#!/bin/bash
s='Continent1_Breed1_Ind-ID1 Continent1_Breed1_Ind-ID1 0 0 0 -9
Continent1_Breed2_Ind-ID2 Continent1_Breed2_Ind-ID1 0 0 0 -0
Continent2_Breed1_Ind-ID1 Continent2_Breed1_Ind-ID1 0 0 0 -9'
awk '{sub(/_[^_]*$/, "", $1)}1' <<< "$s"
IyEvYmluL2Jhc2gKcz0nQ29udGluZW50MV9CcmVlZDFfSW5kLUlEMSBDb250aW5lbnQxX0JyZWVkMV9JbmQtSUQxIDAgMCAwIC05CkNvbnRpbmVudDFfQnJlZWQyX0luZC1JRDIgQ29udGluZW50MV9CcmVlZDJfSW5kLUlEMSAwIDAgMCAtMApDb250aW5lbnQyX0JyZWVkMV9JbmQtSUQxIENvbnRpbmVudDJfQnJlZWQxX0luZC1JRDEgMCAwIDAgLTknCmF3ayAne3N1YigvX1teX10qJC8sICIiLCAkMSl9MScgPDw8ICIkcyI=