Joint-multiple family linkage analysis predicts within-family variation better than single-family analysis of the maize nested association mapping population

Ogut, Funda; Bian, Yang; Bradbury, Peter J.; Holland, James B.

doi:10.1038/hdy.2014.123

Cited by 79 publications

(79 citation statements)

References 39 publications

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“…Population structure is another issue that could be affecting the current results. Controlling for population structure is a standard procedure in GWAS analyses, as we did by using the Q+K model; however, it reduces the statistical power to detect associations when phenotypes strongly correlate with relatedness (Reif et al, 2010;Brachi et al, 2011;Würschum et al, 2012;Ogut et al, 2015;Han et al, 2016;Klasen et al, 2016).…”

Section: Current Challenges and Perspectives Of Gwas In The Blueberrymentioning

confidence: 99%

Insights Into the Genetic Basis of Blueberry Fruit-Related Traits Using Diploid and Polyploid Models in a GWAS Context

et al. 2018

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Polyploidization is an ancient and recurrent process in plant evolution, impacting the diversification of natural populations and plant breeding strategies. Polyploidization occurs in many important crops; however, its effects on inheritance of many agronomic traits are still poorly understood compared with diploid species. Higher levels of allelic dosage or more complex interactions between alleles could affect the phenotype expression. Hence, the present study aimed to dissect the genetic basis of fruit-related traits in autotetraploid blueberries and identify candidate genes affecting phenotypic variation. We performed a genome-wide association study (GWAS) assuming diploid and tetraploid inheritance, encompassing distinct models of gene action (additive, general, different orders of allelic interaction, and the corresponding diploidized models). A total of 1,575 southern highbush blueberry individuals from a breeding population of 117 full-sib families were genotyped using sequence capture and next-generation sequencing, and evaluated for eight fruit-related traits. For the diploid allele calling, 77,496 SNPs were detected; while 80,591 SNPs were obtained in tetraploid, with a high degree of overlap (95%) between them. A linear mixed model that accounted for population and family structure was used for the GWAS analyses. By modeling tetraploid genotypes, we detected 15 SNPs significantly associated with five fruit-related traits. Alternatively, seven significant SNPs were detected for only two traits using diploid genotypes, with two SNPs overlapping with the tetraploid scenario. Our results showed that the importance of tetraploid models varied by trait and that the use of diploid models has hindered the detection of SNP-trait associations and, consequently, the genetic architecture of some commercially important traits in autotetraploid species. Furthermore, 14 SNPs co-localized with candidate genes, five of which lead to non-synonymous amino acid changes. The potential functional significance of these SNPs is discussed.

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Section: Current Challenges and Perspectives Of Gwas In The Blueberrymentioning

confidence: 99%

Insights Into the Genetic Basis of Blueberry Fruit-Related Traits Using Diploid and Polyploid Models in a GWAS Context

et al. 2018

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“…We mapped QTL across the 25 NAM families by joint-linkage (JL) analysis using a composite genetic map of ;14,000 markers (Ogut et al, 2015). This identified 162 QTL, with eight to 21 QTL per trait (Table 2; Supplemental Data Set 3) and phenotypic variance explained (PVE) of 0.6 to 48.2% (Supplemental Data Sets 4 and 5).…”

Section: Genetic Dissection Of Tocochromanol Accumulation In Maize Grainmentioning

confidence: 99%

“…The map was constructed by scoring 4892 available NAM RILs with a genotyping-bysequencing protocol (Elshire et al, 2011;Glaubitz et al, 2014) and imputing SNP markers at evenly spaced 0.1-cM intervals following a previously described procedure (Ogut et al, 2015). Using this consensus map, a previously described JL analysis procedure ) was conducted across the 25 families of the NAM population to identify and define positions of QTL controlling phenotypic variability of the 10 tocochromanol traits.…”

Section: Jl Analysismentioning

confidence: 99%

Novel Loci Underlie Natural Variation in Vitamin E Levels in Maize Grain

et al. 2017

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Tocopherols, tocotrienols, and plastochromanols (collectively termed tocochromanols) are lipid-soluble antioxidants synthesized by all plants. Their dietary intake, primarily from seed oils, provides vitamin E and other health benefits. Tocochromanol biosynthesis has been dissected in the dicot Arabidopsis thaliana, which has green, photosynthetic seeds, but our understanding of tocochromanol accumulation in major crops, whose seeds are nonphotosynthetic, remains limited. To understand the genetic control of tocochromanols in grain, we conducted a joint linkage and genome-wide association study in the 5000-line U.S. maize (Zea mays) nested association mapping panel. Fifty-two quantitative trait loci for individual and total tocochromanols were identified, and of the 14 resolved to individual genes, six encode novel activities affecting tocochromanols in plants. These include two chlorophyll biosynthetic enzymes that explain the majority of tocopherol variation, which was not predicted given that, like most major cereal crops, maize grain is nonphotosynthetic. This comprehensive assessment of natural variation in vitamin E levels in maize establishes the foundation for improving tocochromanol and vitamin E content in seeds of maize and other major cereal crops.

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“…An iterative process of imputation and linkage mapping was conducted to produce a final consensus linkage map with complete map scores at 7386 pseudomarkers with a uniform resolution of 0.2 cM per marker (Swarts et al 2014;Ogut et al 2015).…”

Section: Nam Genotype Datamentioning

confidence: 99%

Genetic Architecture of Domestication-Related Traits in Maize

et al. 2016

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Strong directional selection occurred during the domestication of maize from its wild ancestor teosinte, reducing its genetic diversity, particularly at genes controlling domestication-related traits. Nevertheless, variability for some domestication-related traits is maintained in maize. The genetic basis of this could be sequence variation at the same key genes controlling maize-teosinte differentiation (due to lack of fixation or arising as new mutations after domestication), distinct loci with large effects, or polygenic background variation. Previous studies permit annotation of maize genome regions associated with the major differences between maize and teosinte or that exhibit population genetic signals of selection during either domestication or postdomestication improvement. Genome-wide association studies and genetic variance partitioning analyses were performed in two diverse maize inbred line panels to compare the phenotypic effects and variances of sequence polymorphisms in regions involved in domestication and improvement to the rest of the genome. Additive polygenic models explained most of the genotypic variation for domesticationrelated traits; no large-effect loci were detected for any trait. Most trait variance was associated with background genomic regions lacking previous evidence for involvement in domestication. Improvement sweep regions were associated with more trait variation than expected based on the proportion of the genome they represent. Selection during domestication eliminated large-effect genetic variants that would revert maize toward a teosinte type. Small-effect polygenic variants (enriched in the improvement sweep regions of the genome) are responsible for most of the standing variation for domestication-related traits in maize.KEYWORDS quantitative trait loci; nested association mapping; genome-wide association study; variance components; Zea mays T HE domestication of all major crop plants occurred in a relatively short period in human history, starting 10,000 years ago (Harlan 1992). During the domestication process, seeds of preferred forms were selected and saved to plant subsequent generations. Some alleles favored under domestication may have been neutral or even deleterious for the survival of wild plant species; for example, seed shattering promotes seed dispersal in wild grasses, but alleles for nondisarticulating seed structures were strongly selected for under domestication (Galinat 1983). Consequently, rare alleles favorable for growth and development under agricultural conditions or for traits desired by humans increased in frequency, often reaching fixation and reducing genetic variation very near causal sequence sites (Wang et al. 1999). In addition, domestication was often accompanied by severe genetic bottlenecks from the use of small founder populations. The reduction in effective population sizes also resulted in reduced genetic diversity genome-wide. Population genetics methods to model the strength and duration of bottlenecks provide a means to ...

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Joint-multiple family linkage analysis predicts within-family variation better than single-family analysis of the maize nested association mapping population

Cited by 79 publications

References 39 publications

Insights Into the Genetic Basis of Blueberry Fruit-Related Traits Using Diploid and Polyploid Models in a GWAS Context

Insights Into the Genetic Basis of Blueberry Fruit-Related Traits Using Diploid and Polyploid Models in a GWAS Context

Novel Loci Underlie Natural Variation in Vitamin E Levels in Maize Grain

Genetic Architecture of Domestication-Related Traits in Maize

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