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Association mapping of stigma and spikelet characteristics in rice (Oryza sativa L.).

Yan WG, Li Y, Agrama HA, Luo D, Gao F, Lu X, Ren G - Mol. Breed. (2009)

Bottom Line: Four markers were associated with single stigma exsertion (SStgE), six with dual exsertion (DStgE) and five with total exsertion.Four markers were associated with spikelet length, three with width and seven with L/W ratio.Numerous markers were co-associated with multiple traits that were phenotypically correlated, i.e. RM12521_Chr2 associated with all three correlated spikelet traits.

View Article: PubMed Central - PubMed

ABSTRACT
Stigma and spikelet characteristics play an essential role in hybrid seed production. A mini-core of 90 accessions developed from USDA rice core collection was phenotyped in field grown for nine traits of stigma and spikelet and genotyped with 109 DNA markers, 108 SSRs plus an indel. Three major clusters were built upon Rogers' genetic distance, indicative of indicas, and temperate and tropical japonicas. A mixed linear model combining PC-matrix and K-matrix was adapted for mapping marker-trait associations. Resulting associations were adjusted using false discovery rate technique. We identified 34 marker-trait associations involving 22 SSR markers for eight traits. Four markers were associated with single stigma exsertion (SStgE), six with dual exsertion (DStgE) and five with total exsertion. RM5_Chr1 played major role indicative of high regression with not only DStgE but also SStgE. Four markers were associated with spikelet length, three with width and seven with L/W ratio. Numerous markers were co-associated with multiple traits that were phenotypically correlated, i.e. RM12521_Chr2 associated with all three correlated spikelet traits. The co-association should improve breeding efficiency because single marker could be used to assist breeding for multiple traits. Indica entry 1032 (cultivar 50638) and japonica entry 671 (cultivar Linia 84 Icar) with 80.65 and 75.17% of TStgE, respectively are recommended to breeder for improving stigma exsertion. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1007/s11032-009-9290-y) contains supplementary material, which is available to authorized users.

No MeSH data available.


Related in: MedlinePlus

Marker-trait associations tested with false discovery rate (−log10FDR > 3) corrected from P values with 90 accessions as a mini-core collection and reference cultivars genotyped with 109 molecular markers for percentage of single (SStgE), dual (SStgE) and total stigma exsertion (TStgE), stigma length (StgL), width (StgW) and L/W ratio (StgL/W) and spikelet length (SpkL), width (SpkW) and L/W ratio (SpkL/W)
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Fig6: Marker-trait associations tested with false discovery rate (−log10FDR > 3) corrected from P values with 90 accessions as a mini-core collection and reference cultivars genotyped with 109 molecular markers for percentage of single (SStgE), dual (SStgE) and total stigma exsertion (TStgE), stigma length (StgL), width (StgW) and L/W ratio (StgL/W) and spikelet length (SpkL), width (SpkW) and L/W ratio (SpkL/W)

Mentions: Based on the criterion P-value less than 0.001 with 109 markers for nine traits, we identified 45 significant marker-trait associations involving 33 markers (Fig. 6). After false discovery rate (FDR) correction, 34 of these associations involving 22 markers remained significant at P < 0.001 (−log10FDR > 3.0) (Table 2). Among 34 marker-trait associations, dual stigma exsertion (DStgE) with RM7203_Chr11 (8.7 cM) had the highest—log10FDR value of 5.91 resulting in the lowest probability of 1.22E-06 (Table 2). Regression (R2) was the highest (0.308) between StgL and RM474_Chr10 (0.8 cM), but lowest (0.042) between DStgE and RM455_Chr7 (78.9 cM).Fig. 6


Association mapping of stigma and spikelet characteristics in rice (Oryza sativa L.).

Yan WG, Li Y, Agrama HA, Luo D, Gao F, Lu X, Ren G - Mol. Breed. (2009)

Marker-trait associations tested with false discovery rate (−log10FDR > 3) corrected from P values with 90 accessions as a mini-core collection and reference cultivars genotyped with 109 molecular markers for percentage of single (SStgE), dual (SStgE) and total stigma exsertion (TStgE), stigma length (StgL), width (StgW) and L/W ratio (StgL/W) and spikelet length (SpkL), width (SpkW) and L/W ratio (SpkL/W)
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC2837221&req=5

Fig6: Marker-trait associations tested with false discovery rate (−log10FDR > 3) corrected from P values with 90 accessions as a mini-core collection and reference cultivars genotyped with 109 molecular markers for percentage of single (SStgE), dual (SStgE) and total stigma exsertion (TStgE), stigma length (StgL), width (StgW) and L/W ratio (StgL/W) and spikelet length (SpkL), width (SpkW) and L/W ratio (SpkL/W)
Mentions: Based on the criterion P-value less than 0.001 with 109 markers for nine traits, we identified 45 significant marker-trait associations involving 33 markers (Fig. 6). After false discovery rate (FDR) correction, 34 of these associations involving 22 markers remained significant at P < 0.001 (−log10FDR > 3.0) (Table 2). Among 34 marker-trait associations, dual stigma exsertion (DStgE) with RM7203_Chr11 (8.7 cM) had the highest—log10FDR value of 5.91 resulting in the lowest probability of 1.22E-06 (Table 2). Regression (R2) was the highest (0.308) between StgL and RM474_Chr10 (0.8 cM), but lowest (0.042) between DStgE and RM455_Chr7 (78.9 cM).Fig. 6

Bottom Line: Four markers were associated with single stigma exsertion (SStgE), six with dual exsertion (DStgE) and five with total exsertion.Four markers were associated with spikelet length, three with width and seven with L/W ratio.Numerous markers were co-associated with multiple traits that were phenotypically correlated, i.e. RM12521_Chr2 associated with all three correlated spikelet traits.

View Article: PubMed Central - PubMed

ABSTRACT
Stigma and spikelet characteristics play an essential role in hybrid seed production. A mini-core of 90 accessions developed from USDA rice core collection was phenotyped in field grown for nine traits of stigma and spikelet and genotyped with 109 DNA markers, 108 SSRs plus an indel. Three major clusters were built upon Rogers' genetic distance, indicative of indicas, and temperate and tropical japonicas. A mixed linear model combining PC-matrix and K-matrix was adapted for mapping marker-trait associations. Resulting associations were adjusted using false discovery rate technique. We identified 34 marker-trait associations involving 22 SSR markers for eight traits. Four markers were associated with single stigma exsertion (SStgE), six with dual exsertion (DStgE) and five with total exsertion. RM5_Chr1 played major role indicative of high regression with not only DStgE but also SStgE. Four markers were associated with spikelet length, three with width and seven with L/W ratio. Numerous markers were co-associated with multiple traits that were phenotypically correlated, i.e. RM12521_Chr2 associated with all three correlated spikelet traits. The co-association should improve breeding efficiency because single marker could be used to assist breeding for multiple traits. Indica entry 1032 (cultivar 50638) and japonica entry 671 (cultivar Linia 84 Icar) with 80.65 and 75.17% of TStgE, respectively are recommended to breeder for improving stigma exsertion. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1007/s11032-009-9290-y) contains supplementary material, which is available to authorized users.

No MeSH data available.


Related in: MedlinePlus