Development of a core SNP panel for cacao (Theobroma cacao L.) identity analysis

Genome ◽  
2020 ◽  
Vol 63 (2) ◽  
pp. 103-114 ◽  
Author(s):  
Amrita Mahabir ◽  
Lambert A. Motilal ◽  
David Gopaulchan ◽  
Saila Ramkissoon ◽  
Antoinette Sankar ◽  
...  
Keyword(s):  
Dna Fingerprinting ◽  
Allele Frequency ◽  
Theobroma Cacao ◽  
Nucleotide Polymorphisms ◽  
Major Allele Frequency ◽  
Concomitant Reduction ◽  
Minimum Number ◽  
Snp Panel ◽  
Snp Panels ◽  
Theobroma Cacao L

Single nucleotide polymorphisms (SNPs) are preferred markers for DNA fingerprinting and diversity studies in cacao (Theobroma cacao L.). Yet, a consensus SNP panel with a minimum number of SNPs for optimal identity analysis is unavailable for cacao. An initial set of 146 SNP panels of varying sizes were assembled based on heterozygosity, linkage disequilibrium (LD), linkage group (LG) distribution, major allele frequency, minor allele frequency (MiAF), polymorphism information content (PIC), and random distribution. These panels were assessed to determine their ability to distinguish among a training set of 155 accessions. The panels with the best separation ability were supplemented with additional SNPs to create 16 designer panels, which separated all 155 accessions. The 16 designer SNP panels were then assessed on a dataset of 1220 accessions coming from 10 ancestral groups. Increasing the number of SNPs generally yielded improved resolution of genetic identities with concomitant reduction of synonymous groups. The number and choice of SNPs were critical factors with LD, MiAF, and PIC being important selection attributes but an even LG distribution was unnecessary. A robust set of 96 SNPs is recommended as a minimal core SNP panel for cacao DNA fingerprinting to the international cacao community.

scholarly journals Low-density genotype panel for both parentage verification and discovery in a multi-breed sheep population

2019 ◽  
Vol 58 (1) ◽  
pp. 1-12 ◽  
Author(s):  
D.P. Berry ◽  
N. McHugh ◽  
E. Wall ◽  
K. McDermott ◽  
A.C. O’Brien
Keyword(s):  
Candidate Snps ◽  
Low Density ◽  
Nucleotide Polymorphisms ◽  
Entire Genome ◽  
Sheep Population ◽  
Genome Wide ◽  
Likelihood Approach ◽  
Snp Panel ◽  
Snp Panels ◽  
Breed Sheep

Abstract The generally low usage of artificial insemination and single-sire mating in sheep, compounded by mob lambing (and lambing outdoors), implies that parentage assignment in sheep is challenging. The objective here was to develop a low-density panel of single nucleotide polymorphisms (SNPs) for accurate parentage verification and discovery in sheep. Of particular interest was where SNP selection was limited to only a subset of chromosomes, thereby eliminating the ability to accurately impute genome-wide denser marker panels. Data used consisted of 10,933 candidate SNPs on 9,390 purebred sheep. These data consisted of 1,876 validated genotyped sire–offspring pairs and 2,784 validated genotyped dam–offspring pairs. The SNP panels developed consisted of 87 SNPs to 500 SNPs. Parentage verification and discovery were undertaken using 1) exclusion, based on the sharing of at least one allele between candidate parent–offspring pairs, and 2) a likelihood-based approach. Based on exclusion, allowing for one discordant offspring–parent genotype, a minimum of 350 SNPs was required when the goal was to unambiguously identify the true sire or dam from all possible candidates. Results suggest that, if selecting SNPs across the entire genome, a minimum of 250 carefully selected SNPs are required to ensure that the most likely selected parent (based on the likelihood approach) was, in fact, the true parent. If restricting the SNPs to just a subset of chromosomes, the recommendation is to use at least a 300-SNP panel from at least six chromosomes, with approximately an equal number of SNPs per chromosome.

Situación económica y social de la población de San José del Carmen, San Cristóbal de las Casas, Chiapas

2019 ◽  
Vol 12 (4) ◽  
Author(s):  
Pedro Cadena-Iñiguez ◽  
Eileen Salinas-Cruz ◽  
Jesús Martínez-Sánchez ◽  
Mariano Morales-Guerra ◽  
Romualdo Vásquez-Ortiz ◽  
...  
Keyword(s):  
Solanum Tuberosum ◽  
Theobroma Cacao ◽  
Zea Mays L ◽  
Solanum Tuberosum L ◽  
San Jose ◽  
Phaseolus Vulgaris L ◽  
Las Casas ◽  
Vicia Faba L ◽  
Las Mujeres ◽  
Theobroma Cacao L

Objetivo: Establecer una línea base como fundamento para la intervención e inducción de innovaciones a través de escuelas de campo y planes de negocios. Diseño/metodología/aproximación: El estudio se desarrolló en San José del Carmen, San Cristóbal de Las Casas, Chiapas, México. Se elaboró una encuesta como instrumento para recabar en campo información de familias de la localidad con la finalidad de conocer su situación actual. La localidad de trabajo se eligió utilizando como criterio las poblaciones que se encuentran dentro de Cruzada Nacional contra el hambre y en la clasificación de la pobreza extrema Resultados: La localidad de San José del Carmen es considerada como de alta marginación, la población es bilingüe, su principal lengua es el Tzotzil, el nivel de estudios promedio es hasta el tercer año de primaria, las principales actividades productivas son la siembra de maíz (Zea mays L.), frijol (Phaseolus vulgaris L.), papa (Solanum tuberosum L.) y haba (Vicia faba L.) que son utilizadas principalmente para autoconsumo.  No cuentan con agua potable ya que su sistema es a través de la recaudación de agua de lluvia o a través de un jagüey. Sus principales actividades económicas son la albañilería por parte de los hombres, y venta de productos, tales como el pozol (bebida energética a base de maíz y cacao (Theobroma cacao L.), tostadas y algunos vegetales por parte de las mujeres. Las tostadas son producidas en forma artesanal con un proceso de doble nixtamalización y vendida en bolsas de 20 tostadas cada una, a un costo de MX$10.00 en los mercados de San Cristóbal de las Casas, una a dos veces por semana alrededor de 40 bolsas por día de venta. Limitaciones del estudio/implicaciones: La afiliación zapatista de alguno de los pobladores y el hecho de que algunos habitantes no hablen español, fueron factores que limitaron desarrollar al 100% el estudio; sin embargo, se considera que se tienen los elementos necesarios para establecer la línea base de la situación de San José del Carmen. Conclusiones: El diagnóstico servirá como una herramienta para establecer una intervención a través de innovaciones y planes de negocios en la comunidad de estudio. Los pobladores cuentan con herramientas necesarias para obtener nuevos conocimientos que ayuden a un desarrollo de su producción. El idioma no deberá de ser una limitante para ello.

CLASSIFICAÇÃO DE AMÊNDOAS E QUALIDADE DE LIQUOR DE CACAU (Theobroma cacao L.) SUPERIOR BAHIA

2013 ◽  
Vol 15 (4) ◽  
pp. 391-396 ◽  
Author(s):  
B.A. Melo Neto ◽  
E.A. Carvalho ◽  
D.L.N. Mello ◽  
A.C. Anjos ◽  
A.C.R. Ferreira ◽  
...  
Keyword(s):  
Theobroma Cacao ◽  
Theobroma Cacao L

DETERMINATION OF INCOMPATIBILITY ALLELES OF SCAVINA 6 (Theobroma cacao L.) CLONE IN FARM SELECTIONS

2013 ◽  
Vol 25 (2) ◽  
pp. 93-96
Author(s):  
Milton Macoto Yamada ◽  
Wilson Reis Monteiro ◽  
Uilson Vanderlei Lopes ◽  
José Luis Pires ◽  
Basil G. D. Bartley ◽  
...  
Keyword(s):  
Theobroma Cacao ◽  
Incompatibility Alleles ◽  
Theobroma Cacao L

Ảnh hưởng của dung môi và phương pháp trích ly đến khả năng chiết tách các hợp chất phenolics, saponins và alkaloids từ vỏ quả ca cao (Theobroma cacao L.)

2020 ◽  
Vol 56(4) ◽  
pp. 71
Author(s):  
Nguyễn Văn Tặng ◽  
Trần Thị Mỹ Hạnh ◽  
Phạm Châu An ◽  
Phan Thị Bích Trâm ◽  
Huỳnh Quốc Trung ◽  
...  
Keyword(s):  
Theobroma Cacao ◽  
Theobroma Cacao L

Genetic diversity of native cultivated cacao accessions (Theobroma cacao L.) in Nicaragua

2012 ◽  
Vol 10 (3) ◽  
pp. 254-257
Author(s):  
Erwin Aragon ◽  
Claudia Rivera ◽  
Helena Korpelainen ◽  
Aldo Rojas ◽  
Paula Elomaa ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Theobroma Cacao ◽  
Phytophthora Palmivora ◽  
Genetic Composition ◽  
Breeding Programmes ◽  
Black Pod ◽  
Black Pod Disease ◽  
Parental Lines ◽  
Resistant Genotypes ◽  
Theobroma Cacao L

A total of 60 farmers' cacao accessions (Theobroma cacao L.) from Nicaragua were investigated using microsatellite markers to reveal their genetic composition and to identify potentially resistant genotypes against the black pod disease caused by Phytophthora palmivora. These accessions were compared with 21 breeders' accessions maintained locally, two Criollo accessions from Costa Rica and two accessions from Ecuador. The analyses showed a low level of differentiation among groups of farmers' accessions (FST = 0.06) and that six Nicaraguan accessions were genetically closely related to the two Criollo accessions used as a reference. In addition, seven distinct genotypes were found to have allelic composition that may indicate linkage to resistance alleles, thus being potential parental lines in future breeding programmes.

scholarly journals 99 Breed authentication of five lines comparing Structure, Admixture, and an allele frequency method

2020 ◽  
Vol 98 (Supplement_3) ◽  
pp. 25-25
Author(s):  
Austin M Putz ◽  
Patrick Charagu ◽  
Abe Huisman
Keyword(s):  
Population Structure ◽  
Allele Frequency ◽  
Regression Coefficients ◽  
Frequency Method ◽  
Large White ◽  
Reference Allele ◽  
Software Packages ◽  
The Matrix ◽  
Snp Panel ◽  
Compare And Contrast

Abstract Two commonly used population structure software packages are freely available for breed authentication, Structure and Admixture. Structure uses a Bayesian approach to model population structure, while Admixture uses a frequentist approach. More recently, an allele frequency method has been updated to use quadratic programming to constrain the multiple linear regression coefficients of the regression of genotype count (divided by two) on the matrix of allele frequencies for each known breed or line. This constraint forced coefficients to sum to one and be greater than or equal to 0 and less than or equal to 1. The goal of this research was to compare and contrast these three methods to determine the breed/line authenticity for each of the five genetic lines. These five lines included Large White, Landrace, a lean Duroc, a meat quality Duroc, and a Pietrain line. Only animals with a 50K SNP panel were used in this analysis. Analyses were run five times for Structure and Admixture to check repeatability. The allele frequency method did not need to be repeated because it remains the same as long as the reference allele frequency matrix stays constant. For Structure, results of breed composition were inconsistent across replicates. Structure separated at least one of the maternal lines in three out of the five replicates with only 500 animals and kept the Duroc lines together as one population. Only 500 animals could be utilized in each run of Structure due to computational restraints. Admixture was very consistent across runs for each animal, but also failed to separate the two Duroc lines, instead splitting one of the two maternal lines. Finally, the allele frequency method split all five lines correctly and was 100% reproducible as long as the reference allele frequency matrix stays the same across runs.

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