Abstract
BSA (bulked-segregant analysis) can be defined as a rapid procedure for identifying genomic regions responsible for complex traits in crops. The method involves comparing two bulked DNA samples generated from a segregating population originating from a single cross. With the improvement of next-generation sequencing (NGS) technology, BSA combined with next-generation sequencing (NGS-BSA) has been widely applied to QTL mapping due to its high efficiency. Following a summary of widely used NGS-BSA methods, we present a novel strategy of NGS-BSA application, called as Modified QTL-seq. For Modified QTL-seq, QTL-seq analysis is performed on paired bulks,followed by multiple comparison analysis, which can significantly narrow the candidate intervals. Besides, F4:5 progeny used for additional QTL-seq analysis are only polymorphic at the target locus, which diminishs the heterosis influence on construction of bulked DNA, thus further narrowing candidate regions. Therefore, Modified QTL-seq is another optimization of NGS-BSA application. Compared with previous BSA methods, Modified QTL-seq is potential and cost-effective, and will accelerate QTL-mapping in crops.
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Abbreviations
- BSA:
-
Bulked segregant analysis
- NILs:
-
Near-isogenic lines
- NGS:
-
Next-generation sequencing
- NGS-BSA:
-
Bulked-segregant analysis combined with next-generation sequencing
- QTLs:
-
Quantitative trait loci
- MAS:
-
Marker-assisted selection
- RFLP:
-
Restriction fragment polymorphism
- RAPD:
-
Random amplified polymorphic DNA
- NGM:
-
Next generation mapping
- LD:
-
Linkage disequilibrium
- GPS:
-
Graded Pool-Seq
- PCAMP:
-
Pair-wise Comparison Analysis for Multiple Pool-seq
- SSR:
-
Simple sequence repeat
- SNP:
-
Single nucleotide polymorphism
- X-QTL:
-
Extreme QTL mapping
- RF:
-
Reference
- SV:
-
Structural variation
- WGS:
-
Whole genome sequencing
- ceX-QTL:
-
C. elegans X-QTL
- RIAILs:
-
Recombinant inbred advanced intercross lines
- IDMAS:
-
InDel markers-assisted selection
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Acknowledgements
This study was funded by Key Research Project of Specialty Industry (YCX2019T05) of Shanxi Academy of Agricultural Sciences and was conceived by Genquan Wang. On the basis of consulting a large number of scientific literatures, Xiaoyu Wang is responsible for summary, innovation and paper writing. All authors agree on the final manuscript.
Funding
Key Research Project of Specialty Industry of Shanxi Academy of Agricultural Sciences.
Number: YCX2019T05.
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Wang, X., Wang, G. Application of NGS-BSA and proposal of Modified QTL-seq. J. Plant Biochem. Biotechnol. 32, 31–39 (2023). https://doi.org/10.1007/s13562-022-00778-1
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DOI: https://doi.org/10.1007/s13562-022-00778-1