Bulk segregation analysis in the NGS era: a review of its teenage years

SUMMARY Bulk segregation analysis (BSA) utilizes a strategy of pooling individuals with extreme phenotypes to conduct economical and rapidly linked marker screening or quantitative trait locus (QTL) mapping. With the development of next‐generation sequencing (NGS) technology in the past 10 years, BS...

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Bibliographic Details
Published in:The Plant journal : for cell and molecular biology Vol. 109; no. 6; pp. 1355 - 1374
Main Authors: Li, Zhiqiang, Xu, Yuhui
Format: Journal Article
Language:English
Published: England Blackwell Publishing Ltd 01.03.2022
Subjects:
Algorithms
Aquatic animals
Aquatic insects
bulk segregation analysis (BSA)
bulked segregant RNA‐seq (BSR‐seq)
Chromosome Mapping - methods
Crops
Crops, Agricultural - genetics
fine mapping
Gene mapping
Grain crops
High-Throughput Nucleotide Sequencing - methods
Horticultural crops
horticulture
Insects
landscapes
Mapping
mapping algorithm
next‐generation sequencing (NGS)
Phenotype
Phenotypes
Polymorphism, Single Nucleotide
population
Quantitative trait loci
Quantitative Trait Loci - genetics
threshold
Yeast
yeasts
bulked segregant RNA-seq (BSR-seq)
next-generation sequencing (NGS)
mapping algorithm
threshold
bulk segregation analysis (BSA)
fine mapping
population
ISSN:0960-7412, 1365-313X, 1365-313X
Online Access:Get full text
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Summary:SUMMARY Bulk segregation analysis (BSA) utilizes a strategy of pooling individuals with extreme phenotypes to conduct economical and rapidly linked marker screening or quantitative trait locus (QTL) mapping. With the development of next‐generation sequencing (NGS) technology in the past 10 years, BSA methods and technical systems have been gradually developed and improved. At the same time, the ever‐decreasing costs of sequencing accelerate NGS‐based BSA application in different species, including eukaryotic yeast, grain crops, economic crops, horticultural crops, trees, aquatic animals, and insects. This paper provides a landscape of BSA methods and reviews the BSA development process in the past decade, including the sequencing method for BSA, different populations, different mapping algorithms, associated region threshold determination, and factors affecting BSA mapping. Finally, we summarize related strategies in QTL fine mapping combining BSA. Significance Statement This paper provides a landscape of BSA methods in the next‐generation sequencing (NGS) era and a guideline to select a proper method for bulk segregation analysis mapping design. In addition, quantitative trait locus fine mapping strategies are summarized for researchers in the field.
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ISSN:0960-7412
1365-313X
1365-313X
DOI:10.1111/tpj.15646