Identification and mapping of conserved ortholog set (COS) II sequences of cacao and their conversion to SNP markers for marker-assisted selection in Theobroma cacao and comparative genomics studies

2011 ◽  
Vol 8 (1) ◽  
pp. 97-111 ◽  
Author(s):  
David N. Kuhn ◽  
Don Livingstone ◽  
Dorrie Main ◽  
Ping Zheng ◽  
Chris Saski ◽  
...  
Keyword(s):  
Comparative Genomics ◽  
Theobroma Cacao ◽  
Marker Assisted Selection ◽  
Snp Markers ◽  
Conserved Ortholog Set

scholarly journals Development of genic KASP SNP markers from RNA-Seq data for map-based cloning and marker-assisted selection in maize

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Zhengjie Chen ◽  
Dengguo Tang ◽  
Jixing Ni ◽  
Peng Li ◽  
Le Wang ◽  
...  
Keyword(s):  
Marker Assisted Selection ◽  
Inbred Lines ◽  
Average Density ◽  
Snp Markers ◽  
Data Sets ◽  
Rna Seq ◽  
Specific Pcr ◽  
Maize Inbred Lines ◽  
Allele Specific ◽  
Allele Specific Pcr

Abstract Background Maize is one of the most important field crops in the world. Most of the key agronomic traits, including yield traits and plant architecture traits, are quantitative. Fine mapping of genes/ quantitative trait loci (QTL) influencing a key trait is essential for marker-assisted selection (MAS) in maize breeding. However, the SNP markers with high density and high polymorphism are lacking, especially kompetitive allele specific PCR (KASP) SNP markers that can be used for automatic genotyping. To date, a large volume of sequencing data has been produced by the next generation sequencing technology, which provides a good pool of SNP loci for development of SNP markers. In this study, we carried out a multi-step screening method to identify kompetitive allele specific PCR (KASP) SNP markers based on the RNA-Seq data sets of 368 maize inbred lines. Results A total of 2,948,985 SNPs were identified in the high-throughput RNA-Seq data sets with the average density of 1.4 SNP/kb. Of these, 71,311 KASP SNP markers (the average density of 34 KASP SNP/Mb) were developed based on the strict criteria: unique genomic region, bi-allelic, polymorphism information content (PIC) value ≥0.4, and conserved primer sequences, and were mapped on 16,161 genes. These 16,161 genes were annotated to 52 gene ontology (GO) terms, including most of primary and secondary metabolic pathways. Subsequently, the 50 KASP SNP markers with the PIC values ranging from 0.14 to 0.5 in 368 RNA-Seq data sets and with polymorphism between the maize inbred lines 1212 and B73 in in silico analysis were selected to experimentally validate the accuracy and polymorphism of SNPs, resulted in 46 SNPs (92.00%) showed polymorphism between the maize inbred lines 1212 and B73. Moreover, these 46 polymorphic SNPs were utilized to genotype the other 20 maize inbred lines, with all 46 SNPs showing polymorphism in the 20 maize inbred lines, and the PIC value of each SNP was 0.11 to 0.50 with an average of 0.35. The results suggested that the KASP SNP markers developed in this study were accurate and polymorphic. Conclusions These high-density polymorphic KASP SNP markers will be a valuable resource for map-based cloning of QTL/genes and marker-assisted selection in maize. Furthermore, the method used to develop SNP markers in maize can also be applied in other species.

scholarly journals Assessing hidden parentage and genetic integrity of the “United Fruit Clones” of cacao (Theobroma cacao) from Costa Rica using SNP markers

2018 ◽  
Vol 68 (5) ◽  
pp. 545-553 ◽  
Author(s):  
Allan Mata-Quirós ◽  
Adriana Arciniegas-Leal ◽  
Wilbert Phillips-Mora ◽  
Lyndel W. Meinhardt ◽  
Lambert Motilal ◽  
...  
Keyword(s):  
Costa Rica ◽  
Theobroma Cacao ◽  
Snp Markers ◽  
Genetic Integrity

Molecular Characterization of Cacao (Theobroma cacao) Germplasm from Jamaica Using Single Nucleotide Polymorphism (SNP) Markers

2018 ◽  
Vol 11 (3-4) ◽  
pp. 93-106 ◽  
Author(s):  
Aliza A. Lindo ◽  
Dwight E. Robinson ◽  
Paula F. Tennant ◽  
Lyndel W. Meinhardt ◽  
Dapeng Zhang
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Molecular Characterization ◽  
Theobroma Cacao ◽  
Snp Markers ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide

Correlation Analysis between MyoG Gene Polymorphism and Carcass Characteristics of Egg quails

2020 ◽  
Author(s):  
Jun Yan Bai ◽  
Xiao Ping Jia ◽  
Jun Hao Lu ◽  
Shuai Yang ◽  
You Zhi Pang ◽  
...  
Keyword(s):  
Heart Rate ◽  
Gene Polymorphism ◽  
Control Region ◽  
Marker Assisted Selection ◽  
Sexual Maturity ◽  
Carcass Characteristics ◽  
Snp Markers ◽  
Muscle Weight ◽  
Leg Muscle ◽  
Production Period

Quail is extensively reared in China for characteristic of quick growth, small fodder consumption, early sexual maturity, high egg output and short production period. In this study, the SNP markers in 5’ regulation regions of cytogenin gene (MyoG) among China yellow quail, Beijing white quail and Korean quail were detected by PCR-SSCP method. Moreover, correlations of MyoG 5’ regulation regions with carcass characteristics of quail were analyzed. Results demonstrated thatin egg quail group, six genotypes were detected in Locus A in the control region of MyoG 5’, including AA, BB, CC, AB, AC and BC. The highest frequencies of CC in China yellow quail, Beijing white quail and Korean quail were 0.323, 0.366 and 0.444, respectively. A total of 9 genotypes were detected in locus B in egg quail group, which were AA, BB, CC, DD, EE, AB, AC, AD and AE. AA showed the highest frequency in China yellow quail, Beijing white quail and Korean quail, which were 0.493, 0.385 and 0.406, respectively. There was significant correlation between locus A and leg muscle rate of egg quail (plessthan0.05). Locus B presented significant correlations with carcass net weight, leg muscle weight, dressing percentage, whole net carcass rate and heart rate (plessthan0.05). Loci A and B in the control region of MyoG 5’ can be used as the molecular marker of carcass characteristics of egg quails during marker assisted selection.

scholarly journals Selecting SNP markers reflecting population origin for cacao (Theobroma cacao L.) germplasm identification

2021 ◽  
Vol 1 (0) ◽  
pp. 1-9
Author(s):  
Osman A. Gutiérrez ◽  
◽  
Kathleen Martinez ◽  
Dapeng Zhang ◽  
Donald S. Livingstone ◽  
...  
Keyword(s):  
Theobroma Cacao ◽  
Snp Markers ◽  
Germplasm Identification ◽  
Population Origin

scholarly journals Genome Wide Association Studies for Four Physiological Traits in Groundnut (Arachis hypogaea L.) Minicore Collection

2019 ◽  
Author(s):  
Abdulwahab Saliu Shaibu ◽  
Clay Sneller ◽  
Babu N. Motagi ◽  
Jackline Chepkoech ◽  
Mercy Chepngetich ◽  
...  
Keyword(s):  
Marker Assisted Selection ◽  
Association Studies ◽  
Canopy Temperature ◽  
Snp Markers ◽  
Physiological Traits ◽  
Rapid Decline ◽  
Genome Wide Association Studies ◽  
Area Index ◽  
Trait Association ◽  
Genome Wide

Abstract Background In order to integrate genomics in breeding and development of drought tolerant groundnut genotypes, identification of genomic regions/genetic markers for drought surrogate traits is essential. We used SNP markers for a genetic analysis of the ICRISAT groundnut minicore collection for genome wide marker-trait association for some physiological traits and to determine the magnitude of linkage disequilibrium (LD) present in the genetic resources. Results The LD analysis showed that about 36% of loci pairs were in significant LD (P < 0.05 and r2 > 0.2) and 3.14% of the pairs were in complete LD. There was rapid decline in LD with distance and the LD was <0.2 at a distance of 41635 bp. The marker trait association (MTAs) studies revealed 20 significant MTAs (p <0.001) with 11 markers for leaf area index (4), canopy temperature (13), chlorophyll content (1) and NDVI (2). The markers explained 2 to 21% of the phenotypic variation observed. Most of the MTAs identified on the A subgenome were also identified on the respective homeologous chromosome on the B subgenome. The duplications of effect observed could be due to common ancestor of the A and B genome which explains the linkage detected between markers lying on different chromosomes seen in the current study. Conclusions The present study identified a total of 20 highly significant marker trait associations with 11 markers for four physiological traits of importance in groundnut; LAI, CT, SCMR and NDVI. The markers identified in this study can serve as useful genomic resources to initiate marker-assisted selection and trait introgression of groundnut for drought tolerance. The identified markers in this study may be useful for marker assisted selection after further validation.

scholarly journals Genetic identification of SNP markers linked to a new grape phylloxera resistant locus in Vitis cinerea for marker-assisted selection

2018 ◽  
Vol 18 (1) ◽  
Author(s):  
Harley M. Smith ◽  
Catherine W. Clarke ◽  
Brady P. Smith ◽  
Bernadette M. Carmody ◽  
Mark R. Thomas ◽  
...  
Keyword(s):  
Marker Assisted Selection ◽  
Snp Markers ◽  
Genetic Identification ◽  
Grape Phylloxera
Sign in / Sign up

Export Citation Format

Share Document