Articles
Insights into population structure and genetic diversity in lettuce (Lactuca sativa L.) based on SNP genotyping data
Article number
1454_69
Pages
505 – 512
Language
English
Abstract
Genetic variability is essential in crop breeding.
We have carried out studies on genetic diversity and population structure within lettuce (Lactuca sativa L.), one of the most popular leafy vegetables worldwide.
A panel of 21 commercial and traditional cultivars was genotyped with 13,026 SNPs (single nucleotide polymorphisms). Results from phylogenetic, multidimensional scaling and population structure analyses showed that the cultivars were divided into three groups.
Pop. 1 was composed exclusively of red commercial cultivars, Pop. 2 was the one with the highest admixture including all types of cultivars and Pop. 3 grouped together only green traditional cultivars.
Pop. 1 was the most genetically distant from the rest, whereas Pop. 2 and 3 seemed to be close to each other with results even indicating that Pop. 3 could be a subgroup of Pop. 2. The greatest difference was observed between Pop. 1 and Pop. 3 according to FST index (0.63, compared to 0.36 and 0.43 between Pop. 1 and 2 and Pop. 2 and 3, respectively), as expected because their members do not share any characteristic like horticultural type, leaf color or geographical origin.
Analysis of molecular variance showed that Pop. 2 was the most diverse as it accounted for the highest percentage of the total variation (53.20%, compared to 9.80% and 3.70% of Pop. 1 and 3, respectively). This group also showed the highest gene diversity value (0.31 versus 0.15 and 0.06 in Pop. 1 and 3, respectively). Observed heterozygosity values were quite low in all groups (<4%), in agreement with the predominantly autogamous nature of lettuce.
Even so, traditional cultivars studied here harbour substantial variability, as they cluster separately (i.e., Pop. 2 and 3) albeit all of them come from a small region and most share horticultural type and leaf color.
We have carried out studies on genetic diversity and population structure within lettuce (Lactuca sativa L.), one of the most popular leafy vegetables worldwide.
A panel of 21 commercial and traditional cultivars was genotyped with 13,026 SNPs (single nucleotide polymorphisms). Results from phylogenetic, multidimensional scaling and population structure analyses showed that the cultivars were divided into three groups.
Pop. 1 was composed exclusively of red commercial cultivars, Pop. 2 was the one with the highest admixture including all types of cultivars and Pop. 3 grouped together only green traditional cultivars.
Pop. 1 was the most genetically distant from the rest, whereas Pop. 2 and 3 seemed to be close to each other with results even indicating that Pop. 3 could be a subgroup of Pop. 2. The greatest difference was observed between Pop. 1 and Pop. 3 according to FST index (0.63, compared to 0.36 and 0.43 between Pop. 1 and 2 and Pop. 2 and 3, respectively), as expected because their members do not share any characteristic like horticultural type, leaf color or geographical origin.
Analysis of molecular variance showed that Pop. 2 was the most diverse as it accounted for the highest percentage of the total variation (53.20%, compared to 9.80% and 3.70% of Pop. 1 and 3, respectively). This group also showed the highest gene diversity value (0.31 versus 0.15 and 0.06 in Pop. 1 and 3, respectively). Observed heterozygosity values were quite low in all groups (<4%), in agreement with the predominantly autogamous nature of lettuce.
Even so, traditional cultivars studied here harbour substantial variability, as they cluster separately (i.e., Pop. 2 and 3) albeit all of them come from a small region and most share horticultural type and leaf color.
Authors
I. Medina-Lozano, J. Plieske, M. Ganal, H. Gnad, A. Díaz
Keywords
heterozygosity, high-throughput genotyping, phylogenetic relationships, SNP arrays, traditional cultivars, Wright’s fixation index
Groups involved
- Division Plant Genetic Resources, Breeding and Biotechnology
- Working Group Genetic Transformation and Gene Editing
- Working Group Horticultural Biotechnology and Breeding
- Division Ornamental Plants
- Division Vegetables, Roots and Tubers
- Division Temperate Tree Fruits
- Division Vine and Berry Fruits
- Division Horticulture for Development
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