Future tools for association mapping in crop plantsThis article is one of a selection of papers from the conference “Exploiting Genome-wide Association in Oilseed Brassicas: a model for genetic improvement of major OECD crops for sustainable farming”.

Genome ◽  
2010 ◽  
Vol 53 (11) ◽  
pp. 1017-1023 ◽  
Author(s):  
Chris Duran ◽  
Dominic Eales ◽  
Daniel Marshall ◽  
Michael Imelfort ◽  
Jiri Stiller ◽  
...  
Keyword(s):  
Association Mapping ◽  
Genetic Improvement ◽  
Sequence Data ◽  
Nucleotide Polymorphisms ◽  
Snp Discovery ◽  
Single Nucleotide ◽  
Genome Wide ◽  
Oilseed Brassicas ◽  
Paired Read ◽  
Selection Of

Association mapping currently relies on the identification of genetic markers. Several technologies have been adopted for genetic marker analysis, with single nucleotide polymorphisms (SNPs) being the most popular where a reasonable quantity of genome sequence data are available. We describe several tools we have developed for the discovery, annotation, and visualization of molecular markers for association mapping. These include autoSNPdb for SNP discovery from assembled sequence data; TAGdb for the identification of gene specific paired read Illumina GAII data; CMap3D for the comparison of mapped genetic and physical markers; and BAC and Gene Annotator for the online annotation of genes and genomic sequences.

scholarly journals Statistical genetic issues for genome-wide association studiesThis article is one of a selection of papers from the conference “Exploiting Genome-wide Association in Oilseed Brassicas: a model for genetic improvement of major OECD crops for sustainable farming”.

Genome ◽  
2010 ◽  
Vol 53 (11) ◽  
pp. 869-875 ◽  
Author(s):  
Bruce S. Weir
Keyword(s):  
Quality Control ◽  
Association Mapping ◽  
Genetic Improvement ◽  
Genome Wide Association ◽  
Plant Association ◽  
Similar Activity ◽  
Genome Wide ◽  
Oilseed Brassicas ◽  
Genotyping Technology ◽  
Selection Of

Genotyping technology now allows the rapid and affordable generation of million-SNP profiles for humans, leading to considerable activity in association mapping. Similar activity is anticipated for many plant species, including Brassica . These plant association mapping activities will require the same care in quality control and quality assurance as for humans. The subsequent analyses may draw upon the same body of theory that is described here in the language of quantitative genetics.

scholarly journals Genome-Wide Association Study of Body Weight Traits in Chinese Fine-Wool Sheep

Animals ◽  
2020 ◽  
Vol 10 (1) ◽  
pp. 170 ◽  
Author(s):  
Zengkui Lu ◽  
Yaojing Yue ◽  
Chao Yuan ◽  
Jianbin Liu ◽  
Zhiqiang Chen ◽  
...  
Keyword(s):  
Body Weight ◽  
Muscle Development ◽  
Genome Wide Association Study ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Genome Wide ◽  
Economic Trait ◽  
Significance Levels ◽  
Genomic Regions ◽  
Selection Of

Body weight is an important economic trait for sheep and it is vital for their successful production and breeding. Therefore, identifying the genomic regions and biological pathways that contribute to understanding variability in body weight traits is significant for selection purposes. In this study, the genome-wide associations of birth, weaning, yearling, and adult weights of 460 fine-wool sheep were determined using resequencing technology. The results showed that 113 single nucleotide polymorphisms (SNPs) reached the genome-wide significance levels for the four body weight traits and 30 genes were annotated effectively, including AADACL3, VGF, NPC1, and SERPINA12. The genes annotated by these SNPs significantly enriched 78 gene ontology terms and 25 signaling pathways, and were found to mainly participate in skeletal muscle development and lipid metabolism. These genes can be used as candidate genes for body weight in sheep, and provide useful information for the production and genomic selection of Chinese fine-wool sheep.

scholarly journals Genotyping-by-sequencing enables linkage mapping in three octoploid cultivated strawberry families

2017 ◽  
Author(s):  
Kelly J Vining ◽  
Natalia Salinas ◽  
Jacob A Tennessen ◽  
Jason D Zurn ◽  
Daniel James Sargent ◽  
...  
Keyword(s):  
Reference Genome ◽  
Sequence Data ◽  
Genotyping By Sequencing ◽  
Nucleotide Polymorphisms ◽  
Linkage Groups ◽  
Single Nucleotide ◽  
Ancestral Species ◽  
Polymorphic Snps ◽  
Genome Wide ◽  
Diploid Ancestor

With the goal of evaluating genotyping-by-sequencing (GBS) in a species with a complex octoploid genome, GBS was used to survey genome-wide single-nucleotide polymorphisms (SNPs) in three biparental strawberry (Fragaria ×ananassa) populations. GBS sequence data were aligned to the F. vesca ‘Fvb’ reference genome in order to call SNPs. Numbers of polymorphic SNPs per population ranged from 1,163 to 3,190. Linkage maps consisting of 30-65 linkage groups were produced from the SNP sets derived from each parent. The linkage groups covered 99% of the Fvb reference genome, with three to seven linkage groups from a given parent aligned to any particular chromosome. A phylogenetic analysis performed using the POLiMAPS pipeline revealed linkage groups that were most similar to ancestral species F. vesca for each chromosome. Linkage groups that were most similar to a second ancestral species, F. iinumae, were only resolved for Fvb 4. The quantity of missing data and heterogeneity in genome coverage inherent in GBS complicated the analysis, but POLiMAPS resolved F. ×ananassa chromosomal regions derived from diploid ancestor F. vesca.

scholarly journals Genotyping-by-sequencing enables linkage mapping in three octoploid cultivated strawberry families

PeerJ ◽  
2017 ◽  
Vol 5 ◽  
pp. e3731 ◽  
Author(s):  
Kelly J. Vining ◽  
Natalia Salinas ◽  
Jacob A. Tennessen ◽  
Jason D. Zurn ◽  
Daniel James Sargent ◽  
...  
Keyword(s):  
Reference Genome ◽  
Sequence Data ◽  
Genotyping By Sequencing ◽  
Nucleotide Polymorphisms ◽  
Linkage Groups ◽  
Single Nucleotide ◽  
Ancestral Species ◽  
Polymorphic Snps ◽  
Genome Wide ◽  
Diploid Ancestor

Genotyping-by-sequencing (GBS) was used to survey genome-wide single-nucleotide polymorphisms (SNPs) in three biparental strawberry (Fragaria× ananassa) populations with the goal of evaluating this technique in a species with a complex octoploid genome. GBS sequence data were aligned to theF. vesca‘Fvb’ reference genome in order to call SNPs. Numbers of polymorphic SNPs per population ranged from 1,163 to 3,190. Linkage maps consisting of 30–65 linkage groups were produced from the SNP sets derived from each parent. The linkage groups covered 99% of theFvbreference genome, with three to seven linkage groups from a given parent aligned to any particular chromosome. A phylogenetic analysis performed using the POLiMAPS pipeline revealed linkage groups that were most similar to ancestral speciesF. vescafor each chromosome. Linkage groups that were most similar to a second ancestral species,F. iinumae, were only resolved forFvb4. The quantity of missing data and heterogeneity in genome coverage inherent in GBS complicated the analysis, but POLiMAPS resolvedF.× ananassachromosomal regions derived from diploid ancestorF. vesca.

scholarly journals Genome-wide association mapping for wood characteristics inPopulusidentifies an array of candidate single nucleotide polymorphisms

2013 ◽  
Vol 200 (3) ◽  
pp. 710-726 ◽  
Author(s):  
Ilga Porth ◽  
Jaroslav Klapšte ◽  
Oleksandr Skyba ◽  
Jan Hannemann ◽  
Athena D. McKown ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphisms ◽  
Association Mapping ◽  
Genome Wide Association ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Genome Wide

scholarly journals Genotyping-by-sequencing enables linkage mapping in three octoploid cultivated strawberry families

2017 ◽  
Author(s):  
Kelly J Vining ◽  
Natalia Salinas ◽  
Jacob A Tennessen ◽  
Jason D Zurn ◽  
Daniel James Sargent ◽  
...  
Keyword(s):  
Reference Genome ◽  
Sequence Data ◽  
Genotyping By Sequencing ◽  
Nucleotide Polymorphisms ◽  
Linkage Groups ◽  
Single Nucleotide ◽  
Ancestral Species ◽  
Polymorphic Snps ◽  
Genome Wide ◽  
Diploid Ancestor

With the goal of evaluating genotyping-by-sequencing (GBS) in a species with a complex octoploid genome, GBS was used to survey genome-wide single-nucleotide polymorphisms (SNPs) in three biparental strawberry (Fragaria ×ananassa) populations. GBS sequence data were aligned to the F. vesca ‘Fvb’ reference genome in order to call SNPs. Numbers of polymorphic SNPs per population ranged from 1,163 to 3,190. Linkage maps consisting of 30-65 linkage groups were produced from the SNP sets derived from each parent. The linkage groups covered 99% of the Fvb reference genome, with three to seven linkage groups from a given parent aligned to any particular chromosome. A phylogenetic analysis performed using the POLiMAPS pipeline revealed linkage groups that were most similar to ancestral species F. vesca for each chromosome. Linkage groups that were most similar to a second ancestral species, F. iinumae, were only resolved for Fvb 4. The quantity of missing data and heterogeneity in genome coverage inherent in GBS complicated the analysis, but POLiMAPS resolved F. ×ananassa chromosomal regions derived from diploid ancestor F. vesca.

scholarly journals Using population-specific add-on polymorphisms to improve genotype imputation in underrepresented populations

2021 ◽  
Author(s):  
Zhi Ming Xu ◽  
Sina Rüeger ◽  
Michaela Zwyer ◽  
Daniela Brites ◽  
Hellen Hiza ◽  
...  
Keyword(s):  
Association Studies ◽  
Imputation Accuracy ◽  
Genotype Imputation ◽  
Small Subset ◽  
Study Cohort ◽  
Genome Wide Association Studies ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Genome Wide ◽  
Selection Of

AbstractGenome-wide association studies rely on the statistical inference of untyped variants, called imputation, to increase the coverage of genotyping arrays. However, the results are often suboptimal in populations underrepresented in existing reference panels and array designs, since the selected single nucleotide polymorphisms (SNPs) may fail to capture population-specific haplotype structures, hence the full extent of common genetic variation. Here, we propose to sequence the full genome of a small subset of an underrepresented study cohort to inform the selection of population-specific add-on SNPs, such that the remaining array-genotyped cohort could be more accurately imputed. Using a Tanzania-based cohort as a proof-of-concept, we demonstrate the validity of our approach by showing improvements in imputation accuracy after the addition of our designed addon SNPs to the base H3Africa array.

scholarly journals Improving the Efficiency of Genomic Selection in Chinese Simmental beef cattle

2015 ◽  
Author(s):  
Jiangwei Xia ◽  
Yang Wu ◽  
Huizhong Fang ◽  
Wengang Zhang ◽  
Yuxin Song ◽  
...  
Keyword(s):  
Beef Cattle ◽  
Genomic Relationship Matrix ◽  
Relationship Matrix ◽  
Nucleotide Polymorphisms ◽  
Linear Unbiased Prediction ◽  
Single Nucleotide ◽  
Kinship Matrix ◽  
Genome Wide ◽  
Best Linear Unbiased ◽  
Selection Of

Genomic selection is an accurate and efficient method of estimating genetic merits by using high-density genome-wide single nucleotide polymorphisms (SNPs).In this study, we investigate an approach to increase the efficiency of genomic prediction by using genome-wide markers. The approach is a feature selection based on genomic best linear unbiased prediction (GBLUP),which is a statistical method used to predict breeding values using SNPs for selection in animal and plant breeding. The objective of this study is the choice of kinship matrix for genomic best linear unbiased prediction (GBLUP).The G-matrix is using the information of genome-wide dense markers. We compare three kinds of kinships based on different combinations of centring and scaling of marker genotypes.And find a suitable kinship approach that adjusts for the resource population of Chinese Simmental beef cattle.Single nucleotide polymorphism (SNPs) can be used to estimate kinship matrix and individual inbreeding coefficients more accurately. So in our research a genomic relationship matrix was developed for 1059 Chinese Simmental beef cattle using 640000 single nucleotide polymorphisms and breeding values were estimated using phenotypes about Carcass weight and Sirloin weight. The number of SNPs needed to accurately estimate a genomic relationship matrix was evaluated in this population. Another aim of this study was to optimize the selection of markers and determine the required number of SNPs for estimation of kinship in the Chinese Simmental beef cattle. We find that the feature selection of GBLUP using Xu’s and the Astle and Balding’s kinships model performed similarly well, and were the best-performing methods in our study. Inbreeding and kinship matrix can be estimated with high accuracy using ≥12,000s in Chinese Simmental beef cattle.

scholarly journals Genome-wide identification of ZmHMAs and association of natural variation in ZmHMA2 and ZmHMA3 with leaf cadmium accumulation in maize

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e7877 ◽  
Author(s):  
Yanhua Cao ◽  
Xiongwei Zhao ◽  
Yajuan Liu ◽  
Yalong Wang ◽  
Wenmei Wu ◽  
...  
Keyword(s):  
Natural Variation ◽  
Developmental Stages ◽  
Expression Patterns ◽  
Cadmium Accumulation ◽  
Functional Verification ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Cd Accumulation ◽  
Genome Wide ◽  
Selection Of

P1B-type ATPases, known as heavy metal ATPases (HMAs), play an important role in the control of cadmium (Cd) accumulation in plants. In this study, a total of 12 ZmHMA genes were identified in the maize genome and particularly classified into six clusters based on their phylogenetic relationship and motif compositions. Furthermore, the expression patterns of different ZmHMA genes varied with developmental stages, and were tissue specific under normal conditions. ZmHMA2 and ZmHMA3 genes exhibited significant up-regulation under Cd treatment. Eventually, the association analysis between 103 inbred lines and alleles in ZmHMA2 and ZmHMA3 revealed that one insertion–deletion (InDel) in the intron from ZmHMA2 was associated with leaf Cd concentration under low Cd condition at the seedling stage. Twenty polymorphisms in ZmHMA3 were significantly associated with leaf Cd concentration under various Cd levels at seedling and maturing stages. Five single nucleotide polymorphisms (SNPs) and two InDels of these significantly associated polymorphic loci from ZmHMA3 caused the amino acid substitutions and insertion or deletion events. Importantly, the proteins encoded by ZmHMA2 and ZmHMA3 genes were located in the plasma membrane. This comprehensive analysis will provide an important theoretical basis for future functional verification of ZmHMA genes to unravel the mechanisms of Cd accumulation in leaves of maize. Additionally, the favorable alleles in ZmHMA3 will lay a foundation for the marker-assisted selection of low Cd accumulation in maize.

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