Association mapping: critical considerations shift from genotyping to experimental design
Open accessAbstract
The goal of many plant scientists' research is to explain natural phenotypic variation in terms of simple changes in DNA sequence. Traditionally, linkage mapping has been the most commonly employed method to reach this goal: experimental crosses are made to generate a family with known relatedness, and attempts are made to identify cosegregation of genetic markers and phenotypes within this family. In vertebrate systems, association mapping (also known as linkage disequilibrium mapping) is increasingly being adopted as the mapping method of choice. Association mapping involves searching for genotype-phenotype correlations in unrelated individuals and often is more rapid and cost-effective than traditional linkage mapping. We emphasize here that linkage and association mapping are complementary approaches and are more similar than is often assumed. Unlike in vertebrates, where controlled crosses can be expensive or impossible (e.g., in humans), the plant scientific community can exploit the advantages of both controlled crosses and association mapping to increase statistical power and mapping resolution. While the time and money required for the collection of genotype data were critical considerations in the past, the increasing availability of inexpensive DNA sequencing and genotyping methods should prompt researchers to shift their attention to experimental design. This review provides thoughts on finding the optimal experimental mix of association mapping using unrelated individuals and controlled crosses to identify the genes underlying phenotypic variation.
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Association mapping is a powerful approach for identifying genotype-phenotype correlations within a diverse collection of germplasms or breeding materials.
“Association mapping (also known as linkage disequilibrium mapping) is a powerful approach for identifying genotype (marker)-phenotype (trait) correlations within a diverse collection of germplasms or breeding materials (Myles et al., 2009; Wang M. L. et al., 2011).”
From Development and identification of SSR markers associated with starch properties and β-carotene content in the storage root of sweet potato (Ipomoea batatas L.) (2016) · cites this paper as Myles et al., 2009
Association analyses were performed using various mixed models with subpopulation membership percentages as fixed covariates or kinship as a random effect, including naive, Q, Q+K, and K models.
“We performed association analyses using various mixed models (Yu et al., 2006; Myles et al., 2009), which with subpopulation membership percentages as fixed covariates or kinship as a random effect, including (1) naive model, without controlling for Q and K, (2) Q model, controlling for Q, (3) Q+K model, controlling for both Q and K, and (4) K model, controlling for K (Supplementary Material 6).”
From Development and identification of SSR markers associated with starch properties and β-carotene content in the storage root of sweet potato (Ipomoea batatas L.) (2016) · cites this paper as Myles et al., 2009
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Genotyping‐by‐Sequencing for Plant Breeding and Genetics
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- Authors
- Myles, S., Peiffer, J., Brown, P. J., Ersoz, E. S., Zhang, Z., Costich, D. E., & Buckler, E. S.
- Affiliations
- Cornell University (US)
- Agricultural Research Service (US)
- Venue
- The Plant Cell
- Publisher
- Oxford University Press (OUP)
- Published
- 2009-08
- Volume
- 21
- Issue
- 8
- Pages
- 2194-2202
- ISSN
- 1040-4651 (ISSN-L)
- 1532-298X
- PMC
- PMC2751942
- OpenAlex
- W2100082928
- Cited by
- 857
- References
- 69
- Citations by year
- 2026: 25 · 2025: 31 · 2024: 45 · 2023: 36 · 2022: 53 · 2021: 56 · 2020: 53 · 2019: 52 · 2018: 50 · 2017: 68 · 2016: 62 · 2015: 66 · 2014: 54 · 2013: 63 · 2012: 58
- FWCI
- 4.46
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Locations
- The Plant Cell (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Mapping and Diversity in Plants and Animals
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Associations and Epidemiology
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic and phenotypic traits in livestock
- Keywords
- association mapping, linkage mapping, linkage disequilibrium, experimental design, plant genetics, genotype-phenotype correlation, statistical power, mapping resolution, genotyping, controlled crosses
- MeSH terms
- Animals, Chromosome Mapping, Genotype, Humans, Phenotype, Research Design
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