Ten Years of the Maize Nested Association Mapping Population: Impact, Limitations, and Future Directions

Gage, Joseph L.; Monier, Brandon; Giri, Anju; Buckler, Edward S.

doi:10.1105/tpc.19.00951

Cited by 101 publications

(78 citation statements)

References 76 publications

(112 reference statements)

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“…Temperate maize in the United States is much older with adaptation to temperate highlands occurring over an approximate 2,000 year period starting 4,000 years ago, allowing for more gradual selection and therefore less likely to capture pleiotropic loci 96 . Similarly, many of the lines in the SAP trace their origin to a conversion process where genes needed for temperate adaptation were introgressed through multiple generations of strong phenotypic selection 20,23 , while both the most widely employed maize association panel and the maize nested association panel were assembled from lines already adapted to the temperate United States 6,97 .…”

Section: Discussionmentioning

confidence: 99%

Meta-Analysis Identifies Pleiotropic Loci Controlling Phenotypic Trade-offs in Sorghum

Mural

Grzybowski

Miao

et al. 2020

Preprint

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Community association populations are composed of phenotypically and genetically diverse accessions. Once these populations are genotyped, the resulting marker data can be reused by different groups investigating the genetic basis of different traits. Because the same genotypes are observed and scored for a wide range of traits in different environments, these populations represent a unique resource to investigate both pleiotropy and genotype by environment interactions. Here we assembled a set of 234 separate trait datasets for the Sorghum Association Panel, a group of 406 sorghum genotypes widely employed by the sorghum genetics community. Comparison of genome wide association studies conducted with two independently generated marker sets for this population demonstrate that existing genetic marker sets do not saturate the genome and likely capture only 35-43% of potentially detectable loci controlling variation for traits scored in this population. While limited evidence for pleiotropy was apparent in cross GWAS comparisons, a multivariate adaptive shrinkage approach recovered both known pleiotropic effects of existing loci and new pleiotropic effects, particularly significant impacts of known dwarfing genes on root architecture. In addition, we identified new loci with pleiotropic effects consistent with known trade-offs in sorghum development. These results demonstrate the potential for mining existing trait datasets from widely used community association populations to enable new discoveries from existing trait datasets as new, denser genetic marker datasets are generated for existing community association populations.

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Section: Discussionmentioning

confidence: 99%

Meta-Analysis Identifies Pleiotropic Loci Controlling Phenotypic Trade-offs in Sorghum

Mural

Grzybowski

Miao

et al. 2020

Preprint

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“…However, although the overall diversity can be large, the recurrent founder in NAM limits the haplotypic diversity within any family of RILs (Ladejobi et al 2016). Furthermore, the benefits of increasing genetic diversity by adding founders may need to be balanced against the number of RILs developed from each cross (Gage et al 2020;. We also note that tailored mapping methods may be required to account for differing recombination frequencies among the NAM's constituent bi-parental families (Li et al 2011).…”

Section: Crossing Designmentioning

confidence: 99%

“…Table 2 summarises the traits mapped just in crop MAGIC populations, encompassing simple to complex traits and exemplifying their utility in dissecting the genetic architecture of crop phenotypes. For example, 75-80% of the phenotypic variance in leaf length, width and angle in a large maize NAM population can be accounted for by more than 30 QTL that have been identified (Tian et al 2011;Gage et al 2020). One purpose of mapping QTL is to understand the genetic basis of traits and to identify markers that can be used in breeding programmes.…”

Section: Applications Of Mppsmentioning

confidence: 99%

“…MPPs offer an opportunity to identify correlations between traits that are truly caused by a shared underlying genetic basis. For example, in a maize NAM, leaf length, width and angle have weak correlations (0.03-0.08) and share only 2-6% of QTL (Tian et al 2011) whereas different carbon and nitrogen metabolites are more highly correlated (up to 0.7) and share QTL (Zhang et al 2015;Gage et al 2020).…”

Section: Multi-trait Analysesmentioning

confidence: 99%

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Multi-parent populations in crops: a toolbox integrating genomics and genetic mapping with breeding

Scott¹,

Ladejobi²,

et al. 2020

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Crop populations derived from experimental crosses enable the genetic dissection of complex traits and support modern plant breeding. Among these, multi-parent populations now play a central role. By mixing and recombining the genomes of multiple founders, multi-parent populations combine many commonly sought beneficial properties of genetic mapping populations. For example, they have high power and resolution for mapping quantitative trait loci, high genetic diversity and minimal population structure. Many multi-parent populations have been constructed in crop species, and their inbred germplasm and associated phenotypic and genotypic data serve as enduring resources. Their utility has grown from being a tool for mapping quantitative trait loci to a means of providing germplasm for breeding programmes. Genomics approaches, including de novo genome assemblies and gene annotations for the population founders, have allowed the imputation of rich sequence information into the descendent population, expanding the breadth of research and breeding applications of multi-parent populations. Here, we report recent successes from crop multi-parent populations in crops. We also propose an ideal genotypic, phenotypic and germplasm 'package' that multi-parent populations should feature to optimise their use as powerful community resources for crop research, development and breeding. Over recent years, numerous multi-parent populations (MPPs) have been successfully developed in crops (Huang et al. 2015; Cockram and Mackay 2018). MPPs bring together key genomic, phenotypic and germplasm resources to form a

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“…It represents a highly studied set of ~5,000 recombinant inbred lines, generated from the single seed descent of an F1 crossing between 25 diverse maize inbreds and into a common parent, B73 (McMullen et al, 2009), allowing for the dissection of the genetic components underlying the control of maize phenotypes. The NAM population mapping resource (Buckler et al, 2009) has been utilized to identify quantitative trait loci for various complex traits (Gage et al, 2020). A recent NSF funded project (NAM Genomes Project, 2020) has produced extremely high-quality chromosome level assemblies of the NAM founders by combining long-read sequencing and optical mapping technologies.…”

Section: Introductionmentioning

confidence: 99%

A Maize Practical Haplotype Graph Leverages Diverse NAM Assemblies

Franco

Gage

Bradbury

et al. 2020

Preprint

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As a result of millions of years of transposon activity, multiple rounds of ancient polyploidization, and large populations that preserve diversity, maize has an extremely structurally diverse genome, evidenced by high-quality genome assemblies that capture substantial levels of both tropical and temperate diversity. We generated a pangenome representation (the Practical Haplotype Graph, PHG) of these assemblies in a database, representing the pangenome haplotype diversity and providing an initial estimate of structural diversity. We leveraged the pangenome to accurately impute haplotypes and genotypes of taxa using various kinds of sequence data, ranging from WGS to extremely-low coverage GBS. We imputed the genotypes of the recombinant inbred lines of the NAM population with over 99% mean accuracy, while unrelated germplasm attained a mean imputation accuracy of 92 or 95% when using GBS or WGS data, respectively. Most of the imputation errors occur in haplotypes within European or tropical germplasm, which have yet to be represented in the maize PHG database. Also, the PHG stores the imputation data in a 30,000-fold more space-efficient manner than a standard genotype file, which is a key improvement when dealing with large scale data.

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Ten Years of the Maize Nested Association Mapping Population: Impact, Limitations, and Future Directions

Cited by 101 publications

References 76 publications

Meta-Analysis Identifies Pleiotropic Loci Controlling Phenotypic Trade-offs in Sorghum

Meta-Analysis Identifies Pleiotropic Loci Controlling Phenotypic Trade-offs in Sorghum

Multi-parent populations in crops: a toolbox integrating genomics and genetic mapping with breeding

A Maize Practical Haplotype Graph Leverages Diverse NAM Assemblies

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