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Resolution of genetic map expansion caused by excess heterozygosity in plant recombinant inbred populations.

Truong SK, McCormick RF, Morishige DT, Mullet JE - G3 (Bethesda) (2014)

Bottom Line: We implement this model using the existing open-source genetic map construction code base for R/qtl to estimate recombination fractions.Finally, we show that accounting for excess heterozygosity in a sorghum recombinant inbred mapping population shrinks the genetic map by 213 cM (a 13% decrease corresponding to 4.26 fewer recombinations per meiosis).More accurate estimates of linkage benefit linkage-based analyses used in the identification and utilization of causal genetic variation.

View Article: PubMed Central - PubMed

Affiliation: Interdisciplinary Program in Genetics, Texas A&M University, College Station, Texas 77843 Biochemistry & Biophysics Department, Texas A&M University, College Station, Texas 77843.

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Excess heterozygosity in a sorghum mapping population. Box plot of genotype frequencies of 398 individuals of the BT×623 × IS3620C recombinant inbred population. Each individual has a percentage of its genotypes that are homozygous or heterozygous for a BT×623 parental allele, A, and IS3620C parental allele, a. The dashed red lines represent the expected genotype frequencies under the assumptions of Mendelian segregation. The expected heterozygous frequency is lower than the median observed.
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fig2: Excess heterozygosity in a sorghum mapping population. Box plot of genotype frequencies of 398 individuals of the BT×623 × IS3620C recombinant inbred population. Each individual has a percentage of its genotypes that are homozygous or heterozygous for a BT×623 parental allele, A, and IS3620C parental allele, a. The dashed red lines represent the expected genotype frequencies under the assumptions of Mendelian segregation. The expected heterozygous frequency is lower than the median observed.

Mentions: To demonstrate that accounting for excess heterozygosity can shrink the genetic map of a plant recombinant inbred population (as postulated by Knox and Ellis 2002), we applied our method to a sorghum recombinant inbred population displaying excess heterozygosity (Burow et al. 2011). The members of the population ranged from F7 to F9 and exhibit more than a 300% increase in heterozygosity relative to the expected heterozygosity given a Mendelian model: 6.7% observed after our quality control steps vs. 1.6% given a Mendelian model for t = 7 (Figure 2). Heterozygosity was present at elevated levels throughout the genome relative to expectations under a Mendelian model, although some regions deviated notably from the average (Figure 3, Figure S2, and Figure S3). Previous reports estimating the genetic map as an RIL that has gone to fixation for this sorghum population range from 1279 cM to 1713 cM, a difference of 8.48 recombinations per meiosis (Table S2) (Peng et al. 1999; Hart et al. 2001; Menz et al. 2002; Mace et al. 2009; Burow et al. 2011).


Resolution of genetic map expansion caused by excess heterozygosity in plant recombinant inbred populations.

Truong SK, McCormick RF, Morishige DT, Mullet JE - G3 (Bethesda) (2014)

Excess heterozygosity in a sorghum mapping population. Box plot of genotype frequencies of 398 individuals of the BT×623 × IS3620C recombinant inbred population. Each individual has a percentage of its genotypes that are homozygous or heterozygous for a BT×623 parental allele, A, and IS3620C parental allele, a. The dashed red lines represent the expected genotype frequencies under the assumptions of Mendelian segregation. The expected heterozygous frequency is lower than the median observed.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4199702&req=5

fig2: Excess heterozygosity in a sorghum mapping population. Box plot of genotype frequencies of 398 individuals of the BT×623 × IS3620C recombinant inbred population. Each individual has a percentage of its genotypes that are homozygous or heterozygous for a BT×623 parental allele, A, and IS3620C parental allele, a. The dashed red lines represent the expected genotype frequencies under the assumptions of Mendelian segregation. The expected heterozygous frequency is lower than the median observed.
Mentions: To demonstrate that accounting for excess heterozygosity can shrink the genetic map of a plant recombinant inbred population (as postulated by Knox and Ellis 2002), we applied our method to a sorghum recombinant inbred population displaying excess heterozygosity (Burow et al. 2011). The members of the population ranged from F7 to F9 and exhibit more than a 300% increase in heterozygosity relative to the expected heterozygosity given a Mendelian model: 6.7% observed after our quality control steps vs. 1.6% given a Mendelian model for t = 7 (Figure 2). Heterozygosity was present at elevated levels throughout the genome relative to expectations under a Mendelian model, although some regions deviated notably from the average (Figure 3, Figure S2, and Figure S3). Previous reports estimating the genetic map as an RIL that has gone to fixation for this sorghum population range from 1279 cM to 1713 cM, a difference of 8.48 recombinations per meiosis (Table S2) (Peng et al. 1999; Hart et al. 2001; Menz et al. 2002; Mace et al. 2009; Burow et al. 2011).

Bottom Line: We implement this model using the existing open-source genetic map construction code base for R/qtl to estimate recombination fractions.Finally, we show that accounting for excess heterozygosity in a sorghum recombinant inbred mapping population shrinks the genetic map by 213 cM (a 13% decrease corresponding to 4.26 fewer recombinations per meiosis).More accurate estimates of linkage benefit linkage-based analyses used in the identification and utilization of causal genetic variation.

View Article: PubMed Central - PubMed

Affiliation: Interdisciplinary Program in Genetics, Texas A&M University, College Station, Texas 77843 Biochemistry & Biophysics Department, Texas A&M University, College Station, Texas 77843.

Show MeSH
Related in: MedlinePlus