Advanced Strategies in Bulked Segregant Analysis and its Applications

Bhartiya Krishi Anusandhan Patrika ◽

10.18805/bkap327 ◽

2021 ◽

Author(s):

Harshavardan J. Hilli

Keyword(s):

Genetic Markers ◽

Mapping Population ◽

Bulked Segregant Analysis ◽

High Density ◽

Mutant Phenotype ◽

Linkage Maps ◽

Quick Method ◽

Reduced Time

Bulked segregant analysis (BSA) is a technique used to identify genetic markers associated with a mutant phenotype and is a quick method for identifying markers in particular genome regions. The paper focussed on Advanced methods which escape the requirement of genotyping all the individuals of the mapping population and generation of high-density linkage maps for mapping of the gene for the trait of interest. With the emergence of re-sequencing techniques, quick mapping of genes has become possible with reduced time and cost by using advanced methodologies like MutMap, MutMap+, MutMap-Gap, QTL-Seq, RNAseq BSA, NGS BSA and QTG seq. The procedure for various advanced BSA strategies has been described.

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Selective Mapping: A Strategy for Optimizing the Construction of High-Density Linkage Maps

Genetics ◽

10.1093/genetics/155.1.407 ◽

2000 ◽

Vol 155 (1) ◽

pp. 407-420

Author(s):

Todd J Vision ◽

Daniel G Brown ◽

David B Shmoys ◽

Richard T Durrett ◽

Steven D Tanksley

Keyword(s):

Mapping Population ◽

High Density ◽

Linkage Maps ◽

Radiation Hybrids ◽

Genome Wide ◽

Stochastic Optimization Problem ◽

Radiation Induced ◽

Selective Mapping ◽

Map Resolution ◽

Mapping Populations

Abstract Historically, linkage mapping populations have consisted of large, randomly selected samples of progeny from a given pedigree or cell lines from a panel of radiation hybrids. We demonstrate that, to construct a map with high genome-wide marker density, it is neither necessary nor desirable to genotype all markers in every individual of a large mapping population. Instead, a reduced sample of individuals bearing complementary recombinational or radiation-induced breakpoints may be selected for genotyping subsequent markers from a large, but sparsely genotyped, mapping population. Choosing such a sample can be reduced to a discrete stochastic optimization problem for which the goal is a sample with breakpoints spaced evenly throughout the genome. We have developed several different methods for selecting such samples and have evaluated their performance on simulated and actual mapping populations, including the Lister and Dean Arabidopsis thaliana recombinant inbred population and the GeneBridge 4 human radiation hybrid panel. Our methods quickly and consistently find much-reduced samples with map resolution approaching that of the larger populations from which they are derived. This approach, which we have termed selective mapping, can facilitate the production of high-quality, high-density genome-wide linkage maps.

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Genomic Resource Development for Hydrangea (Hydrangea macrophylla (Thunb.) Ser.)—A Transcriptome Assembly and a High-Density Genetic Linkage Map

Horticulturae ◽

10.3390/horticulturae7020025 ◽

2021 ◽

Vol 7 (2) ◽

pp. 25

Author(s):

Xingbo Wu ◽

Amanda M. Hulse-Kemp ◽

Phillip A. Wadl ◽

Zach Smith ◽

Keithanne Mockaitis ◽

...

Keyword(s):

Genetic Resources ◽

Linkage Map ◽

Genetic Linkage ◽

Genetic Linkage Map ◽

Mapping Population ◽

High Density ◽

Linkage Maps ◽

Map Construction ◽

Hydrangea Macrophylla ◽

Genetic Linkage Maps

Hydrangea (Hydrangea macrophylla) is an important ornamental crop that has been cultivated for more than 300 years. Despite the economic importance, genetic studies for hydrangea have been limited by the lack of genetic resources. Genetic linkage maps and subsequent trait mapping are essential tools to identify and make markers available for marker-assisted breeding. A transcriptomic study was performed on two important cultivars, Veitchii and Endless Summer, to discover simple sequence repeat (SSR) markers and an F1 population based on the cross ‘Veitchii’ × ‘Endless Summer’ was established for genetic linkage map construction. Genotyping by sequencing (GBS) was performed on the mapping population along with SSR genotyping. From an analysis of 42,682 putative transcripts, 8780 SSRs were identified and 1535 were validated in the mapping parents. A total of 267 polymorphic SSRs were selected for linkage map construction. The GBS yielded 3923 high quality single nucleotide polymorphisms (SNPs) in the mapping population, resulting in a total of 4190 markers that were used to generate maps for each parent and a consensus map. The consensus linkage map contained 1767 positioned markers (146 SSRs and 1621 SNPs), spanned 1383.4 centiMorgans (cM), and was comprised of 18 linkage groups, with an average mapping interval of 0.8 cM. The transcriptome information and large-scale marker development in this study greatly expanded the genetic resources that are available for hydrangea. The high-density genetic linkage maps presented here will serve as an important foundation for quantitative trait loci mapping, map-based gene cloning, and marker-assisted selection of H. macrophylla.

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Investigation of genetic markers for intramuscular fat in the hybrid Wagyu cattle with bulked segregant analysis

Scientific Reports ◽

10.1038/s41598-021-91101-w ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Yun Zhu ◽

Liyun Han ◽

Peng Li ◽

Xiaolong Kang ◽

Xingang Dan ◽

...

Keyword(s):

Molecular Markers ◽

Beef Cattle ◽

Genetic Markers ◽

Bulked Segregant Analysis ◽

Low Cost ◽

Intramuscular Fat ◽

Mixed Population ◽

High Density ◽

Genome Wide ◽

Qtls Mapping

Abstractulked Segregant Analysis (BSA) is a rapid strategy for identifying genetic markers in specific regions of the phenotypical population and it has been widely used for QTLs mapping in smaller mixed F2 and F3 populations. We applied a modified BSA method to assessed genome-wide homozygous and heterozygous linkage patterns in the Chinese Wagyu Beef Cattle F2/F3 mixed population. Two overlapped regions from F2 and F3 populations on autosomes were found with high-density heterozygote alleles between high and low intramuscular fat groups. Regions from 24.8 M ~ 29.6 M of chromosome 23 were identified as most significantly correlated to the intramuscular fat in our samples. We also identified other 4 potential loci on chromosomes 5, 9, 15, and 21 correlated with Intramuscular fat. This study provided a novel low-cost method for QTLs mapping and identify molecular markers of phenotypical changes in a small mixed population.

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Investigation of Genetic Markers for Intramuscular Fat in the Hybrid Wagyu Cattle With Bulked Segregant Analysis

10.21203/rs.3.rs-277670/v1 ◽

2021 ◽

Author(s):

Yun Zhu ◽

Liyun Han ◽

Peng Li ◽

Xiaolong Kang ◽

Xingang Dan ◽

...

Keyword(s):

Molecular Markers ◽

Beef Cattle ◽

Genetic Markers ◽

Bulked Segregant Analysis ◽

Low Cost ◽

Intramuscular Fat ◽

Mixed Population ◽

High Density ◽

Genome Wide ◽

Qtls Mapping

Abstract Bulked Segregant Analysis（BSA）is a rapid strategy for identifying genetic markers in specific regions of the phenotypical population and it has been widely used for QTLs mapping in smaller mixed F2 and F3 populations. We applied a modified BSA method to assessed genome-wide homozygous and heterozygous linkage patterns in the Chinese Wagyu Beef Cattle F2/F3 mixed population. Two overlapped regions from F2 and F3 populations on autosomes were found with high-density heterozygote alleles between high and low intramuscular fat groups. Regions from 24.8M~29.6M of chromosome 23 were identified as most significantly correlated to the intramuscular fat in our samples. We also identified other 4 potential loci on chromosomes 5, 9, 15, and 21 correlated with Intramuscular fat. This study provided a novel low-cost method for QTLs mapping and identify molecular markers of phenotypical changes in a small mixed population.

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