Limits...
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: In sorghum, a genomic and morphological model for panicoid cereals, a rich history of research into the genetics of seed size is reflected by a total of 13 likelihood intervals determined by conventional QTL (linkage) mapping in 11 nonoverlapping regions of the genome.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

Genome-wide association studies of seed length, seed mass, and seed width in 2008. (A) Manhattan plot of compressed mixed linear model (CMLM) (see Materials and Methods for details) for 2008 seed length. The 10 sorghum chromosomes are plotted against the negative base-10 logarithm of the association P value, with significance threshold denoted by the gray dashed line. The areas highlighted in green indicate likelihood intervals for seed size determined by QTL mapping. Heterochromatin and centromeres are indicated by the gray areas and black dots, respectively. (B) Manhattan plot of CMLM for 2008 seed mass. (C) Manhattan plot of CMLM for 2008 seed width.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC4478542&req=5

fig3: Genome-wide association studies of seed length, seed mass, and seed width in 2008. (A) Manhattan plot of compressed mixed linear model (CMLM) (see Materials and Methods for details) for 2008 seed length. The 10 sorghum chromosomes are plotted against the negative base-10 logarithm of the association P value, with significance threshold denoted by the gray dashed line. The areas highlighted in green indicate likelihood intervals for seed size determined by QTL mapping. Heterochromatin and centromeres are indicated by the gray areas and black dots, respectively. (B) Manhattan plot of CMLM for 2008 seed mass. (C) Manhattan plot of CMLM for 2008 seed width.

Mentions: For functional loci located in the pericentromeric region, the general lack of recombination can allow QTL likelihood intervals to cross centromeres and to cover broad genomic areas. Of the 13 QTL intervals for seed size, four cross centromeres (Table S2 and Figure 3). Mapped QTL intervals tend to have finer resolution in euchromatin, where there is more recombination generally, such as the intervals identified on chromosomes Sb02 and Sb07 (Figure 3). Rapidly growing genetic/genomic data may provide future information to discern whether additional QTL affecting seed size in sorghum are either consistent in multiple genotypes or specific to single genotypes.


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)

Genome-wide association studies of seed length, seed mass, and seed width in 2008. (A) Manhattan plot of compressed mixed linear model (CMLM) (see Materials and Methods for details) for 2008 seed length. The 10 sorghum chromosomes are plotted against the negative base-10 logarithm of the association P value, with significance threshold denoted by the gray dashed line. The areas highlighted in green indicate likelihood intervals for seed size determined by QTL mapping. Heterochromatin and centromeres are indicated by the gray areas and black dots, respectively. (B) Manhattan plot of CMLM for 2008 seed mass. (C) Manhattan plot of CMLM for 2008 seed width.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

fig3: Genome-wide association studies of seed length, seed mass, and seed width in 2008. (A) Manhattan plot of compressed mixed linear model (CMLM) (see Materials and Methods for details) for 2008 seed length. The 10 sorghum chromosomes are plotted against the negative base-10 logarithm of the association P value, with significance threshold denoted by the gray dashed line. The areas highlighted in green indicate likelihood intervals for seed size determined by QTL mapping. Heterochromatin and centromeres are indicated by the gray areas and black dots, respectively. (B) Manhattan plot of CMLM for 2008 seed mass. (C) Manhattan plot of CMLM for 2008 seed width.
Mentions: For functional loci located in the pericentromeric region, the general lack of recombination can allow QTL likelihood intervals to cross centromeres and to cover broad genomic areas. Of the 13 QTL intervals for seed size, four cross centromeres (Table S2 and Figure 3). Mapped QTL intervals tend to have finer resolution in euchromatin, where there is more recombination generally, such as the intervals identified on chromosomes Sb02 and Sb07 (Figure 3). Rapidly growing genetic/genomic data may provide future information to discern whether additional QTL affecting seed size in sorghum are either consistent in multiple genotypes or specific to single genotypes.

Bottom Line: In sorghum, a genomic and morphological model for panicoid cereals, a rich history of research into the genetics of seed size is reflected by a total of 13 likelihood intervals determined by conventional QTL (linkage) mapping in 11 nonoverlapping regions of the genome.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