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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

UPGMA tree based on Rogers’s genetic distance for 90 accessions (Core entry number used in the chart) and reference cultivars (highlighted) genotyped with 109 molecular markers
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Fig3: UPGMA tree based on Rogers’s genetic distance for 90 accessions (Core entry number used in the chart) and reference cultivars (highlighted) genotyped with 109 molecular markers

Mentions: Three major clusters were obtained using the unweighted pair-group (UPGMA) analysis based on the Rogers’ genetic distance for the 90 accessions plus four reference cultivars (Fig. 3). Two dimensional principal components analysis (PCA) resulted in three clusters (Fig. 4) as well, largely corresponding to the grouping resulted from UPGMA cluster analysis. The PCA provides another perspective on the relationships among the accessions, and generally supports results obtained by the UPGMA. The first (49.2%) and second (20.2%) axes of PCA explained a relatively high percentage (69.4%) of the total variation. Accessions 307, 951 and 1386 were not assigned to any cluster in the PCA, but were instead placed intermediately among the clusters 1, 2 and 3 in the UPGMA. Both the PCA and UPGMA grouped the indica reference cultivars Guichao No2 (Li et al. 2001), Aijiaonante (Xiong et al. 1999) and IR24 (Miyata et al. 2007) in cluster 1, while japonica Koshihikari (Miyata et al. 2007), temperate japonica 718 (PI 584588), and 1321 (PI 439625) (Garris et al. 2005) were placed in cluster 3. Two accessions 259 (PI 303646) and 888 (PI 199542) in Cluster 2 was classified as tropical japonica (Garris et al. 2005). This grouping suggests that cluster 1 accessions are indicas while cluster 2 and 3 accessions correspond to tropical and temperate japonicas, respectively.Fig. 3


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)

UPGMA tree based on Rogers’s genetic distance for 90 accessions (Core entry number used in the chart) and reference cultivars (highlighted) genotyped with 109 molecular markers
© Copyright Policy
Related In: Results  -  Collection

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

Fig3: UPGMA tree based on Rogers’s genetic distance for 90 accessions (Core entry number used in the chart) and reference cultivars (highlighted) genotyped with 109 molecular markers
Mentions: Three major clusters were obtained using the unweighted pair-group (UPGMA) analysis based on the Rogers’ genetic distance for the 90 accessions plus four reference cultivars (Fig. 3). Two dimensional principal components analysis (PCA) resulted in three clusters (Fig. 4) as well, largely corresponding to the grouping resulted from UPGMA cluster analysis. The PCA provides another perspective on the relationships among the accessions, and generally supports results obtained by the UPGMA. The first (49.2%) and second (20.2%) axes of PCA explained a relatively high percentage (69.4%) of the total variation. Accessions 307, 951 and 1386 were not assigned to any cluster in the PCA, but were instead placed intermediately among the clusters 1, 2 and 3 in the UPGMA. Both the PCA and UPGMA grouped the indica reference cultivars Guichao No2 (Li et al. 2001), Aijiaonante (Xiong et al. 1999) and IR24 (Miyata et al. 2007) in cluster 1, while japonica Koshihikari (Miyata et al. 2007), temperate japonica 718 (PI 584588), and 1321 (PI 439625) (Garris et al. 2005) were placed in cluster 3. Two accessions 259 (PI 303646) and 888 (PI 199542) in Cluster 2 was classified as tropical japonica (Garris et al. 2005). This grouping suggests that cluster 1 accessions are indicas while cluster 2 and 3 accessions correspond to tropical and temperate japonicas, respectively.Fig. 3

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