Whole Genome Screening Procures a Holistic Hold of the Russian Chicken Gene Pool Heritage and Demographic History
Abstract
:Simple Summary
Abstract
1. Introduction
2. Materials and Methods
2.1. Breeds, Sampling and Ethics Statement
2.2. DNA Isolation
2.3. SNP Markers and Genotyping Quality Control
2.4. Genetic Diversity, Population Structure and Split and Admixture
2.5. Runs of Homozygosity Analysis
2.6. Demographic History Inference
3. Results
3.1. Genetic Diversity
3.2. ROH Distribution in Chicken Breed Genomes
3.3. Breed Relationship and Admixture
3.4. Demographic History Inference
3.4.1. Population Divergence and Gene Flow
3.4.2. Effective Population Size
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Breed (Population) | Code | n | Breed Type | Origin | Refs | Image Source | |
---|---|---|---|---|---|---|---|
Old Russian indigenous breeds | |||||||
Orloff Mille Fleur | OMF | 29 | DPB/MEB, fancy and semi-game breed (GB), cold and heat tolerant, chicks are late feathering and cannot withstand cold and humidity, incubation instinct | Central Russia, late 18th century, from local chickens, Gilian and Old English Game | [32,33,37,43] | a | |
Poltava Clay | PC | 21 | DPB/MEB | Poltava Governorate, Russia; mid 19th century, from local chickens, Buff Orpington and possibly RIR and NH, Wyandotte, etc., bred at the Ukrainian Poultry Research Institute, USSR since 1951 | [32,33,38,39,40,41] | a | |
Russian Black Bearded (Galan) | RBB | 25 | DPB/MEB and fancy, cold tolerant, incubation instinct | Kursk, Oryol and neighboring governorates, Russia, 19th century (2nd half), from (1) Wyandotte and Crevecoeur or (2) Orloff Black and Wyandotte | [32] | b | |
Russian Crested | RC | 29 | DPB/MEB and fancy, cold tolerant, incubation instinct | Russia, 19th century, from local chickens and possibly Asian breeds | [32] | a | |
Ushanka (or Ukrainian Muffed) | Ush | 30 | DPB/MEB and fancy, sex-linked early feathering in chicks, cold tolerant, incubation instinct | South Russia and territory of Ukraine, 17th century to 1880s, from local chickens, probable random mating to other breeds | [32,33,37] | a | |
Yurlov Crower | YC | 36 | DPB/MEB, long crowing, of two varieties (silver and golden), sex-linked late feathering in chicks | Russia, 19th century (2nd half), from local and GB chickens, Brahma, Cochin and Langshan, almost extinct in 1941–1945, brought to ARPRTI, Zagorsk, USSR in 1948 | [32,33,34,35,36] | a | |
Improved Russian breeds | |||||||
Adler Silver | AS | 30 | DPB/MEB | Adler Poultry Farm, Krasnodar Krai, USSR, 1951–1965, from Pm, RW, NH, White Plymouth Rock and YC | [32] | a | |
Kotlyarevsky | Kt | 28 | DPB/MEB | Kotlyarevsky Breeding Farm, Kabardino-Balkarian ASSR, USSR, 20th century (2nd half), from NH, RW, ZS, Naked Neck and Barred Plymouth Rock | [32] | b | |
Kuchino Jubilee | KJ | 29 | DPB/MEB, sex-linked early feathering in chicks | Kuchinsky State Breeding Farm, Moscow Oblast, USSR, 1947–1990, from RW, NH, RIR, AoB, Plymouth Rock White, YC, Brown Leghorn (Italian Partridge) and Livny | [32] | a | |
Leningrad Mille Fleur | LMF | 7 | DPB/EMB | RRIFAGB, Pushkin, Leningrad Oblast, USSR, 1985, from Australorp Black Speckled, NH and PC | [33] | a | |
Pervomai | Pm | 30 | DPB/MEB | Pervoe Maya State Farm, Kharkov Oblast, Ukrainian SSR, USSR, 1935–1941; Pachelma State Farm, Penza Oblast, RSFSR, USSR, 1942–1963; from White Wyandotte, RIR and YC | [32,33] | a | |
Russian White (ARPRTI) | RW1 | 29 | ETB | USSR, 1929–1953, from local white chickens and WL, bred at ARPRTI, Zagorsk/Sergiev Posad, USSR/Russia | [32,37,42] | b | |
Russian White (RRIFAGB) | RW2 | 71 | ETB, cold tolerant | Bred at RRIFAGB, Pushkin, USSR/Russia since 1952, a single telic mating of an RRIFAGB inbred line of RW, selected for cold tolerance, to WL | [32,33,37,42,44,45,46] | a | |
Ushanka Foot-feathered | UshF | 6 | DPB/MEB and fancy, cold tolerant | ARPRTI, Sergiev Posad, Russia, 20th century (more recently), from Pavlov, Orloff and possibly Ush | [32] | b | |
Zagorsk Salmon | ZS | 27 | DPB/MEB, sex-linked late feathering and down color in chicks | Zagorsk, USSR, 1950–1959, from RW, NH, RIR and YC | [32,33] | a | |
Specialized foreign breeds | |||||||
Australorp Black | AoB | 30 | DPB/MEB | Australia, 1890s to 1929, from Black Orpington, RIR, Black Minorca, WL, Langshan and Barred Plymouth Rock, bred in Russia since 1946 | [32,33] | a | |
Cornish White | CW | 24 | MTB | England, 1886, from local GB chickens, Asil, White Malay, Indian Game and Cochin, used as paternal stock in commercial broiler crosses, bred in Russia | [33,37,42] | a | |
New Hampshire | NH | 10 | DPB/MEB | USA, early 20th century to 1935, from RIR | [32,33] | a | |
Rhode Island Red | RIR | 17 | DPB/EMB | States of Rhode Island and Massachusetts, USA, 1880s to 1904, from Cochin, Java, Malay, Shanghai and Brown Leghorn | [32,47] | a | |
White Leghorn | WL | 20 | ETB, the only Mediterranean breed of economic importance today | Tuscany, Italy, 19th century, from light rural breeds, brought to USA in 1828, a white variety imported to USA in 1853, line G11 bred in Germany since 1965 | [48,49] | a |
Breed | HO (M ± SE) | HE (M ± SE) | UHE (M ± SE) | AR (M ± SE) | FIS [CI 95%] | UFIS [CI 95%] |
---|---|---|---|---|---|---|
Old Russian indigenous breeds | ||||||
OMF | 0.291 ± 0.001 | 0.286 ± 0.001 | 0.291 ± 0.001 | 1.709 ± 0.002 | −0.019 [−0.021; −0.017] | −0.001 [−0.003; 0.001] |
PC | 0.257 ± 0.001 | 0.249 ± 0.001 | 0.255 ± 0.001 | 1.655 ± 0.002 | −0.029 [−0.031; −0.027] | −0.003 [ −0.005; −0.001] |
RBB | 0.250 ± 0.001 | 0.247 ± 0.001 | 0.252 ± 0.001 | 1.624 ± 0.002 | −0.008 [−0.010; −0.006] | 0.012 [0.010; 0.014] |
RC | 0.325 ± 0.001 | 0.327 ± 0.001 | 0.333 ± 0.001 | 1.819 ± 0.002 | 0.005 [0.003; 0.007] | 0.022 [0.020; 0.024] |
Ush | 0.249 ± 0.001 | 0.255 ± 0.001 | 0.259 ± 0.001 | 1.647 ± 0.002 | 0.016 [0.014; 0.018] | 0.033 [0.031; 0.035] |
YC | 0.347 ± 0.001 | 0.358 ± 0.001 | 0.363 ± 0.001 | 1.867 ± 0.001 | 0.029 [0.027; 0.031] | 0.043 [0.041; 0.045] |
Av. | 0.287 ± 0.017 | 0.287 ± 0.019 | 0.292 ± 0.019 | 1.720 ± 0.041 | −0.001 ± 0.009 [−0.031; 0.031] | 0.018 ± 0.008 [−0.005; 0.045] |
Improved Russian breeds | ||||||
AS | 0.321 ± 0.001 | 0.329 ± 0.001 | 0.335 ± 0.001 | 1.811 ± 0.002 | 0.020 [0.018; 0.022] | 0.037 [0.035; 0.039] |
KJ | 0.256 ± 0.001 | 0.252 ± 0.001 | 0.256 ± 0.001 | 1.665 ± 0.002 | −0.018 [−0.020; −0.016] | 0.000 [−0.002; 0.002] |
Kt | 0.257 ± 0.001 | 0.256 ± 0.001 | 0.261 ± 0.001 | 1.650 ± 0.002 | −0.006 [−0.008; −0.004] | 0.012 [0.010; 0.014] |
LMF | 0.249 ± 0.001 | 0.228 ± 0.001 | 0.246 ± 0.001 | 1.606 ± 0.002 | −0.090 [−0.094; −0.086] | −0.011 [−0.015; −0.007] |
Pm | 0.291 ± 0.001 | 0.290 ± 0.001 | 0.295 ± 0.001 | 1.729 ± 0.002 | −0.006 [−0.008; −0.004] | 0.011 [0.009; 0.013] |
RW1 | 0.255 ± 0.001 | 0.248 ± 0.001 | 0.252 ± 0.001 | 1.632 ± 0.002 | −0.016 [−0.018; −0.014] | 0.001 [−0.001; 0.003] |
RW2 | 0.306 ± 0.001 | 0.305 ± 0.001 | 0.307 ± 0.001 | 1.763 ± 0.002 | −0.001 [−0.002; 0.000] | 0.006 [0.005; 0.007] |
UshF | 0.252 ± 0.001 | 0.232 ± 0.001 | 0.253 ± 0.001 | 1.645 ± 0.003 | −0.088 [−0.092; −0.084] | 0.003 [−0.001; 0.007] |
ZS | 0.275 ± 0.001 | 0.271 ± 0.001 | 0.276 ± 0.001 | 1.688 ± 0.002 | −0.015 [−0.017; −0.013] | 0.004 [0.002; 0.006] |
Av. | 0.274 ± 0.009 | 0.268 ± 0.011 | 0.276 ± 0.010 | 1.688 ± 0.022 | −0.024 ± 0.013 [−0.094; 0.022] | 0.007 ± 0.004 [−0.015; 0.039] |
Specialized foreign breeds | ||||||
AoB | 0.296 ± 0.001 | 0.314 ± 0.001 | 0.319 ± 0.001 | 1.777 ± 0.002 | 0.045 [0.043; 0.047] | 0.061 [0.059; 0.063] |
CW | 0.365 ± 0.001 | 0.368 ± 0.001 | 0.371 ± 0.001 | 1.876 ± 0.001 | 0.001 [−0.001; 0.003] | 0.022 [0.020; 0.024] |
NH | 0.233 ± 0.001 | 0.205 ± 0.001 | 0.216 ± 0.001 | 1.542 ± 0.002 | −0.122 [−0.125; −0.119] | −0.067 [−0.070; −0.064] |
RIR | 0.256 ± 0.001 | 0.256 ± 0.001 | 0.264 ± 0.001 | 1.661 ± 0.002 | −0.003 [−0.006; 0.000] | 0.027 [0.024; 0.030] |
WL | 0.164 ± 0.001 | 0.185 ± 0.001 | 0.185 ± 0.001 | 1.452 ± 0.002 | 0.080 [0.077; 0.083] | 0.103 [0.100; 0.106] |
Av. | 0.263 ± 0.033 | 0.266 ± 0.033 | 0.271 ± 0.034 | 1.662 ± 0.077 | 0.000 ± 0.034 [−0.125; 0.083] | 0.029 ± 0.028 [−0.070; 0.106] |
Source of Variation | df 1 | Sum of Squares | Variance Components | Percentage of Variation | p-Value of Fixation |
---|---|---|---|---|---|
Among groups | 2 | 450,114,870.5 | 0.014 | 1.36 | 0.011 |
Among populations within group | 17 | 4,945,631,101 | 0.151 | 14.93 | 0.001 |
Within populations | 508 | 27,729,967,336 | 0.163 | 83.71 | 0.001 |
Total | 527 | 33,125,713,307 | 0.328 | 100 |
Breed | ROH Length, Mb (M ± SE) | ROH No. (M ± SE) | FROH (M ± SE) |
---|---|---|---|
Old Russian indigenous breeds | |||
OMF | 266.42 ± 12.42 | 125.17 ± 4.03 | 0.279 ± 0.013 |
PC | 337.93 ± 15.74 | 145.00 ± 6.50 | 0.354 ± 0.017 |
RBB | 369.41 ± 16.07 | 141.32 ± 5.01 | 0.387 ± 0.017 |
RC | 197.84 ± 19.08 | 89.28 ± 6.88 | 0.207 ± 0.020 |
Ush | 375.63 ± 14.23 | 127.13 ± 2.70 | 0.394 ± 0.015 |
YC | 146.91 ± 11.94 | 70.11 ± 2.62 | 0.154 ± 0.013 |
Average (M ± SE) | 282.36 ± 38.78 | 121.75 ± 12.26 | 0.296 ± 0.041 |
Improved Russian breeds | |||
AS | 205.05 ± 9.33 | 94.87 ± 2.86 | 0.215 ± 0.010 |
KJ | 368.96 ± 7.20 | 142.00 ± 2.71 | 0.387 ± 0.008 |
Kt | 360.79 ± 9.22 | 143.86 ± 3.83 | 0.378 ± 0.010 |
LMF | 375.11 ± 18.37 | 112.14 ± 4.13 | 0.393 ± 0.019 |
Pm | 274.02 ± 9.01 | 139.87 ± 3.77 | 0.287 ± 0.009 |
RW1 | 323.45 ± 15.34 | 151.38 ± 2.41 | 0.339 ± 0.016 |
RW2 | 195.24 ± 5.89 | 130.83 ± 2.74 | 0.205 ± 0.006 |
UshF | 357.71 ± 35.25 | 116.00 ± 4.56 | 0.375 ± 0.037 |
ZS | 301.06 ± 9.48 | 154.04 ± 4.9 | 0.316 ± 0.010 |
Average (M ± SE) | 306.82 ± 23.04 | 131.67 ± 6.66 | 0.322 ± 0.024 |
Specialized foreign breeds | |||
AoB | 260.03 ± 10.18 | 107.03 ± 2.89 | 0.273 ± 0.011 |
CW | 154.61 ± 5.98 | 126.29 ± 3.28 | 0.162 ± 0.006 |
NH | 403.39 ± 11.15 | 120.80 ± 1.43 | 0.423 ± 0.012 |
RIR | 352.15 ± 14.42 | 151.94 ± 8.01 | 0.369 ± 0.015 |
WL | 525.64 ± 6.12 | 249.75 ± 2.48 | 0.551 ± 0.006 |
Average (M ± SE) | 339.16 ± 63.00 | 151.16 ± 25.70 | 0.356 ± 0.066 |
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Romanov, M.N.; Abdelmanova, A.S.; Fisinin, V.I.; Gladyr, E.A.; Volkova, N.A.; Anshakov, D.V.; Stanishevskaya, O.I.; Vakhrameev, A.B.; Dotsev, A.V.; Griffin, D.K.; et al. Whole Genome Screening Procures a Holistic Hold of the Russian Chicken Gene Pool Heritage and Demographic History. Biology 2023, 12, 979. https://doi.org/10.3390/biology12070979
Romanov MN, Abdelmanova AS, Fisinin VI, Gladyr EA, Volkova NA, Anshakov DV, Stanishevskaya OI, Vakhrameev AB, Dotsev AV, Griffin DK, et al. Whole Genome Screening Procures a Holistic Hold of the Russian Chicken Gene Pool Heritage and Demographic History. Biology. 2023; 12(7):979. https://doi.org/10.3390/biology12070979
Chicago/Turabian StyleRomanov, Michael N., Alexandra S. Abdelmanova, Vladimir I. Fisinin, Elena A. Gladyr, Natalia A. Volkova, Dmitry V. Anshakov, Olga I. Stanishevskaya, Anatoly B. Vakhrameev, Arsen V. Dotsev, Darren K. Griffin, and et al. 2023. "Whole Genome Screening Procures a Holistic Hold of the Russian Chicken Gene Pool Heritage and Demographic History" Biology 12, no. 7: 979. https://doi.org/10.3390/biology12070979