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Association mapping for kernel phytosterol content in almond.

Font I Forcada C, Velasco L, Socias I Company R, Fernández I Martí Á - Front Plant Sci (2015)

Bottom Line: The mixed linear model (MLM) approach using co-ancestry values from population structure and kinship estimates (K model) as covariates identified a maximum of 13 significant associations.Most of the associations found appeared to map within the interval where many candidate genes involved in the sterol biosynthesis pathway are predicted in the peach genome.These findings provide a valuable foundation for quality gene identification and molecular marker assisted breeding in almond.

View Article: PubMed Central - PubMed

Affiliation: Genome Center, University of California, Davis Davis, CA, USA.

ABSTRACT
Almond kernels are a rich source of phytosterols, which are important compounds for human nutrition. The genetic control of phytosterol content has not yet been documented in almond. Association mapping (AM), also known as linkage disequilibrium (LD), was applied to an almond germplasm collection in order to provide new insight into the genetic control of total and individual sterol contents in kernels. Population structure analysis grouped the accessions into two principal groups, the Mediterranean and the non-Mediterranean. There was a strong subpopulation structure with LD decaying with increasing genetic distance, resulting in lower levels of LD between more distant markers. A significant impact of population structure on LD in the almond cultivar groups was observed. The mean r(2) -value for all intra-chromosomal loci pairs was 0.040, whereas, the r(2) for the inter-chromosomal loci pairs was 0.036. For analysis of association between the markers and phenotypic traits five models were tested. The mixed linear model (MLM) approach using co-ancestry values from population structure and kinship estimates (K model) as covariates identified a maximum of 13 significant associations. Most of the associations found appeared to map within the interval where many candidate genes involved in the sterol biosynthesis pathway are predicted in the peach genome. These findings provide a valuable foundation for quality gene identification and molecular marker assisted breeding in almond.

No MeSH data available.


Related in: MedlinePlus

Neighbor joining tree of 71 almond accessions based on 40 SSR markers.
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Figure 1: Neighbor joining tree of 71 almond accessions based on 40 SSR markers.

Mentions: Clustering analysis based on Neighbor-joining essentially allowed the detection of three major clusters of different size, further subdivided in other small clusters (Figure 1). A close relationship could be established for some of these groups with their geographical origin. The first cluster (blue) contained only Spanish accessions (36 in total). This group comprises only cultivars from Spain with representative accessions such as “Marcona,” “Desmayo Largueta,” “Atocha” or “Castilla.” Some new releases from different Spanish breeding programs, such as “Mardía” and “Marta,” were also grouped in this cluster. The accessions from the two Spanish archipelagos (Canary Islands and Majorca), such as “Padre Santo,” “Dura de Tijarafe,” “Vivot,” “Garondès” and “Vinagrilla,” were equally clustered in this first group. The second group (red) appeared to be much diversified, with 20 accessions, including a pool of Mediterranean accessions: two from North Africa (“Constantini” and “Zahaf”), four from France (“Belle d'Aurons,” “Lauranne,” “Ferragnès,” and “Ferraduel”), four from Italy (“Tuono,” “Supernova,” “Rachele,” and “Filippo Ceo”), five from Greece (“Picantilli,” “Tsotouliu,” “Truito,” “Symmetrikji,” and “Phyllis”), and five from Portugal (“Cosa Nova,” “Molar de Fuzeta,” “Carreirinha,” “Raposa,” and “Rameira”). The third group (green) clustered accessions from many different countries, although all of them have in common not being strictly Mediterranean. This group included one accession from Bulgaria (“Exinograd”), three from Crimea (“Yaltinskij,” “Primorskij,” and “Sovietskij”), two from Argentina (“Marcona Argentina” and “Emilito”), one from Australia (“Chellastone”) and eight from the United States (“I.X.L.,” “Texas,” “Thompson,” “Tioga,” “Peerless,” “Tokyo,” “Mono,” and “Tardy Nonpareil”).


Association mapping for kernel phytosterol content in almond.

Font I Forcada C, Velasco L, Socias I Company R, Fernández I Martí Á - Front Plant Sci (2015)

Neighbor joining tree of 71 almond accessions based on 40 SSR markers.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4496553&req=5

Figure 1: Neighbor joining tree of 71 almond accessions based on 40 SSR markers.
Mentions: Clustering analysis based on Neighbor-joining essentially allowed the detection of three major clusters of different size, further subdivided in other small clusters (Figure 1). A close relationship could be established for some of these groups with their geographical origin. The first cluster (blue) contained only Spanish accessions (36 in total). This group comprises only cultivars from Spain with representative accessions such as “Marcona,” “Desmayo Largueta,” “Atocha” or “Castilla.” Some new releases from different Spanish breeding programs, such as “Mardía” and “Marta,” were also grouped in this cluster. The accessions from the two Spanish archipelagos (Canary Islands and Majorca), such as “Padre Santo,” “Dura de Tijarafe,” “Vivot,” “Garondès” and “Vinagrilla,” were equally clustered in this first group. The second group (red) appeared to be much diversified, with 20 accessions, including a pool of Mediterranean accessions: two from North Africa (“Constantini” and “Zahaf”), four from France (“Belle d'Aurons,” “Lauranne,” “Ferragnès,” and “Ferraduel”), four from Italy (“Tuono,” “Supernova,” “Rachele,” and “Filippo Ceo”), five from Greece (“Picantilli,” “Tsotouliu,” “Truito,” “Symmetrikji,” and “Phyllis”), and five from Portugal (“Cosa Nova,” “Molar de Fuzeta,” “Carreirinha,” “Raposa,” and “Rameira”). The third group (green) clustered accessions from many different countries, although all of them have in common not being strictly Mediterranean. This group included one accession from Bulgaria (“Exinograd”), three from Crimea (“Yaltinskij,” “Primorskij,” and “Sovietskij”), two from Argentina (“Marcona Argentina” and “Emilito”), one from Australia (“Chellastone”) and eight from the United States (“I.X.L.,” “Texas,” “Thompson,” “Tioga,” “Peerless,” “Tokyo,” “Mono,” and “Tardy Nonpareil”).

Bottom Line: The mixed linear model (MLM) approach using co-ancestry values from population structure and kinship estimates (K model) as covariates identified a maximum of 13 significant associations.Most of the associations found appeared to map within the interval where many candidate genes involved in the sterol biosynthesis pathway are predicted in the peach genome.These findings provide a valuable foundation for quality gene identification and molecular marker assisted breeding in almond.

View Article: PubMed Central - PubMed

Affiliation: Genome Center, University of California, Davis Davis, CA, USA.

ABSTRACT
Almond kernels are a rich source of phytosterols, which are important compounds for human nutrition. The genetic control of phytosterol content has not yet been documented in almond. Association mapping (AM), also known as linkage disequilibrium (LD), was applied to an almond germplasm collection in order to provide new insight into the genetic control of total and individual sterol contents in kernels. Population structure analysis grouped the accessions into two principal groups, the Mediterranean and the non-Mediterranean. There was a strong subpopulation structure with LD decaying with increasing genetic distance, resulting in lower levels of LD between more distant markers. A significant impact of population structure on LD in the almond cultivar groups was observed. The mean r(2) -value for all intra-chromosomal loci pairs was 0.040, whereas, the r(2) for the inter-chromosomal loci pairs was 0.036. For analysis of association between the markers and phenotypic traits five models were tested. The mixed linear model (MLM) approach using co-ancestry values from population structure and kinship estimates (K model) as covariates identified a maximum of 13 significant associations. Most of the associations found appeared to map within the interval where many candidate genes involved in the sterol biosynthesis pathway are predicted in the peach genome. These findings provide a valuable foundation for quality gene identification and molecular marker assisted breeding in almond.

No MeSH data available.


Related in: MedlinePlus