ◽

Rotylenchulus Reniformis ◽

Single Nucleotide ◽

Specific Pcr

This study employed single nucleotide polymorphisms (SNPs) to determine the genetic variability present in 26 isolates of Rotylenchulus reniformis from Louisiana, Mississippi, Arkansas, South Carolina, Georgia, Hawaii, and Alabama. Genomic DNA from reniform nematode was extracted and increased quantitatively using the process of whole genome amplification. More than 162 putative SNPs were identified, 31 of which were tested using a KASP kompetitive allele-specific PCR genotyping assay. Of the SNPs tested, 13, 17, and 19 SNPs revealed genetic variability within reniform nematode isolates from Louisiana, Mississippi, and Arkansas, respectively. Seven SNPs elucidated genetic differences among isolates of reniform nematode from Louisiana, Mississippi, and Arkansas. Eight SNPs determined genetic variability among individual isolates from South Carolina, Georgia, Hawaii, and Alabama. This study is the first to report genetic variability in geographic isolates of reniform nematode employing a SNP assay. This study also demonstrated that SNP markers can be used to evaluate isolates of R. reniformis and could be useful to assess their genetic diversity, origin, and distribution. Such information would be extremely useful in resistance breeding programs.

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Population structure of Brazilian Gyr dairy cattle

Revista Brasileira de Zootecnia ◽

10.1590/s1516-35982010001200012 ◽

2010 ◽

Vol 39 (12) ◽

pp. 2640-2645 ◽

Cited By ~ 12

Author(s):

João Cruz Reis Filho ◽

Paulo Sávio Lopes ◽

Rui da Silva Verneque ◽

Robledo de Almeida Torres ◽

Roberto Luiz Teodoro ◽

...

Keyword(s):

Population Structure ◽

Genetic Structure ◽

Genetic Variability ◽

Inbreeding Coefficient ◽

Mating Strategies ◽

Future Generations ◽

Breeding Value ◽

Effective Number ◽

Generation Interval ◽

Inbreeding Coefficients

The objective of the present study was to evaluate the genetic structure of Gyr cattle selected for milk production. Files of pedigree and production were composed of 27,610 animals. The ENDOG program was used for the calculation of individual inbreeding coefficient (F) and coefficient of average relatedness (AR), effective number of animals(Ne), effective number of founders (f e) and ancestors (f a), and generation interval (GI). Individual inbreeding coefficients and average relatedness in the population were 2.82% and 2.10%, respectively. It was observed a reduction in the effective number of animals, especially after publication of the results of the first progeny test. The estimated effective number of founders was 146 and 75 for the ancestrals. Out of those, only 28 ancestors accounted for the origin of 50% of the population genes. The average generation interval was 8.41 years and it was longer for males than for females. For maintaining genetic variability in future generations, it should be invested mating strategies that reduce inbreeding and which do not use massively only some high breeding value sires.

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Sexual selection strategy and sexism in the Greek system: Mating strategies represented in Greek life

PsycEXTRA Dataset ◽

10.1037/e512142015-155 ◽

2014 ◽

Author(s):

Patrick J. Ewell ◽

C. Veronica Smith ◽

Rosanna E. Guadagno

Keyword(s):

Sexual Selection ◽

Mating Strategies ◽

Selection Strategy ◽

Greek Life ◽

Greek System

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