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Identification of Genetic Loci Associated with Quality Traits in Almond via Association Mapping.

Font i Forcada C, Oraguzie N, Reyes-Chin-Wo S, Espiau MT, Socias i Company R, Fernández i Martí A - PLoS ONE (2015)

Bottom Line: There was a strong subpopulation structure with linkage disequilibrium decaying with increasing genetic distance resulting in lower levels of linkage disequilibrium between more distant markers.A significant impact of population structure on linkage disequilibrium in the almond cultivar groups was observed.The mixed linear model (MLM) approach using co-ancestry values from population structure and kinship estimates (K model) as covariates identified a maximum of 16 significant associations for chemical traits and 12 for physical traits.

View Article: PubMed Central - PubMed

Affiliation: Genome Center, 451 Health Sciences Dr, University of California Davis, Davis, CA 95616, United States of America.

ABSTRACT
To design an appropriate association study, we need to understand population structure and the structure of linkage disequilibrium within and among populations as well as in different regions of the genome in an organism. In this study, we have used a total of 98 almond accessions, from five continents located and maintained at the Centro de Investigación y Tecnología Agroalimentaria de Aragón (CITA; Spain), and 40 microsatellite markers. Population structure analysis performed in 'Structure' grouped the accessions into two principal groups; the Mediterranean (Western-Europe) and the non-Mediterranean, with K = 3, being the best fit for our data. There was a strong subpopulation structure with linkage disequilibrium decaying with increasing genetic distance resulting in lower levels of linkage disequilibrium between more distant markers. A significant impact of population structure on linkage disequilibrium in the almond cultivar groups was observed. The mean r2 value for all intra-chromosomal loci pairs was 0.040, whereas, the r2 for the inter-chromosomal loci pairs was 0.036. For analysis of association between the markers and phenotypic traits, five models comprising both general linear models and mixed linear models were selected to test the marker trait associations. The mixed linear model (MLM) approach using co-ancestry values from population structure and kinship estimates (K model) as covariates identified a maximum of 16 significant associations for chemical traits and 12 for physical traits. This study reports for the first time the use of association mapping for determining marker-locus trait associations in a world-wide almond germplasm collection. It is likely that association mapping will have the most immediate and largest impact on the tier of crops such as almond with the greatest economic value.

No MeSH data available.


A phenogram based on Neighbor-joining analysis showing the genetic relationships of 98 CITA almond collection using 40 SSR markers.Local accessions from Spain are shown in a blue branch line; cultivars from other Mediterranean countries are shown in a red branch line while cultivars from other regions are shown in a green branch line.
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pone.0127656.g001: A phenogram based on Neighbor-joining analysis showing the genetic relationships of 98 CITA almond collection using 40 SSR markers.Local accessions from Spain are shown in a blue branch line; cultivars from other Mediterranean countries are shown in a red branch line while cultivars from other regions are shown in a green branch line.

Mentions: Cluster analysis based on the Neighbor-joining method detected three major clusters and sub-clusters (Fig 1). In some clusters, the groupings concurred with the geographical origin of the accessions. The first and largest cluster (blue) contained only the Spanish accessions (57). This group comprises cultivars from the north-eastern part of Spain including Guara, Bertina, Muel, Desmayo Largueta or Castilla as well as cultivars from the south and south-eastern parts such as Marcona, Ramillete, Coop. Mañán, Atocha, Garrigues, Del Cid or Malagueña. The new releases from different Spanish breeding programs such as Mardía, Soleta, Masbovera, Tarragonès, Marta and Belona were also grouped in this cluster. In addition, this cluster contains a group of cultivars from the Canary Islands (El Paso-4, Colorada, Dura de Tijarafe, Padre Santo and Redonda de Palma) and the Majorca Island (Vivot, Garondès and Vinagrilla).


Identification of Genetic Loci Associated with Quality Traits in Almond via Association Mapping.

Font i Forcada C, Oraguzie N, Reyes-Chin-Wo S, Espiau MT, Socias i Company R, Fernández i Martí A - PLoS ONE (2015)

A phenogram based on Neighbor-joining analysis showing the genetic relationships of 98 CITA almond collection using 40 SSR markers.Local accessions from Spain are shown in a blue branch line; cultivars from other Mediterranean countries are shown in a red branch line while cultivars from other regions are shown in a green branch line.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4482440&req=5

pone.0127656.g001: A phenogram based on Neighbor-joining analysis showing the genetic relationships of 98 CITA almond collection using 40 SSR markers.Local accessions from Spain are shown in a blue branch line; cultivars from other Mediterranean countries are shown in a red branch line while cultivars from other regions are shown in a green branch line.
Mentions: Cluster analysis based on the Neighbor-joining method detected three major clusters and sub-clusters (Fig 1). In some clusters, the groupings concurred with the geographical origin of the accessions. The first and largest cluster (blue) contained only the Spanish accessions (57). This group comprises cultivars from the north-eastern part of Spain including Guara, Bertina, Muel, Desmayo Largueta or Castilla as well as cultivars from the south and south-eastern parts such as Marcona, Ramillete, Coop. Mañán, Atocha, Garrigues, Del Cid or Malagueña. The new releases from different Spanish breeding programs such as Mardía, Soleta, Masbovera, Tarragonès, Marta and Belona were also grouped in this cluster. In addition, this cluster contains a group of cultivars from the Canary Islands (El Paso-4, Colorada, Dura de Tijarafe, Padre Santo and Redonda de Palma) and the Majorca Island (Vivot, Garondès and Vinagrilla).

Bottom Line: There was a strong subpopulation structure with linkage disequilibrium decaying with increasing genetic distance resulting in lower levels of linkage disequilibrium between more distant markers.A significant impact of population structure on linkage disequilibrium in the almond cultivar groups was observed.The mixed linear model (MLM) approach using co-ancestry values from population structure and kinship estimates (K model) as covariates identified a maximum of 16 significant associations for chemical traits and 12 for physical traits.

View Article: PubMed Central - PubMed

Affiliation: Genome Center, 451 Health Sciences Dr, University of California Davis, Davis, CA 95616, United States of America.

ABSTRACT
To design an appropriate association study, we need to understand population structure and the structure of linkage disequilibrium within and among populations as well as in different regions of the genome in an organism. In this study, we have used a total of 98 almond accessions, from five continents located and maintained at the Centro de Investigación y Tecnología Agroalimentaria de Aragón (CITA; Spain), and 40 microsatellite markers. Population structure analysis performed in 'Structure' grouped the accessions into two principal groups; the Mediterranean (Western-Europe) and the non-Mediterranean, with K = 3, being the best fit for our data. There was a strong subpopulation structure with linkage disequilibrium decaying with increasing genetic distance resulting in lower levels of linkage disequilibrium between more distant markers. A significant impact of population structure on linkage disequilibrium in the almond cultivar groups was observed. The mean r2 value for all intra-chromosomal loci pairs was 0.040, whereas, the r2 for the inter-chromosomal loci pairs was 0.036. For analysis of association between the markers and phenotypic traits, five models comprising both general linear models and mixed linear models were selected to test the marker trait associations. The mixed linear model (MLM) approach using co-ancestry values from population structure and kinship estimates (K model) as covariates identified a maximum of 16 significant associations for chemical traits and 12 for physical traits. This study reports for the first time the use of association mapping for determining marker-locus trait associations in a world-wide almond germplasm collection. It is likely that association mapping will have the most immediate and largest impact on the tier of crops such as almond with the greatest economic value.

No MeSH data available.