Genetic Diversity and Population Structure of a Wide Pisum spp. Core Collection
Abstract
:1. Introduction
2. Results
2.1. The Pea Core Collection
2.2. DArTSeq Marker Sequencing and Genetic Diversity Indices
2.3. Marker Distribution and Linkage Disequilibrium
2.4. Genetic Structure of the Pea Core Collection
2.5. Principal Component Analysis
2.6. Phylogenetic Relationship of the Pisum Core Collection
3. Discussion
4. Materials and Methods
4.1. Plant Material
4.2. DNA Extraction, Library Construction, and Sequencing
4.3. Population Structure of the Pea Core Collection
4.4. Phylogenetic Relationship of the Pea Core Collection
4.5. Linkage Disequilibrium
Supplementary Materials
Author Contributions
Funding
Data Availability Statement
Conflicts of Interest
References
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Species | Number of Accessions |
---|---|
P. sativum | 167 |
P. sativum subsp. sativum | 23 |
P. sativum subsp. sativum var. sativum | 37 |
P. sativum subsp. sativum var. arvense | 32 |
P. sativum subsp. elatius | 7 |
P. sativum subsp. elatius var. elatius | 24 |
P. sativum subsp. elatius var. pumilio | 3 |
P. sativum subsp. jomardii | 7 |
P. sativum subsp. transcaucasicum | 2 |
P. sativum subsp. thebaicum | 2 |
P. sativum subsp. cinereum | 1 |
P. abyssinicum | 7 |
P. fulvum | 13 |
Total | 325 |
SilicoDArT | SNP | |||||
---|---|---|---|---|---|---|
Mean | Min | Max | Mean | Min | Max | |
PIC | 0.295 | 0.006 | 0.499 | 0.267 | 0.013 | 0.594 |
MAF | 0.41 | 0.052 | 0.997 | 0.532 | 0.046 | 0.975 |
Ar | 1.783 | 1 | 2.91 | 1.515 | 0.4 | 2 |
Ho | 0.06 | 0 | 0.7 | 0.035 | 0 | 0.78 |
He | 0.217 | 0 | 0.5 | 0.148 | 0 | 0.5 |
FIS | 0.692 | −0.102 | 1 | 0.707 | −0.592 | 1 |
FIS Low | 0.615 | −0.675 | 1 | 0.588 | −0.905 | 1 |
FIS High | 0.762 | −0.058 | 1.1412 | 0.815 | −0.375 | 1.305 |
Total Lenght (Mbp) | Marker Number | Chromosome Coverage | Mean Distance Between Markers | Marker Density | |||||
---|---|---|---|---|---|---|---|---|---|
SilicoDarT | SNP | SilicoDarT | SNP | SilicoDarT | SNP | SilicoDarT | SNP | ||
Chr1 | 372.17 | 2388 | 1284 | 0.04–372.1 | 0.24–372.0 | 0.156 | 0.290 | 6.4 | 3.5 |
Chr2 | 427.6 | 2157 | 1068 | 0.27–427.4 | 0.03–427.4 | 0.198 | 0.401 | 5.0 | 2.5 |
Chr3 | 437.56 | 2331 | 1194 | 0.09–437.5 | 0.09–437.5 | 0.188 | 0.367 | 5.3 | 2.7 |
Chr4 | 446.35 | 2716 | 1341 | 0.03–446.3 | 0.03–446.3 | 0.164 | 0.333 | 6.1 | 3.0 |
Chr5 | 579.27 | 3696 | 1993 | 0.09–579.1 | 0.14–579.1 | 0.157 | 0.291 | 6.4 | 3.4 |
Chr6 | 480.42 | 2970 | 1672 | 0.23–480.4 | 0.21–480.4 | 0.162 | 0.287 | 6.2 | 3.5 |
Chr7 | 491.38 | 3253 | 1573 | 0.05–491.3 | 0.05–491.1 | 0.151 | 0.312 | 6.6 | 3.2 |
Whole genome | 19,514 | 11,511 | 0.166 | 0.319 | 6.0 | 3.1 |
MeanLD | LD90 | Dist LD50 (Mbp) | ||||
---|---|---|---|---|---|---|
SilicoDarT | SNP | SilicoDarT | SNP | SilicoDarT | SNP | |
Chr1 | 0.104 | 0.12 | 0.244 | 0.28 | 0.60 | 1.58 |
Chr2 | 0.091 | 0.104 | 0.206 | 0.239 | 0.32 | 0.82 |
Chr3 | 0.101 | 0.114 | 0.234 | 0.267 | 0.60 | 1.83 |
Chr4 | 0.09 | 0.101 | 0.203 | 0.242 | 0.25 | 0.69 |
Chr5 | 0.104 | 0.112 | 0.239 | 0.264 | 0.54 | 1.20 |
Chr6 | 0.136 | 0.159 | 0.35 | 0.42 | 1.05 | 3.19 |
Chr7 | 0.086 | 0.099 | 0.191 | 0.23 | 0.24 | 0.78 |
Whole genome | 0.103 | 0.118 | 0.236 | 0.28 | 0.48 | 1.38 |
Clusters | Membership a | Average Dist. b | Fst |
---|---|---|---|
K = 3 | |||
1 | 28.16 | 0.2130 | 0.2268 |
2 | 56.83 | 0.2262 | 0.3154 |
3 | 15.01 | 0.1514 | 0.4315 |
K = 6 | |||
1 | 14.25 | 0.1836 | 0.3316 |
2 | 21.08 | 0.2141 | 0.3504 |
3 | 21.39 | 0.1670 | 0.4147 |
4 | 21.35 | 0.1667 | 0.4688 |
5 | 12.57 | 0.1424 | 0.4975 |
6 | 9.37 | 0.1305 | 0.5404 |
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Rispail, N.; Wohor, O.Z.; Osuna-Caballero, S.; Barilli, E.; Rubiales, D. Genetic Diversity and Population Structure of a Wide Pisum spp. Core Collection. Int. J. Mol. Sci. 2023, 24, 2470. https://doi.org/10.3390/ijms24032470
Rispail N, Wohor OZ, Osuna-Caballero S, Barilli E, Rubiales D. Genetic Diversity and Population Structure of a Wide Pisum spp. Core Collection. International Journal of Molecular Sciences. 2023; 24(3):2470. https://doi.org/10.3390/ijms24032470
Chicago/Turabian StyleRispail, Nicolas, Osman Zakaria Wohor, Salvador Osuna-Caballero, Eleonora Barilli, and Diego Rubiales. 2023. "Genetic Diversity and Population Structure of a Wide Pisum spp. Core Collection" International Journal of Molecular Sciences 24, no. 3: 2470. https://doi.org/10.3390/ijms24032470