@article{fdi:010068313,
  title = {{G}enome scan reveals selection acting on genes linked to stress response in wild pearl millet},
  author = {{B}erthouly, {C}{\'e}cile and {T}huillet, {A}nne-{C}{\'e}line and {R}hone, {B}{\'e}n{\'e}dicte and {M}ariac, {C}{\'e}dric and {O}usseini, {I}. {S}. and {C}ouderc, {M}arie and {T}enaillon, {M}. {I}. and {V}igouroux, {Y}ves},
  editor = {},
  language = {{ENG}},
  abstract = {{U}ncovering genomic regions involved in adaption is a major goal in evolutionary biology. {H}igh-throughput sequencing now makes it possible to tackle this challenge in nonmodel species. {Y}et, despite the increasing number of methods targeted to specifically detect genomic footprints of selection, the complex demography of natural populations often causes high rates of false positive in gene discoveries. {T}he aim of this study was to identify climate adaptations in wild pearl millet populations, {C}enchrus americanus ssp. monodii. {W}e focused on two climate gradients, one in {M}ali and one in {N}iger. {W}e used a two-step strategy to limit false-positive outliers. {F}irst, we considered gradients as biological replicates and performed {RNA} sequencing of four populations at the extremities. {W}e combined four methods-three based on differentiation among populations and one based on diversity patterns within populations-to identify outlier {SNP}s from a set of 87 218 high-quality {SNP}s. {A}mong 11 155 contigs of pearl millet reference transcriptome, 540 exhibited selection signals as evidenced by at least one of the four methods. {I}n a second step, we genotyped 762 samples in 11 additional populations distributed along the gradients using {SNP}s from the detected contigs and random {SNP}s as control. {W}e further assessed selection on this large data set using a differentiation-based method and a method based on correlations with environmental variables based. {F}our contigs displayed consistent signatures between the four extreme and 11 additional populations, two of which were linked to abiotic and biotic stress responses.},
  keywords = {adaptation ; {C}enchrus americanus ; climate gradient ; {P}ennisetum glaucum ; {RNA}seq ; {MALI} ; {NIGER}},
  booktitle = {},
  journal = {{M}olecular {E}cology},
  volume = {25},
  numero = {21},
  pages = {5500--5512},
  ISSN = {0962-1083},
  year = {2016},
  DOI = {10.1111/mec.13859},
  URL = {https://www.documentation.ird.fr/hor/fdi:010068313},
}