UNIVERSITY OF AGRICULTURAL SCIENCES, GKVK, BANGALORE
DEPARTMENT OF GENETICS AND PLANT BREEDING
SEMINAR – GPB 581 (0+1)
“Strategies for linkage mapping of oligogenes”
Name: Kuldeep Saikia Date: 13-01-2024
ID No: PAMB 2223 Synopsis Time: 09:00 AM
Plant breeders have traditionally developed crop varieties using phenotype-based selection. With the
development of molecular markers, marker assisted selection (MAS) has become an important tool in plant
breeding. Identification of the genomic regions harboring the gene (s) of interest with a high resolution and
detection of molecular markers tightly linked to the gene (s) of interest (these processes are referred to as gene
mapping) are the prerequisite to implement MAS.
The general approach for gene mapping involves genotyping the entire mapping population with a
large number of polymorphic markers. However, this would involve considerable genotyping work, and the
chances of finding a marker closely linked to the gene of interest would be small1. To address this issue,
alternate strategies such as, bulked segregant analysis (BSA) and selective genotyping have been recommended
mapping genes1. The primary aim of these alternate strategies is to identify markers putatively linked to the
target gene/trait from among a large number of markers without genotyping the entire mapping population.
BSA and selective genotyping strategies are based on the principle of genotyping only extreme
phenotypic groups. The rationale of these strategies is that the extreme phenotypes in a mapping population
contains most of the linkage information. In BSA approach, DNA is bulked from both extreme phenotypic
groups for marker genotyping; and a marker allele showing polymorphism between both the bulks is likely to
be linked to the trait/gene.1 In the first study based on BSA, Michelmore et al. (1991) detected RAPD markers
linked to the Dm518 that confers resistance to downy mildew in lettuce2.
In selective genotyping, DNA is extracted at individual plant level from each of the extreme
phenotypic groups. Within selective genotyping, two strategies, namely (1) unidirectional and (2) bidirectional
mapping are followed. In unidirectional selective genotyping, significant departure of marker allele frequency
from 0.5 is regarded as an evidence for marker-trait linkage. In bidirectional selective genotyping, significant
differences in allelic frequency between the two extreme phenotypic groups is considered as an evidence for
marker-trait linkage. In a study based on selective genotyping, Gonal et al. (2023) detected two SSR markers
linked to the trait flowering time in dolichos bean3.
BSA and selective genotyping strategies can further be coupled with NGS based approaches to
increase precision and efficiency.
References
1
.SINGH, B. D. AND SINGH, A. K., 2015, Linkage Mapping of Molecular Markers and Oligogenes. Marker-
Assisted Plant Breeding: Principles and Practices 151–183.
2
.MLCHELMORE, R. W., PARAN, I. AND KESSELI, R. V., 1991, Identification of markers linked to
disease-resistance genes by bulked segregant analysis: A rapid method to detect markers in
specific genomic regions by using segregating populations. Proceedings of the National
Academy of Sciences U. S. A., 88, 9828–9832.
3
.GONAL, B., RAMESH, S., RANJITHA, G.V., KALPANA, M.P., SIDDU, B.C., SATISH, H.,
KIRANKUMAR, R. AND ANIKET, S., 2023, Selective genotyping for discovery of QTL
controlling flowering time in dolichos bean (Lablab purpureus L.). Crop Breeding and Applied
Biotechnology., 23, p.e44182327.
