GENETICA Mercati Et Al. Electronic Supplementary Material (Eight Tables: S1, S2, S3, S4

GENETICA Mercati et al. Electronic Supplementary Material (Eight Tables: S1, S2, S3, S4, S5, S6 and S7 in word and Table S8 In Excel)

GENETIC DIVERSITY AND POPULATION STRUCTURE OF AN ITALIAN LANDRACE OF RUNNER BEAN (Phaseolus coccineus L.): INFERENCES FOR ITS SAFEGUARD AND ON FARM CONSERVATION

MERCATI F., CATARCIONE G., PAOLACCI A.R., ABENAVOLI M.R., SUNSERI F.+, Ciaffi m.+

+ Corresponding authors:

Ciaffi M.: DIBAF, University of Tuscia, via S.C. de Lellis, 01100 Viterbo, Italy; email address: ; phone number: +39 0761357424; fax number +39 0761357242

Sunseri F.: Dipartimento AGRARIA, Università Mediterranea di Reggio Calabria, 89124 Reggio Calabria, Italy; email address: ; phone number: +39 09651870659; fax number : +39 09651870459

Table S1. Collection sites of the 20 populations (farms) of “Fagiolone” landrace, their geographic coordinates and elevations above sea level, and mean and standard error (St Err) for seed size and shape (calculated on a random sample of 20 seeds for each population).

Accession code / Collection site / Municipality / Lat. / Lon. / Elevation (m) / Seed Weight (g) / Seed Width (mm) / Seed Length (mm) / Seed shape-ratio
Mean / St Err / Mean / St Err / Mean / St Err / Mean / St Err
V1 / Tartaro / Vallepietra / 41.93 / 13.23 / 766 / 1.74 / 0.12 / 13.90 / 0.25 / 22.90 / 0.44 / 1.64 / 0.014
V2 / Cese Angeli / Vallepietra / 41.93 / 13.24 / 800 / 1.98 / 0.05 / 15.70 / 0.12 / 24.50 / 0.40 / 1.56 / 0.021
V3 / Forniglio / Vallepietra / 41,93 / 13.23 / 780 / 1.72 / 0.11 / 14.50 / 0.29 / 22.00 / 0.37 / 1.52 / 0.029
F4 / Pisciarello / Filettino / 41.88 / 13.32 / 980 / 2.00 / 0.05 / 15.10 / 0.32 / 24.90 / 0.47 / 1.65 / 0.026
V5 / Moralli / Vallepietra / 41.93 / 13.21 / 750 / 1.61 / 0.10 / 14.70 / 0.21 / 23.10 / 0.53 / 1.57 / 0.027
V6 / Cannavine / Vallepietra / 41.92 / 13.25 / 820 / 1.85 / 0.09 / 14.80 / 0.27 / 23.30 / 0.55 / 1.58 / 0.028
V7 / Tartaro / Vallepietra / 41.93 / 13.23 / 766 / 1.83 / 0.08 / 14.80 / 0.34 / 23.50 / 0.42 / 1.59 / 0.024
V8 / Tartaro / Vallepietra / 41.93 / 13.23 / 766 / 2.04 / 0.15 / 15.30 / 0.42 / 24.80 / 0.62 / 1.62 / 0.028
V9 / Pantano / Vallepietra / 41.95 / 13.24 / 825 / 1.99 / 0.12 / 14.70 / 0.37 / 24.50 / 0.67 / 1.68 / 0.055
V10 / Tartaro / Vallepietra / 41.93 / 13.23 / 766 / 1.68 / 0.07 / 14.50 / 0.23 / 24.10 / 0.40 / 1.67 / 0.036
V11 / Cese Angeli / Vallepietra / 41.93 / 13.24 / 800 / 1.99 / 0.08 / 15.00 / 0.27 / 24.50 / 0.57 / 1.63 / 0.025
V12 / Cese Angeli / Vallepietra / 41.93 / 13.24 / 800 / 1.87 / 0.08 / 14.60 / 0.27 / 23.50 / 0.57 / 1.61 / 0.037
V13 / Cannavine / Vallepietra / 41.92 / 13.25 / 820 / 1.98 / 0.09 / 15.20 / 0.23 / 24.90 / 0.58 / 1.64 / 0.028
F14 / Faito / Filettino / 41.90 / 13.29 / 930 / 2.56 / 0.13 / 15.90 / 0.20 / 27.10 / 0.51 / 1,70 / 0.033
F15 / Faito / Filettino / 41.90 / 13.29 / 930 / 1.98 / 0.08 / 15.00 / 0.24 / 24.70 / 0.32 / 1.65 / 0.019
F16 / Vardano / Filettino / 41.88 / 13.31 / 900 / 2.01 / 0.10 / 14.80 / 0.22 / 25.20 / 0.66 / 1.71 / 0.030
F17 / Faito / Filettino / 41.90 / 13.29 / 930 / 1.88 / 0.06 / 14.30 / 0.16 / 23.70 / 0.43 / 1.65 / 0.027
T18 / Canapine / Trevi nel Lazio / 41.84 / 13.26 / 650 / 1.97 / 0.05 / 14.90 / 0.19 / 24.90 / 0.23 / 1.68 / 0.027
T19 / Canapine / Trevi nel Lazio / 41.84 / 13.26 / 650 / 1.63 / 0.05 / 13.20 / 0.28 / 23.00 / 0.40 / 1.75 / 0.058
J20 / Ponte Tavole / Jenne / 41.87 / 13.16 / 530 / 2.94 / 0.10 / 16.80 / 0.15 / 28.40 / 0.28 / 1.69 / 0.020

Table S2 – List of the reference landraces/accessions of P. coccineus used in this study (28 landraces/cultivars from Italy and 13 accessions from Mesoamerica), and their geographic coordinates and elevations above sea level.

Donor bank code / Don Inst / Country / Prov. / Location / Lat / Long / Elevation (m)
Acc_24 / CRA / Italy / Ascoli Piceno / Acquasanta Terme / 42.76 / 13.40 / 392
Acc_223 / CRA / Italy / Macerata / Pievebovigliana / 43.06 / 13.08 / 439
Acc_227 / CRA / Italy / Macerata / Castel S. Angelo / 43.19 / 13.00 / 780
Acc_229 / CRA / Italy / Macerata / Castel S. Angelo / 43.19 / 13.00 / 780
Acc_231 / CRA / Italy / Macerata / Visso / 42.92 / 13.08 / 607
Acc_236 / CRA / Italy / Ascoli Piceno / Amandola / 42.97 / 13.35 / 500
Acc_253 / CRA / Italy / Macerata / Pieve Torina / 43.04 / 13.04 / 470
Acc_257 / CRA / Italy / Macerata / Pieve Torina / 43.04 / 13.04 / 470
Acc_264 / CRA / Italy / Macerata / Visso / 42.92 / 13.08 / 607
Acc_267 / CRA / Italy / Macerata / Visso / 42.92 / 13.08 / 607
Acc_275 / CRA / Italy / Macerata / Fiuminata / 43.18 / 12.95 / 479
Acc_397 / CRA / Italy / Macerata / Serravalle / 43.07 / 12.95 / 667
PHA_801 / IPK / Italy / Reggio Calabria / Santurio Polsi / 38.17 / 15.87 / 1524
PHA_803 / IPK / Italy / Cosenza / Aprigliano / 39.22 / 16.32 / 729
PHA_8229 / IPK / Italy / Cosenza / Cavallerizzo / 39.50 / 16.12 / 350
PHA_8277 / IPK / Italy / Vibo Valenzia / Serra S. Bruno / 38.57 / 16.32 / 857
PHA_8347 / IPK / Italy / Vibo Valenzia / Serra S. Bruno / 38.57 / 16.32 / 857
PHA_8365 / IPK / Italy / Vibo Valenzia / Serra S. Bruno / 38.57 / 16.32 / 857
PHA_8291 / IPK / Italy / Isernia / Castel Giudice / 41.85 / 14.22 / 979
PHA_8389 / IPK / Italy / Isernia / Castel Giudice / 41.85 / 14.22 / 979
PHA_8356 / IPK / Italy / Isernia / Castel Giudice / 41.85 / 14.22 / 979
PHA_8284 / IPK / Italy / L'Aquila / Scanno / 41.88 / 13.87 / 1218
PHA_8285 / IPK / Italy / L'Aquila / Campo di Giove / 42.02 / 14.50 / 1224
3615 / UNIPG / Italy / Perugia / Spoleto / 42.65 / 12.95 / 1000
Corona / UNIPG / Italy / Perugia / Colfiorito / 43.02 / 12.89 / 760
Venere / UNIPG / Italy / Perugia / Colfiorito / 43.02 / 12.89 / 760
4392 / UNIPG / Italy / Rieti / Grisciano / 42.67 / 13.30 / 700
Fagiolo Turco / UNIPG / Italy / Lucca / Pieve Fosciana / 44.13 / 10.41 / 369
PI 311920 / USDA / Mexico / Puebla / Tehuacan / 18.45 / -97.37 / 1660
PI 325597 / USDA / Mexico / Puebla / Tezuitlan / 15.18 / -92.65 / 2000
PI 313221 / USDA / Mexico / Lèon / San Diego de A. / 21.75 / -102.17 / 1950
PI 325584 / USDA / Mexico / Puebla / Teletes / 19.81 / -97.81 / 1960
PI 406785 / USDA / Costarica / San Josè / Cartago / 9.85 / -83.90 / 1431
PI 309888 / USDA / Costarica / San Josè / Santa Maria de Dota / 9.65 / -83.97 / 1663
PI 311219 / USDA / Guatemala / Totonicapan / Totonicapan / 14.92 / -91.37 / 2667
PI 311882 / USDA / Guatemala / Huehuetenango / Huehuetenango / 15.03 / -91.50 / 2830
PI 433236 / USDA / Guatemala / Sololà / Sololà / 14.76 / -91.18 / 2113
PI 282119 / USDA / Chile / Cautin / Temuco / -39.51 / -72.43 / 500
PI 313573 / USDA / Colombia / Sonson / Sonson / 5.45 / -75.18 / 2475
PI 406938 / USDA / Honduras / Francisco M. / Tegucigalpa / 14.10 / -87.22 / 980
PI 355423 / USDA / Equador / Guajaquil / Mercado der Sur / -1.46 / -77.98 / 660

Table S3. Mean and standard error (St Err) for seed size and shape, and seed coat attributes (colour) measured on a random sample of 20 seeds for each of the Italian and Mesoamerican accessions of P. coccineus used as a reference in this study

Donor bank code / Seed Weight (g) / Seed Width (mm) / Seed Length (mm) / Seed shape-ratio / Seed Coat
Mean / St Err / Mean / St Err / Mean / St Err / Mean / St Err / Background or main colour / Distribution second colour / Secondary colour
Acc_24 / 0.97 / 0.07 / 12.40 / 0.02 / 19.00 / 0.06 / 1.53 / 0.04 / White / None
Acc_223 / 1.94 / 0.12 / 14.50 / 0.05 / 12.30 / 0.02 / 1.48 / 0.04 / White / None
Acc_227 / 1.81 / 0.17 / 15.70 / 0.08 / 22.30 / 0.09 / 1.44 / 0.06 / White / None
Acc_229 / 1.82 / 0.12 / 14.00 / 0.07 / 22.60 / 0.05 / 1.63 / 0.06 / White / None
Acc_231 / 1.69 / 0.05 / 15.20 / 0.01 / 21.80 / 0.05 / 1.43 / 0.04 / White / None
Acc_236 / 1.82 / 0.08 / 14.70 / 0.05 / 22.20 / 0.07 / 1.52 / 0.07 / White / None
Acc_253 / 2.42 / 0.26 / 15.20 / 0.10 / 25.60 / 0.11 / 1.69 / 0.05 / White / None
Acc_257 / 1.98 / 0.07 / 15.10 / 0.04 / 23.90 / 0.07 / 1.59 / 0.08 / White / None
Acc_264 / 1.24 / 0.09 / 13.30 / 0.07 / 21.10 / 0.05 / 1.61 / 0.06 / Brown / Spotted / Brown
Acc_267 / 2.58 / 0.13 / 15.70 / 0.03 / 26.50 / 0.04 / 1.69 / 0.04 / White / None
Acc_275 / 1.89 / 0.20 / 14.00 / 0.03 / 22.20 / 0.03 / 1.59 / 0.02 / White / None
Acc_397 / 1.77 / 0.03 / 14.40 / 0.02 / 25.10 / 0.05 / 1.75 / 0.04 / Brown / Spotted / Brown
PHA_801 / 1.18 / 0.09 / 12.50 / 0.03 / 19.20 / 0.05 / 1.54 / 0.03 / White / None
PHA_803 / 1.57 / 0.04 / 13.00 / 0.02 / 21.00 / 0.03 / 1.62 / 0.01 / White / None
PHA_8229 / 1.63 / 0.12 / 12.80 / 0.03 / 21.60 / 0.05 / 1.69 / 0.03 / White / None
PHA_8277 / 1.19 / 0.07 / 11.70 / 0.02 / 19.70 / 0.04 / 1.68 / 0.02 / White / None
PHA_8347 / 1.70 / 0.12 / 13.70 / 0.06 / 21.50 / 0.03 / 1.58 / 0.07 / Brown / Spotted / Black
PHA_8365 / 1.13 / 0.08 / 12.10 / 0.03 / 20.10 / 0.03 / 1.66 / 0.04 / Black / Spotted / Brown
PHA_8291 / 1.67 / 0.09 / 13.70 / 0.05 / 21.10 / 0.03 / 1.55 / 0.06 / White / None
PHA_8389 / 1.61 / 0.05 / 13.00 / 0.03 / 21.70 / 0.05 / 1.67 / 0.02 / White / None
PHA_8356 / 1.30 / 0.07 / 12.10 / 0.03 / 20.00 / 0.06 / 1.66 / 0.06 / Black / Spotted / Brown
PHA_8284 / 1.45 / 0.07 / 12.50 / 0.02 / 22.70 / 0.05 / 1.82 / 0.04 / Brown / Spotted / Brown
PHA_8285 / 1.54 / 0.12 / 13.70 / 0.04 / 21.20 / 0.04 / 1.55 / 0.05 / White / None
3615 / 1.05 / 0.07 / 12.10 / 0.06 / 18.70 / 0.06 / 1.56 / 0.08 / White / None
Corona / 2.35 / 0.09 / 26.70 / 0.05 / 26.30 / 0.05 / 1.58 / 0.06 / White / None
Venere / 1.39 / 0.07 / 13.60 / 0.04 / 20.50 / 0.06 / 1.51 / 0.04 / White / None
4392 / 2.13 / 0.12 / 15.20 / 0.03 / 25.20 / 0.14 / 1.66 / 0.08 / White / None
Fagiolo Turco / 1.47 / 0.05 / 14.20 / 0.03 / 21.60 / 0.03 / 1.53 / 0.04 / White / None
PI 311920 / 1.07 / 0.04 / 12.30 / 0.02 / 19.10 / 0.02 / 1.55 / 0.03 / Black / None
PI 325597 / 0.97 / 0.04 / 11.70 / 0.01 / 17.20 / 0.03 / 1.47 / 0.02 / Brown / Mottled / Brown
PI 313221 / 1.21 / 0.07 / 10.80 / 0.04 / 18.10 / 0.04 / 1.69 / 0.07 / White / None
PI 325584 / 0.89 / 0.04 / 11.40 / 0.02 / 17.20 / 0.11 / 1.50 / 0,07 / Black / None
PI 406785 / 0.60 / 0.04 / 10.00 / 0.02 / 14.10 / 0.12 / 1.41 / 0.13 / Brown / None
PI 309888 / 0.95 / 0.02 / 11.40 / 0.03 / 17.30 / 0.02 / 1.52 / 0.05 / Brown / None
PI 311219 / 0.86 / 0.07 / 10.60 / 0.02 / 15.50 / 0.02 / 1.46 / 0.01 / Brown / None
PI 311882 / 0.62 / 0.02 / 9.80 / 0.01 / 14.90 / 0.03 / 1.53 / 0.04 / Black / None
PI 433236 / 1.00 / 0.03 / 11.10 / 0.02 / 15.80 / 0.03 / 1.43 / 0.02 / White / None
PI 282119 / 1.34 / 0.05 / 13.30 / 0.01 / 21.90 / 0.07 / 1.65 / 0.06 / Brown / Spotted / Black
PI 313573 / 0.47 / 0.03 / 7.70 / 0.02 / 12.40 / 0.09 / 1.62 / 0.13 / Brown / None
PI 406938 / 0.66 / 0.02 / 10.90 / 0.01 / 16.20 / 0.05 / 1.49 / 0.06 / Brown / None
PI 355423 / 0.62 / 0.03 / 9.50 / 0.04 / 13.70 / 0.03 / 1.45 / 0.08 / Brown / None

Table S4. Main genetic parameters from the 9 polymorphic SSR loci in the whole analyzed sample including 405 genotypes from 20 populations of “Fagiolone”, 28 Italian landraces and 13 Mesoamerican accessions. Values of the genetic parameters of the 20 populations of “Fagiolone” are reported in brackets.

SSR / Allele size range (bp) / No Alleles / Major Allele Frequency / Hoa / Hea / PICb / fc
X79722 / 140-150 / 5.00 (3.00) / 0.577 (0.627) / 0.376 (0.233) / 0.599 (0.527) / 0.551 (0.463) / 0.374 (0.560)
X74919 / 127-179 / 11.00 (4.00) / 0.810 (0.924) / 0.109 (0.079) / 0.329 (0.144) / 0.310 (0.139) / 0.668 (0.454)
X80051 / 193-231 / 24.00 (20.00) / 0.253 (0.363) / 0.479 (0.570) / 0.885 (0.822) / 0.876 (0.809) / 0.459 (0.309)
M75856 / 126-164 / 12.00 (8.00) / 0.424 (0.400) / 0.369 (0.489) / 0.701 (0.735) / 0.655 (0.696) / 0.474 (0.336)
X60000 / 125-139 / 7.00 (5.00) / 0.734 (0.629) / 0.159 (0.253) / 0.436 (0.532) / 0.408 (0.474) / 0.637 (0.527)
X04660 / 198-208 / 8.00 (6.00) / 0.510 (0.500) / 0.930 (0.968) / 0.636 (0.628) / 0.579 (0.564) / -0.461 (-0.540)
X04001 / 158-164 / 5.00 (3.00) / 0.897 (0.955) / 0.057 (0.026) / 0.189 (0.087) / 0.178 (0.085) / 0.700 (0.697)
U18349 / 226-232 / 4.00 (2.00) / 0.772 (0,889) / 0.162 (0.169) / 0.377 (0.197) / 0.345 (0.178) / 0.570 (0.145)
AF483902 / 150-170 / 8.00 (3.00) / 0.856 (0.891) / 0.059 (0.016) / 0.261 (0.194) / 0.253 (0.177) / 0.775 (0.919)
Mean / 9.33 (6.00) / 0.648 (0.686) / 0.300 (0.311) / 0.490 (0.430) / 0.462 (0.398) / 0.389 (0.278)

a Genetic diversity (average He, Nei 1987) and observed (Ho) heterozygosity

b Polymorphic information content (PIC)

c Inbreeding coefficient (f)

Table S5. Private alleles for population.

Pop / Locus / Allele / Freq
V1 / M75856 / 126 / 0,050
V1 / X60000 / 127 / 0,050
V2 / X04660 / 203 / 0,050
V3 / X80051 / 198 / 0,100
V5 / AF483902 / 150 / 0,100
V10 / X80051 / 214 / 0,056
F15 / X74919 / 147 / 0,050
F17 / X80051 / 212 / 0,143
F18 / X80051 / 231 / 0,150

Table S6. Pairwise Fst values of the “Fagiolone” populations

V1 / V2 / V3 / F4 / V5 / V6 / V7 / V8 / V9 / V10 / V11 / V12 / V13 / F14 / F15 / F16 / F17 / T18 / T19 / J20
V1 / 0.000
V2 / 0.075 / 0.000
V3 / 0.060 / 0.053 / 0.000
F4 / 0.083 / 0.029 / 0.053 / 0.000
V5 / 0.085 / 0.054 / 0.060 / 0.030 / 0.000
V6 / 0.078 / 0.079 / 0.038 / 0.056 / 0.046 / 0.000
V7 / 0.086 / 0.048 / 0.049 / 0.057 / 0.079 / 0.062 / 0.000
V8 / 0.063 / 0.053 / 0.037 / 0.057 / 0.071 / 0.066 / 0.051 / 0.000
V9 / 0.187 / 0.162 / 0.186 / 0.155 / 0.150 / 0.196 / 0.178 / 0.156 / 0.000
V10 / 0.105 / 0.067 / 0.093 / 0.045 / 0.054 / 0.090 / 0.092 / 0.074 / 0.089 / 0.000
V11 / 0.165 / 0.149 / 0.150 / 0.142 / 0.131 / 0.160 / 0.145 / 0.137 / 0.030 / 0.090 / 0.000
V12 / 0.164 / 0.154 / 0.163 / 0.148 / 0.130 / 0.159 / 0.158 / 0.142 / 0.021 / 0.083 / 0.025 / 0.000
V13 / 0.186 / 0.159 / 0.163 / 0.150 / 0.146 / 0.195 / 0.178 / 0.148 / 0.023 / 0.092 / 0.022 / 0.034 / 0.000
F14 / 0.131 / 0.083 / 0.103 / 0.065 / 0.079 / 0.128 / 0.121 / 0.105 / 0.071 / 0.048 / 0.073 / 0.066 / 0.068 / 0.000
F15 / 0.178 / 0.163 / 0.174 / 0.157 / 0.142 / 0.169 / 0.154 / 0.153 / 0.079 / 0.125 / 0.031 / 0.054 / 0.061 / 0.095 / 0.000
F16 / 0.158 / 0.103 / 0.145 / 0.100 / 0.112 / 0.147 / 0.098 / 0.123 / 0.079 / 0.072 / 0.046 / 0.066 / 0.077 / 0.069 / 0.050 / 0.000
F17 / 0.118 / 0.114 / 0.096 / 0.121 / 0.124 / 0.137 / 0.123 / 0.091 / 0.132 / 0.085 / 0.122 / 0.099 / 0.140 / 0.096 / 0.141 / 0.128 / 0.000
T18 / 0.127 / 0.088 / 0.109 / 0.086 / 0.093 / 0.135 / 0.114 / 0.099 / 0.110 / 0.059 / 0.090 / 0.086 / 0.108 / 0.047 / 0.092 / 0.076 / 0.086 / 0.000
T19 / 0.154 / 0.111 / 0.119 / 0.122 / 0.133 / 0.164 / 0.102 / 0.120 / 0.106 / 0.096 / 0.097 / 0.083 / 0.121 / 0.090 / 0.111 / 0.081 / 0.076 / 0.078 / 0.000
J20 / 0.111 / 0.088 / 0.091 / 0.102 / 0.120 / 0.133 / 0.093 / 0.079 / 0.098 / 0.085 / 0.083 / 0.086 / 0.097 / 0.068 / 0.090 / 0.085 / 0.072 / 0.051 / 0.039 / 0.000

*Significant at the P < 0.05 level