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Comparative Genetics of Seed Size Traits in Divergent Cereal Lineages Represented by Sorghum (Panicoidae) and Rice (Oryzoidae).

Zhang D, Li J, Compton RO, Robertson J, Goff VH, Epps E, Kong W, Kim C, Paterson AH - G3 (Bethesda) (2015)

Bottom Line: To complement QTL data and investigate whether the discovery of seed size QTL is approaching "saturation," we compared QTL data to GWAS for seed mass, seed length, and seed width studied in 354 accessions from a sorghum association panel (SAP) that have been genotyped at 265,487 SNPs.Targeted resequencing near four association peaks with the most notable linkage disequilibrium provides further support of the role(s) of these regions in the genetic control of sorghum seed size and identifies two candidate causal variants with nonsynonymous mutations.Identifying intersections between positional and association genetic data are a potentially powerful means to mitigate constraints associated with each approach, and nonrandom correspondence of sorghum (panicoid) GWAS signals to rice (oryzoid) QTL adds a new dimension to the ability to leverage genetic data about this important trait across divergent plants.

View Article: PubMed Central - PubMed

Affiliation: Plant Genome Mapping Laboratory, University of Georgia, Athens, Georgia 30602 Institute of Bioinformatics, University of Georgia, Athens, Georgia 30602.

No MeSH data available.


Related in: MedlinePlus

Germplasm origin and population structure of 354 accessions in a U.S. sorghum association panel (Casa et al. 2008). (A) Geographic origins of 354 sorghum accessions, color-coded by morphological types. A pie chart illustrates proportions of morphology at a location. (B) PCA plots of the first two components for 265,487 SNPs. Three color-coded subgroups for 354 sorghum accessions determined by K-means clustering. (C) The spectrum of allele frequencies at the SNP site (S10_40095764) characterized in gene Sb10g018720.
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fig2: Germplasm origin and population structure of 354 accessions in a U.S. sorghum association panel (Casa et al. 2008). (A) Geographic origins of 354 sorghum accessions, color-coded by morphological types. A pie chart illustrates proportions of morphology at a location. (B) PCA plots of the first two components for 265,487 SNPs. Three color-coded subgroups for 354 sorghum accessions determined by K-means clustering. (C) The spectrum of allele frequencies at the SNP site (S10_40095764) characterized in gene Sb10g018720.

Mentions: Geographic origins and domestication history can result in patterns of phenotypic variation among genotypes within a gene pool. We investigated whether phenotypic data for components of seed size exhibited variation patterns correlated with phylogenetic models for sorghum. The population structure of 354 accessions that broadly sample taxonomic, geographic, and morphological variations in cultivated forms of Sorghum bicolor (Casa et al. 2008) was determined from 265,487 SNPs by using principal component analysis (PCA) (Figure 2B). The 354 accessions were clustered into three subgroups by applying K-means clustering to the first two components of the PCA result (Figure 2B). Group I consists mostly of Kafir-type sorghums originally from southern Africa, which show a distinct genetic pattern relative to other races (Morris et al. 2012). The seeds of Kafir are considered to be medium in size (Magness et al. 1971). Group III is composed of most Caudatum, Zerazera-caudatum, and Milo-feterita types. Caudatum-type sorghums are generally considered to originate from central Africa and have large seeds. Milo and feterita types are found in northeast Africa and generally produce very large seeds (Magness et al. 1971). The remaining sorghum botanical races form group II. Based on t-tests (Table 1), group I and group III differ significantly in 2008 seed mass and seed width (with group III being larger and wider), but not in seed length. However, the variations are not observed in 2009 and 2010 seed mass data. Group II exhibits intermediate values of seed size traits and does not show significant seed size differences with the other two groups.


Comparative Genetics of Seed Size Traits in Divergent Cereal Lineages Represented by Sorghum (Panicoidae) and Rice (Oryzoidae).

Zhang D, Li J, Compton RO, Robertson J, Goff VH, Epps E, Kong W, Kim C, Paterson AH - G3 (Bethesda) (2015)

Germplasm origin and population structure of 354 accessions in a U.S. sorghum association panel (Casa et al. 2008). (A) Geographic origins of 354 sorghum accessions, color-coded by morphological types. A pie chart illustrates proportions of morphology at a location. (B) PCA plots of the first two components for 265,487 SNPs. Three color-coded subgroups for 354 sorghum accessions determined by K-means clustering. (C) The spectrum of allele frequencies at the SNP site (S10_40095764) characterized in gene Sb10g018720.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4478542&req=5

fig2: Germplasm origin and population structure of 354 accessions in a U.S. sorghum association panel (Casa et al. 2008). (A) Geographic origins of 354 sorghum accessions, color-coded by morphological types. A pie chart illustrates proportions of morphology at a location. (B) PCA plots of the first two components for 265,487 SNPs. Three color-coded subgroups for 354 sorghum accessions determined by K-means clustering. (C) The spectrum of allele frequencies at the SNP site (S10_40095764) characterized in gene Sb10g018720.
Mentions: Geographic origins and domestication history can result in patterns of phenotypic variation among genotypes within a gene pool. We investigated whether phenotypic data for components of seed size exhibited variation patterns correlated with phylogenetic models for sorghum. The population structure of 354 accessions that broadly sample taxonomic, geographic, and morphological variations in cultivated forms of Sorghum bicolor (Casa et al. 2008) was determined from 265,487 SNPs by using principal component analysis (PCA) (Figure 2B). The 354 accessions were clustered into three subgroups by applying K-means clustering to the first two components of the PCA result (Figure 2B). Group I consists mostly of Kafir-type sorghums originally from southern Africa, which show a distinct genetic pattern relative to other races (Morris et al. 2012). The seeds of Kafir are considered to be medium in size (Magness et al. 1971). Group III is composed of most Caudatum, Zerazera-caudatum, and Milo-feterita types. Caudatum-type sorghums are generally considered to originate from central Africa and have large seeds. Milo and feterita types are found in northeast Africa and generally produce very large seeds (Magness et al. 1971). The remaining sorghum botanical races form group II. Based on t-tests (Table 1), group I and group III differ significantly in 2008 seed mass and seed width (with group III being larger and wider), but not in seed length. However, the variations are not observed in 2009 and 2010 seed mass data. Group II exhibits intermediate values of seed size traits and does not show significant seed size differences with the other two groups.

Bottom Line: To complement QTL data and investigate whether the discovery of seed size QTL is approaching "saturation," we compared QTL data to GWAS for seed mass, seed length, and seed width studied in 354 accessions from a sorghum association panel (SAP) that have been genotyped at 265,487 SNPs.Targeted resequencing near four association peaks with the most notable linkage disequilibrium provides further support of the role(s) of these regions in the genetic control of sorghum seed size and identifies two candidate causal variants with nonsynonymous mutations.Identifying intersections between positional and association genetic data are a potentially powerful means to mitigate constraints associated with each approach, and nonrandom correspondence of sorghum (panicoid) GWAS signals to rice (oryzoid) QTL adds a new dimension to the ability to leverage genetic data about this important trait across divergent plants.

View Article: PubMed Central - PubMed

Affiliation: Plant Genome Mapping Laboratory, University of Georgia, Athens, Georgia 30602 Institute of Bioinformatics, University of Georgia, Athens, Georgia 30602.

No MeSH data available.


Related in: MedlinePlus