Status and Prospects of Association Mapping in Plants

By Chengsong Zhu, Michael A. Gore, Edward S. Buckler, Jianming Yu. 2008

1,288 citations recorded by the source corpus.

There is tremendous interest in using association mapping to identify genes responsible for quantitative variation of complex traits with agricultural and evolutionary importance. Recent advances in genomic technology, impetus to exploit natural diversity, and development of robust statistical analysis methods make association mapping appealing and affordable to plant research programs. Association mapping identifies quantitative trait loci (QTLs) by examining the marker‐trait associations that can be attributed to the strength of linkage disequilibrium between markers and functional polymorphisms across a set of diverse germplasm. General understanding of association mapping has increased significantly since its debut in plants. We have seen a more concerted effort in assembling various association‐mapping populations and initiating experiments through either candidate‐gene or genome‐wide approaches in different plant species. In this review, we describe the current status of association mapping in plants and outline opportunities and challenges in complex trait dissection and genomics‐assisted crop improvement.

Subfields: Genetics, Plant Science

View Paper: https://www.semanticscholar.org/paper/336861147c14c5218e6203494406cbf43dcd0e1d

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Citations in the corpus

The genetic dissection of quantitative traits in crops (2010, background): “As reviewed by Zhu et al. (2008), population size for several association mapping studies is about 100, which is much lower compared to individuals used for linkage-based QTL mapping.”
Association Mapping: Critical Considerations Shift from Genotyping to Experimental Design (2009, background): “In addition, the number of QTL one canmap for a given phenotype is not limited towhat segregates between parents of a cross, but rather by the number of real QTL underlying the trait and the degree to which the mapping population captures the total genetic diversity available in nature (Zhu et al., ”
Molecular marker-assisted breeding options for maize improvement in Asia (2010, background): “Association mapping has been used in many crop species including maize, rice, wheat, barley, sorghum, sugarcane, soybean, potatoes, tomato, and trees such as eucalyptus, aspen and pine (Zhu et al. 2008).”
Association Mapping in Plant Genomes (2012, background): “In the absence of other forces, recombination through random mating breaks down the LD with Dt = D0 (1 – r)t, where Dt is the remaining LD between two loci after t generations of random mating from the original D0 (Zhu et al., 2008).”
Molecular approaches unravel the mechanism of acid soil tolerance in plants (2013, background): “molecular markers and traits that can be attributed to the strength of linkage disequilibrium in large populations without crossing [123].”
Characterization of a global germplasm collection and its potential utilization for analysis of complex quantitative traits in maize (2011, background): “…and selection by breeders, complex patterns of genetic relatedness are common in maize association panels, generating numerous spurious associations (Yu and Buckler 2006; Zhu et al. 2008; Myles et al. 2009), which makes correcting spurious associations a major challenge for association mapping.”
Next-generation phenotyping: requirements and strategies for enhancing our understanding of genotype–phenotype relationships and its relevance to crop improvement (2013, background): “…that have developed these kinds of publicly shared germplasm resources include rice (Zhao et al. 2011a), maize (Yu et al. 2008), wheat (Neumann et al. 2011) Arabidopsis (Atwell et al. 2010), sorghum (Mitchell et al. 2008), barley (Pasam et al. 2012) and many other species (Zhu et al. 2008).”
Marker-Assisted Plant Breeding: Principles and Practices (2015, background): “Since most plant materials will be adapted to the conditions of various localities in which they have been growing, exposed to natural and/or artificial selection, and are likely to be subjected to breeding, they would belong to the category four listed above (Zhu et al. 2008).”
Zinc nutrition in wheat-based cropping systems (2017, methodology): “Quantitative trait loci are mapped using two methods viz. association and linkage mapping (Zhu et al. 2008; Myles et al. 2009).”
Comprehending crystalline β-carotene accumulation by comparing engineered cell models and the natural carotenoid-rich system of citrus (2011, neutral): “Recently, it has been proposed that AtNRAMP1 is a high-afﬁnity Mn transporter and essential for uptake of Mn from the soil in low Mn conditions (Cailliatte et al. , 2010).”
Genetic mapping of quantitative trait loci in crops (2017, background): “[34] is becoming more and more popular, as it successfully corrects for population structure and family relatedness [2].”
Recent Updates on Salinity Stress in Rice: From Physiological to Molecular Responses (2011, methodology): “This method is more and more widely used in plants (Zhu et al., 2008), notably because sequencing and resequencing efforts now provide SNPs and InDels at the right density for such studies (Delseny et al., 2010).”
Population Structure and Linkage Disequilibrium in U.S. Barley Germplasm: Implications for Association Mapping (2010, background): “Most association studies in crop plants have used populations representing global or regional diversity (see summary in Zhu et al., 2008), including accessions from germplasm banks; the barley CAP collection, in contrast, focuses almost entirely on breeding germplasm from U.S. programs.”