Contribution to the Knowledge of the Populations of Nile Tilapia

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Contribution to the knowledge of the populations of Nile tilapia (Oreochromis niloticus) inhabiting extreme conditions of temperature and alkalinity Titus Chemandwa Ndiwa

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Titus Chemandwa Ndiwa. Contribution to the knowledge of the populations of Nile tilapia (Ore- ochromis niloticus) inhabiting extreme conditions of temperature and alkalinity. Biodiversity. Uni- versité Montpellier II - Sciences et Techniques du Languedoc, 2014. English. NNT : 2014MON20114. tel-01542402

HAL Id: tel-01542402 https://tel.archives-ouvertes.fr/tel-01542402 Submitted on 19 Jun 2017

HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés.

Délivré par UNIVERSITE MONTPELLIER 2 Préparée DXVHLQGHO·pFROHGRFWRUDOH SIBAGHE (WGHO·XQLWpGHUHFKHUFKH ISE-M 6SpFLDOLWp %LRORJLHGHO¶(YROXWLRQHW(FRORJLH Présentée par 7LWXV&KHPDQGZD1GLZD Contribution à la connaissance des populations du tilapia du Nil ( 2UHRFKURPLVQLORWLFXV ) vivant dans des conditions extrêmes de température et G·DOFDOLQLWp

Soutenue le 19/12/2014 devant le jury composé de Mme Janice Briton Davidian, Directeur de Recherche, CNRS Invitée Mme Dorothy Wanja Nyingi, Researcher, NMK Co-encadrant M. Paul Alibert, MC, Université de Bourgogne Rapporteur M. Didier Paugy, Directeur de Recherche, IRD Président M. Jean-François Agnèse, Directeur de Recherche, IRD Dir. de thèse

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78 7DEOHV Water ϮϳʹϮϳΣ ϭϳʹϮϲΣ ϮϳʹϯϮΣ ϮϱʹϮϳΣ ϯϮʹϯϵΣ ϮϳʹϯϮΣ temperature N° N° of males 54 6 4 °C 24.5 - 22 4 6 N° N° of females Ethiopia Ethiopia Lake Turkana Turkana Lake SpringHotel Bogoria Lake Kenya Kenya 10 10 10 7 °C 36 Lake MetaharaLake Ethiopia Basin Localisation Country Volta + Nile Volta+ BouakeStation Coast Ivory 6 7 Nilotic Nile Manzala Lake Eygypt 11 17-25.7 20.5 NiloticNilotic Rift-Valley Rift-Valley NiloticNilotic Rift-ValleyNilotic Baringo Lake Rift-Valley Rift-ValleyChelaba Spring TurtleSpring Kenya Kenya 10 Kenya 10 10 10 10 10°C 36 °C 36 + Nilotic + Regions Ichthyo. EthiopianEthiopianEthiopian Awash AwashHora Lake Awash Koka Lake Sudano-Sahelian VoltaVolta Lake Ghana 11 10 Sudano-Sahelian Oreochromis niloticus Oreochromis pledof O. n.O.niloticus O. n.O.niloticus O. n.O.vulcani n.O.loboi O. n.O.niloticus n.O.baringoensis n.O.loboi n.O.loboi n.O.cancellatus n.O.cancellatus n.O.filoa Wild Wild Wild Wild Wild Wild Wild Wild Wild Characteristics Subspecies DomesticatedStrain DomesticatedStrain

Strain Population or Lake Turkana Lake Bogoria Table 1: Information on the populations and strains sam strains and populations the on Information 1: Table Kpandu Bouake Manzala Baringo Lake Spring Chelaba Spring Turtle Hora Lake Koka Lake Metahara

79 Alignment LOC100701078 ENSONIG00000005545 ENSONIG00000000155 Scaffold GL831420.1 Scaffold GL831234.1 Mod. EF512167 ENSONIT0000000602 AF472620 EF026080 EF512167 KC710223 KC710224 HG518784 ES 814 bp 814 57°C 56°Cbp 1223 58°Cbp 1073 57°Cbp 1081 60°Cbp 988 58°Cbp/ 1047 60°Cbp 925 60°Cbp 293 & ES (5'-3') Tm Size GenBank AACCTGTACCAAATGGCATC GATGGGACAGTTTGAAGTAT AAATCTGGAATCAATGTAATGAAGA GCAGAGATCAGATCCATGAGAA CCCGTTTGCTGTCTGATTTT GGATGGCAACCTCGTTTTAC ACAAACCCTGTGCTGCTCTT GTGGGAGCTGTGGAGTTGAT CTGCAAACCTCCTTCCTTTG CGACAAATTCACGCTAAGCA TGGCCACGGATTCTCTAAAC GCATCTGGCTTGATGGAGAT CGGTCCCAGTGACCTATGAG AAGTACACGTGGTGTATTGTAATTGA CTGGTTTGCAATAGTTAGGGTGCT CAGAAATGTAGACGCCCAGGTATC TAAATTAATGACATTTCAGTTATG TTACAGCAGCACCCAGAGTCAT SCAR-5F-X Wt1b-F938 Wt1b-R1836 cyp19a1a-F1872 cyp19a1a-R2371 Amh-R1308 Amh-F885 Amh-R1958 Amh-F1802 Amh-R2883 Amh-R3328 Amh-R3490 SCAR-5R SCAR-5R-Y SCAR-5F ate gene or marker Exon 5-Exon 7 5-Exon Exon Exon 1-Intron 3 1-Intron Exon Amh-F85 6 3-Exon Exon 6 6-Intron Exon 76-Exon Intron Amh-F2340 76-Exon Intron Amh-F2443 Promoter wt1b X-specific cyp19a1a amh amhy Y-specific Scaffold Gene/ Marker Region Primers Used Primer Sequence scaffold17 scaffold101 scaffold101 LG1 LG23 Group Linkage Table Primers2: used for SNP search for each candid

80 °Ind. gene cyp19a1a T 68.98 187 T 28.26 184 G 4.30 186 A 61.50 187 CT 2.14 187 CT 1.08 184 A/G 18.28 186 d of the aromatase gonadal gonadal aromatase the of d 2308 Promoter none C 28.88 187 2175 Promoter none A 77.42 186 2124 Promoter none G 38.50 187 2016 Promoter none C 70.65 184 cyp19a1a cyp19a1a cyp19a1a cyp19a1a Cyp_2308 Cyp_2175 Cyp_2124 Cyp_2016 SNP Name SNP Gene Position Feature Consequencetype SNP Frequency N Table 3: SNPs identified in the promoter region studie region identified SNPs promoter the in 3: Table

81 SONIG00000000155 /Strain Frequency N°Ind. HoraKoka 100 100 11/11 8/8 Chelaba 15 6/20 A to Tto A Chelaba 30 3/20 promoter region studied vs ref. Genbank AF472620 & EN & AF472620 Genbank ref. vs studied region promoter cyp19a1a 1988 promoter G Metahara 100 10/10 1992 promoter A Bogoria 25 5/20 2036-2037 promoter GTPOP. ALL 100 188 cyp19a1a cyp19a1a cyp19a1a Cyp_1988 Cyp_1993 SNP Name SNP Gene Position Feature Deletion change Nt Population Cyp_2036-2037 Table 4: Nucleotide deletions found in the indeletions Nucleotide found 4: Table

82 Table 5: Pairwise linkage disequilibrium detected for the region of the cyp19a1a gene promoter

Linkage Allele pair Population/strain R2 disequilibrium (%)

Cyp_2016-Cyp_2124 Bogoria 22 0.22 Cyp_2016-Cyp_2175 Baringo 40 0.4 Turtle 12 0.12 Cyp_2016-Cyp_2308 Baringo 2 0.02 Cyp_2016-Cyp_1993 Bogoria 50 0.5 Chelaba 46 0.46 Cyp_2124-Cyp_2175 Bogoria 14 0.14 Chelaba 2 0.02 Cyp_2124-Cyp_2308 Bogoria 10 0.1 Chelaba 6 0.06 Cyp_2124-Cyp_1993 Bogoria 8 0.08 Chelaba 46 0.46 Cyp_2175-Cyp_2308 Baringo 16 0.16 Turtle 10 0.1 Cyp_2175-Cyp_1993 Bogoria 32 0.32 Chelaba 64 0.64 Cyp_2308-Cyp_1993 Bogoria 28 0.28 Chelaba 56 0.56

83 1.62 5.91 5.91 1.08 53.5528.41 18.04 183 79.4618.92 185 89.1910.81 87.10 185 186 T G G G CT CT AG AG NON Codonacid Amino type SNP Frequency N°Ind. Consequence gene 398 12776 Intron none A 464466 1343649 13456 Intron 1528684 none6 Intron 6 Exon5/Exon non-synon. none AGC/AGT 1563 S6 Exon C A C wt1b wt1b wt1b wt1b wt1b wt1b wt1b_398 wt1b_464 wt1b_466 wt1b_649 wt1b_684 SNP Name SNP Generef.* Position gene** Position Feature * Position * withEF026080 respectto Position with** LOC100701078 respectto Table 6: SNPs identified SNPs the in 6: Table

84 Table 7: Pairwise linkage disequilibrium detected for the wt1b gene gene promoter

Linkage Allele pair Population/strain R2 disequilibrium (%)

Wt1b_398-Wt1b_652 Baringo 8 0.8 Wt1b_398-Wt1b_464 Chelaba 6 0.6 Baringo 100 1 Turtle 100 1 Bouake 100 1 Wt1b_398-Wt1b_466 Bouake 10 0.1 Wt1b_398-Wt1b_649 Baringo 8 0.8 Wt1b_652-Wt1b_464 Baringo 100 1 Wt1b_652-Wt1b_466 Turkana 6 0.6 Wt1b_464-Wt1b_466 Bouake 100 1 Kpandu 10 0.1 Wt1b_464-Wt1b_649 Baringo 100 1

85 Table 8: SNPs identified in the amh gene

SNP Name Gene Position Feature Consequence Codon Amino acid SNP type Frequency N°Ind.

amh_202 amh 202 Exon 1 upstream A 74.85 163 G 15.34 AG 9.81 amh_264 amh 264 Exon 1 upstream A 87.58 177 G 6.21 amh_280 amh 280 Exon 1 upstream C 87.36 174 T 4.6 CT 8.04 amh_597 amh 597 Exon 2 synonmous GAG/GAT E/D G 74.29 175 T 18.86 GT 6.86 amh_611 amh 611 Exon 2 synonmous AAC/AGC/ N/S/ A 18.97 175 ACC/ATC T/I G 81.03 C 51.43 175 T 32.57 CT 16.00 amh_754 amh 754 Intron 2 C 51.43 175 T 32.57 CT 16.00 amh_875 amh 875 Exon 3 non-synon. CCA/CCT P A 66.67 141 T 33.33 amh_916 amh 916 Exon 3 synonmous AAT/AGT N/S A 66.67 132 G 33.33 amh_1996 amh 1996 Exon 6 non-synon. AGC/AGT S C 81.32 182 T 18.68 amh_2005 amh 2005 Exon 6 non-synon. TCC/TCT S C 86.74 181 T 6.08 CT 7.18 amh_2127 amh 2127 Exon 6 synonmous CTG/CCG L/P C 74.43 176 T 6.25 CT 19.32 amh_2128 amh 2128 Exon 6 non-synon. CCG/CCA P A 22.29 175 G 72.00 AG 1.71 T 4.00 amh_2245 amh 2245 Intron 6 A/T 68.13 91 T 31.87 amh_2282 amh 2282 Intron 6 G 60.92 174 T 39.08 amh_2486 amh 2487 Intron 6 C 78.12 192 T 12.50 CT 9.38 amh_2509 amh 2509 Intron 6 A 68.62 188 C 25.53 AC 2.85 amh_2586 amh 2586 Intron 6 C 75.42 179 G 23.46 CG 1.12 amh_2618 amh 2618 Intron 6 A 14.29 182 G 81.87 AG 3.84 amh_2643 amh 2643 Intron 6 A 8.99 178 G 76.40 AG 14.61 amh_2655 amh 2655 Intron 6 A 16.11 180 T 80.00 AT 3.89

86 Table 9: Nucleotide Insertions vs ref. Scaffold GL831234.1 and Mod. EF512167 SNP Name Gene Position Feature Deletion Insertion Population/Strain Frequency N°Ind.

amh_2860 amh 2860 Intron 6 G Bouake 100.0 13/13 Kpandu 100.0 21/21 Manzala 100.0 28/28 Hora 100.0 10/10 Koka 100.0 11/11 amh_2867 amh 2867 Intron 6 A ALL POP. 8/8 amh_2871 amh 2871 Intron 6 C Bouake 100.0 13/13 Kpandu 100.0 21/21 Manzala 100.0 28/28 Metahara 100.0 10/10 Hora 100.0 11/11 Koka 100.0 8/8 amh_2898 amh 2898 Intron 6 T Bouake 100.0 13/13 Kpandu 100.0 21/21 Manzala 100.0 28/28 Metahara 100.0 10/10 Hora 100.0 11/11 Koka 100.0 8/8 amh_2909 amh 2909 Intron 6 C Bouake 100.0 13/13 Kpandu 100.0 21/21 Manzala 100.0 28/28 Metahara 100.0 10/10 Hora 100.0 11/11 Koka 100.0 8/8 Turkana 100.0 17/17 Bogoria 60.0 12/20 Chelaba 45.0 9/20 Turtle 100.0 15/15 Baringo 95.0 19/20 amh_2934 amh 2934 Intron 6 T ALL POP. 100.0 192 amh 2677 to Intron 6 17 nt Bogoria 40.0 8/20 2694 Chelaba 55.0 11/20 Turtle 25.0 5/20 Baringo 5.0 1/20 amh 2895 to Intron 6 18 nt Bogoria 40.0 8/20 2914 Chelaba 55.0 11/20 Turtle 25.0 5/20 Baringo 5.0 1/20

87 Table 10: Chi-square test results for the deviation of sex-linked SNP in females and males from the HWE. Bogoria Chelaba Turtle Lake Lake SNP Name SNP Type Phenotype Item Spring Spring Spring Baringo Turkana Amh_597 T Females X2 8.2974 7.4370 10.796 6.8075 3.5451 P 0.0028 0.0316 0.0001 0.0001 0.1048 G Males X2 6.5778 4.3571 9.1000 7.6095 - P 0.0546 0.1035 0.0048 0.0001 - Amh_611 G Females X2 11.962 9.6103 - 10.936 13.888 P 0.0008 0.0001 - 0.0001 0.0001 A Males X2 9.5093 5.9932 - 2.6037 - P 0.0001 0.0034 - 0.5941 - Amh_754 C Female X2 2.1173 9.4780 2.5568 4.2743 - P 0.2985 0.0018 0.1734 0.1180 - T/C Males X2 3.3812 - 6.5714 - P 0.1645 - 0.0001 - Amh_2586 C Female X2 3.2145 7.4370 6.1276 6.5470 7.2193 P 0.1618 0.0301 0.0214 0.0508 0.0001 G Males X2 4.6803 5.9943 8.7575 5.3466 8.6480 P 0.0703 0.0701 0.0040 0.0800 0.0001 Amh_2618 A Female X2 3.2399 6.1864 8.6464 6.9242 - P 0.2683 0.0636 0.0104 0.0001 - G Males X2 3.1738 - 8.6464 - - P 0.1773 - 0.0096 -- Amh_2643 G Female X2 - 2.3331 2.5076 3.0096 16.009 P - 0.3209 0.2716 0.0682 0.0001 A Males X2 - - 5.1361 4.9882 - P-- 0.0084 0.0001 - Amh_2655 A Female X2 3.1644 7.3418 5.5800 6.9327 - P 0.1700 0.0234 0.0760 0.0475 - T Males X2 2.6479 4.9155 5.5800 - - P 0.2591 0.0246 0.0740 - - Amh_2668 A Female X2 - 2.7522 7.5030 1.9226 6.0103 P - 0.2309 0.0290 0.4274 0.0495 C Males X2 1.7287 - 3.9115 3.0720 - P 0.5569 - 0.1639 0.1557 - Amh_2807 T Female X2 7.8671 6.7877 6.3502 1.1015 - P 0.0001 0.0199 0.0350 0.6177 - C Males X2 5.7147 6.2877 10.115 5.9863 - P 0.0680 0.0103 0.0001 0.0836 - Amh_2486 C Female X2 - - - 7.9071 - P--- 0.0001 - T Males X2 5.7193 4.8331 2.7264 2.6300 - P 0.1060 0.1142 0.3524 0.6187 - Amh_2509 A Female X2 8.8034 7.7724 5.5015 5.1160 - P 0.0001 0.0029 0.0232 0.0860 - C Males X2 5.9466 5.5909 6.3127 - 5.4925 P 0.0275 0.0294 0.0182 - 0.0139

X2= chi-square test value, BOLD indicates population showing significant differences in both males and females. P= significance difference at 0.05 P values could not be calculated in all the populations due to their sums being zero.

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