Genome-Wide SNP Analysis Reveals the Population Structure and the Conservation Status of 23 Italian Chicken Breeds
Abstract
Simple Summary
Abstract
1. Introduction
2. Materials and Methods
2.1. Samples and Genotyping
2.2. Admixture and Genetic Relationship
2.3. Runs of Homozygosity
3. Results
3.1. Analysis of Whole-Genome Diversity
3.2. Analysis of Genetic Distance and Population Structure
3.3. Run of Homozygosity Analysis
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Acknowledgments
Conflicts of Interest
References
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Breed | Acronym | N | MAF | Ho | He | FHOM | ||||
---|---|---|---|---|---|---|---|---|---|---|
Mean | SD | Mean | SD | Mean | SD | Mean | SD | |||
Ancona | ANC | 24 | 0.267 | 0.242 | 0.263 | 0.181 | 0.274 | 0.187 | 0.284 | 0.100 |
Bianca di Saluzzo | BSA | 24 | 0.286 | 0.190 | 0.339 | 0.172 | 0.336 | 0.151 | 0.076 | 0.059 |
Bionda Piemontese | BPT | 22 | 0.283 | 0.210 | 0.325 | 0.186 | 0.317 | 0.164 | 0.116 | 0.025 |
Cornuta Caltanissetta | COR | 22 | 0.267 | 0.301 | 0.167 | 0.162 | 0.210 | 0.178 | 0.545 | 0.180 |
Ermellinata di Rovigo | PER | 23 | 0.309 | 0.321 | 0.199 | 0.192 | 0.220 | 0.198 | 0.459 | 0.044 |
Livorno Bianca | PLB | 24 | 0.269 | 0.295 | 0.205 | 0.196 | 0.218 | 0.186 | 0.465 | 0.061 |
Livorno Nera | PLN | 24 | 0.263 | 0.279 | 0.233 | 0.211 | 0.231 | 0.195 | 0.365 | 0.062 |
Mericanel della Brianza | MER | 24 | 0.282 | 0.268 | 0.232 | 0.180 | 0.261 | 0.186 | 0.368 | 0.127 |
Millefiori di Lonigo | PML | 23 | 0.281 | 0.238 | 0.293 | 0.199 | 0.291 | 0.178 | 0.202 | 0.080 |
Modenese | MOD | 24 | 0.273 | 0.252 | 0.260 | 0.197 | 0.27 | 0.181 | 0.296 | 0.083 |
Mugellese | MUG | 24 | 0.284 | 0.231 | 0.281 | 0.182 | 0.300 | 0.175 | 0.236 | 0.115 |
Padovana Argenta | PPA | 24 | 0.241 | 0.331 | 0.151 | 0.198 | 0.146 | 0.185 | 0.588 | 0.098 |
Padovana Camosciata | PPC | 24 | 0.238 | 0.303 | 0.169 | 0.191 | 0.179 | 0.193 | 0.538 | 0.095 |
Padovana Dorata | PPD | 24 | 0.247 | 0.264 | 0.219 | 0.194 | 0.232 | 0.187 | 0.404 | 0.081 |
Pepoi | PPP | 24 | 0.277 | 0.341 | 0.154 | 0.191 | 0.168 | 0.196 | 0.579 | 0.039 |
Polverara Bianca | PPB | 24 | 0.260 | 0.261 | 0.216 | 0.179 | 0.248 | 0.187 | 0.411 | 0.052 |
Polverara Nera | PPN | 24 | 0.257 | 0.290 | 0.201 | 0.193 | 0.213 | 0.194 | 0.454 | 0.062 |
Robusta Lionata | PRL | 23 | 0.305 | 0.345 | 0.181 | 0.199 | 0.185 | 0.195 | 0.508 | 0.039 |
Robusta Maculata | PRM | 24 | 0.304 | 0.358 | 0.157 | 0.190 | 0.166 | 0.193 | 0.572 | 0.032 |
Romagnola | ROM | 24 | 0.271 | 0.241 | 0.281 | 0.197 | 0.278 | 0.182 | 0.235 | 0.091 |
Siciliana | SIC | 24 | 0.259 | 0.361 | 0.129 | 0.205 | 0.123 | 0.189 | 0.648 | 0.034 |
Valdarnese | VLD | 24 | 0.283 | 0.204 | 0.321 | 0.181 | 0.322 | 0.160 | 0.127 | 0.098 |
Valplatani | VLP | 20 | 0.281 | 0.268 | 0.280 | 0.224 | 0.261 | 0.184 | 0.239 | 0.086 |
708 Broiler Ross | 708 | 13 | 0.317 | 0.234 | 0.369 | 0.219 | 0.324 | 0.162 | −0.005 | 0.009 |
Eureka | EUK | 9 | 0.329 | 0.261 | 0.374 | 0.260 | 0.305 | 0.177 | −0.018 | 0.013 |
Hy-lyne white eggs | HYL | 10 | 0.333 | 0.278 | 0.375 | 0.286 | 0.289 | 0.285 | −0.020 | 0.008 |
Isa Brown | ISA | 9 | 0.332 | 0.261 | 0.378 | 0.276 | 0.298 | 0.182 | −0.028 | 0.017 |
Breed | FROH | SD | Mean ROH | SD | Total Number ROH |
---|---|---|---|---|---|
Ancona (ANC) | 0.201 | 0.099 | 56.21 | 14.01 | 1351 |
Bianca di Saluzzo (BSA) | 0.081 | 0.057 | 20.53 | 9.22 | 492 |
Bionda Piemontese (BPT) | 0.081 | 0.024 | 31.52 | 6.82 | 694 |
Cornuta di Caltanissetta (COR) | 0.507 | 0.184 | 80.01 | 29.72 | 1761 |
Ermellinata di Rovigo (PER) | 0.305 | 0.082 | 133.71 | 24.83 | 3077 |
Livorno Bianca (PLB) | 0.427 | 0.059 | 77.72 | 6.15 | 1865 |
Livorno Nera (PLN) | 0.296 | 0.063 | 68.18 | 7.94 | 1636 |
Mericanel della Brianza (MER) | 0.326 | 0.135 | 65.15 | 15.97 | 1563 |
Millefiori di Lonigo (PML) | 0.166 | 0.073 | 56.01 | 20.79 | 1289 |
Modenese (MOD) | 0.264 | 0.086 | 54.14 | 9.42 | 1299 |
Mugellese (MUG) | 0.225 | 0.112 | 39.64 | 16.29 | 951 |
Padovana Argentata (PPA) | 0.509 | 0.118 | 96.76 | 12.71 | 2323 |
Padovana Camosciata (PPC) | 0.410 | 0.109 | 103.52 | 17.74 | 2485 |
Padovana Dorata (PPD) | 0.230 | 0.070 | 100.42 | 20.66 | 2410 |
Pepoi (PPP) | 0.482 | 0.096 | 151.81 | 30.76 | 3645 |
Polverara Bianca (PPB) | 0.310 | 0.068 | 113.85 | 22.07 | 2732 |
Polverara Nera (PPN) | 0.353 | 0.087 | 127.80 | 21.91 | 3069 |
Robusta Lionata (PRL) | 0.353 | 0.109 | 135.11 | 26.44 | 3109 |
Robusta Maculata (PRM) | 0.410 | 0.113 | 157.58 | 22.06 | 3782 |
Romagnola (ROM) | 0.187 | 0.091 | 43.17 | 10.04 | 1054 |
Siciliana (SIC) | 0.607 | 0.037 | 96.09 | 6.90 | 2305 |
Valdarnese (VLD) | 0.121 | 0.095 | 30.76 | 15.60 | 737 |
Valplatani (VLP) | 0.236 | 0.087 | 41.55 | 5.91 | 830 |
708 Broiler ROSS (708) | 0.034 | 0.009 | 17.24 | 4.31 | 224 |
Eureka (EUK) | 0.033 | 0.005 | 17.74 | 2.74 | 160 |
Hy-lyne white eggs (HYL) | 0.038 | 0.008 | 19.23 | 3.59 | 192 |
IsaBrown (ISA) | 0.030 | 0.011 | 16.22 | 5.95 | 146 |
GGA | No. of SNPs | Start | End | Length (bp) | Genes | QTL |
---|---|---|---|---|---|---|
2 | 18 | 53,138,767 | 53,202,574 | 63,807 | TPK1, LOC107051643 | - |
5 | 315 | 2,124,338 | 3,730,724 | 1,606,386 | NELL1, SLC6A5, LOC107053351, LOC107053349, LOC107053350, LOC107053348, ANO5, SLC17A6, FANCF, GAS2, SVIP, ANO3, SLC5A12, BBOX1, SLC5A12, FIBIN, CCDC34, LGR4, LIN7B | Body weight (28 days) QTL (95,416) Body weight (28 days) QTL (95,415) |
7 | 273 | 6,771,434 | 7,892,629 | 1,121,195 | COL6A2, LOC107053768, LOC107053769, LOC107053763, FTCD, MCM3AP, YBEY, LOC107053762, MCM3AP, YBEY, POFUT2, LOC107053766, CD163L1, LSS, S100B, DIP2A, PCNT, KMO, FAM207a, ITGB3, ADARB1 | Feed conversion ratio QTL (139,597) Feed conversion ratio QTL (139,472) Feed conversion ratio QTL (139,435) Feed conversion ratio QTL (139,598) |
8 | 371 | 9,506,680 | 10,604,288 | 1,097,608 | LOC101751732, PLA2G4A, PTGS2, PDC, C8H10RF27, TPR, LOC100859371, HMCN1, LOC107053953, LOC101750397, LOC107053952, INVS1ABP, SWT1, TRMT1L, LOC107053951 | Feed conversion ratio QTL (139,596) |
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Cendron, F.; Perini, F.; Mastrangelo, S.; Tolone, M.; Criscione, A.; Bordonaro, S.; Iaffaldano, N.; Castellini, C.; Marzoni, M.; Buccioni, A.; et al. Genome-Wide SNP Analysis Reveals the Population Structure and the Conservation Status of 23 Italian Chicken Breeds. Animals 2020, 10, 1441. https://doi.org/10.3390/ani10081441
Cendron F, Perini F, Mastrangelo S, Tolone M, Criscione A, Bordonaro S, Iaffaldano N, Castellini C, Marzoni M, Buccioni A, et al. Genome-Wide SNP Analysis Reveals the Population Structure and the Conservation Status of 23 Italian Chicken Breeds. Animals. 2020; 10(8):1441. https://doi.org/10.3390/ani10081441
Chicago/Turabian StyleCendron, Filippo, Francesco Perini, Salvatore Mastrangelo, Marco Tolone, Andrea Criscione, Salvatore Bordonaro, Nicolaia Iaffaldano, Cesare Castellini, Margherita Marzoni, Arianna Buccioni, and et al. 2020. "Genome-Wide SNP Analysis Reveals the Population Structure and the Conservation Status of 23 Italian Chicken Breeds" Animals 10, no. 8: 1441. https://doi.org/10.3390/ani10081441
APA StyleCendron, F., Perini, F., Mastrangelo, S., Tolone, M., Criscione, A., Bordonaro, S., Iaffaldano, N., Castellini, C., Marzoni, M., Buccioni, A., Soglia, D., Schiavone, A., Cerolini, S., Lasagna, E., & Cassandro, M. (2020). Genome-Wide SNP Analysis Reveals the Population Structure and the Conservation Status of 23 Italian Chicken Breeds. Animals, 10(8), 1441. https://doi.org/10.3390/ani10081441